bluuebunny/crossref_metadata_2025 huggingface dataset:
Epidemiological Analysis Defining Concurrent Outbreaks of Serratia marcescens and Methicillin-Resistant Staphylococcus aureus in a Neonatal Intensive-Care Unit
Authors: Campbell Judith R. , Zaccaria Elena , Mason Edward O. , Baker Carol J.
Published: September 2009

Objective:

To describe the epidemiology, interventions, and molecular typing methods used during the investigation and control of concurrent outbreaks of Serratia marcescens and methicillin-resistant Staphylococcus aureus (MRSA) infections in a neonatal intensive-care unit (NICU).

Setting:

A 206-bed women's and infants' hospital with a 48-bed NICU.

Design:

A 22-week, prospective, descriptive study of all NICU infants with S marcescens or MRSA infection or colonization. Repetitive polymerase chain reaction (rep PCR) and pulsed-field gel electrophoresis (PFGE), respectively, were applied to the typing of S marcescens and MRSA isolates.

Interventions:

Infants with S marcescens or MRSA infection or colonization were placed in isolation; all other infants were cohorted. A multidisciplinary task force implemented education for all hospital and medical staff regarding policies essential for outbreak control. Changes in physical setting and patient contact procedure were required to promote adherence to existing policies.

Results:

Two premature infants had S marcescens infection, and five were colonized; rep PCR verified that both invasive and three of five colonizing isolates were related genotypically. Five bacteremic and 10 MRSA-colonized infants were identified; PFGE confirmed that 12 of the isolates had similar electrophoretic patterns. S marcescens infection was eliminated from the NICU 3 weeks after interventions were initiated. MRSA infections also were eliminated, and MRSA colonization fell to below pre-outbreak rates within 8 weeks. Despite a 100% increase in NICU patient days per month during the subsequent 2 years, no further clusters of S marcescens or MRSA infection have occurred.

Conclusions:

Concurrent outbreaks of S marcescens and MRSA in an NICU were confirmed by genotyping of strains. Control was achieved by isolation and cohorting of patients and strict adherence to NICU policies and procedures.
Identification of genes involved in the same pathways using a Hidden Markov Model-based approach
Authors: Senf Alexander , Chen Xue-wen
Published: September 2009

Motivation: The sequencing of whole genomes from various species has provided us with a wealth of genetic information. To make use of the vast amounts of data available today it is necessary to devise computer-based analysis techniques.

Results: We propose a Hidden Markov Model (HMM) based algorithm to detect groups of genes functionally similar to a set of input genes from microarray expression data. A subset of experiments from a microarray is selected based on a set of related input genes. HMMs are trained from the input genes and a group of random gene input sets to provide significance estimates. Every gene in the microarray is scored using all HMMs and significant matches with the input genes are retained. We ran this algorithm on the life cycle of Drosophila microarray data set with KEGG pathways for cell cycle and translation factors as input data sets. Results show high functional similarity in resulting gene sets, increasing our biological insight into gene pathways and KEGG annotations. The algorithm performed very well compared to the Signature Algorithm and a purely correlation-based approach.

Availability: Java source codes and data sets are available at http://www.ittc.ku.edu/∼xwchen/software.htm

Contact:  xwchen@ittc.ku.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Why compare marine ecosystems?
Authors: Murawski Steven A. , Steele John H. , Taylor Phillip , Fogarty Michael J. , Sissenwine Michael P. , Ford Michael , Suchman Cynthia
Published: September 2009

Murawski, S. A., Steele, J. H., Taylor, P., Fogarty, M. J., Sissenwine, M. P., Ford, M., and Suchman, C. 2010. Why compare marine ecosystems? – ICES Journal of Marine Science, 67: 1–9. Effective marine ecosystem-based management (EBM) requires understanding the key processes and relationships controlling the aspects of biodiversity, productivity, and resilience to perturbations. Unfortunately, the scales, complexity, and non-linear dynamics that characterize marine ecosystems often confound managing for these properties. Nevertheless, scientifically derived decision-support tools (DSTs) are needed to account for impacts resulting from a variety of simultaneous human activities. Three possible methodologies for revealing mechanisms necessary to develop DSTs for EBM are: (i) controlled experimentation, (ii) iterative programmes of observation and modelling (“learning by doing”), and (iii) comparative ecosystem analysis. We have seen that controlled experiments are limited in capturing the complexity necessary to develop models of marine ecosystem dynamics with sufficient realism at appropriate scales. Iterative programmes of observation, model building, and assessment are useful for specific ecosystem issues but rarely lead to generally transferable products. Comparative ecosystem analyses may be the most effective, building on the first two by inferring ecosystem processes based on comparisons and contrasts of ecosystem response to human-induced factors. We propose a hierarchical system of ecosystem comparisons to include within-ecosystem comparisons (utilizing temporal and spatial changes in relation to human activities), within-ecosystem-type comparisons (e.g. coral reefs, temperate continental shelves, upwelling areas), and cross-ecosystem-type comparisons (e.g. coral reefs vs. boreal, terrestrial vs. marine ecosystems). Such a hierarchical comparative approach should lead to better understanding of the processes controlling biodiversity, productivity, and the resilience of marine ecosystems. In turn, better understanding of these processes will lead to the development of increasingly general laws, hypotheses, functional forms, governing equations, and broad interpretations of ecosystem responses to human activities, ultimately improving DSTs in support of EBM.
PLZF is a regulator of homeostatic and cytokine-induced myeloid development
Authors: Doulatov Sergei , Notta Faiyaz , Rice Kim L. , Howell Louise , Zelent Arthur , Licht Jonathan D. , Dick John E.
Published: September 2009

A major question in hematopoiesis is how the system maintains long-term homeostasis whereby the generation of large numbers of differentiated cells is balanced with the requirement for maintenance of progenitor pools, while remaining sufficiently flexible to respond to periods of perturbed cellular output during infection or stress. We focused on the development of the myeloid lineage and present evidence that promyelocytic leukemia zinc finger (PLZF) provides a novel function that is critical for both normal and stress-induced myelopoiesis. During homeostasis, PLZF restricts proliferation and differentiation of human cord blood-derived myeloid progenitors to maintain a balance between the progenitor and mature cell compartments. Analysis of PLZF promoter-binding sites revealed that it represses transcription factors involved in normal myeloid differentiation, including GFI-1, C/EBPα, and LEF-1, and induces negative regulators DUSP6 and ID2. Loss of ID2 relieves PLZF-mediated repression of differentiation identifying it as a functional target of PLZF in myelopoiesis. Furthermore, induction of ERK1/2 by myeloid cytokines, reflective of a stress response, leads to nuclear export and inactivation of PLZF, which augments mature cell production. Thus, negative regulators of differentiation can serve to maintain developmental systems in a primed state, so that their inactivation by extrinsic signals can induce proliferation and differentiation to rapidly satisfy increased demand for mature cells.
The Starlet Sea Anemone Nematostella vectensis: An Anthozoan Model Organism for Studies in Comparative Genomics and Functional Evolutionary Developmental Biology
Authors: Genikhovich Grigory , Technau Ulrich
Published: September 2009

INTRODUCTION

Nematostella vectensis is a brackish water sea anemone of the family Edwardsiidae. The polyps can be reared with a full life cycle in laboratories with direct access to seawater or in inland laboratories. Robust protocols for the induction of gametogenesis have been established, which can yield thousands of embryos every day and allow for fairly synchronized development of individual batches. Embryos develop into primary polyps within 7-9 d and sexual maturity is reached after 3-6 mo. Zygotes are accessible for most modern molecular and developmental techniques, including gene knockdown by morpholino injection, generation of transgenics, in situ hybridization, and antibody staining. Various cDNA libraries and a bacterial artificial chromosome (BAC) library are available and the genome has been sequenced at ~6.5X coverage. The diploid set of chromosomes is 30 and, based on the sequence assembly, the genome size is 450 Mbp. Expressed sequence tag (EST) and genome analyses have emphasized the striking degree of sequence conservation and complexity in terms of gene content between Nematostella and vertebrates. This indicates that many ancestral traits have been preserved in Nematostella. Taken together with its experimental tractability, this makes Nematostella a very attractive model system among the representatives of basal metazoan lineages.
In Vivo Imaging of Mammalian Cells: Image Acquisition and Analysis: Figure 1.
Authors: Swedlow Jason R. , Andrews Paul D. , Platani Melpomeni
Published: September 2009

INTRODUCTION

Live cell imaging provides a powerful technique for the analysis of molecular dynamics within cells. Advances in imaging technology and probe design have established this approach as an important tool in modern biology. It is now possible to obtain commercial turnkey systems for digital imaging using a number of different imaging modalities. Nevertheless, it still requires considerable technical care and expertise to conduct a successful experiment. To perform a successful imaging experiment, it is important to maximize the signal-to-noise ratio (S:N) while minimizing damage to the cells. In this article, we focus on the use of fluorescence microscopy in live cell imaging, although most of the points discussed are relevant to any type of imaging. We describe many of the methods and considerations that are required for performing a successful imaging experiment in living cells. However, we do not provide a single recipe for success: The approach is much too empirical and depends on careful observation of the particular cells under investigation.
In Vivo DNase I, MNase, and Restriction Enzyme Footprinting via Ligation-Mediated Polymerase Chain Reaction (LM-PCR): Figure 1.
Authors: Carey Michael F. , Peterson Craig L. , Smale Stephen T.
Published: September 2009

INTRODUCTION

Genomic footprinting and related methods can reveal important protein-DNA interactions not detected using other methods. This protocol presents procedures for DNase I genomic footprinting, micrococcal nuclease (MNase) mapping of nucleosome positioning, and monitoring nucleosome remodeling via restriction enzyme accessibility. These procedures rely on a technique known as ligation-mediated polymerase chain reaction (LM-PCR), which can be used in concert with a variety of agents that cleave or modify genomic DNA within an intact cell or nucleus, with each agent providing unique insight into the regulation of a gene. LM-PCR is a powerful technique for detecting DNA strand breaks within a complex sample because of its extreme sensitivity and specificity. This general method has proven to be invaluable for several purposes, in particular, in analysis of the properties of an endogenous DNA locus. Coupling LM-PCR to DNase I digestion results in assays that are analogous to in vitro DNase I footprinting or methylation protection. Coupling to MNase digestion allows for the high-resolution analysis of nucleosome positioning. Coupling to restriction enzyme digestion in isolated nuclei provides evidence of nucleosome remodeling. For each of these methods, nuclei must first be isolated by lysis of the cells with a non-ionic detergent, followed by centrifugation. The isolated nuclei are then treated with the appropriate nuclease, followed by purification of the genomic DNA. LM-PCR is then performed on the cleaved genomic DNA.
In Situ Hybridization of Starlet Sea Anemone (Nematostella vectensis) Embryos, Larvae, and Polyps
Authors: Genikhovich Grigory , Technau Ulrich
Published: September 2009

INTRODUCTION

Whole-mount in situ hybridization is used to reveal the spatiotemporal expression pattern of a gene in tissue samples without sectioning the tissue. This protocol describes procedures for fixing starlet sea anemone (Nematostella vectensis) embryos, larvae, and polyps, hybridizing with a digoxigenin (DIG)-labeled RNA probe, and detecting the bound probe.
Extraction of DNA from Adult Amphioxus Tissue
Authors: Yu J.K. Sky , Holland Linda Z.
Published: September 2009

INTRODUCTION

This protocol describes the extraction of DNA from adult amphioxus (Branchiostoma floridae). Generally, we use adult B. floridae animals for extracting genomic DNA because the embryos are more precious and are only available during the summer breeding season. Whole adult amphioxus or dissected tissues are rapidly frozen and crushed to produce readily digestible pieces. The processed tissue is incubated in a buffer with proteinase K and sodium dodecyl sulfate (SDS) until most of the cellular protein is degraded. After removing protein from the samples by successive organic extractions, genomic DNA is recovered by ethanol precipitation. The resulting DNA can be used for Southern blotting, polymerase chain reaction (PCR), or other applications.
Construction of Gene-Targeting Vectors by Recombineering
Authors: Lee Song-Choon , Liu Pentao
Published: September 2009

INTRODUCTION

The critical step in generating a knockout mouse is gene-targeting vector construction. Recombineering technology has greatly streamlined the vector construction process. This protocol describes a method for making conditional knockout (cko) targeting vectors using the pSim18 plasmid. This plasmid carries the three λ phage Red genes (Gam, Bet, and Exo) under the control of the pL promoter, which is in turn regulated by the temperature-sensitive CI857 repressor. Hence, the heat-inducible recombineering functions can be easily delivered to bacterial artificial chromosomes (BACs) using a simple plasmid transformation, allowing one to manipulate any cloned mouse genomic region in Escherichia coli for cko vector construction. The conditional targeting vectors described in this protocol generate a flexible reporter/null/conditional allele in the mouse.
Egg Collection and In Vitro Fertilization of the Western Clawed Frog Xenopus tropicalis
Authors: Showell Chris , Conlon Frank L.
Published: September 2009

INTRODUCTION

The eggs of Xenopus laevis have been widely used in studies investigating a variety of aspects of biology, such as control of the cell cycle, RNA processing, and the cytoskeleton. The Western clawed frog Xenopus tropicalis is likely to prove useful for such studies in the future, because of the potential to combine traditional experimental approaches with genetic analysis and the available genome sequence. The eggs of X. tropicalis are also a key starting material for transgenesis. Here, we describe a method for the routine collection of eggs from X. tropicalis, together with a method for in vitro fertilization. Very large numbers of eggs, often more than 2000, can be obtained from a single X. tropicalis female. In vitro fertilization is a valuable alternative to natural mating for generating embryos. It is particularly useful for microinjection experiments and when collecting embryos at a series of defined developmental stages (e.g., for studies of gene expression), because it produces embryos that develop synchronously during early embryonic development. The typical yield of embryos ranges from several hundred to more than 1000 per fertilization.
Effects of data incompleteness on the relative performance of parsimony and Bayesian approaches in a supermatrix phylogenetic reconstruction of Mustelidae and Procyonidae (Carnivora)
Authors: Wolsan Mieczyslaw , Sato Jun J.
Published: September 2009

Missing data are commonly thought to impede a resolved or accurate reconstruction of phylogenetic relationships, and probabilistic analysis techniques are increasingly viewed as less vulnerable to the negative effects of data incompleteness than parsimony analyses. We test both assumptions empirically by conducting parsimony and Bayesian analyses on an approximately 1.5 × 106‐cell (27 965 characters × 52 species) mustelid–procyonid molecular supermatrix with 62.7% missing entries. Contrary to the first assumption, phylogenetic relationships inferred from our analyses are fully (Bayesian) or almost fully (parsimony) resolved topologically with mostly strong support and also largely in accord with prior molecular estimations of mustelid and procyonid phylogeny derived with parsimony, Bayesian, and other probabilistic analysis techniques from smaller but complete or nearly complete data sets. Contrary to the second assumption, we found no compelling evidence in support of a relationship between the inferior performance of parsimony and taxon incompleteness (i.e. the proportion of missing character data for a taxon), although we found evidence for a connection between the inferior performance of parsimony and character incompleteness (i.e. no overlap in character data between some taxa). The relatively good performance of our analyses may be related to the large number of sampled characters, so that most taxa (even highly incomplete ones) are represented by a sufficient number of characters allowing both approaches to resolve their relationships.

© The Willi Hennig Society 2009.
Fibroblast growth factor receptor 3 mutation in voided urine is a useful diagnostic marker and significant indicator of tumor recurrence in non‐muscle invasive bladder cancer
Authors: Miyake Makito , Sugano Kokichi , Sugino Hitomi , Imai Kazuho , Matsumoto Eri , Maeda Koshi , Fukuzono Shinich , Ichikawa Hiroki , Kawashima Kiyotaka , Hirabayashi Kaoru , Kodama Tetsuro , Fujimoto Hiroyuki , Kakizoe Tadao , Kanai Yae , Fujimoto Kiyohide , Hirao Yoshihiko
Published: September 2009

The fibroblast growth factor receptor (FGFR)‐3 gene encodes a receptor tyrosine kinase that is frequently mutated in non‐muscle invasive bladder cancer (NMIBC). A sensitive and quantitative assay using peptide nucleic acid‐mediated real‐time PCR was developed for detecting FGFR3 mutations in the urine samples and evaluated as a molecular marker for detecting intravesical recurrence of NMIBC in patients undergoing transurethral resection of bladder tumor. FGFR3 mutation was examined in tumor tissues and serially taken pre‐ and postoperative urine sediments in 45 NMIBC patients with a median follow up of 32 months. FGFR3 mutations were detected in 53.3% (24/45) of primary tumor tissues, among which intravesical recurrence developed in 37.5% (9/24) of cases. FGFR3 mutation in the primary tumor was not a significant prognostic indicator for recurrence, while the proportion of FGFR3 mutation (i.e. tumor cellularity was ≥11%) in the preoperative urine sediments was a significant indicator for recurrence in patients with FGFR3 mutations in the primary tumors. FGFR3 mutations were detected in 78% (7/9) of postoperative urine samples from recurrent cases with FGFR3 mutations in the tumor, while no mutations were detected in the urine of 15 non‐recurrent cases. Urine cytology was negative in all cases with FGFR3 mutations in the primary tumors, while the sensitivity of cytological examination was as high as 56% (5/9) in cases showing wild‐type FGFR3 in the primary tumors. Urine FGFR3 mutation assay and cytological examination may be available in the future as complementary diagnostic modalities in postoperative management of NMIBC. (Cancer Sci 2009)
The role of mitogen‐activated protein (MAP) kinase signalling components and the Ste12 transcription factor in germination and pathogenicity of Botrytis cinerea
Authors: SCHAMBER ASTRID , LEROCH MICHAELA , DIWO JANINE , MENDGEN KURT , HAHN MATTHIAS
Published: September 2009

In all fungi studied so far, mitogen‐activated protein (MAP) kinase cascades serve as central signalling complexes that are involved in various aspects of growth, stress response and infection. In this work, putative components of the yeast Fus3/Kss1‐type MAP kinase cascade and the putative downstream transcription factor Ste12 were analysed in the grey mould fungus Botrytis cinerea. Deletion mutants of the MAP triple kinase Ste11, the MAP kinase kinase Ste7 and the MAP kinase adaptor protein Ste50 all resulted in phenotypes similar to that of the previously described BMP1 MAP kinase mutant, namely defects in germination, delayed vegetative growth, reduced size of conidia, lack of sclerotia formation and loss of pathogenicity. Mutants lacking Ste12 showed normal germination, but delayed infection as a result of low penetration efficiency. Two differently spliced ste12 transcripts were detected, and both were able to complement the ste12 mutant, except for a defect in sclerotium formation, which was only corrected by the full‐sized transcript. Overexpression of the smaller ste12 transcript resulted in delayed germination and strongly reduced infection. Bc‐Gas2, a homologue of Magnaporthe grisea Gas2 that is required for appressorial function, was found to be non‐essential for growth and infection, but its expression was under the control of both Bmp1 and Ste12. In summary, the role and regulatory connections of the Fus3/Kss1‐type MAP kinase cascade in B. cinerea revealed both common and unique properties compared with those of other plant pathogenic fungi, and provide evidence for a regulatory link between the BMP1 MAP kinase cascade and Ste12.
Stable isotope evidence for impala Aepyceros melampus diets at Akagera National Park, Rwanda
Authors: Copeland Sandi R. , Sponheimer Matt , Spinage Clive A. , Lee‐Thorp Julia A. , Codron Daryl , Reed Kaye E.
Published: September 2009

Stable isotope analysis of tooth enamel was used to investigate the relative proportions of grass and browse in seasonal and overall diets of impala Aepyceros melampus at Akagera National Park, Rwanda. Bulk enamel samples suggest that on average, impala ate c. 86% C4 grass year‐round, far more than in most previously studied impala populations across Africa. Intra‐tooth samples show that seasonal changes in the proportion of C4 grass versus C3 browse are minimal (c. 10%), the diet being dominated by C4 grass year‐round in contrast to other impala populations that consume ≥50% browse during the dry season. Intra‐tooth oxygen isotope values track carbon isotope changes to a moderate degree, but are not patterned clearly enough to permit identification of wet versus dry seasons. As other studies have shown that impala select high‐protein diets, the foraging behaviour at Akagera is probably because of the availability of palatable grass for much of the year in the edaphic grasslands around the lacustrine environments of the eastern portions of Akagera National Park.
Understanding the multiple meanings of ‘inbreeding’ and ‘effective size’ for genetic management of African rhinoceros populations
Authors: Braude Stanton , Templeton Alan R.
Published: September 2009

Although some African rhinoceros populations are currently increasing, others are critically endangered. Even healthy populations are extensively managed in the wild and in captivity. While political and demographic considerations are of primary concern, many decisions are made in the name of genetic management. Such decisions should be informed by a full understanding of the multiple meanings of inbreeding and effective population size. In this essay, we examine inbreeding and effective size of wild and captive populations of African rhinoceroses. We conclude by showing how misunderstanding of effective size and Franklin’s 50/500 rule can make a crucial difference in informing management decisions.
High temporal variation in the assemblage of Lepidopteran larvae on a constant resource
Authors: Skippari Sini , Veteli Timo Olavi , Kasenene John , Niemelä Pekka , Roininen Heikki
Published: September 2009

We studied variation in the assemblage of lepidopteran larvae between individual trees, and temporal variation in the diversity and species composition of the assemblage in a medium‐altitude rainforest in Kibale National Park, Uganda. Monthly samples of lepidopteran larvae were collected from the leaves of Neoboutonia macrocalyx Pax. between January 1995 and December 1996. During this period, a total of 1961 specimens representing 76 lepidopteran morphospecies were found. The numbers of individuals within species varied enormously, ranging from one to 707 individuals. Assemblages of individual trees were highly similar and dominated by geometrid larvae. Temporal variation in herbivore abundance was high. The number of individuals peaked during the major rainy season in 1995 but not in 1996 and was not correlated significantly with rainfall within these 2 years. In contrast, a negative correlation was found between lepidopteran diversity and rainfall that seems to cause a semi‐annual trend in diversity with one or two peaks per year. Furthermore, there was seasonality in the similarity of the assemblage. Consequently, the same species were found in the assemblage during certain times of the year. Our study shows that short‐term biodiversity assessments can give a skewed picture of the diversity of tropical forests.
Enrichment planting does not improve tree restoration when compared with natural regeneration in a former pine plantation in Kibale National Park, Uganda
Authors: Omeja Patrick A. , Chapman Colin A. , Obua Joseph
Published: September 2009

Given the high rates of deforestation and subsequent land abandonment, there are increasing calls to reforest degraded lands; however, many areas are in a state of arrested succession. Plantations can break arrested succession and the sale of timber can pay for restoration efforts. However, if the harvest damages native regeneration, it may be necessary to intervene with enrichment planting. Unfortunately, it is not clear when intervention is necessary. Here, we document the rate of biomass accumulation of planted seedlings relative to natural regeneration in a harvested plantation in Kibale National Park, Uganda. We established two 2‐ha plots and in one, we planted 100 seedlings of each of four native species, and we monitored all tree regeneration in this area and the control plot. After 4 years, naturally regenerating trees were much taller, larger and more common than the planted seedlings. Species richness and two nonparametric estimators of richness were comparable between the plots. The cumulative biomass of planted seedlings accounted for 0.04% of the total above‐ground tree biomass. The use of plantations facilitated the growth of indigenous trees, and enrichment planting subsequent to harvesting was not necessary to obtain a rich tree community with a large number of new recruits.
Growth response of woody species to elephant foraging in Mwea National Reserve, Kenya
Authors: Chira Robert M. , Kinyamario J. I.
Published: September 2009

The African elephant (Loxodonta africana) is known to greatly affect the structure and dynamics of vegetation. In Mwea National Reserve, elephants foraged mainly on Acacia ataxacantha and Grewia bicolor out of the five most preferred woody species. However, out of the five preferred woody species, only Grewia virosa and G. bicolor showed a positive association between their fresh use and past elephant use. All the five selected woody species showed high coppicing response after foraging, with the highest coppice growth rates recorded for Acacia brevispica and lowest for Grewia tembensis. The mean heights of woody species utilized by elephants were highest for A. brevispica and lowest for G. bicolor. The mean heights of coppices emerging after utilization by elephants were not significantly different for A. ataxacantha but were significantly shorter in the rest of the foraged species. Elephants avoided the coppices of many other woody species notably C. africana, A. tortilis, A. mellifera, Combretum aculeatum among others in the reserve. The objective of this study was to understand the capacity of woody species to recover after utilization by elephants and feeding response of elephants to new woody species re‐growth; a cycle that would define the dynamics of food resources and elephant population within the reserve.
Impact of land use on the ecology of uncultivated plant species in the Rwenzori mountain range, mid western Uganda
Authors: Muhumuza Moses , Byarugaba Dominic
Published: September 2009

Rwenzori mountain range is important for its high diversity of unique species and as a water catchment area and yet very fragile to human interference. The study documented the impact of land use on ecology of uncultivated plant species in the Rwenzori mountain range using Bugoye sub‐county as a reference site. The ecological aspects of the plants studied included distribution, abundance and diversity of the plant species in and around the various land uses as well as in degraded, disturbed and undisturbed areas. Land uses identified were; agriculture, built up area and land with other activities (conservation and abandoned fields). The study revealed that agriculture was the main land use category taking up 69.7% of land use area. Plants distributed in and around the land uses were mainly trees with species diversity of 34.5%. Generally, there was no relationship in the distribution of plant species in degraded, undisturbed and disturbed areas (a = 0.01). In disturbed areas, there was vegetation cover especially of plant species that occur as secondary re‐growth, and in degraded areas, the ground was sparsely covered by primary succession species while in the undisturbed areas, plant species growing in a ‘natural. habitat dominated and most of them were climax species.
The distribution of temperature, oxygen and nutrients in Lake Bukoni, Uganda
Authors: Nyakoojo Clement , Byarujali Stephen M.
Published: September 2009

Temperature, oxygen and nutrients were determined in the permanently stratified Lake Bukoni from July 2004 to December 2005. Meromixis has resulted from the nature of the surrounding hilly topography and the almost vertical crater walls that exclude the effects of light winds. These circumstances and the tropical temperature regime ensure permanent stratification in the offshore part of the lake. From about 20 m to the bottom, the water was out of circulation and devoid of oxygen. Water samples from such depths had a strong smell of hydrogen sulphide gas. The inshore site, with greater turbulence and littoral area, had a uniformly oxygenated water column compared with the offshore site. According to information from members of the community around the lake, ‘fish kills’ have taken place but on irregular occasions. The nutrients (N, P and Si) were well distributed in the inshore site. In the offshore site, the concentrations were generally lower in the uppermost 20 m but more than double near the mud surface. Soluble reactive phosphorous was the least abundant nutrient while soluble reactive silicon was the most abundant nutrient. The high Si : P ratios have led to the dominance of species like Synedra ulna Ehr.
Potentially inappropriate prescribing in an Irish elderly population in primary care
Authors: Ryan Cristín , O'Mahony Denis , Kennedy Julia , Weedle Peter , Byrne Stephen
Published: September 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Potentially inappropriate prescribing in older people is a well‐documented problem and has been associated with adverse drug reactions and hospitalization.

• Beers' criteria, Screening Tool of Older Persons' potentially inappropriate Prescriptions (STOPP) and Screening Tool to Alert doctors to Right Treatment (START) are screening tools that have been formulated to help physicians and pharmacists identify potentially inappropriate prescribing and potential prescribing omissions.

• The prevalence of potentially inappropriate prescribing and prescribing omissions in the elderly population presenting to hospital with acute illness is high according to STOPP and START criteria.

WHAT THIS STUDY ADDS

• Potential errors of prescribing and of omission of medicines are prevalent among medically stable older people in primary care.

• Screening tools should be incorporated into the everyday practice of primary care doctors and community pharmacists as a means of preventing potential errors of prescribing commission and prescribing omission in older people.

AIMS Screening tools have been formulated to identify potentially inappropriate prescribing (IP) in older people. Beers' criteria are the most widely used but have disadvantages when used in Europe. New IP screening tools called Screening Tool of Older Person's Prescriptions (STOPP) and Screening Tool to Alert doctors to Right Treatment (START) have been developed to identify potential IP and potential prescribing omissions (PPOs). The aim was to measure the prevalence rates of potential IP and PPOs in primary care using Beers' criteria, STOPP and START.

METHODS Case records of 1329 patients ≥65 years old from three general practices in one region of southern Ireland were studied. The mean age ± SD of the patients was 74.9 ± 6.4 years, 60.9% were female. Patients' current diagnoses and prescription medicines were reviewed and the Beers' criteria, STOPP and START tools applied.

RESULTS The total number of medicines prescribed was 6684; median number of medicines per patient was five (range 1–19). Overall, Beers' criteria identified 286 potentially inappropriate prescriptions in 18.3% (243) of patients, whilst the corresponding IP rate identified by STOPP was 21.4% (284), in respect of 346 potentially inappropriate prescriptions. A total of 333 PPOs were identified in 22.7% (302) of patients using the START tool.

CONCLUSION Potentially inappropriate drug prescribing and errors of drug omission are highly prevalent among older people living in the community. Prevention strategies should involve primary care doctors and community pharmacists.
Pharmacokinetic and clinical profile of a novel formulation of bosentan in children with pulmonary arterial hypertension: the FUTURE‐1 study
Authors: Beghetti Maurice , Haworth Sheila G. , Bonnet Damien , Barst Robyn J. , Acar Philippe , Fraisse Alain , Ivy Dunbar D. , Jais Xavier , Schulze‐Neick Ingram , Galiè Nazzareno , Morganti Adele , Dingemanse Jasper , Kusic‐Pajic Andjela , Berger Rolf M. F.
Published: September 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Exposure to bosentan was lower in paediatric pulmonary arterial hypertension (PAH) patients treated with the marketed adult formulation at a dose of about 2 mg kg−1 when compared with adult PAH patients.

• In healthy adult subjects, bosentan pharmacokinetics are less than dose‐proportional at doses of ≥500 mg.

WHAT THIS STUDY ADDS

• The pharmacokinetics of a new paediatric bosentan formulation were characterized in paediatric PAH patients.

• The level of exposure to bosentan as observed in adult PAH patients cannot be reached in paediatric patients with b.i.d. dosing.

• In paediatric PAH patients, nondose‐proportional pharmacokinetics of bosentan occur at lower doses when compared with healthy adult subjects.

AIM To show equivalent bosentan exposure in paediatric patients with pulmonary arterial hypertension (PAH) when compared with a cohort of historical controls of adult PAH patients using a newly developed paediatric formulation.

METHODS Thirty‐six paediatric PAH patients were enrolled in this multicentre, prospective, open‐label, noncontrolled study and treated for 4 weeks with bosentan 2 mg kg−1 b.i.d. and then for 8 weeks with 4 mg kg−1 b.i.d. Blood samples were taken for pharmacokinetic purposes. Exploratory efficacy measurements included World Health Organization (WHO) functional class and parent's and clinician's Global Clinical Impression scales.

RESULTS Comparing children with a historical group of adults, the geometric mean ratio (90% confidence interval) of the area under the plasma concentration–time curve was 0.54 (0.37, 0.78), i.e. children had lower exposure to bosentan than adults. Bosentan concentrations following doses of 2 and 4 mg kg−1 were similar. Improvements in WHO functional class and the Global Clinical Impression scales occurred mainly in bosentan‐naive patients, whereas the rare worsenings occurred in patients already on bosentan prior to study initiation. The paediatric formulation was well accepted and bosentan well tolerated in this study. No cases of elevated liver enzymes or anaemia were reported.

CONCLUSIONS Exposure to bosentan, as shown comparing the results from this study with those from a study in adults, was different in paediatric and adult PAH patients. Since FUTURE‐1 and past studies suggest a favourable benefit–risk profile for bosentan at 2 mg kg−1 b.i.d., this dose is recommended for children with PAH. The new paediatric formulation was well tolerated.
Effect of renal impairment on the pharmacokinetics of the GLP‐1 analogue liraglutide
Authors: Jacobsen Lisbeth V. , Hindsberger Charlotte , Robson Richard , Zdravkovic Milan
Published: September 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Patients with Type 2 diabetes are likely to have or to develop renal impairment, which affects the pharmacokinetics of some antidiabetic treatments.

• Whether dosing of the once‐daily human glucagon‐like peptide‐1 analogue liraglutide should be modified in patients with renal impairment has not previously been studied.

WHAT THIS STUDY ADDS

• Renal dysfunction was not found to increase the exposure of liraglutide.

• Hence, no dose adjustment is expected to be required in patients with Type 2 diabetes and renal impairment treated with liraglutide.

AIMS To investigate whether dose adjustment of the once‐daily human glucagon‐like peptide‐1 analogue liraglutide is required in patients with varying stages of renal impairment.

METHODS A cohort of 30 subjects, of whom 24 had varying degrees of renal impairment and six had normal renal function, were given a single dose of liraglutide, 0.75 mg subcutaneously, and completed serial blood sampling for plasma liraglutide measurements for pharmacokinetic estimation.

RESULTS No clear trend for change in pharmacokinetics was evident across groups with increasing renal dysfunction. While the between‐group comparisons of the area under the liraglutide concentration–curve (AUC) did not demonstrate equivalence [estimated ratio AUCsevere/AUChealthy 0.73, 90% confidence interval (CI) 0.57, 0.94; and AUC (continuous ambulatory peritoneal dialysis)CAPD/AUChealthy 0.74, 90% CI 0.56, 0.97], the regression analysis of log(AUC) for subjects with normal renal function and mild‐to‐severe renal impairment showed no significant effect of decreasing creatinine clearance on the pharmacokinetics of liraglutide. The expected AUC ratio between the two subjects with the lowest and highest creatinine clearance in the study was estimated to be 0.88 (95% CI 0.58, 1.34) (NS). Degree of renal impairment did not appear to be associated with an increased risk of adverse events.

CONCLUSIONS This study indicated no safety concerns regarding use of liraglutide in patients with renal impairment. Renal dysfunction was not found to increase exposure of liraglutide, and patients with Type 2 diabetes and renal impairment should use standard treatment regimens of liraglutide. There is, however, currently limited experience with liraglutide in patients beyond mild‐stage renal disease.
Genetic and environmental controls of microbial communities on leaf litter in streams
Authors: MARKS JANE C. , HADEN G. A. , HARROP BRENDA L. , REESE ELIZABETH G. , KEAMS JEANNA L. , WATWOOD MARY E. , WHITHAM THOMAS G.
Published: September 2009

1. Despite the importance of microorganisms for leaf litter decomposition in streams, little is known about which factors affect community composition of bacterial and fungal communities. Standard morphological techniques probably underestimate microbial diversity.

2. We used terminal restriction fragment length polymorphisms of the ITS regions for fungi, and the 16S region for bacteria, to compare fungal and bacterial communities on four cross types of cottonwood leaves (Populus fremontii, P. angustifolia, and their naturally occurring F1 and backcross hybrids). Decomposing leaves were studied in two Arizona rivers that differ in water chemistry and macroinvertebrates.

3. Hybridising cottonwoods are an ideal model system to test how genetic differences in leaf litter chemistry affect microbial communities because cross types have different decomposition rates and leaf litter chemistry. Leaves were incubated in litter bags for 2 weeks and brought to the laboratory for genetic analysis. Communities were analysed using non‐metric multi dimensional scaling (NMDS) and diversity indices.

4. Fungal and bacterial communities differed between the two rivers, even when growing on identical substrates. There were also significant differences in microbial communities among the four cross types, indicating that genetically based differences in leaf litter translate to differences in microbial communities.

5. Diversity increased along the hybridising complex from P. fremontii to P. angustifolia, with hybrids showing intermediate values. Fungal and bacterial diversity were significantly higher on cross types with higher tannin concentrations and slower decomposition rates.

6. Environmental conditions most strongly structured microbial communities, but within an environment, genetic‐based differences in leaf litter quality yielded differences in diversity and community structure.

7. Molecular tools are making it possible to understand patterns of microbial diversity in river ecosystems, paving the way for a better understanding of how differences in microbial species affect ecosystem processes and higher trophic levels.
Colour phases of the eastern screech owl: a comparison of biomechanical variables of body contour feathers
Authors: Pannkuk Evan L. , Siefferman Lynn M. , Butts Jeffrey A.
Published: September 2009

1.
 Melanin is a ubiquitous pigment in the animal kingdom and has been reported to increase biological tissue strength. Melanin is responsible for many observed cases of colour polymorphism, or existence of two or more distinct plumage colours in one species (regardless of age, sex, or mass). Researchers have postulated that the relative concentration of melanin pigments deposited in feathers may function to strengthen feathers but colour polymorphic species have been ignored. Here, we investigate whether different morphs of a polymorphic bird species exhibit differential plumage strength.

2.
 While colour polymorphism is widespread in birds, there is no consensus on the adaptive significance of polymorphism or the maintenance of clinal variation in colour morphs. The eastern screech owl (Megascops asio) is a polymorphic species; individuals exhibit rufous, intermediate, or grey coloration that is likely caused by relative amounts or concentration of black or rufous melanin subtype (eumelanin and pheomelanin respectively). This species exhibits clinal variation in morph prevalence; the rufous morph predominates in humid deciduous forests while the grey morph is more common in dry or cold environments.

3.
 Here, we test the hypothesis that differences in feather strength may select for darker plumage in drier climates. First, we use reflectance spectrometry to objectively verify differences in colour morphs of the eastern screech owl. Second, we measure mechanical variables and morphology of dorsal feather barbs.

4.
 While reflectance spectrometry objectively separated the three colour morphs, we found no significant differences in the mechanical variables of plumage morphs. These results fail to demonstrate differences in plumage strength among eastern screech owl colour variants.

5.
 This conclusion rejects the hypothesis that melanin subtype affects the strength of body contour feathers in the eastern screech owl and may not factor in the maintenance of the observed clinal variation.
When sea‐ice clock is ahead of Adélie penguins’ clock
Authors: Beaulieu Michaël , Dervaux Antoine , Thierry Anne‐Mathilde , Lazin David , Le Maho Yvon , Ropert‐Coudert Yan , Spée Marion , Raclot Thierry , Ancel André
Published: September 2009

1.  In Polar Regions, the extent and dynamics of sea‐ice are changing. This affects the ocean productivity which consecutively impacts plankton communities and polar top predators like penguins. Yet, the underlying behavioural and physiological mechanisms remain poorly understood.

2.
 Here we monitored the ecophysiological responses of Adélie penguin (Pygoscelis adeliae) pairs during two seasons of contrasting timing of sea‐ice retreat. Beside classical breeding parameters like foraging trip duration, body mass and reproductive success, we also investigated food‐related stress (via plasma corticosterone concentration), nutritional state (via metabolite levels) and the use of penguins’ habitat (via blood isotopic values).

3.  Body mass and reproductive success remained unchanged but foraging trips were shorter when sea‐ice retreated earlier. Constant plasma corticosterone concentrations indicated that none of the feeding conditions resulted in a food‐related stress. However metabolite levels were lower when sea‐ice retreated early, suggesting that the foraging performance and the quality/quantity of food differed. Indeed isotopic ratios indicated that coastal prey like fish contributed more to the penguins’ diet when sea‐ice retreated prematurely.

4.  The early sea‐ice retreat was related to higher chlorophyll concentrations, known to favour krill recruitment. Paradoxically, this was not associated to a higher krill contribution in the penguins’ diet. We propose that a shift in the phytoplankton quality (rather than quantity), affecting krill recruitment, forced penguins to switch to more available prey like coastal fish.

5.  In some Antarctic regions, sea‐ice is retreating earlier and earlier. In the present study, even though the timing of sea‐ice retreat and the consecutive ocean productivity differed drastically between the 2 years, Adélie penguins were not severely affected because they were able to adjust their at‐sea behaviour and thus maintained their body condition and reproductive success unchanged.

6.  This suggests that the timing of sea‐ice retreat does not represent an important threat to populations of Adélie penguins at least as long as alternative resources are still available and other environmental parameters like winter sea‐ice extent are not dramatically altered.