bluuebunny/crossref_metadata_2025 huggingface dataset:
A protein kinase network regulates the function of aminophospholipid flippases
Authors: Roelants Françoise M. , Baltz Alexander G. , Trott Amy E. , Fereres Sol , Thorner Jeremy
Published: December 2009

Limited exposure of aminophospholipids on the outer leaflet of the plasma membrane is a fundamental feature of eukaryotic cells and is maintained by the action of inward-directed P-type ATPases (“flippases”). Yeast
S. cerevisiae
has five flippases (Dnf1, Dnf2, Dnf3, Drs2, and Neo1), but their regulation is poorly understood. Two paralogous plasma membrane-associated protein kinases, Pkh1 and Pkh2 (orthologs of mammalian PDK1), are required for viability of
S. cerevisiae
cells because they activate several essential downstream protein kinases by phosphorylating a critical Thr in their activation loops. Two such targets are related protein kinases Ypk1 and Ypk2 (orthologs of mammalian SGK1), which have been implicated in multiple processes, including endocytosis and coupling of membrane expansion to cell wall remodeling, but the downstream effector(s) of these kinases have been elusive. Here we show that a physiologically relevant substrate of Ypk1 is another protein kinase, Fpk1, a known flippase activator. We show that Ypk1 phosphorylates and thereby down-regulates Fpk1, and further that a complex sphingolipid counteracts the down-regulation of Fpk1 by Ypk1. Our findings delineate a unique regulatory mechanism for imposing a balance between sphingolipid content and aminophospholipid asymmetry in eukaryotic plasma membranes.
A demonstration that the hippocampus supports both recollection and familiarity
Authors: Kirwan C. Brock , Wixted John T. , Squire Larry R.
Published: December 2009

Recognition memory is thought to depend on two distinct processes: recollection and familiarity. There is debate as to whether damage to the hippocampus selectively impairs recollection or whether it impairs both recollection and familiarity. If hippocampal damage selectively impairs recollection but leaves familiarity intact, then patients with circumscribed hippocampal lesions should exhibit the full normal range of low-confidence and high-confidence familiarity-based recognition. High-confidence, familiarity-based decisions are ordinarily accompanied by successful recollection (when memory is intact). However, patients with hippocampal lesions, if recollection is impaired, should frequently experience high-confidence, familiarity-based recognition in the absence of recollection, and this circumstance (termed the “butcher-on-the-bus” phenomenon) should occur more often in patients than in healthy controls. We tested five patients with circumscribed hippocampal damage, asking them to recognize recently studied words as well as to remember the context in which the items were studied. Relative to controls, the patients exhibited no increased tendency to experience the butcher-on-the-bus phenomenon. The simplest explanation of the results is that hippocampal damage impairs familiarity as well as recollection. The same conclusion was suggested when two competing models of recognition memory were used to analyze the data.
A nonsynaptic mechanism underlying interictal discharges in human epileptic neocortex
Authors: Roopun Anita K. , Simonotto Jennifer D. , Pierce Michelle L. , Jenkins Alistair , Nicholson Claire , Schofield Ian S. , Whittaker Roger G. , Kaiser Marcus , Whittington Miles A. , Traub Roger D. , Cunningham Mark O.
Published: December 2009

Very fast oscillations (VFOs, >80 Hz) are important for physiological brain processes and, in excess, with certain epilepsies. Putative mechanisms for VFO include interneuron spiking and network activity in coupled pyramidal cell axons. It is not known whether either, or both, of these apply in pathophysiological conditions. Spontaneously occurring interictal discharges occur in human tissue in vitro, resected from neocortical epileptic foci. VFO associated with these discharges was manifest in both field potential and, with phase delay, in excitatory synaptic inputs to fast spiking interneurons. Recruitment of somatic pyramidal cell and interneuron spiking was low, with no correlation between VFO power and synaptic inputs to principal cells. Reducing synaptic inhibition failed to affect VFO occurrence, but they were abolished by reduced gap junction conductance. These data suggest a lack of a causal role for interneurons, and favor a nonsynaptic pyramidal cell network origin for VFO in epileptic human neocortex.
The γ isoform of CaM kinase II controls mouse egg activation by regulating cell cycle resumption
Authors: Backs Johannes , Stein Paula , Backs Thea , Duncan Francesca E. , Grueter Chad E. , McAnally John , Qi Xiaoxia , Schultz Richard M. , Olson Eric N.
Published: December 2009

Fertilization triggers a rise in intracellular Ca
2+
concentration ([Ca
2+
]
i
) in the egg that initiates a series of events known as egg activation. These events include cortical granule exocytosis that establishes a block to polyspermy, resumption of meiosis, and recruitment of maternal mRNAs into polysomes for translation. Several calcium-dependent proteins, including calcium/calmodulin-dependent protein kinase II (CaMKII), have been implicated in egg activation. However, the precise role of CaMKII in mediating specific events of egg activation and the identity of the isoform(s) present in mouse eggs have not been unequivocally established. Through targeted deletion of the γ isoform of CaMKII, we find that CaMKIIγ is the predominant CaMKII isoform in mouse eggs and that it is essential for egg activation. Although CaMKIIγ
−/−
eggs exhibit a normal pattern of Ca
2+
oscillations after insemination and undergo cortical granule exocytosis, they fail to resume meiosis or to recruit maternal mRNAs. Surprisingly, we find that the recruitment of maternal mRNAs does not directly depend on CaMKII, but requires elevated [Ca
2+
]
i
and metaphase II exit. We conclude that CaMKIIγ specifically controls mouse egg activation by regulating cell cycle resumption.
TRPM1 is a component of the retinal ON bipolar cell transduction channel in the mGluR6 cascade
Authors: Koike Chieko , Obara Takehisa , Uriu Yoshitsugu , Numata Tomohiro , Sanuki Rikako , Miyata Kentarou , Koyasu Toshiyuki , Ueno Shinji , Funabiki Kazuo , Tani Akiko , Ueda Hiroshi , Kondo Mineo , Mori Yasuo , Tachibana Masao , Furukawa Takahisa
Published: December 2009

An essential step in intricate visual processing is the segregation of visual signals into ON and OFF pathways by retinal bipolar cells (BCs). Glutamate released from photoreceptors modulates the photoresponse of ON BCs via metabotropic glutamate receptor 6 (mGluR6) and G protein (Go) that regulates a cation channel. However, the cation channel has not yet been unequivocally identified. Here, we report a mouse TRPM1 long form (TRPM1-L) as the cation channel. We found that TRPM1-L localization is developmentally restricted to the dendritic tips of ON BCs in colocalization with mGluR6. TRPM1 null mutant mice completely lose the photoresponse of ON BCs but not that of OFF BCs. In the TRPM1-L-expressing cells, TRPM1-L functions as a constitutively active nonselective cation channel and its activity is negatively regulated by Go in the mGluR6 cascade. These results demonstrate that TRPM1-L is a component of the ON BC transduction channel downstream of mGluR6 in ON BCs.
The upper surface of an
Escherichia coli
swarm is stationary
Authors: Zhang Rongjing , Turner Linda , Berg Howard C.
Published: December 2009

When grown in a rich medium on agar, many bacteria elongate, produce more flagella, and swim in a thin film of fluid over the agar surface in swirling packs. Cells that spread in this way are said to swarm. The agar is a solid gel, with pores smaller than the bacteria, so the swarm/agar interface is fixed. Here we show, in experiments with
Escherichia coli
, that the swarm/air interface also is fixed. We deposited MgO smoke particles on the top surface of an
E. coli
swarm near its advancing edge, where cells move in a single layer, and then followed the motion of the particles by dark-field microscopy and the motion of the underlying cells by phase-contrast microscopy. Remarkably, the smoke particles remained fixed (diffusing only a few micrometers) while the swarming cells streamed past underneath. The diffusion coefficients of the smoke particles were smaller over the virgin agar ahead of the swarm than over the swarm itself. Changes between these two modes of behavior were evident within 10–20 μm of the swarm edge, indicating an increase in depth of the fluid in advance of the swarm. The only plausible way that the swarm/air interface can be fixed is that it is covered by a surfactant monolayer pinned at its edges. When a swarm is exposed to air, such a monolayer can markedly reduce water loss. When cells invade tissue, the ability to move rapidly between closely opposed fixed surfaces is a useful trait.
Optimal hematocrit for maximal exercise performance in acute and chronic erythropoietin-treated mice
Authors: Schuler Beat , Arras Margarete , Keller Stephan , Rettich Andreas , Lundby Carsten , Vogel Johannes , Gassmann Max
Published: December 2009

Erythropoietin (Epo) treatment increases hematocrit (Htc) and, consequently, arterial O
2
content. This in turn improves exercise performance. However, because elevated blood viscosity associated with increasing Htc levels may limit cardiac performance, it was suggested that the highest attainable Htc may not necessarily be associated with the highest attainable exercise capacity. To test the proposed hypothesis that an optimal Htc in acute and chronic Epo-treated mice exists—i.e., the Htc that facilitates the greatest O
2
flux during maximal exercise—Htc levels of wild-type mice were acutely elevated by administering novel erythropoiesis-stimulating protein (NESP; wtNESP). Furthermore, in the transgenic mouse line tg6 that reaches Htc levels of up to 0.9 because of constitutive overexpression of human Epo, the Htc was gradually reduced by application of the hemolysis-inducing compound phenylhydrazine (PHZ; tg6PHZ). Maximal cardiovascular performance was measured by using telemetry in all exercising mice. Highest maximal O
2
uptake

and maximal time to exhaustion at submaximal exercise intensities were reached at Htc values of 0.58 and 0.57 for wtNESP, and 0.68 and 0.66 for tg6PHZ, respectively. Rate pressure product, and thus also maximal working capacity of the heart, increased with elevated Htc values. Blood viscosity correlated with

Apart from the confirmation of the Htc hypothesis, we conclude that tg6PHZ adapted better to varying Htc values than wtNESP because of the higher optimal Htc of tg6PHZ compared to wtNESP. Of note, blood viscosity plays a critical role in limiting exercise capacity.
Sleep–wake regulation and hypocretin–melatonin interaction in zebrafish
Authors: Appelbaum Lior , Wang Gordon X. , Maro Geraldine S. , Mori Rotem , Tovin Adi , Marin Wilfredo , Yokogawa Tohei , Kawakami Koichi , Smith Stephen J. , Gothilf Yoav , Mignot Emmanuel , Mourrain Philippe
Published: December 2009

In mammals, hypocretin/orexin (HCRT) neuropeptides are important sleep–wake regulators and HCRT deficiency causes narcolepsy. In addition to fragmented wakefulness, narcoleptic mammals also display sleep fragmentation, a less understood phenotype recapitulated in the zebrafish HCRT receptor mutant (
hcrtr
−/−). We therefore used zebrafish to study the potential mediators of HCRT-mediated sleep consolidation. Similar to mammals, zebrafish HCRT neurons express vesicular glutamate transporters indicating conservation of the excitatory phenotype. Visualization of the entire HCRT circuit in zebrafish stably expressing
hcrt:EGFP
revealed parallels with established mammalian HCRT neuroanatomy, including projections to the pineal gland, where
hcrtr
mRNA is expressed. As pineal-produced melatonin is a major sleep-inducing hormone in zebrafish, we further studied how the HCRT and melatonin systems interact functionally. mRNA level of arylalkylamine-N-acetyltransferase (AANAT2), a key enzyme of melatonin synthesis, is reduced in
hcrtr
−/− pineal gland during the night. Moreover, HCRT perfusion of cultured zebrafish pineal glands induces melatonin release. Together these data indicate that HCRT can modulate melatonin production at night. Furthermore,
hcrtr
−/− fish are hypersensitive to melatonin, but not other hypnotic compounds. Subthreshold doses of melatonin increased the amount of sleep and consolidated sleep in
hcrtr
−/− fish, but not in the wild-type siblings. These results demonstrate the existence of a functional HCRT neurons-pineal gland circuit able to modulate melatonin production and sleep consolidation.
Copper in Lake Pontchartrain bottom sediment: Relationship to sediment properties
Authors: Delaune R. D. , Wang Jim J. , Jugsujinda A.
Published: December 2009

Several watersheds in the Louisiana Pontchartrain Basin are listed as impaired, with dissolved Cu as one of the impairments. In this study we determine Cu levels in sediment of Lake Pontchartrain (which comprises part of one of the largest estuaries in the Gulf Coast region) which receives water from impaired watersheds. Sediment samples were collected along an 8 km sampling grid (174 sites) and analyzed for total Cu in sediment. The average Cu content in sediment was 13.6 ± 6.7 mg.kg−1 ranging from 0 to 31.5 mg.kg−1 (n = 174). Results show that there was little Cu pollution in the lake sediment. Cu level was correlated with Al content (r = 0.888**) and Fe content (r = 0.907**) of sediment. Higher Cu was also found in sediment with high clay content (r = 0.429**). Cu was inversely correlated with sand content of sediment (r = −0.520**).
Multivariate methods distinguishing mangrove community structure of Coringa in the Godavari Delta, East coast of India
Authors: Satyanarayana B. , Raman A. V. , Mohd-Lokman H. , Dehairs F. , Sharma V. S. , Farid Dahdouh-Guebas
Published: December 2009

Multivariate analysis (PRIMER) based on mangrove tree density and basal area measurements in Coringa, a Bay-Mangrove ecosystem in the Indian sub-continent, revealed 6 different floristic groups. While Group-1 and Group 2 characterized by a combination of Sonneratia apetala and S. caseolari-Avicennia alba, reflected conditions typical of low-lying swamps, Group-3, consisting of Xylocarpus mekongensis, Rhizophora mucronata, R. apiculata and Bruguiera gymnorrhiza, was found close to the sea where high saline conditions prevailed. Group-4 species, Avicennia marina, A. officinalis and Excoecaria agallocha, represented widespread distribution and were found almost everywhere within Coringa. Group-5 consisted of Lumnitzera racemosa, Ceriops decandra and Aegiceras corniculatum which occurred at sites not very far from the influence of Gautami-Godavari estuary, suggestive of their preference to low salinity regimes. Finally, Group-6 typically represented by Bruguiera cylindrica was seen interiorally at sites under the direct influence of Bay waters. Delineation of sample sites and species records based on extensive field data will be invaluable for appropriate management (e.g. plantation) and conservation measures for Coringa.
Plant-promoted dissipation of four submerged macrophytes to phenanthrene
Authors: Jia-hua Li , Hong-yan Guo , Xiao-rong Wang , Hong Wong Ming , ShiHe Wang , Da-qiang Yin , Ying Yin , Jingfei Zhang
Published: December 2009

In order to investigate the function of submerged aquatic plants for recovery of water polluted by typical organic pollutants, and select potential plants for phytoremediation of polycyclic aromatic hydrocarbons contaminated water, removal efficiencies of four submerged macrophytes to phenanthrene were investigated, following 40-day exposure to phenanthrene solutions in an outdoor-simulated experiment. During the exposure period, phenanthrene concentration in water, sediments and the roots of submerged macrophytes were observed. Results showed that Elodeacanadensi exhibited the highest concentrations in roots, while Ceratophyllum demersum contained the lowest among these four submerged macrophytes. The disparity of phenanthrene in roots would come from plant properties including the shape and surface area of both shoots and roots. These plants enhanced the remediation of phenanthrene in solution through plant-promoted sedimentation and biodegradation. Potamogetoncrispu and Elodeacanadensi showed the higher performance to remove phenanthrene due to plant-promoted biodegradation.
Studies on physico-chemical characteristics and sediment environment along the coastal waters in Pulau Tuba, Langkawi, Malaysia
Authors: Jalal K. C. A. , Faizul H. N. Noor , Kamaruzzaman B. Y. , Shahbudin S. , Alam M. Z. , Irwandi Jaswir
Published: December 2009

Field observations on physico-chemical characteristics of water and sediment quality were carried out from March, 2005 to Dec, 2005 at 4 different stations (Station 1 – Main Jetty Pulau Tuba, Station 2 – Pulau Tuba Jetty number 2, Station 3 – Simpan Tiga Mangrove Area and Station 4 – Kuah Jetty) along the coastal waters iin Pulau Tuba, Langkawi. The physico-chemical parameters such as temperature (27.43–28.88°C), DO (3.79–6.49 mg/l), pH (7.72–8.20), salinity (33.10–33.96 ppt), TDS (32.27–32.77) g l−1) and specific conductivity (49.83-51.63 mS cm−1) did not show much variation among the stations. While nitrate, nitrite and phosphate were found among the stations, their concentrations varied and ranged from 2.04–26.93 μ g N l−1, 0.86–4.03 μ g N l−1 and 0.27–1.33 μ g P l−1, respectively. Although the textures of the bottom sediment were limited to sand, silt and clay, most of the stations were dominated by black clay with the highest amount (82.97%) being found at station 4. The amount of organic carbon in the sediment ranged from 1.92 – 3.0%, while the highest amount of Fe (366.90 μg g−1 was also found in station 4. Mn (39.75 μg g−1) and Pb (3.15 μ g g−1) were found in stations 3 and 1 respectively. The results showed that there are no significant differences (P > 0.05) among the physico-chemical profiles of the different stations; while the heavy metals and nutrients showed significant differences (P < 0.05) among the stations. Station 4 was the most man induced polluted area due to being the dumping zone of waste materials throughout the year. Nevertheless, all the sampling areas should be given utmost importance for continuous monitoring of nutrients and heavy metals, which could be alarming for the habitat of the aquatic organisms in the near future.
Fatty acid markers as an indicator for temporal changes in food sources of the bivalve Quidnipagus palatum
Authors: Bachok Zainudin , Meziane Tarik , Mfilinge Prosper L. , Tsuchiya Makoto
Published: December 2009

Changes in the fatty acid composition in the tissues of the bivalve Quidnipagus palatum from the Tomigusuku intertidal flat, Okinawa, Japan, collected in four different seasons (November 2000, the beginning of cold season; January 2001, the cold season; May 2001, the rainy season; and July 2001, the warm season) were examined and compared to the composition of surface sediments and suspended particulate materials. Assessment of fatty acid markers suggested that the food sources of Q. palatum differed between seasons and depended on the sources of organic material present in the sediment and water column. Vascular plants and bacteria were the main dietary components from July to November because of their abundance in the sediment. From November to January, macroalgae and phytoplankton were the major food sources of Q. palatum, corresponding to their predominance in sediments and algal blooms, respectively. During the May rainy season, organic matter in the sediment was dominated by diatoms, whereas the water column contained diatoms and resuspended macroalgal detritus. The transition to the warm season by July significantly increased the contribution of diatoms to the organic matter present in both the sediment and the water column. Consequently, from May to July, diatoms became the main food source for Q. palatum.
Physiological responses of Chaetoceros sp. and Nannochloropsis sp. to short-term 2, 4-D, dimethylamine and endosulfan exposure
Authors: Hii Yii Siang , Shia Kwee Luan , Chuah Tse Seng , Hing Lee Siang
Published: December 2009

The effects of two widely used pesticides in paddy fields, 2, 4-D, dimethylamine and endosulfan, on growth, photosynthetic rate and the photosynthetic pigments of Chaetoceros sp. and Nannochloropsis sp. were assessed in this study. The 48 hour 50% inhibitory concentration (IC50) value for 2, 4-D dimethylamine on Chaetoceros sp. and Nannochloropsis sp. were 142.2 mg l−1 and 211.8 mg l−1, respectively, and the 48 hour IC50 value for endosulfan on Chaetoceros sp. and Nannochloropsis sp. were 21.9 μ g l−1 and 45.8 μ g l−1, respectively. Endosulfan was much more toxic to the microalgae than 2, 4-D dimethylamine. Both pesticides reduced photosynthetic pigments and oxygen production rate of the microalgae. After 48 hours exposure to the pesticides, the microalgae were transferred to a pesticide-free medium to investigate the post-exposure effect. 2, 4-D dimethylamine and endosulfan did not cause irreversible damage on the microalgae. However, there was a prolonged lag phase and the maximum specific growth rate (μ) of the microalgae was significantly retarded.
Hypoxia in the Pearl River Estuary, the South China Sea, in July 1999
Authors: Luo L. , Li S. , Wang D.
Published: December 2009

The Pearl River Estuary empties into the South China Sea in southeastern China, and hypoxia is one of the major environmental problems here during summer. It can be caused by coastline, topography, hydrodynamics, tidal dynamics and biological processes (mainly by stratification and oxidation reaction). Since ecological processes are closely related to dynamic processes, we revise and link together both a physical and a biological model to establish a coupled hydrodynamic-ecological numerical model to study the summertime hypoxia. The model simulates physical and biological processes and reproduces the observed hypoxia in the bottom layer in two regions located in west shallow water and around Nei Lingding Island. A low-salinity plume forms after the freshwater drifts offshore. Strong stratification exists in the water body shoreward where the vertical mixing is weak. The salinity front and stratification cause a poor exchange in the vertical direction and greatly influence biological processes for nutrients, phytoplankton, and detritus, which induce the hypoxia occurrence in the bottom layer of the Pearl River Estuary. On the other hand, in two troughs the tide diminishes the strength of stratification and prohibits the large-scale growth of the hypoxia. The physical processes related to topography, run off and tidal mixing regulate the distribution of biological factors and the occurrence of hypoxia.
Impacts of jetty construction on the wave heights off the Kiashahr lagoon
Authors: Azarmsa S. A. , Esmaeili M. , Khaniki A. Karami
Published: December 2009

Coastal managers and ecologists are confronted with tasks to estimate wave heights in the Kiashahr sea area, since hydrodynamic factors can profoundly impact this environment. In this study, wind data and an empirical wind wave predicting model were used to estimate deepwater wave characteristics in the Kiashahr sea area; while a numerical model was used to determine wave characteristics in shallow waters. Wave heights were also determined and compared at different stations before and after construction of 2 jetties at the lagoon mouth to evaluate their efficiency in wave height reduction. Results revealed that wave height is in the range of 0.8 to 1.2 m at Sefid Rud river mouth. Significant wave height reduction in the range of 0.15 to 1.2 m occurred at the entrance of the lagoon due to construction of the jetties. This attenuation of wave energy may result in some impacts on the ecosystem health of Kiashahr lagoon such as increased sedimentation, reduction in flushing rates, dumping of garbage and consequently, more pollution.
Groundwater conditions beneath beaches of Lake Huron, Ontario, Canada
Authors: Crowe Allan S. , Meek Gregory A.
Published: December 2009

Groundwater flow conditions below beaches of Lake Huron have been examined at eight sites. Groundwater below beaches flows towards the lake throughout the year. However, water table conditions vary between beaches with a shallow water table (< 1 m) and beaches with a deep water table (> 2 m). Where the water table is deep, the water table across a beach will rise and fall proportionally to fluctuations in lake levels. The hydraulic gradient is essentially linear across a beach. Beaches with a shallow water table exhibit very little change in the elevation of the water table over time, do not fluctuate proportionally with lake level changes, and have a break in the hydraulic gradient at ∼ 20 m from shore. Long term and season fluctuations in the surface of Lake Huron will change the elevation and location of the groundwater discharge area, resulting in the water table beneath the entire beach where the water table is deep to rise and fall proportionally and maintaining essentially the same hydraulic gradient. However, fluctuations in the lake levels have little impact on water table conditions at beaches where the water table is shallow.
Some institutional implications of an ecosystems approach to capture fisheries management
Authors: Torell Magnus
Published: December 2009

An ecosystems approach to capture fisheries management has some practical implications for institutions. The goal should be to achieve, at the local or sub-regional level, an integration of fisheries and habitat management. To succeed, cooperation among the various departments of fisheries, environment, and marine and coastal resources together with those responsible for zoning of activities along the coast and in coastal waters must be fostered. In addition, fishermen and coastal villagers must be involved. Here, an introduction is given to some of the institutional and social aspects that must be addressed, based on experiences in Southeast Asia. The paper includes: a) an overview of institutional implications at various levels; b) participatory and local approaches to fisheries and environmental management; c) the uses of various types of fisheries resources and environmental conservation areas; d) coastal planning activities, that have increasing importance due to the rise in natural hazards in the wake of climate change; and e) the need to manage fishing capacity to reduce conflicts and to provide a balance between fishing effort and ecosystem productivity. Positive actions in these areas should move ecosystems towards sustainability and create a less conflict prone environment.
The floristic composition and ecology of periphytic diatoms from the man-made tropical lake Tasik Kenyir, in Malaysia
Authors: Rouf A. J. M. Abdur , Ambak M. A. , Phang Siew-Moi
Published: December 2009

A total of 159 diatom taxa, mostly pennates, under 35 genera, were encountered on the submersed surface of standing dead trees in Lake Kenyir, Malaysia, during one year of sampling in 1995. Their station wise distribution was 101 taxa at the Dam side (site 1) and 145 taxa at the Petang River (site 2), showing 50% more taxa at the latter station. The spatial variability of diatoms is corroborated by the value of the Jaccard similarity index which was found to be 0.48 between the two stations. The monthly species richness ranged from 22 (November) to 60 (September) at the Dam side, whereas it was 32 (January) to 82 (September) at Petang River. The species diversity ranged from 2.87 to 3.70 and showed a positive correlation with species richness.

The pattern in frequency of occurrence of the diatom community was similar at both sites; 35% of the total taxa occurred only once a year in the samples; 31% of the taxa occurred 2–4 times. 15% taxa occurred 5–8 times, and the last 20% occurred 9–12 times in a year. The results of Principal Component Analysis showed that the first and second components comprised 59.4% variability in the data. A general pattern in diatom assemblages can be categorised into four groups along pH gradients. These are group 1: alkalibiont taxa, group 2: heterogeneous mixture of alkaliphilous, circumneutral taxa, group 3: acidobiontic taxa, and group 4: acidophilous taxa.

This study showed that the diatom species pool of Lake Kenyir is very rich, like that expected in a tropical waterbody, and the frequency of occurrence of diatom taxa may be related to the niche availability which requires further investigation. Moreover, the spatial variability of diatom communities within the lake is conspicuous, which is probably linked with habitat heterogeneity: Dam side is the main basin of the lake with open deep pelagic zone, and Petang River is a small shallow flowing stream bed comprised of cobbles and boulders.
Plastic pellets on the beaches of the northern Gulf of Aqaba, Red Sea
Authors: Abu-Hilal Ahmad H. , Al-Najjar Tariq H.
Published: December 2009

The occurrence of plastic pellets on the Jordanian beaches along the northeastern side of the Gulf of Aqaba (Red Sea) is being reported for the first time. Five beaches of about 4,650 m in length and 134,000 m2 in area were surveyed for the presence of these spherules during two successive years. Pellets with a variety of colors, shapes and sizes were found. The presence of these pellets is most likely due to accidental spillages: cargo loss during sea transport and sweeping of raw plastic materials, such as those imported as feedstock for local plastic factories in Jordan, into shore by wave action. When compared with other beaches of other parts of the world, the Jordanian beaches on the Gulf of Aqaba are considered heavily polluted with these pellets. This report discusses type, degree of degradation, sources and possible effects on the marine environment and suggests actions to reduce the input of plastic pellets to the marine environment at the source.
Protecting and managing the Arabian Gulf: Past, present and future
Authors: Hamza Waleed , Munawar Mohiuddin
Published: December 2009

The Arabian Gulf (also known as Persian Gulf and ROPME Sea) represents an extremely important economic, political and strategic aquatic resource. Although the Gulf region is known world wide for its oil-gas deposits and production, very little is known about its ecosystem health, food web dynamics, fisheries, biodiversity and sustainability. The present study reviews and highlights the major anthropogenic stressors which threaten the marine and coastal ecosystems of the Gulf. The Arabian Gulf environment lacks the holistic, ecosystem-based research and monitoring that have been conducted in other marine ecosystems. There is a need for multi-disciplinary, multi-trophic and multi-agency international investigations including the application of emerging technology. Such an integrated strategy is urgently needed to save the rapidly changing marine ecosystems from the impact of rapid and vigorous coastal development across the entire Gulf region. The necessity of developing and implementing ecosystem health agreements between the various riparian countries is emphasized for expeditious protection, conservation and management of this precious but threatened natural heritage.
Distribution and sources of hydrocarbons in lagoon sediments of Setiu Wetland, Terengganu, Malaysia
Authors: Tahir Norhayati Mohd , Rahim Hasra Masrifah Abd. , Hui Tay Joo , Seng Tan Hock , Fadzil Muhammad Fais , Abas Mhd. Radzi
Published: December 2009

Hydrocarbon compounds viz. aliphatic hydrocarbons, polycyclic aromatic hydrocarbons (PAHs), sterols, long chain fatty acids, alkanones and alkanals in surface sediment of Setiu Wetland were analysed and characterized using GCMS. The concentration of total identified resolved n-alkanes (TIRNA) in sediment ranged from 2.99–11.6 μ g g− 1 dry weight. The distribution of the aliphatic fraction showed the presence of n-alkanes ranging from C12 to C36 with high predominance for long chain homologues (C25-C31) and a carbon maximum at C29 and C31 with CPI > 3; these observations provide evidence for the presence of biogenic terrigenous input corresponding to epicuticular plant waxes into the lagoon sediments. Positive and strong correlation between n-alkanes associated with terrigenous input (ALK TER) and TIRNA suggest terrestrial input is the main sources of TIRNA in this study area. The absence of unresolved complex mixture (UCM) in the chromatogram and the absence of hopanes, steranes and PAHs compounds are indicative of uncontaminated sediment by petrogenic and pyrogenic hydrocarbons. The concentration of total identified sterols (TIS) ranged from 1.41 μ g g− 1 dry weight to 3.11 μ g g− 1 dry weight with cholesterol, β -Sitosterol and stigmasterol were generally the most dominant and abundant components detected at almost all stations. A positive and strong correlation was observed between B-Sitosterol and TIS and the distribution of long chain n-alkan-2-ones in the range of C21 to C27 with odd to even predominance and n-alkanals (C20 to C28), n-alkanols (C22–C30) and n-alkanoic acids (C22–C30) with even to odd predominance provide further evidence for biogenic sources of hydrocarbons with terrestrial plant input as the predominant source. It was noted that a minor contribution associated with marine phytoplankton (algae) as well as bacteria were also observed in some of the sediment samples superimposing with the terrigenous plant wax input. In general results from this study clearly showed the lagoon sediment of Setiu Wetland is still in uncontaminated condition where terrestrial plants input are the dominant contributor of organic compounds in the sediments with a minor input from marine organisms.
Progressive Diseases: Interpretation of Genetic Data
Authors: Baum Larry , Baum Eric
Published: December 2009

Simple modeling is proposed to represent the screening of gene polymorphisms for association with a progressive disease of insidious onset such as Alzheimer′s disease. The modeling demonstrates that when a polymorphism affects the rate of progression as well as the risk of disease, the correct interpretation of DNA data requires an accurate sampling of the living, diseased population. Furthermore, in this population, the effect of the polymorphism on disease risk cannot be distinguished from a corresponding effect on the rate of progression of the disease, and a null result does not preclude a significant effect of the gene on the disease. By contrast, when the population is sampled either at time of diagnosis or at autopsy, the effect of the polymorphism on disease frequency can be directly related to the frequency of the polymorphism in the sample, but evaluating the rate of disease progression requires additional data. When the only available data are obtained from a live patient population, substantial differences in interpretation can result from subtle differences in the patient selection protocol. When existing DNA databases are used in which this protocol is not well characterized, there is a corresponding uncertainty introduced into the deduced effect of the polymorphism on disease risk and rate of progression.
A Simple Mathematical Method to Predict the Course of a First Episode of Liver Viral Cytolysis
Authors: Dioguardi Nicola , Barbieri Antonio , Daccò Renato , Grizzi Fabio
Published: December 2009

Early detection of the self‐limiting or chronic tendency towards disease at the beginning of the hepatitis process is a canonical element of the analysis and synthesis to formulate the diagnosis and to decide the most useful and economic therapeutic strategy. Early treatment with antiviral drugs before liver functions undergo deterioration may reduce death and disability especially in young patients.

A formula suggested by a Max Planck equation provides mathematical curves that can be obtained very early during the course of hepatitis using just a few initial serum measurements of the alanine‐aminotransferase (ALT) enzyme. The clinical ALT data forming the unpredictable early natural curve of ALT can be transformed into mathematical values capable of providing a deterministic curve that intersects the normal ALT value at what is known as the G point, and allows some predictions to be made concerning the acute or chronic evolution of the disease.

The G point seems to be a good predictor of whether or not a patient with clinically evident first episode of viral hepatitis will develop chronic liver disease as it revealed the initial phase of the first cytolytic episode in 56 untreated patients of our 59 cases; the three wrong predictions involved patients being treated with interferon.
The Power‐Law Formalism as a Tool for Modeling Hormonal Systems
Authors: Sorribas Albert , González Angel
Published: December 2009

Modeling a hormone system requires a number of simplifying assumptions. Often, the final conceptual model incorporates a number of aggregated processes that have no correspondence with a single enzyme‐catalyzed reaction. In such cases, it is discussible using models based on classical biochemical kinetics rate laws that are valid only under specific conditions. The power‐law formalism provides an alternative framework for building up a mathematical model in such cases. The resulting model is a set of ordinary differential equations with a special structure that allows efficient symbolic and numerical analysis of the system′s properties. In these equations, the underlying rate‐laws of each of the component processes are represented by a power‐law that is an exact representation of the actual rate‐law at the operating point. The particular form of these equations allows representation of a wide range of kinetic features without changing the basic power‐law form. Moreover, its parameters have an immediate interpretation as apparent kinetic‐orders and rate‐constants. This is especially helpful for incorporating both quantitative and qualitative information in the process of model definition. This is particularly useful when detailed kinetic information concerning system′s components is not available. In this paper we show the utility of the power‐law approach in this context by deriving an illustrative model of a complex physiological system: the hypothalamus‐anterior pituitary‐thyroid network. First, we derive a conceptual model that incorporates the key features of this system. Then, we derive an S‐system model, one of the preferred variants within the power‐law formalism, and we show its utility in exploring the system properties. The model qualitatively reproduces the response of normal, hyperthyroid, and hypothyroid patients to a clinical test involving a thyrotropin releasing hormone injection. Finally, we illustrate the utility of this modeling strategy for studying the system′s response to different dynamic patterns of regulatory signals, and for exploring how altered dynamic patterns of stimulatory signals can cause pathological states.
The Potential Distribution due to a Dipole Source in the Fetal Heart: A Numerical Model of the Maternal Abdomen
Authors: Abboud Shimon , Arbel Michael , Rosenfeld Moshe , Udom-Rice Izuka , Skupski Dan , Friedman Deborah , Chervenak Frank A.
Published: December 2009

The potential distribution in a three dimensional model of the abdomen during pregnancy was studied numerically. Magnetic Resonance Imaging scans were used to construct a three dimensional model with eight different compartments of the abdomen: fetal body, vernix caseosa layer, placenta, uterus fluid, soft tissue, spinal cord, fat and muscles. Each compartment was assigned with its own conductivity and the integral form of the conservation volume conductor equation was solved by a finite volume method. The surface potential distribution of the maternal abdomen was studied for different compartment conductivity and for varying dipole source locations and orientations in the fetal heart. The present study supports the hypothesis that the reduction in the amplitude of the abdominal fetal electrocardiogram around the 30th week of gestation is related to the appearance of a low conductive isolating layer around the fetus. The study shows that an opening in the vernix caseosa layer increases the amplitude of the abdominal fetal ECG with the creation of a preferred signal pathway. It is also shown that the surface potential distribution depends on the fetal posture. Thus, choosing the correct bipolar recording and the appropriate sites of the recording electrodes may result in an increase in the peak to peak amplitude of the fetal ECG.
The Non‐Uniform Spatial Development of a Micrometastasis
Authors: Bloor Malcolm I. G. , Wilson Michael J.
Published: December 2009

This paper presents a mathematical model for the growth of a cancer micrometastasis in the form of a vascular cuff. The model postulates the possibility of a local imbalance between the rate of cell proliferation and the rate of cell death through apoptosis which is taken as dependent on the concentration of an angiogenesis‐inhibitor such as angiostatin. This imbalance produces non‐zero cell velocities within the micrometastasis. The local cell velocity is related to an interstitial pressure gradient through a Darcy′s Law type of equation, and the spatio‐temporal development of the micrometastasis in an environment with a non‐uniform nutrient concentration is followed by treating its outer boundary as an advancing front.
Book Reviews
Authors: Jonsson Kjell
Published: December 2009

MRI Atlas of Orthopedics and Traumatology of the Knee. By P. Teller, H. König, U. Weber and P. Hertel. Springer 2003. ISBN 3-540-44034-8. Price hardcover: €99.95.
The Gene Interaction Miner: a new tool for data mining contextual information for protein–protein interaction analysis
Authors: Ikin Aaron , Riveros Carlos , Moscato Pablo , Mendes Alexandre
Published: December 2009

Motivation: This work was motivated by the need for an automated tool for discovery of genetic networks and the availability of extensive contextual protein–protein interaction information in the iHOP repository. At the moment, this information cannot be explored to its full potential due to the lack of software tools to reliably collect, process and display that information in a way that life scientists can quickly analyze genes of interest and search for potential interaction networks. Commercial tools can perform a similar job, but results appear to be less informative than those obtained using contextual information.

Results: The Gene Interaction Miner (GIM) could successfully uncover complex network structures of protein–protein interactions for a test dataset composed of genes already related to Alzheimer's disease. That same set, when examined using two other analysis tools, namely STRING and Pathway Studio, resulted in incomplete protein–protein interaction networks, which indicate that the use of curated databases only gives a partial picture of the biological processes behind the disease.

Availability: The dataset used in this work and a running version of the software tool is available for download from the web site http://www.cs.newcastle.edu.au/∼mendes/softwareGIM.html.

Contact:  alexandre.mendes@newcastle.edu.au
PathGen: a transitive gene pathway generator
Authors: Clement Kendell , Gustafson Nathaniel , Berbert Amanda , Carroll Hyrum , Merris Christopher , Olsen Ammon , Clement Mark , Snell Quinn , Allen Jared , Roper Randall J.
Published: December 2009

Summary: Many online sources of gene interaction networks supply rich visual data regarding gene pathways that can aid in the study of biological processes, disease research and drug discovery. PathGen incorporates data from several sources to create transitive connections that span multiple gene interaction databases. Results are displayed in a comprehensible graphical format, showing gene interaction type and strength, database source and microarray expression data. These features make PathGen a valuable tool for in silico discovery of novel gene interaction pathways, which can be experimentally tested and verified. The usefulness of PathGen interaction analyses was validated using genes connected to the altered facial development related to Down syndrome.

Availability:  http://dna.cs.byu.edu/pathgen

Contact:  clement@cs.byu.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online. Further information is available at http://dna.cs.byu.edu/pathgen/PathGenSupplemental.pdf
Quantifying the biological significance of gene ontology biological processes—implications for the analysis of systems-wide data
Authors: Chagoyen Monica , Pazos Florencio
Published: December 2009

Motivation: Gene Ontology (GO), the de facto standard for representing protein functional aspects, is being used beyond the primary goal for which it is designed: protein functional annotation. It is increasingly used to evaluate large sets of relationships between proteins, e.g. protein–protein interactions or mRNA co-expression, under the assumption that related proteins tend to have the same or similar GO terms. Nevertheless, this assumption only holds for terms representing functional groups with biological significance (‘classes’), and not for the ones representing human-imposed aggregations or conceptualizations lacking a biological rationale (‘categories’).

Results: Using a data-driven approach based on a set of high-quality functional associations, we quantify the functional coherence of GO biological process (GO:BP) terms as well as their explicit and implicit relationships, trying to distinguish classes and categories. We show that the quantification used is in agreement with the distinction one would intuitively make between these two concepts. As not all GO:BP terms and relationships are equally supported by current functional associations, any detailed validation of new experimental data using GO:BP, beyond whole-system statistics, should take such unbalance into account.

Contact:  pazos@cnb.csic.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
Optimization of minimum set of protein–DNA interactions: a quasi exact solution with minimum over-fitting
Authors: Temiz N. A. , Trapp A. , Prokopyev O. A. , Camacho C. J.
Published: December 2009

Motivation: A major limitation in modeling protein interactions is the difficulty of assessing the over-fitting of the training set. Recently, an experimentally based approach that integrates crystallographic information of C2H2 zinc finger–DNA complexes with binding data from 11 mutants, 7 from EGR finger I, was used to define an improved interaction code (no optimization). Here, we present a novel mixed integer programming (MIP)-based method that transforms this type of data into an optimized code, demonstrating both the advantages of the mathematical formulation to minimize over- and under-fitting and the robustness of the underlying physical parameters mapped by the code.

Results: Based on the structural models of feasible interaction networks for 35 mutants of EGR–DNA complexes, the MIP method minimizes the cumulative binding energy over all complexes for a general set of fundamental protein–DNA interactions. To guard against over-fitting, we use the scalability of the method to probe against the elimination of related interactions. From an initial set of 12 parameters (six hydrogen bonds, five desolvation penalties and a water factor), we proceed to eliminate five of them with only a marginal reduction of the correlation coefficient to 0.9983. Further reduction of parameters negatively impacts the performance of the code (under-fitting). Besides accurately predicting the change in binding affinity of validation sets, the code identifies possible context-dependent effects in the definition of the interaction networks. Yet, the approach of constraining predictions to within a pre-selected set of interactions limits the impact of these potential errors to related low-affinity complexes.

Contact:  ccamacho@pitt.edu; droleg@pitt.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.