bluuebunny/crossref_metadata_2025 huggingface dataset:
Antitumorigenesis of antioxidants in a transgenic Rac1 model of Kaposi's sarcoma
Authors: Ma Qi , Cavallin Lucas E. , Yan Bin , Zhu Shoukang , Duran Elda Margarita , Wang Huili , Hale Laura P. , Dong Chunming , Cesarman Ethel , Mesri Enrique A. , Goldschmidt-Clermont Pascal J.
Published: May 2009

Kaposi's sarcoma (KS) is the major AIDS-associated malignancy. It is characterized by the proliferation of spindle cells, inflammatory infiltrate, and aberrant angiogenesis caused by Kaposi's sarcoma herpesvirus (KSHV) infection. Small GTPase Rac1, an inflammatory signaling mediator triggering reactive oxygen species (ROS) production by NADPH-oxidases, is implicated in carcinogenesis and tumor angiogenesis. Here, we show that expression of a constitutively active Rac1 (RacCA) driven by the α-smooth muscle actin promoter in transgenic mice is sufficient to cause KS-like tumors through mechanisms involving ROS-driven proliferation, up-regulation of AKT signaling, and hypoxia-inducible factor 1-α–related angiogenesis. RacCA-induced tumors expressed KS phenotypic markers; displayed remarkable transcriptome overlap with KS lesions; and were, like KS, associated with male gender. The ROS scavenging agent
N
-acetyl-cysteine inhibited angiogenesis and completely abrogated transgenic RacCA tumor formation, indicating a causal role of ROS in tumorigenesis. Consistent with a pathogenic role in KS, immunohistochemical analysis revealed that Rac1 is overexpressed in KSHV
+
spindle cells of AIDS-KS biopsies. Our results demonstrate the direct oncogenicity of Rac1 and ROS and their contribution to a KS-like malignant phenotype, further underscoring the carcinogenic potential of oxidative stress in the context of chronic infection and inflammation. They define the RacCA transgenic mouse as a model suitable for studying the role of oxidative stress in the pathogenesis and therapy of KS, with relevance to other inflammation-related malignancies. Our findings suggest host and viral genes triggering Rac1 or ROS production as key determinants of KS onset and potential KS chemopreventive or therapeutic targets.
Menaquinone as pool quinone in a purple bacterium
Authors: Schoepp-Cothenet Barbara , Lieutaud Clément , Baymann Frauke , Verméglio André , Friedrich Thorsten , Kramer David M. , Nitschke Wolfgang
Published: May 2009

Purple bacteria have thus far been considered to operate light-driven cyclic electron transfer chains containing ubiquinone (UQ) as liposoluble electron and proton carrier. We show that in the purple γ-proteobacterium
Halorhodospira halophila
, menaquinone-8 (MK-8) is the dominant quinone component and that it operates in the Q
B
-site of the photosynthetic reaction center (RC). The redox potentials of the photooxidized pigment in the RC and of the Rieske center of the
bc
1
complex are significantly lower (
E
m
= +270 mV and +110 mV, respectively) than those determined in other purple bacteria but resemble those determined for species containing MK as pool quinone. These results demonstrate that the photosynthetic cycle in
H. halophila
is based on MK and not on UQ. This finding together with the unusual organization of genes coding for the
bc
1
complex in
H. halophila
suggests a specific scenario for the evolutionary transition of bioenergetic chains from the low-potential menaquinones to higher-potential UQ in the proteobacterial phylum, most probably induced by rising levels of dioxygen 2.5 billion years ago. This transition appears to necessarily proceed through bioenergetic ambivalence of the respective organisms, that is, to work both on MK- and on UQ-pools. The establishment of the corresponding low- and high-potential chains was accompanied by duplication and redox optimization of the
bc
1
complex or at least of its crucial subunit oxidizing quinols from the pool, the Rieske protein. Evolutionary driving forces rationalizing the empirically observed redox tuning of the chain to the quinone pool are discussed.
PDK1 coordinates survival pathways and β-adrenergic response in the heart
Authors: Ito Kaoru , Akazawa Hiroshi , Tamagawa Masaji , Furukawa Kensuke , Ogawa Wataru , Yasuda Noritaka , Kudo Yoko , Liao Chien-hui , Yamamoto Rie , Sato Toshiaki , Molkentin Jeffery D. , Kasuga Masato , Noda Tetsuo , Nakaya Haruaki , Komuro Issei
Published: May 2009

The 3-phosphoinositide-dependent kinase-1 (PDK1) plays an important role in the regulation of cellular responses in multiple organs by mediating the phosphoinositide 3-kinase (PI3-K) signaling pathway through activating AGC kinases. Here we defined the role of PDK1 in controlling cardiac homeostasis. Cardiac expression of PDK1 was significantly decreased in murine models of heart failure. Tamoxifen-inducible and heart-specific disruption of
Pdk1
in adult mice caused severe and lethal heart failure, which was associated with apoptotic death of cardiomyocytes and β
1
-adrenergic receptor (AR) down-regulation. Overexpression of Bcl-2 protein prevented cardiomyocyte apoptosis and improved cardiac function. In addition, PDK1-deficient hearts showed enhanced activity of PI3-Kγ, leading to robust β
1
-AR internalization by forming complex with β-AR kinase 1 (βARK1). Interference of βARK1/PI3-Kγ complex formation by transgenic overexpression of phosphoinositide kinase domain normalized β
1
-AR trafficking and improved cardiac function. Taken together, these results suggest that PDK1 plays a critical role in cardiac homeostasis in vivo by serving as a dual effector for cell survival and β-adrenergic response.
Directed, efficient, and versatile modifications of the
Drosophila
genome by genomic engineering
Authors: Huang Juan , Zhou Wenke , Dong Wei , Watson Annie M. , Hong Yang
Published: May 2009

With the completion of genome sequences of major model organisms, increasingly sophisticated genetic tools are necessary for investigating the complex and coordinated functions of genes. Here we describe a genetic manipulation system termed “genomic engineering” in
Drosophila
. Genomic engineering is a 2-step process that combines the ends-out (replacement) gene targeting with phage integrase φC31-mediated DNA integration. First, through an improved and modified gene targeting method, a founder knock-out line is generated by deleting the target gene and replacing it with an integration site of φC31. Second, DNA integration by φC31 is used to reintroduce modified target-gene DNA into the native locus in the founder knock-out line. Genomic engineering permits directed and highly efficient modifications of a chosen genomic locus into virtually any desired mutant allele. We have successfully applied the genomic engineering scheme on 6 different genes and have generated at their loci more than 70 unique alleles.
Coexistence and transition between Cassie and Wenzel state on pillared hydrophobic surface
Authors: Koishi Takahiro , Yasuoka Kenji , Fujikawa Shigenori , Ebisuzaki Toshikazu , Zeng Xiao Cheng
Published: May 2009

Water droplets on rugged hydrophobic surfaces typically exhibit one of the following two states: (
i
) the Wenzel state [Wenzel RN (1936)
Ind Eng Chem
28:988–994] in which water droplets are in full contact with the rugged surface (referred as the wetted contact) or (
ii
) the Cassie state [Cassie, ABD, Baxter S (1944)
Trans Faraday Soc
40:546–551] in which water droplets are in contact with peaks of the rugged surface as well as the “air pockets” trapped between surface grooves (the composite contact). Here, we show large-scale molecular dynamics simulation of transition between Wenzel state and Cassie state of water droplets on a periodic nanopillared hydrophobic surface. Physical conditions that can strongly affect the transition include the height of nanopillars, the spacing between pillars, the intrinsic contact angle, and the impinging velocity of water nanodroplet (“raining” simulation). There exists a critical pillar height beyond which water droplets on the pillared surface can be either in the Wenzel state or in the Cassie state, depending on their initial location. The free-energy barrier separating the Wenzel and Cassie state was computed on the basis of a statistical-mechanics method and kinetic raining simulation. The barrier ranges from a few tenths of
k
B
T
0
(where
k
B
is the Boltzmann constant, and
T
0
is the ambient temperature) for a rugged surface at the critical pillar height to ≈8
k
B
T
0
for the surface with pillar height greater than the length scale of water droplets. For a highly rugged surface, the barrier from the Wenzel-to-Cassie state is much higher than from Cassie-to-Wenzel state. Hence, once a droplet is trapped deeply inside the grooves, it would be much harder to relocate on top of high pillars.
RNAi screen for rapid therapeutic target identification in leukemia patients
Authors: Tyner Jeffrey W. , Deininger Michael W. , Loriaux Marc M. , Chang Bill H. , Gotlib Jason R. , Willis Stephanie G. , Erickson Heidi , Kovacsovics Tibor , O'Hare Thomas , Heinrich Michael C. , Druker Brian J.
Published: May 2009

Targeted therapy has vastly improved outcomes in certain types of cancer. Extension of this paradigm across a broad spectrum of malignancies will require an efficient method to determine the molecular vulnerabilities of cancerous cells. Improvements in sequencing technology will soon enable high-throughput sequencing of entire genomes of cancer patients; however, determining the relevance of identified sequence variants will require complementary functional analyses. Here, we report an RNAi-assisted protein target identification (RAPID) technology that individually assesses targeting of each member of the tyrosine kinase gene family. We demonstrate that RAPID screening of primary leukemia cells from 30 patients identifies targets that are critical to survival of the malignant cells from 10 of these individuals. We identify known, activating mutations in JAK2 and K-RAS, as well as patient-specific sensitivity to down-regulation of FLT1, CSF1R, PDGFR, ROR1, EPHA4/5, JAK1/3, LMTK3, LYN, FYN, PTK2B, and N-RAS. We also describe a previously undescribed, somatic, activating mutation in the thrombopoietin receptor that is sensitive to down-stream pharmacologic inhibition. Hence, the RAPID technique can quickly identify molecular vulnerabilities in malignant cells. Combination of this technique with whole-genome sequencing will represent an ideal tool for oncogenic target identification such that specific therapies can be matched with individual patients.
Endothelium‐dependent Vasodilation in Myogenically Active Mouse Skeletal Muscle Arterioles: Role of EDH and K+ Channels
Authors: POTOCNIK SIMON J. , MCSHERRY IAIN , DING HONG , MURPHY TIMOTHY V. , KOTECHA NEELA , DORA KIM A. , YUILL KATHRYN H. , TRIGGLE CHRIS R. , HILL MICHAEL A.
Published: May 2009

As smooth muscle cell (SMC) membrane potential (Em) is critical for vascular responsiveness, and arteriolar SMCs are depolarized at physiological intraluminal pressures, we hypothesized that myogenic tone impacts on dilation mediated by endothelium‐derived hyperpolarization (EDH). Studies were performed on cannulated mouse cremaster arterioles [diameter, 33±2 μm (n=23) at 60 mmHg; SMC Em ‐34.6±1.2 mV (n=7)]. Myogenic activity was assessed as tone developed in response to intraluminal pressure. Functional observations were related to mRNA, protein expression, and anatomy. Acetylcholine concentration‐response curves showed a modest shift following indomethacin (10 μM) and L‐NAME (100 μM), although maximal vasodilation was achieved. Residual dilation was removed by apamin (1 μM) in combination with TRAM‐34 (1 μM) or charybotoxin (0.1 μM), indicating the requirement of small (S) and intermediate (I) calcium‐activated potassium channels (KCa). Charybdotoxin, but not TRAM‐34, caused vasoconstriction, presumably through the inhibition of SMC BKCa. Expression of SK3 and IK1 was confirmed by immunohistochemistry and polymerase chain reaction, while myoendothelial junctions were common, suggesting a high degree of cell coupling. Also consistent with a role for endothelial KCa channels, acetylcholine increased endothelium [Ca2+]i. Apamin and TRAM‐34 similarly blocked EDH‐mediated dilation at intraluminal pressures of 30 and 90 mmHg, suggesting that in mouse arterioles, SKCa ‐ and IKCa ‐ mediated mechanisms predominate and operate independently of physiological levels of myogenic activation.
Threatened and stressed mountain lakes of Europe: Assessment and progress
Authors: Battarbee Richard W. , Kernan Martin , Rose Neil
Published: May 2009

Mountain regions are cold environments that are hostile to human occupation and widely regarded as places where the air is clean, water is pure and ecosystems are pristine. Yet many mountain regions, especially in Europe, are far from pristine. In the 1980s, research showed that mountain lakes were especially vulnerable to acid deposition and sediment core studies at many sites demonstrated that some mountain lakes had become acidified over the course of the last century. Since then, studies of the water chemistry, biology and history of lakes across the different European mountain regions have increased our understanding of the processes within these systems, their ecological condition and the threats facing them. These studies have demonstrated that: i) gradients of sulphur, nitrogen, metals and persistent organic pollutant deposition occur from relatively uncontaminated regions in Spain and Central Norway to regions of heavy pollution loading in central and eastern Europe;ii) nitrate and sulphate concentrations in lake water reflect the gradients in atmospheric deposition;iii) concentrations of mercury, lead and cadmium in fish tissue show marked regional differences;iv) the spatial pattern of organochlorine concentrations in fish and in sediments follow the pattern for other pollutants, although there is also good evidence for the selective cold trapping of some compounds both at high latitudes and at high altitudes;v) fish suffer physiological stress in mountain lake-water of low ionic strength;vi) climate change over the last century is likely to have induced significant changes in lake ice-cover and water column stratification and mixing in some regions and these have in turn influenced the structure and productivity of biological communities;

This paper provides a review of the research undertaken on European mountain lakes over the past 30 years. In particular, it highlights the stresses faced by these vulnerable systems and the effects these have had, continue to have, and are likely to have on mountain lake ecosystems in future.
Use of predictive models and rapid methods to nowcast bacteria levels at coastal beaches
Authors: Francy Donna S.
Published: May 2009

The need for rapid assessments of recreational water quality to better protect public health is well accepted throughout the research and regulatory communities. Rapid analytical methods, such as quantitative polymerase chain reaction (qPCR) and immunomagnetic separation/adenosine triphosphate (ATP) analysis, are being tested but are not yet ready for widespread use.

Another solution is the use of predictive models, wherein variable(s) that are easily and quickly measured are surrogates for concentrations of fecal-indicator bacteria. Rainfall-based alerts, the simplest type of model, have been used by several communities for a number of years. Deterministic models use mathematical representations of the processes that affect bacteria concentrations; this type of model is being used for beach-closure decisions at one location in the USA. Multivariable statistical models are being developed and tested in many areas of the USA; however, they are only used in three areas of the Great Lakes to aid in notifications of beach advisories or closings. These “operational” statistical models can result in more accurate assessments of recreational water quality than use of the previous day's Escherichia coli (E. coli) concentration as determined by traditional culture methods. The Ohio Nowcast, at Huntington Beach, Bay Village, Ohio, is described in this paper as an example of an operational statistical model. Because predictive modeling is a dynamic process, water-resource managers continue to collect additional data to improve the predictive ability of the nowcast and expand the nowcast to other Ohio beaches and a recreational river. Although predictive models have been shown to work well at some beaches and are becoming more widely accepted, implementation in many areas is limited by funding, lack of coordinated technical leadership, and lack of supporting epidemiological data.
The potential future impact of climate warming and other human activities on the productive capacity of Canada’s lake fisheries: a meta-model
Authors: Minns Charles K.
Published: May 2009

A simple meta-model was used to examine how climate warming and stresses due to other human activities might affect the productive capacity of fisheries in all of Canada’s lakes. Recent estimates of lake resource characteristics by secondary watershed and area size-class provided the basis for the model. Potential fishery productivity was estimated using a variant of the Schlesinger and Regier (1982) model which had lake mean depth, total dissolved solids concentration, and mean annual air temperature as inputs. A business-as-usual climate change scenario (SRES A2) was used to estimate worst case future temperature increases (4.5–8.3°C by the 2080s). The stress index from Chu et al. (2003) was used as a proxy for the impact on fisheries of other human activities. Projected populations for the SRES A2 scenario were used to scale future stress index levels. Potential biotic responses to warming were represented in two ways; the first as potential biotic displacement of currently dominant species when temperature rose beyond their preferred range and the second as potential biotic adaptation of other species, particularly in species rich areas, replacing displaced species. Potential productive capacity of fisheries in all Canadian lakes was 361,000 tonnes for the baseline climate norms period of 1961–1990. Climate warming increased productivity by 80.7% in the 2080s but stress reduced levels by 19.4% in the norms period and held the increase to 10.3% in the 2080s. Biotic displacement alone resulted in large decreases in productivity, by 65.2% in the 2080s and, when stress was added, by 79.5%. Biotic adaptation largely offset displacement. Applying stress and both biotic responses productivity was reduced by 31.4% in the 2080s from the unstressed norms baseline or 12% with stress added. Further investigations are needed to better establish the likely extent of stress impacts and potential biotic responses to climate warming in Canada’s lakes.
Empirical evidence of monsoon influences on Asian Lakes
Authors: Jones J. R. , McEachern P. , Seo D.
Published: May 2009

Limited information is available on how the Asian monsoon influences contemporary lake processes, seasonal patterns and interannual variation. Data sets from Nepal (Indian monsoon region) and South Korea (East Asian monsoon region) along with published literature show a wide range in the response of Asian lakes to the seasonal monsoon. Cross-system patterns show nutrients and algal biomass peak in most lakes in response to monsoon inflow, which suggests nonpoint sources dominate external loading. This seasonal increase may be the general phenological model for nutrients and phytoplankton in lakes in monsoon regions. Major ions show dilution by surface runoff during the monsoon and post-monsoon increases. Dilution of nutrients in fertile systems during the monsoon suggests point source inputs dominate peak loads during the non-monsoon period. Peak monsoon runoff can enter the water column of large stratified lakes as a density-dependent interflow at depth in the water column with little direct influence on the mixed layer. In these water bodies nutrients in surface water can be lower during strong monsoon seasons because of sub-surface loading. Short-interval data from individual lakes show the linkage between nutrients and phytoplankton biomass can be uncoupled by physical processes and light limitation, resulting in considerable temporal variation. Collectively these mixed responses limit our ability to generalize patterns or predict conditions in individual lakes during the monsoon.
Success of science-based best management practices in reducing swimming bans—a case study from Racine, Wisconsin, USA
Authors: Kinzelman Julie L. , McLellan Sandra L.
Published: May 2009

The Great Lakes region possesses over 10,000 miles of shoreline (US EPA and Government of Canada, 1995) which are home to over 1,000 beaches. These beaches represent a recreational outlet for over 30 million people (US EPA and Government of Canada, 1995) and yet many of them remain inaccessible for periods of time each bathing season due to water quality advisories. The reason for these advisories is often elusive to beach managers, hence impeding their ability to craft appropriate mitigation measures. Even when the sources of contamination are known, remediation measures may not be put into practice due to the perception that they are too costly. However, a recent study has demonstrated that investing in environmental improvements which increase the number of days available for swimming in the Great Lakes region by 20% would generate $2–$3 billion dollars in direct economic effects. Therefore, while beach closings and advisories continue to rise overall, some Great Lakes communities have recognized the potential for municipal beaches to generate revenue and increase the quality of life for their citizens and have undertaken comprehensive studies to improve recreational water quality. In Racine, Wisconsin, USA, research conducted to identify pollution sources guided the development of better beach management practices such as ecologically appropriate beach modifications, improved mechanical beach grooming strategies, and the redesign of a major storm water outlet (including installation of a constructed wetland area). Resulting improvements have reduced bathing water quality advisories from 66% of days during the swimming season in 2000 to 5% or less in four consecutive years (2005–2008). These improvements to Racine beaches facilitated Blue Wave certification from the Clean Beaches Council (Washington, DC); thereby restoring public confidence, increasing beach use by the residents and tourists, and expanding the role of the beachfront in the local economy.
Bathing water signage and predictive water quality models in Scotland
Authors: McPhail Calum D. , Stidson Ruth T.
Published: May 2009

The Scottish Environment Protection Agency (SEPA) has developed, and runs, real-time bathing water quality predictions at ten sites throughout Scotland since 2004. Daily bathing water quality predictions are posted on electronic variable message signs at 10 beach locations networked to a central communication centre and updates are simultaneously made on the SEPA website, phone and text message service.

Antecedent rainfall and subsequent river flow can significantly increase the concentrations of faecal indicator organisms in bathing waters. The SEPA signage prediction tool, an Excel spreadsheet based model, was developed and used to set site-specific criteria for rainfall and river flow to predict bathing water quality based on historical data. Real-time predictions against the current EU Bathing Water Directive were correct or precautionary on 99% of days and correct for 82% of compliance samples during 2007, and 81% of compliance samples during the 2008 season.

The revised 2006 Directive sets out more stringent bathing water quality standards which require increased model performance. New predictive models are now being trailed using decision tree statistical software and are intended to replace the existing prediction tool by 2012.
Macroinvertebrate Index of Biotic Integrity (M-IBI) for monitoring rivers in the upper catchment of Lake Victoria Basin, Kenya
Authors: Raburu Phillip Okoth , Masese Frank Onderi , Mulanda Christopher Aura
Published: May 2009

The water quality of many streams in Lake Victoria Basin, Kenya is affected by agricultural intensification, municipal and industrial effluent, as well as water abstraction, livestock and deforestation. Management efforts have been hampered by lack of clear standards against which to judge the degree of environmental degradation. To achieve this goal, a macroinvertebrate-based Index of Biotic Integrity was developed to monitor ecological integrity of selected rivers occurring in the same ecological zone in the upper reaches of the basin. Macroinvertebrates were sampled with a Surber sampler at 22 stations. The stations were grouped into three condition categories (reference, intermediate and impaired stations) according to the level of degradation. Twenty metrics representing the structural and functional organization of macroinvertebrates were computed using Mann-Whitney U tests. The separation power of the metrics was evaluated using box plots. Final metrics were evaluated for responsiveness by Pearson’s correlations with physicochemical parameters. Of the 20 metrics, 9 met the test criteria, as they displayed variability across the stations, and were used to provide the final scores for Macroinvertebrate Index of Biotic Integrity (M-IBI). Metric values at both reference and impaired sites were used to establish the scoring criteria using inter-quartile ranges. This index provided preliminary evidence of response to changes in ecosystem integrity exhibited by resident macroinvertebtrate assemblages in rivers in the upper reaches of Lake Victoria Basin. It was recommended that the index developed be used to assess and monitor rivers in the upper catchments of Lake Victoria Basin in Kenya.
Caribbean beach changes and climate change adaptation
Authors: Cambers Gillian
Published: May 2009

Beach monitoring data are presented and show an average beach erosion trend of 0.5 m yr −1 in eight Caribbean islands over the period 1985–2000, with elevated rates in those islands impacted by a higher number of hurricanes. The data are based on 5 to 15 years of continuous monitoring, conducted at three-month intervals, at 113 beaches (200 profile sites) on eight islands, using standard methodology. The causes of the erosion are discussed and include anthropogenic factors, climate variability and projected climate change. Based on the Intergovernmental Panel on Climate Change projections for the Caribbean region, and the likely increase of anthropogenic stresses such as coastal development, it is likely that the beach erosion trend will continue and increase. Nonexclusive approaches to help beaches adapt to climate change include structural, planning or ecological measures. Two case studies illustrating climate change adaptation measures are discussed, one focuses on coastal planning measures in Anguilla and Nevis, and the second focuses on ecological measures, specifically the rehabilitation of a coastal forest in Puerto Rico. These case studies have not reached a stage where their effectiveness can be evaluated, however preliminary outcomes show that community-based climate change adaptation measures require careful planning such that the entire community is involved in a participatory manner and sufficient time is allocated for awareness-raising, information-sharing and discussion.
Cytochrome P450 induction inIctalurus punctatusfollowing exposure to wastewater treatment plant effluent
Authors: Whatley Alicia , Stewart Paul M. , Bhattarai Smriti Subedi , Magrath Christi
Published: May 2009

Induction of the cytochrome P450 enzymes in fish, measured as ethoxyresorufin-O-deethylase (EROD) activity, has been extensively used as a biomarker in assessing exposures and responses of aquatic organisms to contaminants. This study focused on whether exposure to Troy (Alabama) wastewater treatment plant (TWWTP) effluent at the Walnut Creek mixing zone, induced transcription of mRNA for cytochrome P4501A1 enzyme production and increased EROD activity in channel catfish (Ictalurus punctatus). Water from Big Creek (Barbour County, AL), regarded as least impacted by pollutants, was used as a reference source for administration of a positive control chemical (PCB – Aroclor 1254). All water samples were transported from field sites to the Troy University laboratory for conducting the study. Reverse transcriptase-polymerase chain reaction (RT-PCR) indicated the presence of compounds capable of inducing transcription of CYP1A1 mRNA in catfish liver. Increased transcription of mRNA for cytochrome P4501A1 enzyme production, confirmed by a 3-fold induction of EROD activity, was found in catfish exposed to water from the TWWTP mixing zone on Walnut Creek compared to catfish exposed to Walnut Creek Upstream. Catfish exposed to water from Big Creek treated with PCBs were found to have only slightly higher enzyme activities than those exposed to water from Big Creek Control, but a 2.7-fold EROD level was found in catfish exposed to Big Creek Control compared to Walnut Creek Upstream. Determining the induction of cytochrome P450 and subsequent enzymatic activity in catfish and other fish species common to this region could be useful early molecular warnings of possible pollution effects, beyond those methods typically used to characterize water quality.
Assessment of ecosystem health of tropical shallow waterbodies in eastern India using turbulence model
Authors: Samal N. R. , Mazumdar A. , Jöhnk K. D. , Peeters F.
Published: May 2009

In the present study, a numerical model of the hydrodynamic and thermal structure of artificial shallow lakes in eastern India has been developed as a tool to assess the ecological water quality, driven by the meteorological forcings. It allows quantification of the vertical mixing processes that govern not only the thermal structure but also nutrient exchanges and the distribution of dissolved and particulate matter among water layers. Vertical temperature profiles were calculated by solving coupled partial differential equations for temperature (heat energy balance equation), one-dimensional momentum equation and a second order closure scheme for small-scale turbulence effects, i.e. turbulent kinetic energy and turbulent dissipation rates numerically using an implicit time integration method. The effect of advection due to the inflow and outflow is not taken into consideration as these shallow waterbodies are assumed to behave as a closed lake. The oxygen level measured at different layers during the simulation period in these waterbodies reflects hypolimnetic oxygen depletion due to the thermal stratification in the aquatic environment. The changes in the stratification regime in these waterbodies are expected to affect the water quality and the health of the ecosystem, primarily based on temperature and dissolved oxygen parameter and in particular, the certain features of the oxygen resources of the hypolimnion.
Assessing the impact of climate change on inland fisheries in River Ganga and its plains in India
Authors: Vass K. K. , Das M. K. , Srivastava P. K. , Dey S.
Published: May 2009

Perceptible changes on a global and regional scale are evident in earth's climate. In India, observed changes include an increase of air temperature, regional monsoon variation, frequent droughts and a regional increase in severe storm incidence in coastal states of India, along with indication of Himalayan glacier recession. The impact is being felt in the inland aquatic resources and their fisheries. Analysis of time series data of 30 years from published literature and from current investigations on the River Ganga and water bodies in its plains, indicate increased minimum water temperatures; 1.5°C in colder stretches of the Ganga and 0.2 to 1.6°C in the aquaculture farms of the State of West Bengal in the Gangetic plains. Rainfall has also increased in the post monsoon months of September–December. The impact is manifested in the breeding failure of the Indian Major Carps (IMC) and a consequent decline in fish spawn availability in river Ganga. Whereas, in fish farm hatcheries on the plains, a positive impact on breeding was observed in the advancement and extension of the breeding period of IMC by 45–60 days. A geographic shift of warm water fish species Glossogobius gurius and Xenentodon cancila to the colder stretch of the river Ganga was recorded. The predator prey ratio in the middle stretch in the river Ganga has also declined from 1:4.2 to 1:1.4 in the last three decades. Fish production has shown a distinct change in the last two decades in the middle stretch of river Ganga where the contribution of IMC has decreased from 41.4% to 8.3% and that of miscellaneous and catfish species increased. Climate change in India will put an additional stress on ecological and socio-economic systems that are already facing pressure. Thus the specific climate variables of importance to inland fisheries viz. enhanced water temperature, extreme events like flood and drought, storms and water stress require specific adaptation actions. An integrated water shed management strategy is essential going from the village level to the river basin level in a unified manner. Finally, it is suggested that assessments of inland fisheries vulnerability to climate change should also assess economic scenarios since adaptive capacity is closely linked to the financial capabilities.
FlexServ: an integrated tool for the analysis of protein flexibility
Authors: Camps Jordi , Carrillo Oliver , Emperador Agustí , Orellana Laura , Hospital Adam , Rueda Manuel , Cicin-Sain Damjan , D'Abramo Marco , Gelpí Josep Lluís , Orozco Modesto
Published: May 2009

Summary: FlexServ is a web-based tool for the analysis of protein flexibility. The server incorporates powerful protocols for the coarse-grained determination of protein dynamics using different versions of Normal Mode Analysis (NMA), Brownian dynamics (BD) and Discrete Dynamics (DMD). It can also analyze user provided trajectories. The server allows a complete analysis of flexibility using a large variety of metrics, including basic geometrical analysis, B-factors, essential dynamics, stiffness analysis, collectivity measures, Lindemann's indexes, residue correlation, chain-correlations, dynamic domain determination, hinge point detections, etc. Data is presented through a web interface as plain text, 2D and 3D graphics.

Availability:  http://mmb.pcb.ub.es/FlexServ; http://www.inab.org

Contact:  modesto@mmb.pcb.ub.es or gelpi@mmb.pcb.ub.es

Supplementary information: Additional information and methodology details can be found at http://mmb.pcb.ub.es/FlexServ/help.
MaHCO: an ontology of the major histocompatibility complex for immunoinformatic applications and text mining
Authors: DeLuca David S. , Beisswanger Elena , Wermter Joachim , Horn Peter A. , Hahn Udo , Blasczyk Rainer
Published: May 2009

Motivation: The high level of polymorphism associated with the major histocompatibility complex (MHC) poses a challenge to organizing associated bioinformatic data, particularly in the area of hematopoietic stem cell transplantation. Thus, this area of research has great potential to profit from the ongoing development of biomedical ontologies, which offer structure and definition to MHC-data related communication and portability issues.

Results: We introduce the design considerations, methodological foundations and implementational issues underlying MaHCO, an ontology which represents the alleles and encoded molecules of the major histocompatibility complex. Importantly for human immunogenetics, it includes a detailed level of human leukocyte antigen (HLA) classification. We then present an ontology browser, search interfaces for immunogenetic fact and document retrieval, and the specification of an annotation language for semantic metadata, based on MaHCO. These use cases are intended to demonstrate the utility of ontology-driven bioinformatics in the field of immunogenetics.

Availability and Implementation: The MaHCO Ontology is available via the BioPortal: http://www.bioontology.org/tools/portal/bioportal.html, and at: http://purl.org/stemnet/

Contact:  david_deluca@dfci.harvard.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Measuring herring densities with one real and several phantom research vessels
Authors: Patel Ruben , Ona Egil
Published: May 2009

Patel, R., and Ona, E. 2009. Measuring herring densities with one real and several phantom research vessels. – ICES Journal of Marine Science 66: 1264–1269. Vessel-induced avoidance can potentially cause a large bias in acoustic estimates of schooling, pelagic-fish biomass. This paper presents a method for quantifying this uncertainty. Volume-backscattering strength (Sv) from a horizontally projecting, multibeam sonar (Simrad MS70) is resampled to form synthetic, vertical, echosounder beams to the side of the survey vessel. These data are analysed as if they were collected from phantom vessels surveying parallel transects at fixed ranges from the real vessel. The nautical-area-backscattering coefficients (sA) from the synthetic echograms are compared with those measured by conventional 70 and 120 kHz echosounders (Simrad EK60) on the real vessel. Data collected in 2006 from schools of Norwegian spring-spawning herring are used to illustrate the method and explore its limitations. Potential effects of vessel-induced avoidance are evaluated by comparing the mean sA values observed from the phantom vessels with those observed from the real vessel. The technique also allows direct estimates of the mean lateral-aspect target strength of in situ herring.
Zooplankton spatial distribution along the South African coast studied by multifrequency acoustics, and its relationships with environmental parameters and anchovy distribution
Authors: Lebourges-Dhaussy Anne , Coetzee Janet , Hutchings Larry , Roudaut Gildas , Nieuwenhuys Cornelia
Published: May 2009

Lebourges-Dhaussy, A., Coetzee, J., Hutchings, L., Roudaut, G., and Nieuwenhuys, C. 2009. Zooplankton spatial distribution along the South African coast studied by multifrequency acoustics, and its relationships with environmental parameters and anchovy distribution. – ICES Journal of Marine Science, 66: 1055–1062. The Central Agulhas Bank (CAB) is an important component of the southern Benguela ecosystem. Despite relatively low primary production, secondary production supports large populations of mid-trophic-level pelagic fish. Exhaustive sampling of the Agulhas Bank ecosystem was performed during a routine acoustic biomass survey in November 2006. A TAPS-6 was deployed with near-simultaneous, plankton-net sampling. Concurrent collections of fish-school and environmental data permitted a detailed study of the water column. Zooplankton was classified by equivalent spherical diameter (ESD; mm): 0.0–0.35 (Class I), 0.35–0.8 (Class II), 0.8–2 (Class III), and >2.0 mm (Class IV). Clear relationships with environmental parameters were only evident at night on the CAB (west of 23°E) for Classes II and III. Class III exhibited pronounced diel vertical migrations, whereas Class I exhibited a reverse pattern. Also observed were the effects of anchovy predation on small zooplankton aggregated in areas of high chlorophyll a.
Collar Rot on Italian Alder Trees in California Caused by Phytophthora siskiyouensis
Authors: Rooney-Latham Suzanne , Blomquist Cheryl L. , Pastalka Tomas , Costello Laurence
Published: May 2009

In November 2006, trees of Italian alder (Alnus cordata) were observed declining in association with bleeding trunk cankers in a commercial landscape in Foster City, CA. A species of Phytophthora was isolated on PARP selective medium from the leading edge of the cankers. The Phytophthora species was homothallic with primarily paragynous antheridia and had oospores that were mostly globose and aplerotic. Sporangia were produced from mycelia on plugs of carrot piece agar in soil extraction solution and were semi-papillate and ovoid to ellipsoid in shape. The intergenic transcribed spacer region of rDNA from an alder isolate matched with 100% identity to isolates in GenBank of Phytophthora siskiyouensis, a recently described species associated with tanoak and found in the soil and waterways of coastal Oregon. Pathogenicity was tested on young alder trees growing in pots. Pathogenicity was confirmed on Italian alder trees and potential pathogenicity was demonstrated on red and white alder trees.

Accepted for publication 11 March 2009. Published 13 April 2009.
Stress hormone dynamics: an adaptation to migration?
Authors: Nilsson Anna L. K. , Sandell Maria I.
Published: May 2009

The hormone corticosterone (CORT) is an important component of a bird’s response to environmental stress, but it can also have negative effects. Therefore, birds on migration are hypothesized to have repressed stress responses (migration-modulation hypothesis). In contrast to earlier studies on long-distance migrants, we evaluate this hypothesis in a population containing both migratory and resident individuals. We use a population of partially migratory blue tits (
Cyanistes caeruleus
) in southern Sweden as a model species. Migrants had higher CORT levels at the time of capture than residents, indicating migratory preparations, adaptation to stressors, higher allostatic load or possibly low social status. Migrants and residents had the same stress response, thus contradicting the migration-modulation hypothesis. We suggest that migrants travelling short distances are more benefited than harmed by retaining the ability to respond to stress.
A Redox-Mediated Modulation of Stem Bolting in TransgenicNicotiana sylvestrisDifferentially Expressing the External Mitochondrial NADPH Dehydrogenase
Authors: Liu Yun-Jun , Nunes-Nesi Adriano , Wallström Sabá V. , Lager Ida , Michalecka Agnieszka M. , Norberg Fredrik E.B. , Widell Susanne , Fredlund Kenneth M. , Fernie Alisdair R. , Rasmusson Allan G.
Published: May 2009

Cytosolic NADPH can be directly oxidized by a calcium-dependent NADPH dehydrogenase, NDB1, present in the plant mitochondrial electron transport chain. However, little is known regarding the impact of modified cytosolic NADPH reduction levels on growth and metabolism. Nicotiana sylvestris plants overexpressing potato (Solanum tuberosum) NDB1 displayed early bolting, whereas sense suppression of the same gene led to delayed bolting, with consequential changes in flowering time. The phenotype was dependent on light irradiance but not linked to any change in biomass accumulation. Whereas the leaf NADPH/NADP+ ratio was unaffected, the stem NADPH/NADP+ ratio was altered following the genetic modification and strongly correlated with the bolting phenotype. Metabolic profiling of the stem showed that the NADP(H) change affected relatively few, albeit central, metabolites, including 2-oxoglutarate, glutamate, ascorbate, sugars, and hexose-phosphates. Consistent with the phenotype, the modified NDB1 level also affected the expression of putative floral meristem identity genes of the SQUAMOSA and LEAFY types. Further evidence for involvement of the NADPH redox in stem development was seen in the distinct decrease in the stem apex NADPH/NADP+ ratio during bolting. Additionally, the potato NDB1 protein was specifically detected in mitochondria, and a survey of its abundance in major organs revealed that the highest levels are found in green stems. These results thus strongly suggest that NDB1 in the mitochondrial electron transport chain can, by modifying cell redox levels, specifically affect developmental processes.
FRIGIDA Delays Flowering in Arabidopsis via a Cotranscriptional Mechanism Involving Direct Interaction with the Nuclear Cap-Binding Complex
Authors: Geraldo Nuno , Bäurle Isabel , Kidou Shin-ichiro , Hu Xiangyang , Dean Caroline
Published: May 2009

A major determinant of flowering time in natural Arabidopsis (Arabidopsis thaliana) variants is FRIGIDA (FRI). FRI up-regulates expression of the floral repressor FLOWERING LOCUS C (FLC), thereby conferring a vernalization requirement and a winter annual habit. FRI encodes a novel nuclear protein with no conserved domains except for two coiled-coil regions. A mutation in the large subunit of the nuclear cap-binding complex (CBC) suppresses FRI activity, so we have explored the connection between FRI and the nuclear CBC in order to gain further insight into FRI biochemical activity. Mutations in the small subunit of the CBC (CBP20) also suppress FRI up-regulation of FLC. CBP20 interacted directly with FRI in yeast and in planta, and this association of FRI with the 5′ cap was reinforced by an RNA ligase-mediated rapid amplification of cDNA ends assay that showed FRI decreased the proportion of FLC transcripts lacking a 5′ cap. Loss of CBP20 resulted in very low FLC mRNA levels and an increased proportion of unspliced FLC transcripts. FRI compensated for CBP20 loss, partially restoring FLC levels and normalizing the unspliced-spliced transcript ratio. Our data suggest that FRI up-regulates FLC expression through a cotranscriptional mechanism involving direct physical interaction with the nuclear CBC with concomitant effects on FLC transcription and splicing.
Site-Specific Integration of Transgenes in Soybean via Recombinase-Mediated DNA Cassette Exchange
Authors: Li Zhongsen , Xing Aiqiu , Moon Bryan P. , McCardell Richard P. , Mills Kelly , Falco S. Carl
Published: May 2009

A targeting method to insert genes at a previously characterized genetic locus to make plant transformation and transgene expression predictable is highly desirable for plant biotechnology. We report the successful targeting of transgenes to predefined soybean (Glycine max) genome sites using the yeast FLP-FRT recombination system. First, a target DNA containing a pair of incompatible FRT sites flanking a selection gene was introduced in soybean by standard biolistic transformation. Transgenic events containing a single copy of the target were retransformed with a donor DNA, which contained the same pair of FRT sites flanking a different selection gene, and a FLP expression DNA. Precise DNA cassette exchange was achieved between the target and donor DNA via recombinase-mediated cassette exchange, so that the donor DNA was introduced at the locus previously occupied by the target DNA. The introduced donor genes expressed normally and segregated according to Mendelian laws.
A Visual Reporter System for Virus-Induced Gene Silencing in Tomato Fruit Based on Anthocyanin Accumulation
Authors: Orzaez Diego , Medina Aurora , Torre Sara , Fernández-Moreno Josefina Patricia , Rambla José Luis , Fernández-del-Carmen Asun , Butelli Eugenio , Martin Cathie , Granell Antonio
Published: May 2009

Virus-induced gene silencing (VIGS) is a powerful tool for reverse genetics in tomato (Solanum lycopersicum). However, the irregular distribution of the effects of VIGS hampers the identification and quantification of nonvisual phenotypes. To overcome this limitation, a visually traceable VIGS system was developed for fruit, comprising two elements: (1) a transgenic tomato line (Del/Ros1) expressing Antirrhinum majus Delila and Rosea1 transcription factors under the control of the fruit-specific E8 promoter, showing a purple-fruited, anthocyanin-rich phenotype; and (2) a modified tobacco rattle virus VIGS vector incorporating partial Rosea1 and Delila sequences, which was shown to restore the red-fruited phenotype upon agroinjection in Del/Ros1 plants. Dissection of silenced areas for subsequent chemometric analysis successfully identified the relevant metabolites underlying gene function for three tomato genes, phytoene desaturase, TomloxC, and SlODO1, used for proof of concept. The C-6 aldehydes derived from lipid 13-hydroperoxidation were found to be the volatile compounds most severely affected by TomloxC silencing, whereas geranial and 6-methyl-5-hepten-2-one were identified as the volatiles most severely reduced by phytoene desaturase silencing in ripening fruit. In a third example, silencing of SlODO1, a tomato homolog of the ODORANT1 gene encoding a myb transcription factor, which regulates benzenoid metabolism in petunia (Petunia hybrida) flowers, resulted in a sharp accumulation of benzaldehyde in tomato fruit. Together, these results indicate that fruit VIGS, enhanced by anthocyanin monitoring, can be a powerful tool for reverse genetics in the study of the metabolic networks operating during fruit ripening.