bluuebunny/crossref_metadata_2025 huggingface dataset:
Grass Growth in Response to Time of Rainfall and Season Along a Climate Gradient in Australian Rangelands.
Authors: Walker BH , Mcfarlane FR , Langridge JL
Published: December 2005

Percentage green leaf and height of the major perennial grass species was estimated fortnightly at six locations along a rainfall predictability gradient from Katherine (most predictable) to Lake Mere near Cobar (aseasonal), and regressed on estimated plant available soil moisture (PASM) and time of year (T). Green leaf is more strongly related to T at Katherine and to PASM at Lake Mere with the other sites in-between. Differences between species in terms of seasonal growth phenology were minor, at all sites, and there were no meaningful patterns in percentage contributions by the species to sward biomass. A strong inter-seasonal rainfall pattern over the period of the study may have masked phenological differences between species, but it is also possible that changes in species composition very soon after livestock were introduced resulted in a decline in phenological differentiation. Whatever the reason, the differences observed in this study would ~ot warrant their use in the formulation of management strategies.
An Evaluation of Feral Goat Control Methods on Currawinya National Park, South-Western Queensland.
Authors: Edwards GP , Clancy TF , Lee J , Mcdonnell J
Published: December 2005

This study was designed to develop monitoring techniques based on aerial survey and to evaluate the effectiveness of control methods for large feral herbivores (especially goats) in the mulga woodlands. It was conducted on a study site in south-western Queensland encompassing Currawinya National Park. Two control programs were undertaken on the park: a ground-based shooting program and a two-stage live-muster and aerial culling program.

Population estimates of feral goats based on 100 m strip counts from a fixed-wing aircraft were 4.6/km2 for the survey block for the initial survey with a decline to less than 2/km2 by the end of the project. It was concluded that fixed-wing aerial surveys provide an accurate estimate of the density of large feral herbivores, such as goats.

The first control program, based on ground-based shooting, was of only limited success. The second control program, based on contract mustering with the aid of fixed-wing aircraft followed by aerial culling using a helicopter, was very successful in reducing the number of feral goats and other feral animals. This approach represents best practice management of feral goats in the mulga woodlands. The effect of the reduction in goat numbers on goat impact within the park is yet to be evaluated.
Consequences of Some One-Off Events and Exclosure on a Red Grass (Bothriochloa Macra)-Wallaby Grass (Danthonia Eriantha) Pasture in the Central West of Nsw.
Authors: Semple WS , Koen TB , Waterhouse D
Published: December 2005

The effects of exotic grass introduction and cultivation, herbicide (glyphosate), burning or nil treatments on an exclosed red grass (Bothriochloa macra (Steud.) S.T. Blake) - wallaby grass (Danthonia eriantha Lindl.) pasture in the Central West of NSW were monitored for 3� years. The exotic grasses (Chloris gayana Kunth cv. Pioneer and Erogrostis curvula (Schrad.) Nees cv. Consol) established only in the cultivated plots but soil erosion also occurred in this treatment. Danthonia eriantha was killed by the glyphosate and cultivation treatments and had not re-established after 3� years. Cultivation also killed B. macra plants but limited recruitment subsequently occurred. Burning had little effect on the survival of either of the dominant native grasses. Seedling recruitment of the two dominant grasses was apparently minimal. However, where plants were not killed by the treatments, they expanded to fill some of the gaps created and D. eriantha appeared to be more competitive than B. macra. An unexpected result was the synchronised ripening of the Bothriochloa seedheads in the first summer following either burning or glyphosate application.
The Use of the Land Survey Record to Assess Changes in Vegetation Structure. A Case Study From the Darling Downs, Queensland, Australia.
Authors: Fensham RJ , Holman JE
Published: December 2005

Fifteen references to vegetation structure from the historical land survey record for the eastern Darling Downs were calibrated with historical photographs to determine the use of the surveyors' structural terminology (Open: 'open', 'light': Dense: 'heavy', 'thick', 'dense'). Sites with less than 40% canopy cover were only described by terms included within the Open category, and sites with greater than 50% canopy cover were only described by terms included within the Dense category. These results provide calibrations of the surveyors' structural terminology indicating terms were unambiguously applied outside the 40-50% canopy cover range. The use of corner tree distances as an absolute measure of vegetation density is warned against because corner trees had to meet certain criteria and were not necessarily the nearest tree to any corner. However, the distance from allotment corners to "corner trees" provided a measure of the relative use of the surveyor's structural epithets and is consistent with standard application among their fraternity. Survey records dating from 1864-1910 were compared with the structure of existing remnants (projective crown cover measured from recent 1:25,000 aerial photography) to assess changes in vegetation structure. The analysis suggests that 88% of the 34 sites included in the analysis have not changed from the broad structural category that was assigned by the surveyors. Using the assumptions developed by this study, two sites were assessed as having thickened substantially. These results suggest that only minor vegetation thickening has occurred in the Darling Downs since the early land surveys. This conclusion is supported by direct comparison of the historical photographs with existing remnants. indicating that only one site out of 17 has thickened substantially.
Palaeodrainage at Uluru-Kata Tjuta National Park and implications for water resources.
Authors: English P
Published: December 2005

The stakeholders in the atypical rangeland area of Uluyu-Kata Tjufa National Park in the Northern Territory are the Aboriginal owners, hundreds of thousands of tourists, and vulnerable desert wildlife species. Sustainable water resources and maintenance of the integrity of the unique geological, ecological and cultural environment at Uluyu are major issues being addressed by the trustees of the Park. The Dune Plains area between Uluyu (Ayers Rock) and Kata Tjula (the Olgas) is the setting for a deep palaeovalley. The flat, dune-covered landscape of the present-day Dune Plains area provides no indication of the existence of the underlying palaeovalley. Integrated datasets including aeromagnetic and airborne gamma-ray spectrometric imagery, processed Landsat Thematic Mapper imagery, a digital elevation model, and water-bore logs, have enabled reconstruction of the Dune Plains palaeoriver valley. The datasets reveal a heterogeneous basement topography of domes and basins with 100 m of vertical relief (a buried 'mini-Kata Tjuia') at depth beneath the Dune Plains area, between the rock monoliths. The ancient valley became completely infilled with lake, river and wind-borne sediments during the Tertiary and Quaternary. Major faults traversing the basement beneath the area influenced early erosion and valley initiation. The palaeovalley was originally a closed valley which later evolved to a through-flowing river that fed Lake Amadeus to the north. The Dune Plains palaeovalley is now the setting for a compound bedrock- Cainozoic-sediment aquifer system which is the major source of water supply for the inhabitants and tourists of Uluyu-Kata Tjufa National Park. Major landscape units making up the Uluyu area include groundwater calcrete, sheetwash slopes of red earth, sandplains and dunefields, and modern ephemeral alluvial braidplains that are constrained to corridors afforded by swale networks. The sheetwash unit forms gently sloping aprons around outcrops and supports banded mulga shrubland. During rainfall, surface run-off acts as a 'sheetflow recharge mechanism'. This mechanism maximises water conservation allowing survival of the mulga groves and associated ecosystems. During major rainfall events, the sheetflow processes augment replenishment of the aquifer system at the base of the slopes. The palaeodrainage configuration and hydrodynamics of both the surface environment and the subsurface aquifer system are complex. The methodology used to reconstruct the Dune Plains palaeodrainage and associated aquifer system, and the hydrodynamic processes described for the Uluru area are applicable to widespread rangeland areas elsewhere across the continent. Keywords: Uluyu, Kata Tjula, Dune Plains, palaeovalley, palaeodrainage, hydrology, groundwater, aquifer, sheetwash, red earths, calcrete, hydrodynamics, mulga (Acacia aneura), run-off, run-on, recharge.
Movement Patterns of Feral Goats in a Semi-Arid Woodland in Eastern Australia.
Authors: Freudenberger D , Barber J
Published: December 2005

The movement patterns of ten feral goats fitted with radio transmitters were examined over a 20 month period in a semi-arid woodland of western New South Wales. The mean distance between locations (fixes) was 3.1 km at 42 day intervals. The mean interfix distance for male goats was 1.1 km greater than for females. The mean home range for the five males was 29.4 km2 and 10.9 km2 for the five females (95% convex polygon). The movement patterns of feral goats in this woodland system were predictable. Goats usually moved small distances and remained close to intermittent lakes and creeks with abundant tree and shrub cover. Goats commercially harvested in this area were likely to have come from local populations living in an area of 15-35 km2, an area encompassed by 1-2 paddocks on a single property.
Recovery of Populations of the Soil Lichen Psora Crenata After Disturbance in Arid South Australia.
Authors: Eldridge DJ , Ferris JM
Published: December 2005

Measurements were made of density, size and shape of colonies of the soil lichen Psora crenata at sites with varying disturbance histories at Maralinga in arid South Australia. Lichens were measured along transects at 10 sites with recovery intervals ranging from 3 to 42 years, and on four undisturbed control sites. As the time since disturbance increased, the number of lichen colonies increased markedly, colony size declined, but colony shape remained unchanged. We tentatively suggest that at least 60 years is required for disturbed sites to approach the condition of undisturbed sites. These results reinforce the notion that lichen recovery is very slow, and suggest that colony density of Psora could be a useful indicator of recovery after disturbance in rangelands where crusts are a common component of the soil surface. Keywords: Psora crenata, rangelands, soil crusts, cryptogams, rangeland health
A Technique for Near-Ground Remote Sensing of Herbaceous Vegetation in Tropical Woodlands.
Authors: Northup BK , Brown JR , Dias CD , Skelly WC , Radford B
Published: December 2005

Cost-effective, accurate, repeatable methods for assaying characteristics of vegetative communities are critical for developing management strategies for grasslands in dry tropical Australia. We outline a set of flexible and adaptable techniques that will allow the description of plant canopy cover, bare ground, and standing crop through near-ground remote sensing. The system consists of a gantry frame and telescoping boom arm mounted on a quad bike, digital camera (or analog camera using slide film) to capture plot images, Leica TClOlO total station (electronic theodolite with data capture card) to measure distance and bearings to centres of imaged plots, and a suite of readily available software packages to process the images. During 1997, data were collected from three experimental paddocks in different stages of degradation within a dry tropical woodland located near Charters Towers, Queensland. Comparisons of data quality and time requirements for digital and standard field estimation techniques (BOTANAL) are made, and the strengths and weaknesses of the two systems discussed.
An Analysis of the Private Returns From Three Land Development Options in the Southern Mallee of Nsw.
Authors: Patton DA , Mullen JD
Published: December 2005

In early 1993, the DLWC initiated a project to develop regional planning strategies for clearing and cultivation activities in the Southern Mallee and Northern Floodplain areas of the Western Division of NSW. Concentrating on the Southern Mallee region, a benefit-cost analysis of current clearing and cultivation proposals and their impact on the financial viability of the individual landholder has been conducted. While the development proposals all had the potential to return much higher levels of expected net income to farmers than the existing extensive grazing strategy, market and climatic uncertainty meant that the probability of the extensive grazing activity returning more than cropping was as high as 50% for some proposals. This means that farmers have to weigh up higher incomes on average from cropping against the more certain income from grazing. Clearly, this is a personal choice with the more risk averse decision makers favouring the extensive grazing option. However, we found that for levels of risk aversion that research suggests typifies Australian farmers, the development proposals were dominant over the extensive grazing option except where there was a higher proportion of land devoted to conservation at a discount rate of 12%. No attempt has been made in the present study to evaluate the public benefits and costs, in the form of changes in environmental resources, associated with such development proposals Key words: Western Division, conservation, clearing and cultivation, stochastic dominance, economics.
The SET domain protein Metnase mediates foreign DNA integration and links integration to nonhomologous end-joining repair
Authors: Lee Suk-Hee , Oshige Masahiko , Durant Stephen T. , Rasila Kanwaldeep Kaur , Williamson Elizabeth A. , Ramsey Heather , Kwan Lori , Nickoloff Jac A. , Hromas Robert
Published: December 2005

The molecular mechanism by which foreign DNA integrates into the human genome is poorly understood yet critical to many disease processes, including retroviral infection and carcinogenesis, and to gene therapy. We hypothesized that the mechanism of genomic integration may be similar to transposition in lower organisms. We identified a protein, termed Metnase, that has a SET domain and a transposase/nuclease domain. Metnase methylates histone H3 lysines 4 and 36, which are associated with open chromatin. Metnase increases resistance to ionizing radiation and increases nonhomologous end-joining repair of DNA doublestrand breaks. Most significantly, Metnase promotes integration of exogenous DNA into the genomes of host cells. Therefore, Metnase is a nonhomologous end-joining repair protein that regulates genomic integration of exogenous DNA and establishes a relationship among histone modification, DNA repair, and integration. The data suggest a model wherein Metnase promotes integration of exogenous DNA by opening chromatin and facilitating joining of DNA ends. This study demonstrates that eukaryotic transposase domains can have important cell functions beyond transposition of genetic elements.
Somatic mtDNA mutations cause aging phenotypes without affecting reactive oxygen species production
Authors: Trifunovic Aleksandra , Hansson Anna , Wredenberg Anna , Rovio Anja T. , Dufour Eric , Khvorostov Ivan , Spelbrink Johannes N. , Wibom Rolf , Jacobs Howard T. , Larsson Nils-Göran
Published: December 2005

The mitochondrial theory of aging proposes that reactive oxygen species (ROS) generated inside the cell will lead, with time, to increasing amounts of oxidative damage to various cell components. The main site for ROS production is the respiratory chain inside the mitochondria and accumulation of mtDNA mutations, and impaired respiratory chain function have been associated with degenerative diseases and aging. The theory predicts that impaired respiratory chain function will augment ROS production and thereby increase the rate of mtDNA mutation accumulation, which, in turn, will further compromise respiratory chain function. Previously, we reported that mice expressing an error-prone version of the catalytic subunit of mtDNA polymerase accumulate a substantial burden of somatic mtDNA mutations, associated with premature aging phenotypes and reduced lifespan. Here we show that these mtDNA mutator mice accumulate mtDNA mutations in an approximately linear manner. The amount of ROS produced was normal, and no increased sensitivity to oxidative stress-induced cell death was observed in mouse embryonic fibroblasts from mtDNA mutator mice, despite the presence of a severe respiratory chain dysfunction. Expression levels of antioxidant defense enzymes, protein carbonylation levels, and aconitase enzyme activity measurements indicated no or only minor oxidative stress in tissues from mtDNA mutator mice. The premature aging phenotypes in mtDNA mutator mice are thus not generated by a vicious cycle of massively increased oxidative stress accompanied by exponential accumulation of mtDNA mutations. We propose instead that respiratory chain dysfunction
per se
is the primary inducer of premature aging in mtDNA mutator mice.
Somatic events modify hypertrophic cardiomyopathy pathology and link hypertrophy to arrhythmia
Authors: Wolf Cordula M. , Moskowitz Ivan P. G. , Arno Scott , Branco Dorothy M. , Semsarian Christopher , Bernstein Scott A. , Peterson Michael , Maida Michael , Morley Gregory E. , Fishman Glenn , Berul Charles I. , Seidman Christine E. , Seidman J. G.
Published: December 2005

Sarcomere protein gene mutations cause hypertrophic cardiomyopathy (HCM), a disease with distinctive histopathology and increased susceptibility to cardiac arrhythmias and risk for sudden death. Myocyte disarray (disorganized cell–cell contact) and cardiac fibrosis, the prototypic but protean features of HCM histopathology, are presumed triggers for ventricular arrhythmias that precipitate sudden death events. To assess relationships between arrhythmias and HCM pathology without confounding human variables, such as genetic heterogeneity of disease-causing mutations, background genotypes, and lifestyles, we studied cardiac electrophysiology, hypertrophy, and histopathology in mice engineered to carry an HCM mutation. Both genetically outbred and inbred HCM mice had variable susceptibility to arrhythmias, differences in ventricular hypertrophy, and variable amounts and distribution of histopathology. Among inbred HCM mice, neither the extent nor location of myocyte disarray or cardiac fibrosis correlated with
ex vivo
signal conduction properties or
in vivo
electrophysiologically stimulated arrhythmias. In contrast, the amount of ventricular hypertrophy was significantly associated with increased arrhythmia susceptibility. These data demonstrate that distinct somatic events contribute to variable HCM pathology and that cardiac hypertrophy, more than fibrosis or disarray, correlates with arrhythmic risk. We suggest that a shared pathway triggered by sarcomere gene mutations links cardiac hypertrophy and arrhythmias in HCM.
The role of large-scale spatially explicit and small-scale localized processes on the population dynamics of cereal aphids
Authors: Winder L. , Griffiths G.J.K. , Perry J.N. , Alexander C.J. , Holland J.M. , Kennedy P.J. , Birt A.
Published: December 2005

A field-scale study of the spatially explicit interaction between the carabid Poecilus cupreus Linnaeus, and two common aphid species (Sitobion avenae (Fabricius) and Metopolophium dirhodum (Walker)) in winter wheat was conducted. All three species showed considerable spatial pattern at the field scale. Activity-density of P. cupreus was an order of magnitude higher in the central part of the field compared to its periphery. Where P. cupreus activity-density was highest, S. avenae and M. dirhodum population peaks were delayed. Additionally, in the case of M. dirhodum, lower maximum counts were evident where P. cupreus activity-density was highest. An analysis of the movement of individual P. cupreus using release–recapture indicated that those beetles within the centre of the field exhibited reduced displacement, which may have caused the generation or maintenance of spatial pattern. Crop density was also measured throughout the field. Although crop density had no large-scale spatial pattern, its variability at the small-scale was consistent with an influence on aphid population dynamics. This study demonstrates empirically that both large-scale spatially explicit and small-scale localized processes influenced aphid population dynamics simultaneously.
Development of mass trapping technique for control of brinjal shoot and fruit borer, Leucinodes orbonalis (Lepidoptera: Pyralidae)
Authors: Cork A. , Alam S.N. , Rouf F.M.A. , Talekar N.S.
Published: December 2005

Locally-produced clear plastic water traps (12 cm × 14 cm base and 21 cm height) were optimized for use in large-scale mass trapping trials for control of brinjal fruit and shoot borer, Leucinodes orbonalis Guenée. Changing the shape (square and triangular) and number (two and four) of entry holes in the water trap had no significant effect on trap catch. Significantly more male moths were caught in traps treated with water containing powdered detergent than liquid detergent, light gear oil or insecticide. All water traps tested caught significantly higher numbers of moths than sticky delta traps with open sides under farmers' field conditions. Trap catches per 100 m2 were found to increase with increasing number of traps from 3 to 6 but the difference in catch between 4 and 6 traps per 100 m2 was not significant. Two small-scale replicated integrated pest management (IPM) trials were conducted consisting of the optimized water trap placed out with 10 m spacing (4 per 100 m2) and infested shoots pruned and destroyed. The first season trial had two treatments, IPM and farmers' practice in which farmers applied insecticide every two days in the peak harvest period. Overall, the percentage of healthy fruit and yields in both treatments were comparable at 53.8 and 49.6% and 20 and 19.4 tonnes per ha in the IPM and farmers' practice plots respectively. However, the initial infestations in the IPM plots (68%) were significantly higher than in farmers' practice plots (16%) due to the proximity of the nurseries used for the IPM plots to stacks of brinjal crop residues from the previous season that acted as a source of infestation. The second season's trials contained a third treatment in which IPM and farmers' practice were combined. The percent total healthy fruits harvested were 46.1, 58.6 and 69.1% respectively for the farmers' practice, farmers' practice plus IPM and IPM alone. Averaged total fruit yields were approximately 12 tonnes per ha for the farmers' practice plots and 30 tonnes per ha for each of the IPM-treated plots. The IPM plot had significantly fewer infested fruit than the IPM plus farmers practice plots and this was attributed to the activity of the larval parasitoid Trathala flavo-orbitalis (Cameron) that was suppressed in trial plots treated with insecticides.
Endocrine control of calcium and magnesium metabolism in
ruminants
Authors: Care A. D.
Published: December 2005

Although the importance of calcium and magnesium homoeostasis has been
recognized for many years the precise mechanisms by which this is achieved
are still not clearly understood. Over recent years interest in blood
calcium regulation has been stimulated by the discovery, isolation and
synthesis of calcitonin. Its significance in normal adults, however, remains
in some doubt (vide infra). In this paper is outlined our
present knowledge of the endocrine factors which help to regulate the
control of plasma calcium and magnesium concentration in ruminants through
the operation of negative feedback mechanisms. Mention will also be made of
those hormones which, although capable of altering the plasma concentrations
of either calcium or magnesium, are secreted independently of these
concentrations. It will be seen that in many instances the chemical
similarity between calcium and magnesium is reflected in hormone effects or
in hormone secretion rates. However, this is not always found to be so, e.g.
the control of calcitonin secretion appears to be affected in different
directions by plasma calcium and magnesium concentrations.
Enzymes and the assessment of protein nutrition
Authors: Waterlow J. C. , Stephen Joan M. L.
Published: December 2005

This symposium is concerned with the assessment of protein nutritional status in man. The question we have to examine is whether measurements of enzyme activity are, or may be in the future, of any value for this purpose. There are several concepts which may be useful in considering this problem, such as the nature of enzymes and the regulation of their amount in the body, the effect on activity of a biochemical lesion at the cellular level, and the adaptive changes that reflect an altered balance of metabolic pathways.
DNAVis: interactive visualization of comparative genome annotations
Authors: Fiers Mark W. E. J. , van de Wetering Huub , Peeters Tim H. J. M. , van Wijk Jarke J. , Nap Jan-Peter
Published: December 2005

Summary: The software package DNAVis offers a fast, interactive and real-time visualization of DNA sequences and their comparative genome annotations. DNAVis implements advanced methods of information visualization such as linked views, perspective walls and semantic zooming, in addition to the display of heterologous data in dot plot-like matrix views.

Availability: The software is freely available at ; the source code is available upon request.

Contact:  janpeter.nap@wur.nl

Supplementary information: Figures are available at Bioinformatics online; documentation and data are available at
Lateral gene transfer of a dermonecrotic toxin between spiders and bacteria
Authors: Cordes Matthew H. J. , Binford Greta J.
Published: December 2005

Motivation: Spiders in the genus Loxosceles, including the notoriously toxic brown recluse, cause severe necrotic skin lesions owing to the presence of a venom enzyme called sphingomyelinase D (SMaseD). This enzyme activity is unknown elsewhere in the animal kingdom but is shared with strains of pathogenic Corynebacteria that cause various illnesses in farm animals. The presence of the same toxic activity only in distantly related organisms poses an interesting and medically important question in molecular evolution.

Results: We use superpositions of recently determined structures and sequence comparisons to infer that both bacterial and spider SMaseDs originated from a common, broadly conserved domain family, the glycerophosphoryl diester phosphodiesterases. We also identify a unique sequence/structure motif present in both SMaseDs but not in the ancestral family, supporting SMaseD origin through a single divergence event in either bacteria or spiders, followed by lateral gene transfer from one lineage to the other.

Contact: cordes@email.arizona.edu; binford@lclark.edu
A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data
Authors: MacIsaac Kenzie D. , Gordon D. Benjamin , Nekludova Lena , Odom Duncan T. , Schreiber Joerg , Gifford David K. , Young Richard A. , Fraenkel Ernest
Published: December 2005

Motivation: Genome-wide chromatin-immunoprecipitation (ChIP-chip) detects binding of transcriptional regulators to DNA in vivo at low resolution. Motif discovery algorithms can be used to discover sequence patterns in the bound regions that may be recognized by the immunoprecipitated protein. However, the discovered motifs often do not agree with the binding specificity of the protein, when it is known.

Results: We present a powerful approach to analyzing ChIP-chip data, called THEME, that tests hypotheses concerning the sequence specificity of a protein. Hypotheses are refined using constrained local optimization. Cross-validation provides a principled standard for selecting the optimal weighting of the hypothesis and the ChIP-chip data and for choosing the best refined hypothesis. We demonstrate how to derive hypotheses for proteins from 36 domain families. Using THEME together with these hypotheses, we analyze ChIP-chip datasets for 14 human and mouse proteins. In all the cases the identified motifs are consistent with the published data with regard to the binding specificity of the proteins.

Availability: THEME is freely available for download.

Contact:  fraenkel-admin@mit.edu

Supplementary information:
Clusterv: a tool for assessing the reliability of clusters discovered in DNA microarray data
Authors: Valentini Giorgio
Published: December 2005

Summary: We present a new R package for the assessment of the reliability of clusters discovered in high-dimensional DNA microarray data. The package implements methods based on random projections that approximately preserve distances between examples in the projected subspaces.

Availability:  

Contact:  valentini@dsi.unimi.it

Supplementary information:
PubMed Assistant: a biologist-friendly interface for enhanced PubMed search
Authors: Ding Jing , Hughes LaRon M. , Berleant Daniel , Fulmer Andy W. , Wurtele Eve Syrkin
Published: December 2005

Summary: MEDLINE is one of the most important bibliographical information sources for biologists and medical workers. Its PubMed interface supports Boolean queries, which are potentially expressive and exact. However, PubMed is also designed to support simplicity of use at the expense of query expressiveness and exactness. Many PubMed users have never tried explicit Boolean queries. We developed a Java program, PubMed Assistant, to make literature access easier in several ways. PubMed Assistant provides an interface that efficiently displays information about the citations and includes useful functions such as keyword highlighting, export to citation managers, clickable links to Google Scholar and others that are lacking in PubMed.

Availability: PubMed Assistant and a detailed online manual are freely available at under a GPL (GNU General Public License).

Contact:  berleant@iastate.edu
Reorganization of hair follicles in human skin organ culture induced by cultured human follicle‐derived cells
Authors: Krugluger Walter , Rohrbacher Wolfgang , Laciak Katharina , Moser Karl , Moser Claudia , Hugeneck Joerg
Published: December 2005

Abstract:  Studies of human hair follicle (HF) induction by follicle‐derived cells have been limited due to a lack of suitable test systems. In this study, we established a skin organ culture system which supports HF formation by follicle‐derived cells. Long‐term skin organ cultures were set up from human retroauricular skin specimens and maintained in culture for up to 8 weeks. In vitro expanded human HF‐derived cells from the dermal papilla (DP) and the outer root sheath (ORS) were injected together into the skin specimens and evaluated for their ability to induce reorganization of HFs. Macroscopic analysis of the cultured skin specimens demonstrated the growth of velus‐like hair after 4 weeks in culture. Histologic evaluation of the cultured skin specimens after 8 weeks of culture revealed multiple miniaturized HFs with sebaceous glands. In addition, cell clusters of various differentiation stages could be demonstrated in serial sections of the cultured skin specimens. Labeling of HF‐derived cells with the fluorescence dye CFDA‐1 prior to injection suggested a de novo reorganization of HFs out of the injected cells. In conclusion, the study demonstrated HF formation by HF‐derived cells in an in vitro skin organ culture model.
Modulation of vascular endothelial growth factor receptors in melanocytes
Authors: Kim Ellen J. , Park Hee‐Young , Yaar Mina , Gilchrest Barbara A.
Published: December 2005

Abstract:  Vascular endothelial growth factor (VEGF) is constitutively produced by keratinocytes, but has no known epidermal target cell. We now report that normal human melanocytes (Mc) maintained in serum‐free, hormone‐, and growth factor‐supplemented medium lacking phorbol ester and choleragen constitutively express VEGF receptor‐1 (VEGFR‐1), VEGFR‐2, and neuropilin‐1. Furthermore, stimulation of Mc with VEGF165 isoform leads to phosphorylation of VEGFR‐2, the receptor responsible for most of the VEGF‐mediated effects in endothelial cells, suggesting that the receptor is functional. Interestingly, in Mc, VEGFR‐2 expression is induced by ultraviolet irradiation and is downregulated by VEGF and tumor necrosis factor‐α. Prolonged culture (>8 weeks) in the presence of phorbol ester abrogates VEGFR‐2 expression, explaining previous reports that Mc do not express VEGFR‐1 and VEGFR‐2. These data suggest that VEGF may play a role in Mc behavior in skin.
Defining the caspase‐containing apoptotic machinery contributing to cornification in human epidermal equivalents
Authors: Chaturvedi Vijaya , Sitailo Leonid A. , Bodner Barbara , Denning Mitchell F. , Nickoloff Brian J.
Published: December 2005

Abstract:  Whether terminal differentiation/stratum corneum formation of keratinocytes (KCs) represents a form of programmed cell death, utilizing mediators of classical apoptosis, is unclear. Apoptosis, an evolutionarily conserved death process, is comprised of extrinsic and intrinsic pathways, which converge using caspase 3. To define upstream and downstream caspases involved in terminal differentiation, we utilized human epidermal equivalents (EEs). Using submerged cultures comprised of human KCs, EEs were sequentially analyzed before and after being raised to an air/liquid (A/L) interface at 3–24 h intervals. At each time point, EEs were analyzed morphologically and for specific enzyme activity to distinguish different initiator (caspases 1, 2, 8, 9) and effector caspases (3, 6, 7). Terminal differentiation began at 6–8 h, as defined by stratum corneum with loricirin expression and completed at 18–24 h producing an epidermis resembling normal skin. Enzyme activity for caspases 1, 2, 3, 6, 7, 8, and 9 (but not 4, 5) was enhanced (>two‐fold nmol/mg/h) at 3–6 h compared with submerged cultures. Processing of caspase 14 occurred at 18 h, and cleaved caspase 14 was increased at 24 h. Activated caspase 3‐positive and terminal deoxynucleotidyl transferase‐mediated nick end labeling‐positive KCs were identified in EEs at 3–6 h corresponding to initiation sites of terminal differentiation. Addition of caspase inhibitors reduced levels of involucrin and loricrin in EEs raised to an A/L interface. We conclude caspases function as important death effectors strategically positioned at intersection of intrinsic and extrinsic pathways in KCs undergoing stratum corneum formation.
Dietary constituents are able to play a beneficial role in canine epidermal barrier function
Authors: Watson Adrian L. , Fray Tim R. , Bailey Julie , Baker Claire B. , Beyer Sally A. , Markwell Peter J.
Published: December 2005

Abstract:  Epidermal barrier function is a critical attribute of mammalian skin. The barrier is responsible for preventing skin‐associated pathologies through controlling egress of water and preventing ingress of environmental agents. Maintaining the quality and integrity of the epidermal barrier is therefore of considerable importance. Structurally, the barrier is composed of two main parts, the corneocytes and the intercellular lamellar lipid. The epidermal lamellar lipid comprises mainly ceramides, sterols and fatty acids. Twenty‐seven nutritional components were screened for their ability to upregulate epidermal lipid synthesis. Seven of the 27 nutritional components (pantothenate, choline, nicotinamide, histidine, proline, pyridoxine and inositol) were subsequently retested using an in vitro transepidermal diffusion experimental model, providing a functional assessment of barrier properties. Ultimately, the best performing five nutrients were fed to dogs at supplemented concentrations in a 12‐week feeding study. Barrier function was measured using transepidermal water loss (TEWL). It was found that a combination of pantothenate, choline, nicotinamide, histidine and inositol, when fed at supplemented concentrations, was able to significantly reduce TEWL in dogs after 9 weeks.
Phytocomponents of triterpenoids, oleanolic acid and ursolic acid, regulated differently the processing of epidermal keratinocytes via PPAR‐α pathway
Authors: Lee Hae Kwang , Nam Gae Won , Kim Seung Hun , Lee Seung Hun
Published: December 2005

Abstract:  Naturally occurring triterpenoids such as oleanolic acid (OA) and ursolic acid (UA) are known to have anti‐inflammatory and anticarcinogenic activities in some types of cells. Although it has been reported that UA increases the amount of ceramide in keratinocytes, there is little study on the mechanism of triterpenoids involved in the differentiation of keratinocytes as well as their effects on epidermal permeability barrier. A study was therefore conducted to determine whether OA and UA could stimulate the differentiation of epidermal keratinocytes through peroxisome proliferator‐activated receptor (PPAR)‐α activation. This work was then extended to investigate the rate of formation of cornified envelope as a marker in the terminal differentiation of keratinocytes and the amount of transglutaminase in human keratinocytes treated with OA and UA. It was shown that OA induced the differentiation of keratinocytes, whereas UA had little effect. In addition, reporter gene assay using PPAR response element activity demonstrated that OA might be related to the increase of PPAR‐α activity in CV‐1 cells. Moreover, it enhanced the recovery of epidermal permeability barrier function as well as increased ceramides in epidermis after topical application. We therefore propose that the effect of OA on the stimulation of differentiation in epidermal keratinocytes seems to be highly related to activation of PPAR‐α.
Diagnosis of transfusion‐associated graft‐vs.‐host disease: the importance of short tandem repeat analysis
Authors: Sage D. , Stanworth S. , Turner D. , Navarrete C.
Published: December 2005

summary.  Transfusion‐associated graft‐vs.‐host disease (TA‐GvHD) can occur following transfusion of blood products containing immunocompetent lymphocytes, usually from HLA homozygous donors, into immunocompromised patients sharing one HLA haplotype with the donor. The diagnosis of TA‐GvHD may be delayed due to the initial nonspecific clinical features involved. Investigations to detect the presence of donor‐derived cells in the blood and/or affected tissues of the recipient are essential to confirm the diagnosis.

We report the investigation of suspected TA‐GvHD using short tandem repeat (STR) analysis, to detect the presence of donor cells (chimerism), in an immunocompetent patient admitted for coronary artery bypass surgery. Peripheral blood and skin biopsies (from affected and nonaffected sites) from the patient and peripheral blood samples from the implicated donors were taken for HLA typing and STR analysis.

STR analysis revealed the presence of donor material in the patient's peripheral blood sample and in DNA extracted from the affected skin biopsy but not the unaffected biopsy, suggesting lymphocytes from this donor were responsible for the development of TA‐GvHD. Furthermore, HLA typing results supported the diagnosis of TA‐GvHD. These data demonstrate the use of STR and HLA analysis as effective tools in the diagnosis of TA‐GvHD.
Donors' blood group declaration before donation can be used as a tool for electronic crossmatching
Authors: Arslan Ö.
Published: December 2005

summary.  Electronic crossmatching (E‐XM) is used to detect ABO incompatibility. In developing countries, as many of the donations are from first‐time donors, it is difficult to guarantee the accuracy of the ABO/Rh label on these units to use them for E‐XM. This problem was overcome with a new software ‘hemosoft’, using donors' blood group declaration before donation as a tool for E‐XM.

During registration, donors either declare their blood group or give no comment. For, ABO/Rh grouping, either two results from different donations or only one in concordant with the declaration before donation is needed. If there is a conflict, second typing is performed from the unit segment. If donors give no declaration, two different technicians perform typing, one from the sample tube and the other from the unit segment.

Of 18 618 donations performed, 640 (3%) were repeated and the rest were first‐time donations. In 16 327, typing was performed once, as the blood group declaration and the typing results were identical. In 2407, grouping was performed twice, as donors gave no declaration or conflicts between declaration and typing results were found. No labelling or wrong unit‐release errors were detected in units donated, typed and labelled in our centre. In 26 402 donations, 16 314 (61·8%) E‐XMs were performed. No major haemolytic transfusion reaction was recorded.

Donors' ABO/Rh declaration before donation can be used as a tool for E‐XM, instead of the requirement for serological confirmation or a second donation to guarantee grouping.
Novel method for screening for the presence of haemoglobin S in blood
Authors: Higgins T. N. , Ridley B. , Clarke G.
Published: December 2005

summary.  A high‐performance liquid chromatography (HPLC) method designed for the measurement of haemoglobin (Hb)A1c in blood was investigated for use as a screening method for the presence of HbS in blood. In the Bio‐Rad VARIANT II HbA1c method, HbS was found to have a specific retention time and percentage Hb value that enabled the detection of HbS in blood. Other Hb variants did not have the same combination of retention time and percentage Hb as HbS. The HPLC method was superior to the HbS solubility test in ease of performance and readability. Also, the proposed method showed less interference than the solubility test and could be used with samples from all age groups. The proposed method takes 3 min per sample to perform and is thus suitable for large‐scale screening.
Oral malignant melanoma – the effect of coarse fractionation radiotherapy alone or with adjuvant carboplatin therapy
Authors: Murphy S. , Hayes A. M. , Blackwood L. , Maglennon G. , Pattinson H. , Sparkes A. H.
Published: December 2005

A retrospective study was undertaken of dogs presented to the Animal Health Trust for treatment of oral malignant melanoma, without radiographic evidence of pulmonary metastases. Group 1 (n = 13) received radiotherapy of the primary and any lymph node metastases (4 weekly fractions of 9 Gy); and group 2 (n = 15) were treated the same but additionally received between two and six doses carboplatin at 300 mg m−2every 3 weeks. Median survival times for the two groups were 307 and 286 days, respectively (P > 0.05). In addition, carboplatin therapy did not significantly reduce the proportion of dogs dying due to metastases (three from group 1 and four from group 2). We found no evidence of a beneficial effect of carboplatin therapy over radiotherapy alone.
The newly synthesized linoleic acid derivative DCP‐LA ameliorates memory deficits in animal models treated with amyloid‐β peptide and scopolamine
Authors: NAGATA Tetsu , YAMAMOTO Satoshi , YAGUCHI Takahiro , ISO Hiroyuki , TANAKA Akito , NISHIZAKI Tomoyuki
Published: December 2005

Background:  In our earlier study, 8‐[2‐(2‐pentyl‐cyclopropylmethyl)‐cyclopropyl]‐octanoic acid (DCP‐LA), a newly synthesized linoleic acid derivative with cyclopropane rings instead of cis‐double bonds, facilitated hippocampal synaptic transmission by stimulating glutamate release from presynaptic terminals as mediated via α7 acetylcholine (Ach) receptors under the influence of protein kinase C. The present study assessed the possibility of using DCP‐LA as a cognitive enhancer in animal models.

Methods:  Amyloid‐β1−40 peptide (300 pM/day) or saline was continuously injected in the right lateral ventricle of rats for 2 weeks. Then, the water maze test was carried out, once per day for 7 days, 1 h after the intraperitoneal injection with DCP‐LA or saline. In a different set of experiments, rats were intraperitoneally injected with scopolamine (1 mg/kg) and the water maze test was performed twice per day, with the first test taking place 1 h after the intraperitoneal injection with DCP‐LA, galantamine or saline, and the second test starting 2 min after the end of the first.

Results:  Continuous intraventricular injection with amyloid‐β1−40 peptide in the rat lateral ventricle prolonged the latency for acquisition in the water maze test. DCP‐LA (1 mg/kg, intraperitoneal (i.p.)) significantly improved the impairment, which reached a level similar to the latency for sham. Furthermore, DCP‐LA (1 mg/kg, i.p.) significantly ameliorated learning and memory deficits in rats treated with scopolamine and was, if not more, effective than galantamine, a modest inhibitor of acetylcholinesterase with nicotinic ACh receptor modulation.

Conclusion:  The results of the present study show that DCP‐LA ameliorates learning and memory deficits induced by amyloid‐β1−40 peptide or scopolamine. DCP‐LA may thus offer new hope for dementia patients.
The Aryl Hydrocarbon Receptor Nuclear Translocator Gene Polymorphism in Patients With Recurrent Miscarriage
Authors: Sullivan Amy E. , Nelson Leesa , Frias Antonio E. , Porter T. Flint , Branch D. Wane , Silver Robert M.
Published: December 2005

Objective  The human aryl hydrocarbon receptor nuclear translocator gene (ARNT) is crucial for embryonic development. Knockout of ARNT is embryonic lethal. We thus hypothesized that some cases of recurrent miscarriage (RM) may be due to a polymorphism in the ARNT gene.

Methods  Polymerase chain reaction was used to compare the gene frequencies of a polymorphism in codon 511 of the ARNT gene in 170 women with idiopathic RM and 105 controls.

Results  Using the Hardy–Weinberg equilibrium calculation, the predicted ARNT genotype frequencies for the N511/N511, N511/D511, and D511/D511 genotypes were 0, 2, and 167 respectively. The observed frequencies were 0, 2, and 168 (NS). The N/511/D511 genotype was detected in 1.2% of cases and 2.8% of controls, and the D511/D511genotype was detected in 98.8% of cases and 97.2% of controls (NS).

Conclusions  In our cohort of patients, the polymorphism in codon 511 of the ARNT gene is not associated with RM.
Insights on the female reproductive system in Hippolyte inermis (Decapoda, Caridea): is this species really hermaphroditic?
Authors: Cobos Vanesa , Díaz Vanessa , Raso García , Enrique Jose , Manjón‐Cabeza María Eugenia
Published: December 2005

Abstract. The majority of the published data about the reproductive biology of the decapod shrimp, Hippolyte inermis support the idea that this species is a protandric hermaphrodite, as is reported to be the case for certain other caridean species. However, our studies, based on the relative growth of the male reproductive appendage and histological examinations of the ovary, testes, oviducts, and deferentia vasa, indicate that there is no evidence supporting the occurrence of protandry. The first report of anomalies in the process of sexual inversion is credited to Reverberi (1950); however, we have obtained no evidence to support this phenomenon in H. inermis. We have not found either ovotestes or testes transforming into ovotestes. Therefore, we propose that H. inermis is a gonochoric species.