bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deciphering the Golgi Apparatus: From Imaging to Genes
Authors: Boulaflous Aurelia , Faso Carmen , Brandizzi Federica 
Published: May 2008

The Golgi apparatus is a vital organelle in eukaryotic cells. It grabs and processes secretory materials synthesized by the endoplasmic reticulum (ER) before sorting them to their destination. The Golgi also receives materials from vacuoles/lysosomes and the plasma membrane for further recycling to other compartments within the cell (1) (Figure 1). Given the vital role of the Golgi in a cell, it is important to understand how this organelle attains and maintains its structural and functional integrity during the intense processes of membrane traffic. Despite an equally central role of the Golgi in membrane traffic in eukaryotes, the organization of this organelle has some unique features in each cell system. Therefore, the wealth of information available on the structure and activity of the Golgi in one system is not always directly transferable to others. However, certain morphological and functional aspects are common among cell systems. Therefore, studying the factors that regulate organelle biogenesis and organization of the Golgi apparatus is important in basic cell biology of eukaryotes and may also contribute to a better understanding of how different cell systems have evolved. In this study, we report on the identification of Golgi mutants in plant cells. We have developed a screen that is a promising strategy not only for the identification of genes responsible for the morphological and functional integrity of the plant Golgi but could also provide fundamental information on other multicellular systems for which the power of forward genetics cannot be exploited as easily as in Arabidopsis. The Golgi occupies a central role in membrane traffic. A) Schematic representation of trafficking pathways in a plant cell (reviewed in 1). (a) Anterograde and retrograde protein transport from the ER to the cis Golgi and back. Proteins leaving the Golgi may have different destinations: some will be directed to the lytic (b) or protein storage vacuole (PSV, c), others will reach the plasma membrane (PM, d). The Golgi also receives retrograde flow of proteins from the PM (d). The Golgi appears to be also involved in a transport route to the chloroplast (28) (e). B) Confocal microscopy image of a tobacco leaf epidermal cell expressing the known ER/Golgi marker, ERD2–GFP (3), and an ER membrane marker, yellow fluorescent protein–Vap (unpublished data). A Golgi stack and an ER tubule are labeled with an arrowhead and an arrow, respectively. Scale bar = 5 μm.image
Characterization of Crystalline Bedrock Contaminated by Dense Nonaqueous Liquid
Authors: Cho H. Jean , Fiacco R. Joseph , Daly Matthew 
Published: May 2008

AbstractA systematic hydrogeologic site characterization has been completed in a fractured rock flow system, with the objective of identifying contaminant migration and fate pathways from a historical release of 1,1,1‐trichloroethane (TCA). The study integrated hydrogeologic analysis techniques such as borehole geophysical logging, pumping test analysis, and hydrochemical facies analysis to study the impact of a dense nonaqueous phase liquid (DNAPL) in a sparsely fractured crystalline bedrock. The assessment methodology can be divided into two parts: (1) characterization of the source area, where DNAPL is acting as a residual source of TCA, and (2) characterization of the downgradient plume. Reduction in DNAPL mass in the source area has resulted in significant and sustained reductions in downgradient concentrations, suggesting that remediation of fractured crystalline bedrock contaminated with DNAPL is possible and not “technically infeasible.”
Effect of Well Disinfection on Arsenic in Ground Water
Authors: Gotkowitz Madeline , Ellickson Kristie , Clary Alois , Bowman George , Standridge Jon , Sonzogni William 
Published: May 2008

AbstractDomestic water wells are routinely subjected to in situ chemical disinfection treatments to control nuisance or pathogenic bacteria. Most treatments are chlorine based and presumably cause strongly oxidizing conditions in the wellbore. Water resource managers in Wisconsin were concerned that such treatments might facilitate release of arsenic from sulfide minerals disseminated within a confined sandstone aquifer. To test this hypothesis, a well was subjected to four disinfection treatments over 9 months time. The first treatment consisted of routine pumping of the well without chemical disinfection; three subsequent treatments included chlorine disinfection and pumping. Pretreatment arsenic concentrations in well water ranged from 7.4 to 18 μg/L. Elevated arsenic concentrations up to 57 μg/L in the chemical treatment solutions purged from the well are attributed to the disintegration or dissolution of biofilms or scale. Following each of the four treatments, arsenic concentrations decreased to less than 10 μg/L during a period of pumping. Arsenic concentrations generally returned to pretreatment levels under stagnant, nonpumping conditions imposed following each treatment. Populations of iron‐oxidizing, heterotrophic, and sulfate‐reducing bacteria decreased following chemical treatments but were never fully eradicated from the well. Strongly oxidizing conditions were induced by the chlorine‐based disinfections, but the treatments did not result in sustained increases in well water arsenic. Results suggest that disruption of biofilm and mineral deposits in the well and the water distribution system in tandem with chlorine disinfection can improve water quality in this setting.
An In Situ Device to Measure Oxygen in the Vadose Zone and in Ground Water: Laboratory Testing and Field Evaluation
Authors: Patterson Bradley M , Davis Greg B. 
Published: May 2008

AbstractOxygen probes developed to measure in situ oxygen concentrations in gaseous and aqueous environments were evaluated in laboratory tests and during long‐term field evaluation trials at contaminated sites. The oxygen probes were shown to have a linear calibration and to be accurate compared to conventional dissolved oxygen electrodes and gas chromatography, both of which require labor‐intensive sample collection and processing. The probes, once calibrated, required no maintenance or recalibration for up to a period of 7 years in low‐oxygen environments, demonstrating long‐term stability. Times to achieve 90% of the stabilized concentration (t90) after a step change in aqueous oxygen concentration were 100–120 min in laboratory experiments and up to 180 min in field experiments, which is adequate for monitoring subsurface changes. Field application data demonstrated that the oxygen probes could monitor oxygen concentrations in hydrocarbon‐contaminated ground water to a depth of 20 m below the water table or in pyritic vadose zones over extended periods. During bioremediation field trials, oxygen monitoring enabled estimation of oxygen utilization rates by microorganisms and hydrocarbon biodegradation rates. Also, probes were able to monitor the development of ground water desaturation during air sparging trials, enabling the automated assessment of the distribution of injected air.
Ground Water Contamination in Kuwait Resulting from the 1991 Gulf War: A Preliminary Assessment
Authors: Mukhopadhyay A. , Al‐Awadi E. , Quinn M. , Akber A. , Al‐Senafy M. , Rashid T. 
Published: May 2008

AbstractA large number of oil wells in Kuwait were damaged and ignited by the retreating Iraqi troops during the 1991 Gulf War. The resulting spillage of huge volumes of crude oil on the surface gave rise to oil lakes and crude oil–impregnated soil. Moreover, products of crude oil combustion had spread over a large tract of the ground surface, causing widespread contamination of soil. Hydrocarbon contamination of ground water by the infiltrating runoff water carrying the contaminants from the surface soil to the water table and/or through direct contact with the crude oil leaking through the damaged casing in the subsurface was feared. This preliminary study was carried out to investigate the extent and nature of this possible contamination of ground water. The results indicate that the shallow fresh water lenses present under the Umm Al‐Aish water field and in the southeastern parts of the Raudhatain water field in North Kuwait were affected by hydrocarbon pollution. Standard methods like the determination of the contents of the total petroleum hydrocarbon by the Fourier transform infrared method and 16 polyaromatic hydrocarbons using the gas chromatography‐mass spectrometry method did not work well, possibly due to the environmental degradation of the crude oil over time. The fluorescence methods and the total organic carbon and total organic matter gave better indications of the intensity and the extent of ground water pollution. The brackish water fields of South and Central Kuwait were, however, free of any indications of hydrocarbon contamination.
Zero‐Order Kinetics Model for the Christensen‐Larsen Method for Fugitive Fuel Age Estimates
Authors: Galperin Yakov , Kaplan Isaac R. 
Published: May 2008

AbstractEstimating time of a middle distillate fuel release in soil can be performed under certain restricting environmental conditions using the Christensen‐Larsen method (CLM). This method is based on the linear correlation between the time since a diesel fuel release and the corresponding value of n‐heptadecane to pristane ratio (n‐C17/Pr) but requires knowledge of the initial ratio value. The empirical nature of this method does not, however, allow accounting for variance in the initial fuel value used by CLM. Based on the zero‐order approximation of the Monod model, we have deduced a generalized equation that can be used for estimating release ages of middle distillate fuels with different initial values. When combined with other site‐specific factors, this equation provides a useful tool for the time of release estimates.
Demonstration of Enhanced Bioremediation in a TCE Source Area at Launch Complex 34, Cape Canaveral Air Force Station
Authors: Hood E.D. , Major D.W. , Quinn J.W. , Yoon W.‐S. , Gavaskar A. , Edwards E.A. 
Published: May 2008

AbstractThe ability of bioremediation to treat a source area containing trichloroethene (TCE) present as dense nonaqueous phase liquid (DNAPL) was assessed through a laboratory study and a pilot test at Launch Complex 34, Cape Canaveral Air Force Center. The results of microcosm testing indicate that the indigenous microbial community was capable of dechlorinating TCE to ethene if amended with electron donor; however, bioaugmentation with a dechlorinating culture (KB‐1; SiREM, Guelph, Ontario, Canada) significantly increased the rate of ethene formation. In microcosms, the activity of the dechlorinating organisms in KB‐1 was not inhibited at initial TCE concentrations as high as 2 mM. The initially high TCE concentration in ground water (1.2 mM or 155 mg/L) did not inhibit reductive dechlorination, and at the end of the study, the average concentration of ethene (2.4 mM or 67 mg/L) was in stoichiometric excess of this initial TCE concentration. The production of ethene in stoichiometric excess in comparison to the initial TCE concentration indicates that the bioremediation treatment enhanced the removal of TCE mass (either sorbed to soil or present as DNAPL). Detailed soil sampling indicated that the bioremediation treatment removed greater than 98.5% of the initial TCE mass. Confirmatory ground water samples collected 22 months after the bioremediation treatment indicated that chloroethene concentrations had continued to decline in the absence of further electron donor addition. The results of this study confirm that dechlorination to ethene can proceed at the high TCE concentrations often encountered in source areas and that bioremediation was capable of removing significant TCE mass from the test plot, suggesting that enhanced bioremediation is a potentially viable remediation technology for TCE source areas. Dehalococcoides abundance increased by 2 orders of magnitude following biostimulation and bioaugmentation.
Impact of Substrate Physical Characteristics on Grow Out of Freshwater Prawn,Macrobrachium rosenbergii, in Ponds and Pond Microcosm Tanks
Authors: Tidwell James , Coyle Shawn 
Published: May 2008

AbstractTwo independent trials were conducted to evaluate the effects of different physical characteristics of substrate materials on growth and survival of freshwater prawn. In Trial 1, juvenile prawns (0.4 ± 0.2 g) were stocked at 123 prawns/m2of tank bottom into twenty‐one 18,000‐L fiberglass tanks managed as pond microcosms. Six substrate materials were chosen to allow comparisons of surface area, mesh size, color, and texture. A control treatment received no added substrate. There were three replicate tanks per treatment. Substrates were positioned vertically at a rate sufficient to increase the bottom surface area by 100%. Prawns were fed a 32% protein sinking diet according to a feed chart. After 110 d, there was no significant difference (P > 0.05) in survival among treatments, averaging 72.6% overall. Prawns in the control treatment (no substrate) had significantly lower (P ≤ 0.05) average weights (9.5 g), lower production (1342 kg/ha), and higher feed conversion ratio (FCR; 2.5) than those in substrate treatments, which were not significantly different (P > 0.05) and averaged 13.4 g, 2404 kg/ha, and 1.3, respectively. For Trial 2, the least expensive substrate material from Trial 1 (lightweight polyethylene bird netting) was compared with the substrate most commonly used in commercial production (heavyweight orange polyethylene safety fencing) under practical pond conditions. Juvenile prawns (0.8 ± 0.3 g) were stocked at 61,600/ha into six 0.04‐ha earthen ponds. Each was randomly assigned one of the two substrate materials, and there were three replications per treatment. After 101 d, there were no significant differences (P > 0.05) between treatments in terms of survival (91%), average weight (34 g), total production (2150 kg/ha), or FCR (3.1). In these studies, physical characteristics of the substrate materials had little impact. The lightweight netting represents a 68% cost savings compared to the currently recommended substrate material.
Gene Knockdown: A Powerful Tool for Gene Function Study in Fish
Authors: Boonanuntanasarn Surintorn 
Published: May 2008

Abstract So far, there are a number of fish genome projects, including experimental and economically important fish that provide available DNA sequence information. However, the function of a gene cannot be deduced only by its DNA sequence. Therefore, a technique with which to investigate the function of the fish gene is needed. Gene knockdown (GKD), or antisense technology, is now being used as a powerful technique to study gene functions in living organisms. GKD effects result from the introduction of an antisense molecule into living cells. The antisense agents bind to target messenger RNA, thus inactivating the target gene expression. The appropriately spatial inhibitory effects on protein production from corresponding gene resulted in the phenotypic change. Therefore, the function of the gene can be understood. To date, there are a number of antisense molecules that can affect efficient GKD in fish. These include antisense oligonucleotides, small interfering RNA, and ribozyme. These antisense molecules cause specific gene inhibitor effects with different mechanisms. The various antisense mechanism types facilitate a number of GKD applications with various approaches in animals. In this review, we demonstrate the characteristics of each antisense molecule, its mechanism, and its application, especially for gene functional analysis in fish.
Effects of Graded Levels of Carbohydrate on Growth and Survival of Largemouth Bass, Micropterus salmoides
Authors: Amoah Akua , Coyle Shawn D. , Webster Carl D. , Durborow Robert M. , Bright Leigh Anne , Tidwell James H. 
Published: May 2008

Abstract Excessive carbohydrates (CHO) in diets for largemouth bass (LMB), Micropterus salmoides, are suspected of accumulating glycogen in hepatocytes, which may result in liver dysfunction. This study evaluated the effect of graded levels of dietary CHO on growth, survival, and liver histology of LMB. One hundred feed‐trained advanced fingerling LMB (128.5 ± 21.5 g) were stocked into each of nine 3400‐L polyethylene tanks. Tanks were randomly assigned one of three experimental diets containing different CHO levels (13, 19, or 25% of diet). The extruded diets were approximately isonitrogenous (42% crude protein) and isocaloric (3 kcal/g energy). There were three replicate tanks per dietary treatment. Bass were fed to apparent satiation twice daily for 148 d. Survival was significantly higher (P ≤ 0.05) for fish fed the 13 and 19% CHO diets (89 and 90%, respectively) compared to those fed the 25% CHO diets (82%). Average harvest weight of fish fed the 13% CHO diet (380 g) was significantly greater (P ≤ 0.05) than for fish fed other diets. Average harvest weight of fish fed the 19% CHO diet (347 g) was significantly greater (P ≤ 0.05) than for fish fed the 25% CHO diet (310 g). Specific growth rates (%/d) were significantly higher (P ≤ 0.05) in fish fed the 13 and 19% CHO diets than in fish fed 25% CHO diet. Feed conversion ratios for fish fed the 13 and 19% CHO diets (2.3 and 2.4, respectively) were both significantly lower (P ≤ 0.05) than in fish fed the 25% CHO diet (3.6). There were no significant differences (P > 0.05) in condition factor, protein efficiency ratio, hepatosomatic index, or liver glycogen concentration among fish fed the different experimental diets. Overall, mean blood glucose levels in fish fed the 13 and 19% CHO diets (61.0 and 71.2 mg/dL, respectively) were significantly lower (P ≤ 0.05) than in fish fed the 25% CHO diet (87 mg/dL). Histopathological examination of livers from fish fed the three diets was used to score the degree of vacuolization of hepatic tissues (0 = normal, 1 = slight, 2 = mild, 3 = moderate, and 4 = severe). Regression of vacuolization scores on dietary CHO levels was statistically significant (P ≤ 0.05) and indicated a direct positive relationship between liver vacuolization and dietary CHO level (R2 = 0.57). These data indicate that LMB grow faster and use feeds more efficiently when CHO are maintained at <20% of diet. CHO levels >20% negatively impacted liver histology, but a liver tissue analyses did not document glycogen accumulation.
Finfish Mariculture in Inland Australia: A Review of Potential Water Sources, Species, and Production Systems
Authors: Partridge G. J. , Lymbery A. J. , George R. J. 
Published: May 2008

Abstract Secondary salinization has rendered over 100 million hectares of arable land throughout the world, and over 5 million hectares in Australia, unsuitable for conventional agriculture. The use of this land and associated water for mariculture is an adaptive approach to this environmental problem with many potential economic, social, and environmental benefits. In this article, we review three key technical aspects for the development of a finfish mariculture industry in inland Australia, namely the potential sources of water, the species suitable for culture, and the production systems available to produce them. Based on factors such as their quality, quantity, and proximity to infrastructure, the most appropriate water sources are groundwater obtained from interception schemes and waters from operational or disused mines. Pond‐based culture methods using these water sources have many specific advantages; however, few species can thrive in the wide range of seasonal water temperatures experienced within the temperate regions where secondary salinity is most abundant. Recirculating aquaculture systems (RAS) would enable production of more species in a greater number of water sources; however, the benefits typically associated with RAS are not as apparent in rural areas. Mulloway, Argyrosomus japonicus, are a temperate species that appear to have many positive attributes for inland mariculture; however, more data are required on their rate of growth across a wider range of temperatures. Seasonal production of barramundi, Lates calcarifer, in ponds has been demonstrated in the temperate climatic zones but may be more appropriate for those salinized water sources located in the warmer parts of the country. Freshwater species, such as silver perch, Bidyanus bidyanus, and Murray cod, Maccullochella peelii peelii, are likely to be suitable for low‐salinity waters. Rainbow trout, Oncorhynchus mykiss, also have excellent potential provided water temperature can be maintained below the upper lethal limit.
Spontaneous Spawning of Captive Red Snapper, Lutjanus campechanus, and Dietary Lipid Effect on Reproductive Performance
Authors: Papanikos Nikolaos , Phelps Ronald P. , Davis D. Allen , Ferry Amy , Maus David 
Published: May 2008

Abstract Two experiments addressed the spontaneous spawning of red snapper, Lutjanus campechanus, under controlled temperatures and photoperiods and the effect of broodstock diets supplemented with oils rich in polyunsaturated fatty acids. In Experiment 1, broodfish were fed a standard diet (ST1) and one enriched with menhaden oil (ER1) over a 355‐d period. ER1‐influenced egg fatty acid profile, however, did not positively influence egg production. Both diets produced highly viable eggs and larvae but results varied within treatments. In Experiment 2, broodfish were fed either a standard diet (ST2) or one supplemented with oils (ER2) rich in docosahexaenoic and arachidonic acid using a 203‐d cycle. Both treatments produced eggs but fertilization rates ranged 0–10%. There was no clear influence of the diets on egg fatty acid profiles. These results indicate that red snapper can spawn spontaneously in tanks under controlled environmental conditions and produce viable eggs and larvae when fed diets based on squid, shrimp, and fish. The fatty acid composition of the diets was reflected in the eggs to some degree, but the oil enrichments did not further enhance the reproductive performance and egg quality under the conditions of this study.
Population Growth and Production of Apocyclops dengizicus (Copepoda: Cyclopoida) Fed on Different Diets
Authors: Farhadian Omidvar , Yusoff Fatimah Md , Arshad Aziz 
Published: May 2008

Abstract This study was carried out to investigate the effects of various diets: 4 monoalgal diets: Nannochloropsis oculata (N), Isochrysis galbana (I), Chaetoceros calcitrans (C), and Tetraselmis tetrathele (T); 4 mixed algal diets: N+I+C+T(NICT), N+I+C(NIC), C+T(CT), and I+T(IT); and 2 nonalgal diets: baker’s yeast (BY) and prepared shrimp feed (SF) on population growth and density of Apocyclops dengizicus. The type and density of diet had significant effects on the growth and density of A. dengizicus (P < 0.01). Of tested diets, T and CT were optimum diets due to higher density and growth rate of A. dengizicus compared to other diets. Their high dietary value was related to the higher contents of polyunsaturated fatty acid, particularly docosahexaenoic acid (22:6n‐3), eicosapentaenoic acid (20:5n‐3), and arachidonic acid (20:4n‐6) compared to A. dengizicus cultured on other diets. The results of the present study illustrated that T. tetrathele was the most suitable food for the culture of A. dengizicus.