bluuebunny/crossref_metadata_2025 huggingface dataset:
A computational framework for a nutrient flow representation of energy utilization by growing monogastric animals
Authors: Birkett Stephen , Lange Kees de
Published: May 2008

A computational framework to represent nutrient utilization for body protein and lipid accretion by growing monogastric animals is presented. Nutrient and metabolite flows, and the biochemical and biological processes which transform these, are explicitly represented. A minimal set of calibration parameters is determined to provide five degrees of freedom in the adjustment of the marginal input–output response of this nutritional process model for a particular (monogastric) animal species. These parameters reflect the energy requirements to support the main biological processes: nutrient intake, faecal and urinary excretion, and production in terms of protein and lipid accretion. Complete computational details are developed and presented for these five nutritional processes, as well as a representation of the main biochemical transformations in the metabolic processing of nutrient intake. Absolute model response is determined as the residual nutrient requirements for basal processes. This model can be used to improve the accuracy of predicting the energetic efficiency of utilizing nutrient intake, as this is affected by independent diet and metabolic effects. Model outputs may be used to generate mechanistically predicted values for the net energy of a diet at particular defined metabolic states.
Calibration of a nutrient flow model of energy utilization by growing pigs
Authors: Birkett Stephen , de Lange Kees
Published: May 2008

A computational framework to represent energy utilization for body protein and lipid accretion by growing pigs is presented. Nutrient and metabolite flows, and the biochemical and biological processes which transform these, are explicitly represented in this nutritional process model. A calibration procedure to adjust the marginal input–output response is described, and applied, using reported experimental results, to determine a complete set of parameters for representing energy utilization by growing pigs. A reasonable value for minimum basal energy requirements is also determined. Although model inputs and outputs need not at any time be converted to equivalent energy flows, to facilitate comparison of model response with that of conventional energy-based models, a simple means to estimate energy flows from model-predicted nutrient flows is described. The well-known hierarchy of marginal (biological) energetic efficiencies with which pigs use different classes of nutrients is predicted by the model, based only on simple biological and biochemical principles. The significance of independent diet and metabolic effects on both energetic efficiency and maintenance requirements is examined using model predictions from simulated experiments.
Changes in fatty acid concentrations in tissues of African catfish,Clarias gariepinusBurchell, as a consequence of dietary carnitine, fat and lysine supplementation
Authors: Ozório R. O. A , Uktoseja J. L. A , Huisman E. A. , Verreth J. A. J
Published: May 2008

A study was undertaken to examine the effect of different dietary carnitine (200 and 1000 mg/kg diet) and fat (90 and 190 g/kg diet) supplementation on growth and fatty acid concentrations of fish fed either with a low- (13 g/kg) or a high-lysine (21 g/kg) diet. African catfish (22·7 g/fish),Clarias gariepinusBurchell, juveniles were stocked (sixteen aquaria, twenty-five fish per aquarium) and fed for a maximum of 74 d. Dietary lysine had a clear effect on growth performance and feed conversion ratios, but dietary carnitine supplements had no effect. High-carnitine supplements increased total carnitine content (P<0·0004) and reduced tissue free carnitine: acyl-carnitine ratio (P<0·05) compared with low-carnitine supplements. High-fat supplements decreased liver carnitine concentrations. Clear effects on liver fatty acid concentrations were observed in high-carnitine-fed fish compared with low-carnitine-fed fish. The primary liver fatty acids affected were 18:2n-6 (linoleic acid), 20:5n-3 (eicosapentanoic acid) and 22:6n-3 (docosahexanoic acid). The whole-body fatty acid balance suggested that 20:5n-3 disappeared (apparently by β-oxidation) more readily than 18:2n-6 and/or 22:6n-3. From 774 mg 20:5n-3 eaten by high-lysine–high-fat–low-carnitine fish, 58 % was not assimilated into body tissues. High-carnitine-fed fish showed an increase in 20:5n-3 oxidation by 7 % compared with low-carnitine fish. Although dietary carnitine did not improve body growth, these results support the hypothesis that carnitine can enhance the mobilisation of long-chain fatty acids towards oxidation.
Energy intake by multiple pass 24 h recall and total energy expenditure: a comparison in a representative sample of 3–4-year-olds
Authors: Reilly John J. , Montgomery Colette , Jackson Dian , MacRitchie Jane , Armstrong Julie
Published: May 2008

The accuracy of the multiple pass 24 h recall for assessment of habitual energy intake in pre-school children is unclear. The primary aim of this study was to assess its accuracy by comparison with measurement of total energy expenditure by doubly-labelled water in a representative sample of forty-one 3–4-year-olds. The recall method was well tolerated by subjects and was administered quickly and easily. However, it produced estimates of energy intake which significantly exceeded measures of total energy expenditure from doubly-labelled water, mean paired difference 660 kJ/d (P<0·01). Agreement between the two methods was poor at the individual level: limits of agreement 660+/-3018 kJ/d. Error and imprecision in both methods contribute to individual differences, but the present study suggests that the multiple pass 24 h recall does not provide accurate estimates of dietary energy intake in individual children.
Obesity in African women in the North West Province, South Africa is associated with an increased risk of non-communicable diseases: the THUSA study
Authors: Kruger H. S. , Venter C. S. , Vorster H. H.
Published: May 2008

The objective of the present study was to assess the relationship between anthropometric measurements and risk factors for non-communicable diseases (NCD) in South African black women. A cross-sectional sample of 1040 apparently healthy black female volunteers, 15–70 years old, was recruited from thirty-seven randomly selected sites in the North West Province, stratified according to level of urbanisation. We analysed the association between BMI, waist:hip (WHR), waist circumference (WC) and skinfold measurements and the following risk factors for NCD: blood pressure, serum lipids, fasting serum glucose and insulin and plasma fibrinogen, by using age-adjusted correlation analyses and stepwise regression analysis. Of the subjects, 28·6 % were obese (BMI>30). After adjustment for age and smoking status, BMI correlated significantly with diastolic blood pressure (r0·21,P=0·037), serum triacylglycerols (TG) (r0·30,P=0·003), fasting glucose (r0·29,P=0·005) and log fasting insulin (r0·24,P=0·02). There was a significant negative correlation between BMI and HDL-cholesterol (r-0·38,P<0·001). Similar but stronger correlations were found between both WC and WHR and these risk factors. Together with age, WC was a significant predictor of TG, HDL-cholesterol and fasting glucose in regression analysis, while subscapular skinfold was a significant predictor of diastolic blood pressure and fasting glucose concentration. Triceps skinfold was a significant predictor of total serum cholesterol, LDL-cholesterol, plasma fibrinogen and the insulin sensitivity index. Measures of obesity, particularly WC, are associated with the risk for NCD in black South African women, in which a high rate of obesity has been found.
Evaluation of weed control provided by three winter cereals in conservation-tillage soybean
Authors: Price Andrew J. , Wayne Reeves D. , Patterson Michael G.
Published: May 2008

Information is needed on the role of cover crops as a weed control alternative due to the high adoption of conservation tillage in soybean [Glycine max (L.) Merr.] production. Field experiments were conducted from fall 1994 through fall 1997 in Alabama to evaluate three winter cereal cover crops in a high-residue conservation-tillage, soybean production system. Black oat (Avena strigosa Schreb.), rye (Secale cereale L.), and wheat (Triticum aestivum L.) were evaluated for their weed-suppressive characteristics compared to a winter fallow system. Three herbicide systems were utilized: no herbicide, a mixture of two pre-emergence (PRE) herbicides, or PRE plus post-emergence (POST) herbicides. The PRE system contained pendimethalin plus metribuzin. The PRE plus POST system contained pendimethalin plus a prepackage of metribuzin and chlorimuron ethyl applied PRE, followed by an additional chlorimuron ethyl POST application. No cover crop was effective in controlling weeds without a herbicide. However, when black oat or rye was utilized with only PRE herbicides, weed control was similar to the PRE plus POST input system. Thus, herbicide reductions may be attained by utilizing cover crops that provide weed suppression. Rye and black oat provided more effective weed control in the PRE only herbicide input system than wheat in conservation-tillage soybean. The winter fallow, PRE plus POST herbicide input system yielded significantly less soybean one out of three years when compared to systems that included a winter cover crop.
Do the new organic producers differ from the ‘old guard’? Empirical results from Norwegian dairy farming
Authors: Flaten Ola , Lien Gudbrand , Ebbesvik Martha , Koesling Matthias , Valle Paul S.
Published: May 2008

Conventional farmers converting to organics have contributed to most of the rapid expansion of organic farming in recent years. The new organic farmers may differ from their more established colleagues, which may have implications for the development of the organic farming sector and its distinctiveness vis-à-vis conventional production and marketing practices. The aim of this study was to explore Norwegian organic dairy farmers' personal and farm production characteristics, farming goals, conversion motives, and attitudes to organic farming, grouped by year of conversion (three groups). A postal survey was undertaken among organic dairy farmers (n=161). The results show that the newcomers (converted in 2000 or later) were less educated than the early entrants (the so-called ‘old guard’) who converted in 1995 or earlier. The frequency of activities like vegetable growing and poultry farming among the old guard was high. The late-entry organic herds were fed with more concentrates and had a higher milk production intensity, showed a higher incidence of veterinary treatments and less frequent use of alternative medicine than the herds of the two earlier converting groups. For all groups of farmers, the highest ranked farming goals were sustainable and environment-friendly farming and the production of high-quality food. Late entrants more often mentioned goals related to profit and leisure time. On average, the most frequently mentioned motives for conversion were food quality and professional challenges. The old guard was more strongly motivated by food quality and soil fertility/pollution issues than the others, whereas financial reasons (organic payments included) were relatively more important among the newcomers. All groups held very favorable views about the environmental qualities of organic farming methods, albeit with different strengths of beliefs. Even though trends towards more pragmatic and business-oriented farming were found, the majority of the newcomers were fairly committed.
Strategic market planning for value-added natural beef products: A cluster analysis of Colorado consumers
Authors: Thilmany Dawn D. , Umberger Wendy J. , Ziehl Amanda R.
Published: May 2008

In the past decade, sales of meat products labeled as natural (minimally processed) and produced without antibiotics and hormones have increased dramatically. In response to growing demand for meat products differentiated by various production attributes, many smaller-scale beef enterprises are considering direct marketing of their beef products to end-consumers as a viable approach to sustaining their family farming operations. This research uses survey data from Colorado consumers, and factor and cluster analysis to determine market segments for various (varied by production protocols and other meat attributes) natural beef products. Findings from the cluster analysis indicate that there are multiple segments of consumers who are likely to purchase natural beef, and that different segments are motivated by different factors. The most important factor explaining almost two-thirds of the differences among consumer responses relates to consumers' perceptions of the importance of meat attributes related to production practices (e.g. use of antibiotics, hormones and environmentally friendly grazing). Interestingly, the two consumer segments that are willing to pay a significantly higher premium for natural, local beef are motivated by different aspects of the meat and its intrinsic production attributes. One segment, representing 12.5% of consumers, ranked the importance of all production attributes significantly lower than the sample average. Consumers in this segment appear to be motivated by their perceptions of the extrinsic quality of natural beef products. The other segment, 13% of consumers, appears to be altruistic, ranking all production attributes such as ‘no antibiotics’, ‘no hormones’, and ‘humane treatment’, significantly higher than all of the other clusters. These results indicate the potential strength of production methods (and marketing of such quality differences) as product differentiation criteria. This paper illustrates the type of market research that may be useful for beef producers seeking value-added marketing opportunities, and portrays the types of consumers who are fueling the growth in natural meats in the United States. Such market analysis can facilitate producers' ability to effectively develop product concepts, labeling and promotional strategies targeted at the most receptive consumer segments, and illustrates that there is more than one type of consumer interested in purchasing products differentiated by sustainable production methods.
Profitability of coupled potato and dairy farms in Maine
Authors: Hoshide Aaron K. , Dalton Timothy J. , Stewart Smith N.
Published: May 2008

After decades of farm specialization, re-integrating crop and livestock farming systems is being reconsidered as a key step toward sustainable agriculture. The relative profitability of Maine farms integrating crops and livestock is compared to non-integrated or conventional farms. Crop and livestock integration in Maine occurs through either diversified on-farm integration or, more commonly, through coupled interactions between specialized crop and livestock producers. Potato and dairy systems coupled for only 2 years (short-term) had greater profitability compared to conventional systems. Profitability increased in the short term in two ways. First, potato farms grew more of their primary cash crop. Secondly, dairy farms expanded cow numbers, increasing profitability assuming increasing returns to scale. Coupled systems integrated for more than 10 years (long-term) had more favorable profitability than short-term couplers since greater manure-nutrient credits were taken for potatoes and silage corn. The advantages of potato–dairy integration were even greater if potato yields increased in the long term, as suggested by long-term rotation plot studies in Maine. Even if coupling is more profitable than non-integrated systems, it requires that farms be in close proximity and for farmers to have adequate working relationships and management skills. Despite these challenges to re-integrating crops and livestock, short- and long-term economic benefits may encourage farmers in appropriate areas to consider coupling with other producers.
A comparison of anhydrous fixation methods for the observation of pea embryonic axes (Pisum sativum L. cv. Alaska)
Authors: Ramsay Jodie L. , Koster Karen L.
Published: May 2008

To develop an effective protocol for observation of dry pea embryonic axes (Pisum sativum L. cv. Alaska), several fixation methods were compared for ease of infiltration and sectioning and for quality of sections. These methods included osmium vapour fixation, freeze-substitution followed by an aqueous wash, and freeze-substitution using anhydrous methanol. Axes fixed with osmium vapour were brittle and difficult to section. Cells fixed using vapour from an aqueous OsO4 solution had cell walls separated from plasma membranes, while cells fixed using osmium crystals exhibited folded walls tightly appressed to plasma membranes. Axes fixed using freeze-substitution followed by an aqueous wash sectioned easily, but appeared plasmolysed, with cell walls completely separated from plasma membranes. Even a brief (10 min) rinse in 90% acetone led to separation of the walls from the membranes. Tissues infiltrated with anhydrous methanol and Spurr’s resin were difficult to section, but showed extensive folding of the cell walls, with plasma membranes appressed to the walls. Additional modifications to the infiltration protocol led to improved sectioning. The highest-quality sections were obtained using freeze-substitution with anhydrous methanol as a solvent, followed by infiltration using methanol and Spurr’s resin, with the catalyst (dimethylaminoethanol) omitted from the infiltration protocol until the final step. Through comparison of several protocols recommended in the literature for the preparation of dry tissues, it is apparent that the presence of water, even in the vapour phase, at any step can cause swelling of the cell walls and the artefactual separation of the walls from the fixed protoplast.
Dispersal mechanisms in Lavandula stoechas subsp. pedunculata: autochory and endozoochory by sheep
Authors: Sánchez Ana M. , Peco Begoña
Published: May 2008

It is normally assumed that Lavandula stoechas subsp. pedunculata (Miller) Samp. ex Rozeira (Labiatae) is dispersed by autochory in spite of the clear pioneer nature of the species. This paper examines the efficiency of autochorous dispersal (seed rain) and the possibility that the species is also dispersed endozoochorally by sheep. Seed rain was measured using pitfall traps and adhesive strips in summer 1999. The viable seed content in sheep dung was measured by greenhouse germination of dung collected monthly in the summers of 1998 and 1999. Two experimental tests were also conducted to ascertain whether dung-borne seeds could be established under field conditions and to evaluate the effect of added dung in the establishment of seeds taken from plants. The recorded seed rain was 2544 seeds m-2 inside the Lavandula patches, with an aggregated distribution. Autochory around the mother plant fitted a negative exponential distribution, with 90.5% concentrated in a 0–30 cm radius and a maximum distance of 1 m. Viable Lavandula seeds were found in 73% of the examined dung samples, with an average of 5.5 seeds per sample (6 g) and a high inter- and intra-annual variation. This high seed content, together with the daily sheep movements over several kilometres, make the species highly dispersible, possibly explaining its clear pioneer nature. Moreover, available data suggest that seeds in sheep dung can germinate and establish under natural conditions, and that dung addition has a positive effect on species establishment.
The role of epizoochorous seed dispersal of forest plant species in a fragmented landscape
Authors: Graae Bente Jessen
Published: May 2008

A domestic dog was used in two experiments to elucidate the role of epizoochorous seed dispersal of forest plants. First, the dog was walked through forest vegetation at different times of year and its coat analysed for seeds retained within it. The seed content of the coat was compared to seed frequencies in the vegetation. Secondly, seeds of 11 plant species were placed in different positions on the dog, and their persistence in the coat analysed with respect to distance subsequently travelled. The experiments demonstrate that seeds with morphological adaptations to seed dispersal and small seeds of tall species can be caught effectively by a dog’s coat. The morphologically adapted seeds can be dispersed over large distances as long as the dog moves steadily along a road. The same is true for species with small and smooth seeds if they are deposited on the back of the dog, but not if they are placed on its side. Comparisons of these results with the distribution of forest species in a fragmented landscape, indicated that tall species with small seeds and species with morphological adaptations for epizoochorous dispersal are good at colonizing new forest habitats.
Physical dormancy in Geraniaceae seeds
Authors: Meisert A.
Published: May 2008

Seed dormancy was analysed in Geraniaceae, testing 29,103 seeds of 35 species for seed-coat impermeability to water. Seeds of wild and cultivated species from a number of different climatic/ecological zones (northern Germany, the Canary Islands and South Africa) were investigated. Seeds from cultivated plants and natural populations had similar (±2%) percentages of water-impermeable seeds. The percentages of impermeable seeds at maturity were also mostly constant (±2%) for two different years. The species analysed contained from 0 to 100% impermeable seeds at maturity, and could be classified into three quantitative types of physical dormancy: four species with no impermeable seeds (PY0), 10 species with a maximum of 80% impermeable seeds (PY80), and 21 species with more than 80% impermeable seeds (PY100). Species with different life cycles and from very different habitats, e.g. Geranium pratense or Pelargonium capitatum, belonged to the PY100 group. However, all of the succulent shrubs investigated from the genus Pelargonium were PY0 species. Five years of dry storage at 20 ± 5°C decreased physical dormancy in a species-dependent fashion. Erodium cicutarium, for example, had 95% impermeable seeds at maturity; all of them became permeable during the dry storage and began to germinate immediately after placing them on a moist substrate. Physical dormancy of other species, e.g. Pelargonium zonale, Pelargonium vitifolium or Geranium pratense, was not affected by dry storage. Thus, physical dormancy is a diversely differentiated feature in Geraniaceae with regard to both percentages of impermeable seeds at maturity and maintenance of dormancy under particular conditions.
Use of the hydrothermal time model to analyse interacting effects of water and temperature on germination of three grass species
Authors: Larsen Søren Ugilt , Bailly Christophe , Côme Daniel , Corbineau Françoise
Published: May 2008

The temperate grass species, red fescue (Festuca rubrassp.litoralis), perennial ryegrass (Lolium perenne) and Kentucky bluegrass (Poa pratensis), are often sown in mixtures for turfgrass. Differences in germination response to environmental conditions often result in different establishment success. The three species were compared in a study of imbibition at reduced water potential (Ψ) and in a study of the effects of Ψ and temperature on germination. In all three species, imbibition rate and extent were reduced with decreasing Ψ, causing a prolonged lag-phase before germination, particularly in Kentucky bluegrass. In perennial ryegrass and Kentucky bluegrass, water content at radicle emergence decreased non-linearly with decreasing Ψ, with a lower asymptote expressing the critical water content for germination. Seeds were germinated in factorial combinations of two temperatures (10 and 25°C) and nine Ψ levels (–2 to 0 MPa). Kentucky bluegrass required a longer thermal time to germinate than the other species and exhibited conditional dormancy at 25°C, which affected the use of the thermal time model. The effects of Ψ were described by a hydrotime model. Kentucky bluegrass had higher base water potential (Ψb) and required a longer hydrotime for germination than the other species. However, Ψbincreased with temperature in Kentucky bluegrass and red fescue, but decreased in perennial ryegrass, and the base temperatures also changed with Ψ. The interacting effects of Ψ and temperature affected the ability of the hydrothermal time model to predict germination performance across all temperature and Ψ conditions.
The utility of aged seeds in DNA banks
Authors: Walters Christina , Reilley Ann A. , Reeves Patrick A. , Baszczak Jennifer , Richards Christopher M.
Published: May 2008

The long-term utility of DNA banks is predicated on the stability of DNA during storage. The quality and yield of DNA extracted from seeds from four garden species, which varied in age from 1 to 135 years old, was used to examine the early stages of DNA degradation. Seeds that were 70 years old yielded high molecular weight DNA, which permitted amplification of a 650 bp segment of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA and a 487 bp segment of the plastid-encoded large subunit of rubisco (rbcL). DNA extracted from seeds estimated to be about 135 years old was degraded, but still permitted amplification when routine extraction procedures were used. TherbcLsequences obtained fromc. 135-year-old cucurbit seed DNA were consistent with species identifications based on seed morphological features; however,ITSsequences from the same samples were determined to be of fungal origin. A comparison of our results with studies of DNA stability in leaf specimens suggested that DNA degraded within both tissues, but perhaps more slowly within seeds. Evidence that high-quality DNA can be extracted from old, non-viable seeds expands the utility of seed banks in preserving genetic resources.
Mistakes in germination ecology and how to avoid them
Authors: Baskin Carol C. , Thompson Ken , M. Baskin Jerry
Published: May 2008

Frequently, in studies on seed germination ecology, mistakes are made that lead to problems in determining the kind of dormancy and in extrapolating data to the field situation. In this paper, we discuss 22 of these issues and offer suggestions on how to avoid them.
Phospholipase D Activity Regulates Integrin-mediated Cell Spreading and Migration by Inducing GTP-Rac Translocation to the Plasma Membrane
Authors: Chae Young Chan , Kim Jung Hwan , Kim Kyung Lock , Kim Hyun Wook , Lee Hye Young , Heo Won Do , Meyer Tobias , Suh Pann-Ghill , Ryu Sung Ho
Published: May 2008

Small GTPase Rac is a crucial regulator of actin cytoskeletal rearrangement, and it plays an important role in cell spreading, migration, mitogenesis, phagocytosis, superoxide generation, and axonal growth. It is generally accepted that Rac activity is regulated by the guanosine triphosphate (GTP)/guanosine diphosphate (GDP) cycle. But, it is suggested that in addition to Rac-GTP loading, membrane localization is required for the initiation of downstream effector signaling. However, the molecular mechanisms that control the targeting of GTP-Rac to the plasma membrane remain largely unknown. Here, we have uncovered a signaling pathway linking phospholipase D (PLD) to the localized functions of Rac1. We show that PLD product phosphatidic acid (PA) acts as a membrane anchor of Rac1. The C-terminal polybasic motif of Rac1 is responsible for direct interaction with PA, and Rac1 mutated in this region is incapable of translocating to the plasma membrane and of activating downstream target p21-activated kinase upon integrin activation. Finally, we show that PA induces dissociation of Rho-guanine nucleotide dissociation inhibitor from Rac1 and that PA-mediated Rac1 localization is important for integrin-mediated lamellipodia formation, cell spreading, and migration. These results provide a novel molecular mechanism for the GTP-Rac1 localization through the elevating PLD activity, and they suggest a general mechanism for diverse cellular functions that is required localized Rac activation.
Novel Genetic Tools Reveal Cdk5's Major Role in Golgi Fragmentation in Alzheimer's Disease
Authors: Sun Kai-Hui , de Pablo Yolanda , Vincent Fabien , Johnson Emmanuel O. , Chavers Angela K. , Shah Kavita
Published: May 2008

Golgi fragmentation is a common feature in multiple neurodegenerative diseases; however, the precise mechanism that causes fragmentation remains obscure. A potential link between Cdk5 and Golgi fragmentation in Alzheimer's disease (AD) was investigated in this study. Because Golgi is physiologically fragmented during mitosis by Cdc2 kinase and current Cdk5-specific chemical inhibitors target Cdc2 as well, development of novel tools to modulate Cdk5 activity was essential. These enzyme modulators, created by fusing TAT sequence to Cdk5 activators and an inhibitor peptide, enable specific activation and inhibition of Cdk5 activity with high temporal control. These genetic tools revealed a major role of Cdk5 in Golgi fragmentation upon β-amyloid and glutamate stimulation in differentiated neuronal cells and primary neurons. A crucial role of Cdk5 was further confirmed when Cdk5 activation alone resulted in robust Golgi disassembly. The underlying mechanism was unraveled using a chemical genetic screen, which yielded cis-Golgi matrix protein GM130 as a novel substrate of Cdk5. Identification of the Cdk5 phosphorylation site on GM130 suggested a mechanism by which Cdk5 may cause Golgi fragmentation upon deregulation in AD. As Cdk5 is activated in several neurodegenerative diseases where Golgi disassembly also occurs, this may be a common mechanism among multiple disorders.
Live Cell Dynamics of Promyelocytic Leukemia Nuclear Bodies upon Entry into and Exit from Mitosis
Authors: Chen Yi-Chun M. , Kappel Constantin , Beaudouin Joel , Eils Roland , Spector David L.
Published: May 2008

Promyelocytic leukemia nuclear bodies (PML NBs) have been proposed to be involved in tumor suppression, viral defense, DNA repair, and/or transcriptional regulation. To study the dynamics of PML NBs during mitosis, we developed several U2OS cell lines stably coexpressing PML-enhanced cyan fluorescent protein with other individual marker proteins. Using three-dimensional time-lapse live cell imaging and four-dimensional particle tracking, we quantitatively demonstrated that PML NBs exhibit a high percentage of directed movement when cells progressed from prophase to prometaphase. The timing of this increased dynamic movement occurred just before or upon nuclear entry of cyclin B1, but before nuclear envelope breakdown. Our data suggest that entry into prophase leads to a loss of tethering between regions of chromatin and PML NBs, resulting in their increased dynamics. On exit from mitosis, Sp100 and Fas death domain-associated protein (Daxx) entered the daughter nuclei after a functional nuclear membrane was reformed. However, the recruitment of these proteins to PML NBs was delayed and correlated with the timing of de novo PML NB formation. Together, these results provide insight into the dynamic changes associated with PML NBs during mitosis.
Intrinsic and Cyclin-dependent Kinase-dependent Control of Spindle Pole Body Duplication in Budding Yeast
Authors: Simmons Kovacs Laura A. , Nelson Christine L. , Haase Steven B.
Published: May 2008

Centrosome duplication must be tightly controlled so that duplication occurs only once each cell cycle. Accumulation of multiple centrosomes can result in the assembly of a multipolar spindle and lead to chromosome mis-segregation and genomic instability. In metazoans, a centrosome-intrinsic mechanism prevents reduplication until centriole disengagement. Mitotic cyclin/cyclin-dependent kinases (CDKs) prevent reduplication of the budding yeast centrosome, called a spindle pole body (SPB), in late S-phase and G2/M, but the mechanism remains unclear. How SPB reduplication is prevented early in the cell cycle is also not understood. Here we show that, similar to metazoans, an SPB-intrinsic mechanism prevents reduplication early in the cell cycle. We also show that mitotic cyclins can inhibit SPB duplication when expressed before satellite assembly in early G1, but not later in G1, after the satellite had assembled. Moreover, electron microscopy revealed that SPBs do not assemble a satellite in cells expressing Clb2 in early G1. Finally, we demonstrate that Clb2 must localize to the cytoplasm in order to inhibit SPB duplication, suggesting the possibility for direct CDK inhibition of satellite components. These two mechanisms, intrinsic and extrinsic control by CDK, evoke two-step system that prevents SPB reduplication throughout the cell cycle.
Rapid Cycling and Precocious Termination of G1 Phase in Cells Expressing CDK1AF
Authors: Pomerening Joseph R. , Ubersax Jeffrey A. , Ferrell James E.
Published: May 2008

In Xenopus embryos, the cell cycle is driven by an autonomous biochemical oscillator that controls the periodic activation and inactivation of cyclin B1-CDK1. The oscillator circuit includes a system of three interlinked positive and double-negative feedback loops (CDK1 -> Cdc25 -> CDK1; CDK1 ⊣ Wee1 ⊣ CDK1; and CDK1 ⊣ Myt1 ⊣ CDK1) that collectively function as a bistable trigger. Previous work established that this bistable trigger is essential for CDK1 oscillations in the early embryonic cell cycle. Here, we assess the importance of the trigger in the somatic cell cycle, where checkpoints and additional regulatory mechanisms could render it dispensable. Our approach was to express the phosphorylation site mutant CDK1AF, which short-circuits the feedback loops, in HeLa cells, and to monitor cell cycle progression by live cell fluorescence microscopy. We found that CDK1AF-expressing cells carry out a relatively normal first mitosis, but then undergo rapid cycles of cyclin B1 accumulation and destruction at intervals of 3–6 h. During these cycles, the cells enter and exit M phase-like states without carrying out cytokinesis or karyokinesis. Phenotypically similar rapid cycles were seen in Wee1 knockdown cells. These findings show that the interplay between CDK1, Wee1/Myt1, and Cdc25 is required for the establishment of G1 phase, for the normal ∼20-h cell cycle period, and for the switch-like oscillations in cyclin B1 abundance characteristic of the somatic cell cycle. We propose that the HeLa cell cycle is built upon an unreliable negative feedback oscillator and that the normal high reliability, slow pace and switch-like character of the cycle is imposed by a bistable CDK1/Wee1/Myt1/Cdc25 system.
The PCH Family Member Proline-Serine-Threonine Phosphatase–interacting Protein 1 Targets to the Leukocyte Uropod and Regulates Directed Cell Migration
Authors: Cooper Kate M. , Bennin David A. , Huttenlocher Anna
Published: May 2008

Pombe Cdc15 homology (PCH) family members have emerged as important regulators of membrane–cytoskeletal interactions. Here we show that PSTPIP1, a PCH family member expressed in hematopoietic cells, regulates the motility of neutrophil-like cells and is a novel component of the leukocyte uropod where it colocalizes with other uropod components, such as type I PIPKIγ. Furthermore, we show that PSTPIP1 association with the regulator of endocytosis, dynamin 2, and PSTPIP1 expression impairs transferrin uptake and endocytosis. We also show that PSTPIP1 localizes at the rear of neutrophils with a subpopulation of F-actin that is specifically detected by the binding of an F-actin probe that detects a more stable population of actin. Finally, we show that actin polymerization, but not the microtubule network, is necessary for the polarized distribution of PSTPIP1 toward the rear of the cell. Together, our findings demonstrate that PSTPIP1 is a novel component of the leukocyte uropod that regulates endocytosis and cell migration.
ProBias: a web-server for the identification of user-specified types of compositionally biased segments in protein sequences
Authors: Kuznetsov Igor B.
Published: May 2008

Summary: Most proteins contain compositionally biased segments (CBS) in which one or more amino acid types are significantly overrepresented. CBS that contain amino acids with similar chemical properties can have functional and structural importance. This article describes ProBias, a web-server that searches a protein sequence for CBS composed of user-specified amino acid types. ProBias utilizes the discrete scan statistics to estimate statistical significance of CBS and is able to detect even subtle local deviations from the random independence model. The web-server also analyzes the global compositional bias of the input sequence. In the case of novel proteins that lack functional annotation, statistically significant CBS reported by ProBias can be used to guide the search for potential functionally important sites or domains.

Availability: Freely available at http://lcg.rit.albany.edu/ProBias

Contact:  IKuznetsov@albany.edu

Supplemantary information: Supplementary data are available at Bioinformatics online.
Economic value of damage caused by marine bio-invasions: lessons from two European case studies
Authors: Nunes Paulo A. L. D. , Markandya Anil
Published: May 2008

Nunes, P. A. L. D., and Markandya, A. 2008. Economic value of damage caused by marine bio-invasions: lessons from two European case studies. – ICES Journal of Marine Science, 65: 775–780. We illustrate the use of alternative, non-market valuation methods to estimate the economic value of the social damage caused by marine bio-invasions. First, we present and discuss the motivation to perform an economic valuation of marine ecosystem quality in general and the protection of marine ecosystems against invasive species in particular. Second, we examine in detail two empirical applications of economic value assessment of social damage attributable to marine bio-invasions. One of these looks at ballast water management programmes in Rotterdam harbour, the Netherlands, and the second investigates management practices for the Manila clam in Venice Lagoon. Finally, we explore the relevance of this economic information for cost–benefit analysis and policy guidance.
Coordinated regulation of transcriptional repression by the RBP2 H3K4 demethylase and Polycomb-Repressive Complex 2
Authors: Pasini Diego , Hansen Klaus H. , Christensen Jesper , Agger Karl , Cloos Paul A.C. , Helin Kristian
Published: May 2008

Polycomb group (PcG) proteins regulate important cellular processes such as embryogenesis, cell proliferation, and stem cell self-renewal through the transcriptional repression of genes determining cell fate decisions. The Polycomb-Repressive Complex 2 (PRC2) is highly conserved during evolution, and its intrinsic histone H3 Lys 27 (K27) trimethylation (me3) activity is essential for PcG-mediated transcriptional repression. Here, we show a functional interplay between the PRC2 complex and the H3K4me3 demethylase Rbp2 (Jarid1a) in mouse embryonic stem (ES) cells. By genome-wide location analysis we found that Rbp2 is associated with a large number of PcG target genes in mouse ES cells. We show that the PRC2 complex recruits Rbp2 to its target genes, and that this interaction is required for PRC2-mediated repressive activity during ES cell differentiation. Taken together, these results demonstrate an elegant mechanism for repression of developmental genes by the coordinated regulation of epigenetic marks involved in repression and activation of transcription.
Comparative analysis of human chromosome 7q21 and mouse proximal chromosome 6 reveals a placental-specific imprinted gene, TFPI2/Tfpi2, which requires EHMT2 and EED for allelic-silencing
Authors: Monk David , Wagschal Alexandre , Arnaud Philippe , Müller Pari-Sima , Parker-Katiraee Layla , Bourc’his Déborah , Scherer Stephen W. , Feil Robert , Stanier Philip , Moore Gudrun E.
Published: May 2008

Genomic imprinting is a developmentally important mechanism that involves both differential DNA methylation and allelic histone modifications. Through detailed comparative characterization, a large imprinted domain mapping to chromosome 7q21 in humans and proximal chromosome 6 in mice was redefined. This domain is organized around a maternally methylated CpG island comprising the promoters of the adjacent PEG10 and SGCE imprinted genes. Examination of Dnmt3l−/+ conceptuses shows that imprinted expression for all genes of the cluster depends upon the germline methylation at this putative “imprinting control region” (ICR). Similarly as for other ICRs, we find its DNA-methylated allele to be associated with trimethylation of lysine 9 on histone H3 (H3K9me3) and trimethylation of lysine 20 on histone H4 (H4K20me3), whereas the transcriptionally active paternal allele is enriched in H3K4me2 and H3K9 acetylation. Our study reveals a novel placenta-specific transcript, TFPI2, which is expressed from the maternal allele in both humans and mice. Deficiency for the histone methyltransferase EHMT2 (also known as G9A) or for the Polycomb group protein EED, involved in repressive H3K9me2 and H3K27me3 respectively, leads to biallelic expression of Tfpi2 in the extra-embryonic lineages, whereas the other genes in the cluster maintain correct imprinting. Apart from the putative ICR, however, no other promoter regions within the domain exhibited allele-specific repressive histone modifications. This unexpected general lack of repressive histone modifications suggests that this domain may utilize a different silencing mechanism as compared to other imprinted domains.
RNA-Directed RNA Polymerase3fromNicotiana attenuataIs Required for Competitive Growth in Natural Environments
Authors: Pandey Shree P. , Gaquerel Emmanuel , Gase Klaus , Baldwin Ian T.
Published: May 2008

SDE1/SGS2/RdR6, a putative RNA-directed RNA polymerase, maintains plant defenses against viruses in Arabidopsis (Arabidopsis thaliana) and Nicotiana benthamiana, but its function has not been examined in natural habitats or with respect to other ecological stresses. We evaluated the organismic-level function of this gene (NaRdR3) in an ecological model species, Nicotiana attenuata, by transforming plants to stably silence RdR3 (irRdR3). Minor morphological changes (elongated leaves and reduced leaf number) and increased susceptibility to tobamoviruses typical of RdR6 silencing in other species were observed, but these changes did not alter the reproductive performance of singly grown plants (measured as seed and capsule production) or herbivore resistance in laboratory trials. 454-sequencing of irRdR3's small RNA (smRNA) transcriptome revealed that 21- and 24-nucleotide smRNAs were not affected, but the abundance of 22- to 23-nucleotide smRNAs was reduced. When planted in pairs with wild-type plants in N. attenuata's natural habitat in the Great Basin Desert, irRdR3 plants produced shorter stalks with significantly reduced flower and capsule numbers, but did not influence the ability of plants to resist the native herbivore community, indicating that silencing RdR3 reduced a plant's competitive ability. We tested this hypothesis in the glasshouse by planting irRdR3 and wild-type pairs in communal containers; again irRdR3 plants had severely reduced stalk elongation and reproductive measures. The reduced competitive ability of irRdR3 plants was associated with altered phytohormone homeostasis, especially as reflected in the distribution of auxin. We suggest that RdR3 helps to regulate hormone balance when plants compete with conspecifics in natural environments.
Vacancy-ordering effects in AlB2-type ErGe2 − x
(0.4 < x ≤ 0.5)
Authors: Christensen Jeppe , Lidin Sven , Malaman Bernard , Venturini Gerard
Published: May 2008

In the Er–Ge system, the compostion range ErGe2 to Er2Ge3 has been investigated. Eight samples were produced by arc melting of the elements, and analyzed using X-ray powder diffraction. Nine crystal structures were found to be present in the samples. The structures are described as a homologous series and presented within the superspace formalism using the superspace group X2/m(α0γ)0s, X representing the centring vector (½, ½, 0, ½). In this description the modulation vector q = (αa* + γc*) is shown to be a direct measure of the Ge content as ErGe2 − α (α falls in the range 1\over 3 to ½). The large composition range is achieved by extended vacancy ordering in the planar 63 net of Ge with subsequent relaxation.
Structural analysis of perovskite LaCr1 − x
Ni
x
O3 by Rietveld refinement of X-ray powder diffraction data
Authors: Yang J.
Published: May 2008

The crystal structure of perovskite LaCr1 − x
Ni
x
O3 (0 ≤ x ≤ 1.0) has been systematically investigated by analyzing X-ray powder-diffraction data taken at room temperature. Rietveld refinement has confirmed the structural evolution from the orthorhombic phase (Pbnm, Z = 4) to the two-phase (the orthorhombic and the rhombohedral phases) region around x = 0.7, then to the rhombohedral (R\bar 3c, Z = 2) phase for 0.8 ≤ x ≤ 1.0. The lattice parameters are also obtained in the refinement process. The results are discussed in terms of reduced Cr/Ni—O bond length with increasing Ni-doping level, leading to an increased tolerance factor caused by the substitution of smaller Ni3+ (R_{\rm Ni^{3 + } } = 0.60 Å, six-coordinate) ions for larger Cr3+ (R_{\rm Cr^{3 + } } = 0.615 Å, six-coordinate) ions.
A bond-valence investigation of two series of isostructural lanthanide compounds
Authors: Liebau F. , Wang X.
Published: May 2008

Since the days of Pauling it has been tacitly assumed that the valence, which is distributed between the bonds to neighbouring atoms, is the stoichiometric valence, stoich
V, which has integer values. It is shown here that this is not true. Instead, bond-valence sums (BVS) calculated for lanthanide (Ln) atoms of a series of garnet-type compounds Ln_3^{\rm III}Te_2^{\rm VI}Li_3^{\rm I}O_{12} deviate significantly from stoich
V. Values of (BVS)Ln of this series, plotted versus the element number Z
Ln, show the same irregular sequence as: (i) the third ionization potentials of Ln atoms, (ii) the valence values previously calculated with quantum-chemical methods for lanthanide metals and sulfides, and (iii) the experimental efficiencies of the reactions between LnI and SF6 in the gas phase. This indicates that in the Ln3Te2Li3O12 series the BVS values of the Ln atoms, which are `rattling' in rather large and rigid voids of the structure, reflect the electronic structure of Ln. It is, therefore, concluded that BVS represent a non-integer valence, which is based on the electronic structure of bonded atoms, rather than stoich
V. For this non-integer valence the term `structural valence' and the symbol struct
V have been proposed. In another series of lanthanide chelates the (BVS)Ln values deviate even more from stoich
V
Ln = 3 v.u. than in the garnet-type series. In the chelates the Ln atoms are `squeezed' in rather small voids so that the electronic effects of Ln acting on (BVS)Ln are overridden by stronger steric effects exerted by the organic ligands.
Hydrogen bond strength and bond geometry in cyclic dimers of crystalline carboxylic acids
Authors: Gavezzotti Angelo
Published: May 2008

In a study of 101 crystal structures of carboxylic acids we have observed a clear trend in the difference between the formally single and formally double C—O bond distances, as observed by X-ray diffraction, with a clear-cut distinction between aromatic acids, where the two distances are similar, and non-aromatic acids, where the two distances distinctly differ by 0.06–0.12 Å. A tentative energy classification – within the limits of the many assumptions – and a correlation with the O...O separation over the hydrogen bond indicate that the stability of the carboxylic acid dimer increases as the difference between the two apparent C—O distances becomes smaller, owing to an increasing Coulombic contribution to the dimerization energy. No simple hypothesis is adequate for a complete explanation of the origin, of the details and of the variations of this phenomenon. As often happens in crystal chemistry problems, one is presumably confronted with a balance of several subtle intra- and intermolecular factors.