bluuebunny/crossref_metadata_2025 huggingface dataset:
Liver nitrogen movements during short-term infusion of high levels of ammonia into the mesenteric vein of sheep
Authors: Milano G. D. , Lobley G. E.
Published: May 2008

Sources of viscous soluble fibre, such as barley and oats, have often been included in the weaning diet of the pig to accelerate development of the large intestine. Inclusion of a non-fermentable, viscous compound, sodium carboxymethylcellulose (CMC), in a low-fibre weaning diet was tested to assess the influence of digesta viscosity on the gut in the absence of increased fermentation. Two CMC sources, of low and high viscosity, were added to cooked rice-based diet at 40 g/kg total diet. A third control rice diet did not contain any CMC. Diets were fed for 13 d following weaning at 3 weeks of age. Addition of CMC to the diet significantly increased the intestinal viscosity of digesta within the small (P<0·001) and large (P<0·05) intestine. No simple association was found between increases in intestinal viscosity and effects on intestinal morphology and whole-body growth. The average empty-body-weight gain and the small intestinal villus height increased with low-viscosity CMC, but decreased with the high-viscosity CMC group. The full large intestinal weight increased in all pigs fed CMC. Dietary CMC (both low- and high-viscosity) increased the percentage moisture of digesta and faeces, and was associated with increased faecal shedding of enterotoxigenic haemolytic Escherichia coli. Feed ingredients in weaning diets that excessively increase the viscosity of the intestinal digesta may be detrimental to pig health and production.
Exposure to purified lignan from flaxseed (Linum usitatissimum) alters bone development in female rats
Authors: Ward Wendy E. , Yuan Yvonne V. , Cheung Angela M , Thompson Lilian U.
Published: May 2008

Due to the potential oestrogenic effects of secoisolariciresinol diglycoside (SDG), the mammalian lignan precursor in flaxseed (Linum usitatissimum), we hypothesized that exposure to purified SDG during early life would have a positive effect on developing bone. This present study determined whether exposure to SDG purified from flaxseed during suckling via mother's milk or continuously to adolescence (postnatal day (PND) 50) or adulthood (PND 132) increased bone mineral content (BMC) or bone strength in female rat offspring. Offspring were exposed to basal diet (BD) or one of two doses of SDG (50S, 100S) equivalent to that in a 50 or 100 g flaxseed/kg diet during lactation only or through to PND 50 or 132. At PND 50 and 132, femurs were analysed for BMC by dual energy X-ray absorptiometry and biomechanical strength by a 3-point bending test. Compared with BD group, rats exposed to continuous 50S or 100S diet had stronger femurs at PND 50 without changes in BMC. At PND 132 there were no differences in femur strength despite the fact that continuous exposure to BD resulted in a higher (P<0·05) BMC than rats exposed to 100S during lactation only or to 50S or 100S during lactation through to adulthood. In conclusion, female rat bone is more sensitive to the oestrogen-like action of lignans during early life when endogenous levels of sex hormones are low, but by adulthood the improved bone strength does not persist. Importantly, exposure to purified lignan does not have negative effects on bone strength.
Acute effects of dietary fat composition on postprandial plasma bile acid and cholecystokinin concentrations in healthy premenopausal women
Authors: Costarelli Vassiliki , Sanders T. A. B.
Published: May 2008

Bile acids derived from intestinal bacterial metabolism and transported to the breast in plasma may influence risk of breast cancer. The purpose of the present study was to test the hypothesis that fatty acid chain length and degree of unsaturation differ with regard to their influence on the postprandial release of cholecystokinin (CCK) and the subsequent increase in plasma bile acid concentrations that occur following a meal. A randomized crossover design was used to compare five high-fat test meals (50 g fat) with a low-fat test meal (15 g) on plasma bile acid and CCK concentrations in eighteen healthy premenopausal women. The high-fat meals were enriched in oleate or palmitate, or linoleate or medium-chain triacylglycerols (MCT) or a blend of oleate and long-chain n-3 fatty acids. The postprandial increase in plasma CCK concentration was lower on the MCT meal compared with all meals and was greater following the linoleate compared with the low-fat meal. Plasma bile acid concentrations increased 2–3-fold postprandially but the increase was lower following the MCT meal compared with the other meals and was greater on the linoleate meal compared with the low-fat meal. The postprandial increases in plasma chenodeoxycholic acid concentration showed a trend to rise with increasing unsaturation of the test meal. In conclusion, meals rich in linoleate are a potent stimulus for CCK release and lead to prolonged elevations of plasma bile acids and meals containing MCT inhibit CCK release and the subsequent increase in plasma bile acid concentrations.
Weaning affects lipoprotein lipase activity and gene expression in adipose tissues and inmasseterbut not in other muscles of the calf
Authors: Hocquette Jean-François , Graulet Benoît , Vermorel Michel , Bauchart Dominique
Published: May 2008

The nutritional and physiological modifications that occur during the weaning period induce adaptations of tissue metabolism in all mammal species. Among the adaptations due to weaning in ruminants, the regulation of lipoprotein lipase (LPL) activity, one of the rate-limiting steps of fatty acid utilization by tissues, was still unknown. The present study aimed at comparing LPL activity and gene expression in the heart, seven skeletal muscles and three adipose tissue sites between two groups of seven preruminant (PR) or ruminant (R) calves having a similar age (170 d), similar empty body weight (194 kg) at slaughter, and similar net energy intake from birth onwards. Triacylglycerol content of adipose tissues was 16 % lower in R than in PR calves, (P<0·01). This could be partly the result from a lower LPL activity (-57 %, P<0·01). LPL mRNA levels were also lower in R calves (-48 % to -68 %, P<0·01) suggesting a pretranslational regulation of LPL activity. Activity and mRNA levels of LPL did not differ significantly in the heart and skeletal muscles except in themasseterin which LPL activity and mRNA levels were higher (+50 % and +120 % respectively, P<0·01) in the R calves. Regulation of LPL inmassetercould be explained by the high contractile activity of this muscle after weaning due to solid food chewing. In conclusion, weaning in the calf affects LPL activity and expression in adipose tissues, but not in skeletal muscles except themasseter.
Use of water-miscible retinyl palmitate as markers of chylomicrons gives earlier peak response of plasma retinyl esters compared with oil-soluble retinyl palmitate
Authors: Renuka K. D. , Silva R. , Williams Christine M. , Lovegrove Julie A.
Published: May 2008

Delayed peak response of plasma retinyl esters (RE) relative to plasma triacylglycerols (TAG) and apolipoprotein (Apo) B-48 responses following a fat load supplemented with vitamin A raised doubts about the use of vitamin A to label dietary-derived lipids and lipoproteins. The present study compared the use of water-miscible and oil-soluble retinyl palmitate (RP) as markers of dietary-derived lipoproteins in healthy subjects along with the measurements of postprandial plasma TAG and ApoB-48 responses to investigate whether the delayed peak response observed was due to delayed intestinal output of RE from oil-based solutions. Nine healthy female subjects were given a standard test meal containing a dose (112 mg) of RP in either water-miscible or oil-soluble form in random order, on two separate occasions after a 12 h overnight fast. The results showed that the mean plasma RE concentrations reached a peak significantly later than mean plasma TAG and ApoB-48 concentrations when oil-soluble RP was consumed, whereas plasma RE peaked earlier relative to plasma TAG and ApoB-48 responses when water-miscible RP was used. The results suggested a more rapid absorption with a significantly higher and earlier peak response of plasma RE when water-miscible RP was consumed. This was in contrast to the delayed initial appearance and later sustained higher concentrations of plasma RE during the late postprandial period when oil-soluble RP was consumed. The RE response to the water-miscible RP showed better concordance with plasma TAG response than that of oil-soluble RP.
Dietary conjugated linoleic acid (CLA) induces apoptosis of colonic mucosa in 1,2-dimethylhydrazine-treated rats: a possible mechanism of the anticarcinogenic effect by CLA
Authors: Park Hyun S. , Ryu Ji H. , Ha Yeong L. , Park Jung H. Y.
Published: May 2008

One of the objectives of the present study was to investigate whether 1 % conjugated linoleic acid (CLA) in the diet reduced tumour incidence in the colon of 1,2-dimethylhydrazine (DMH)-treated rats. Colon cancer was induced by injecting 6-week-old, male, Sprague–Dawley rats with 15 mg/kg DMH twice per week for 6 weeks. They were fed either 1 % CLA or a control dietad libitumfor 30 weeks. Dietary CLA significantly decreased colon tumour incidence (P<0·05). Our second objective was to investigate whether apoptosis in the colon mucosa of DMH-treated rats was affected by the amount of dietary CLA and whether the changes in apoptosis were related to those in fatty acid-responsive biomarkers. For this purpose, rats were killed after being fed a diet containing 0 %, 0·5 %, 1 % or 1·5 % CLA for 14 weeks. CLA was undetected in the mucosa of rats fed the 0 % CLA diet and increased to 5·9 mg/g phospholipid in rats fed the 0·5 % diet. The apoptotic index estimated by the terminal deoxynucleotidyl transferase-mediated dUTP nick and labelling technique was increased by 251 % and the 1,2-diacylglycerol content was decreased by 57 % in rats fed 0·5 % CLA. No further changes in these variables were observed when CLA in the diet was raised to 1·0 % or 1·5 %. However, dietary CLA decreased mucosal levels of prostaglandin E2, thromboxane B2and arachidonic acid in a dose-dependent manner. The present data indicate that dietary CLA can inhibit DMH-induced colon carcinogenesis by mechanisms probably involving increased apoptosis.
Flow cytometric analysis of spontaneous and dexamethasone-induced apoptosis in thymocytes from severely malnourished rats
Authors: Ortiz Rocío , Corté Leticia , Gonz´lez–M´rquez Humberto , Gómez José Luis , Gonz´lez Cristina , Cortés Edith
Published: May 2008

Severe malnutrition is widely distributed throughout the world, showing a high prevalence in developing countries. Experimental animal models have been useful to study the effects of malnutrition at different levels and ages. Apoptosis is a well recognised process of cell death occurring under several physiological and pathological conditions. It represents the principal mechanism involved in cell selection in the thymus. Thymocyte apoptosis induction by dexamethasone is one of the best characterised experimental models of programmed cell death. The aim of the present study was to determine whether severe malnutrition increased spontaneous and/or dexamethasone-induced apoptosisin vivoin thymocytes of experimentally malnourished rats during lactation. Thymocytes were obtained from malnourished rats at weaning (21d of age). Apoptosis frequency was estimated by the terminal transferase-mediated dUTP nick end labelling assay. Spontaneous apoptosis was 1·9 (SD 1·0) % IN WELL NOURISHED RATS IN CONTRAST TO 13·3 (sd 3·8) % in malnourished animals; this is seven times greater (P<0·001). Interestingly, the frequency of dexamethasone-induced apoptosis was similar in both groups of animals (47·9 (sd 10·1) % in well nourished rats and 53·8 (sd 8·0) % in malnourished rats). The results obtained in the present study indicate that malnutrition is associated with a significant increase of spontaneously apoptotic cells. In addition, the data showed that the fraction of thymocytes susceptible to dexamethasone-induced apoptosis was similar in well nourished and malnourished animals. The greater levels of spontaneously apoptotic cells associated with malnutrition could be related to alterations of the microenvironment of the thymus and/or to an obstruction of early thymocyte maturation.
Is resting metabolic rate different between men and women?
Authors: Buchholz Andrea C. , Rafii M. , Pencharz P. B.
Published: May 2008

A low resting metabolic rate (RMR) has been proposed as a possible cause for the increased body fat commonly seen in women compared with men. Absolute RMR is higher in men, but whether RMR adjusted for lean body mass (LBM) remains higher is unresolved. The objective of the present study was to determine whether RMR adjusted for various body composition factors differed between healthy adult men and women. Thirty men (28·3±8·0 years, BMI 23·7±2·1 kg/m2) and twenty-eight women (28·7±6·9 years, BMI 22·2±1·9 kg/m2) were included in the analyses. RMR was measured by open-circuit indirect calorimetry for 60 min. Extracellular water (ECW) was measured by corrected Br-space and total body water (TBW) by2H dilution. LBM was estimated as TBW/0·732. Intracellular water (ICW) was calculated as TBW-ECW, and body cell mass (BCM) as ICW/0·732. Men were heavier and had higher BMI, LBM, BCM and ECW, but less fat mass. Absolute RMR was higher in men than women (7280±844v.5485±537 kJ/d,P<0·0001). This difference became non-significant when RMR was adjusted for LBM by ANCOVA (6536±630v.6282±641 kJ/d,P=0·2191), but remained significant when adjusted for BCM (6680±744v.6128±756 kJ/d,P=0·0249). Fat mass explained a significant amount of variation in RMR in women (r20·28,P=0·0038), but not in men (r20·03,P=0·3301). The relationships between body fat and the various subcompartments of BCM and RMR require further elucidation.
Net flux of folates and vitamin B12 through the gastrointestinal tract and the liver of lactating dairy cows
Authors: Girard Christiane L. , Lapierre Hélène , Desrochers André , Benchaar Chaouki , Jacques Matte J. , Rémond Didier
Published: May 2008

In study 1, four cows had a ruminal canula, a catheter in the right ruminal vein and an ultrasonic flow probe around the right ruminal artery; a catheter was placed in the auricular artery on experimental days. Blood samples were taken every 10 min from -20 to 60 min after ruminal infusion of 5·79 mmol pteroylmonoglutamic acid and cyanocobalamin. There was a net release of these vitamins across the rumen wall following the infusion (P=0·06). In studies 2 and 3, four cows had catheters in the portal, one hepatic and two mesenteric veins and one mesenteric artery. Plasma flow was determined using p-aminohippurate. In study 2, blood samples were taken before and every 30 min for 6 h after feeding 0 or 4 mg of pteroylmonoglutamic acid. Flow of folates through the portal-drained viscera (PDV) and the total splanchnic tissues (TSP) tended to increase with the ingestion of pteroylmonoglutamic acid (P=0·19). In study 3, blood samples were collected every 30 min for the first 3 h to calculate plasma flow and basal net fluxes of folates and vitamin B12. The cows were fed 2·6 g pteroylmonoglutamic acid and 500 mg cyanocobalamin; blood samples were taken every 2 h for 24 h. Vitamin supplements increased the net release of folates and vitamin B12 from PDV (P=0·04) and TSP (P=0·13). The present results demonstrate that, in dairy cows, at doses reported to improve animal performance, passage of pteroylmonoglutamic acid to the portal blood appears during the 6 h following its ingestion, whereas for cyanocobalamin, it is a slow process, not yet completed 24 h after its ingestion.
Folate protects against oxidative modification of human LDL
Authors: Nakano Emi , Higgins John A. , Powers Hilary J.
Published: May 2008

Elevated plasma total homocysteine is considered to be a graded risk factor for cardiovascular disease. Folate, through its homocysteine-lowering potential, may therefore be protective. Folate, however, may have protective effects independent of homocysteine-lowering. We have measured the effects of folate on Cu-catalysed oxidative damage to the unsaturated lipids in human LDL. Experiments were carried out in the presence of citrate, and followed increases in absorption at 234 nm, which measures the amount of conjugated diene produced. There is a lag time during which endogenous antioxidants are oxidised, followed by rapid oxidation of lipid. Addition of 0–6 μM-5-methyltetrahydrofolate produced a dose-dependent increase in the lag time, suggesting that folate may have a direct anti-oxidant role in vivo, which is independent of any indirect effects through lowering of homocysteine levels.
Linkages between organic agriculture and agro-ecotourism
Authors: Kuo Nae-Wen , Chen Yin-Jen , Huang Chiou-Lien
Published: May 2008

Organic agriculture is regarded as one important approach to agriculture and food production that is environmentally sustainable and can generate several positive impacts to rural society. However, organic agriculture development is still limited in Taiwan and the major reason is lack of economic incentives to farmers. Hence, one approach to link organic agriculture with agro-ecotourism is proposed in this study to maximize the economic benefit of organic agriculture.

Chrshang Township in Taiwan was selected as an example to develop such eco-organic tourism based on organic agriculture. First, five appropriate activities were designed according to the fundamental principles for guiding the development of eco-organic tourism. In addition, the maximum willingness to pay (WTP) method was employed to estimate potential revenues from eco-organic tourism and then the economic value could be compared with that of other economic activities. Under a conservative scenario, the total annual revenue from eco-organic tourism is about NT$421,293,559, which is about 20 times that of the rice production in the study area.

In addition to the direct economic revenues, the following additional benefits can also be found: (1) the linkage can create additional value of organic agriculture; (2) organic agriculture can contribute to service economy and experience economy; (3) people can increase their confidence in organic products through better understanding; (4) a one-step relationship between organic producer and consumer can be established; and (5) local food supply will be connected with demands in the tourism industry. In summary, under a symbiotic relationship, organic agriculture is not only commodities and goods production, it can become one important service economy and even create experience economy within the tourism industry.
The influence of organic transition systems on beneficial ground-dwelling arthropods and predation of insects and weed seeds
Authors: Lundgren Jonathan G. , Shaw John T. , Zaborski Edmond R. , Eastman Catherine E.
Published: May 2008

The influence of farm management practices on ground-dwelling natural enemy communities and predation of insects and weed seeds was investigated over the first 2 years of the transition from conventional to organic production. Three transition strategies were selected that differed in their management and input intensities, and were characteristic of pasture/ley systems (low intensity), cash grain systems (intermediate intensity), and vegetable production (high intensity). Beneficial arthropods (insectivores and granivores) were monitored using pitfall (arthropod activity) and quadrat (arthropod density) samples. The frequency of predation on restrained larvae ofGalleria mellonellaand the species observed feeding were recorded. Weekly removal rates of weed seeds representative of abundant species at our site were monitored over a 3-week period during fall. Management intensity affected the activity and abundance of biological control agents. In year two of the transition, biological control agent densities were higher in the low-intensity treatment than in the other two treatments, but activity of insectivores and granivores was reduced in this treatment relative to the higher intensity systems. The patterns in the abundances of biological control agents may be explained by habitat stability within the different cropping systems. Quadrat samples were strongly correlated with the insectivory index, although pitfall samples were not. Insectivory rates were highest (>80% ofG. mellonellalarvae) in the low-intensity treatment. Predation patterns over a 17-h period differed substantially among the management treatments, indicating behaviorally distinct insectivore communities. Seed removal was also highest in the low-intensity treatment. We conclude that low-intensity cropping systems are most favorable to the abundance and function of beneficial ground-dwelling arthropod communities (insectivores and granivores) during the transition process.
Weed suppression with hydramulch, a biodegradable liquid paper mulch in development
Authors: Warnick J.P. , Chase C.A. , Rosskopf E.N. , Simonne E.H. , Scholberg J.M. , Koenig R.L. , Roe N.E.
Published: May 2008

Cost-effective, laborsaving, and environmentally sound weed management practices are needed for sustainable vegetable production. Organic production, in particular, precludes the use of synthetic herbicides and requires that organic farmers utilize practices that reduce harmful environmental impact. Although polyethylene film mulch is used extensively in vegetable production in Florida, its use has a number of drawbacks, among which is the susceptibility of opaque polyethylene mulch to penetration by yellow and purple nutsedge. Appreciable labor and disposal/environmental costs are associated with its removal. A durable mulch material that would effectively control nutsedge and other weeds but with no associated environmental and disposal costs is highly desirable. Hydramulch, a paper-like material applied as a slurry consisting of cotton waste, newsprint, gypsum and a proprietary adhesive, was tested as a biodegradable alternative to polyethylene mulch during the spring of 2003. Experiments were conducted in southeastern and north-central Florida to compare the effects of three hydramulch formulations, polyethylene mulch and a no mulch control on soil temperature, soil moisture and weed infestation. Soil temperature under hydramulch was 1–4°C lower than that under polyethylene. In the absence of rain, the use of hydramulch resulted in soil moisture levels that were 1–4% lower than with polyethylene mulch. Higher soil moisture with hydramulch than polyethylene was coincident with rainfall. Hydramulch remained intact on most beds and suppressed broadleaf weeds and grasses, particularly at the north-central site where the mulch was applied at a greater thickness. However, purple nutsedge readily penetrated hydramulch. Therefore, hydramulch may be applicable for use for the suppression of broadleaf weeds and grasses at sites with little or no nutsedge pressure in fall or in crops for which cooler soils are desirable or crops that are rainfed or overhead irrigated.
Histological and biochemical characterization of Theobroma cacao L. endosperm during seed development
Authors: Dangou Justine Sossou , Hocher Valérie , Ferrière Nicole , Fulcheri Corinne , Morard Philippe , Alemanno Laurence
Published: May 2008

The histological and biochemical characteristics of cacao (Theobroma cacao) endosperm were determined at different stages of seed development. At various stages, the endosperm was analysed for minerals, organic acids, carbohydrates, free amino acids, abscisic acid (ABA), indole-3-acetic acid (IAA) and cytokinins. Cacao endosperm was coenocytic and became progressively cellularized from the micropylar zone. From stage I to IIz, the endosperm started to degenerate all around the embryo. Among the minerals detected, potassium and sulphate were the most abundant. Ammonium was the major source of mineral nitrogen, and glutamine was the most abundant free amino acid. Total nitrogen concentration was quite low. No sulphur-containing amino acids could be detected. Malate was present at all endosperm stages and was the most abundant organic acid. The sugars in cacao endosperm were mainly reducing sugars: glucose and fructose. ABA was only detected from stage IIz. IAA and three cytokinins [zeatin, zeatin-riboside and isopentenyl adenosine (iPA)] were present at all stages of development. Cacao endosperm resembled the endosperm of other species in (1) the abundance of organic acids and phosphate; and (2) a unique combination of sugars. However, three features seemed to be specific to cacao: (1) nitrogen was supplied mainly in the form of ammonium and amino acids, whereas, in other species, amino acids represent the predominant form; (2) there was a relatively small amount of nitrogen, and (3) a high concentration of sulphate and the absence of sulphur amino acids.
Membranes and seed dormancy: beyond the anaesthetic hypothesis
Authors: Hallett Barbara P. , Bewley J. Derek
Published: May 2008

The breaking of dormancy in seeds can be elicited by many factors, including temperature and short exposure to low molecular weight amphipathic molecules such as primary alcohols, monocarboxylic acids and anaesthetics. Their action has been suggested to be mediated through effecting changes to membranes. Paradoxically, though, these molecules can inhibit the germination of some non-dormant seeds. Here, we review the structure–activity relationships between amphipathic molecules and dormancy breaking and, based on the known responses of membranes to them and to temperature changes, offer an alternative interpretation of the data and a new hypothesis to explain their action. We suggest that amphipathic molecules break dormancy by partitioning into the membrane, thereby increasing and optimizing phospholipid headgroup spacing. This, in turn, facilitates the binding and activation of a peripheral membrane protein component of a signal transduction pathway that is essential for the completion of germination. In cases where amphipathic molecules inhibit germination, it is predicted that they cause the optimal headgroup spacing to be exceeded, thus preventing subsequent association of the membrane with the peripheral protein component. The hypothesis is extended to explain membrane changes that can lead to dormancy breaking during dry after-ripening.
A classification system for seed dormancy
Authors: Baskin Jerry M. , Baskin Carol C.
Published: May 2008

The proposal is made that seed scientists need an internationally acceptable hierarchical system of classification for seed dormancy. Further, we suggest that a modified version of the scheme of the Russian seed physiologist Marianna G. Nikolaeva be adopted. The modified system includes three hierarchical layers – class, level and type; thus, a class may contain levels and types, and a level may contain only types. The system includes five classes of dormancy: physiological dormancy (PD), morphological dormancy (MD), morphophysiological dormancy (MPD), physical dormancy (PY) and combinational dormancy (PY + PD). The most extensive classification schemes are for PD, which contains three levels and five types (in the non-deep level), and MPD, which contains eight levels but no types. PY is not subdivided at all but probably should be, for reasons given. Justifications are presented for not including mechanical dormancy or chemical dormancy in the modified scheme. PD (non-deep level) is the most common kind of dormancy, and occurs in gymnosperms (Coniferales,Gnetales) and in all major clades of angiosperms. Since, first, this is the class and level of dormancy in seeds of wild populations ofArabidopsis thalianaand, secondly, Type 1 (to which seeds ofA. thalianabelong) is also common, and geographically and phylogenetically widespread, it seems that biochemical, molecular and genetic studies on seed dormancy in this model species might have rather broad application in explaining the basic mechanism(s) of physiological dormancy in seeds.
Decline in a seed-specific abscisic acid-responsive glycine-rich protein (GRPF1) mRNA may reflect the release of seed dormancy in Fagus sylvatica during moist prechilling
Authors: Mortensen Lars Christian , Rodríguez Dolores , Nicolás Gregorio , Eriksen Erik Nymann , Nicolás Carlos
Published: May 2008

Dormancy and desiccation tolerance were studied inFagus sylvaticaseeds subsequent to 0–26 weeks of either moist prechilling (5°C) or warm (15°C) pretreatment at a restricted water content of 34% (fresh weight basis), i.e.c. 5% below full imbibition. After the pretreatments, seeds were either fully imbibed at 5 or 15°C, or dried for 7 d to around 13% moisture content and then fully imbibed at 5°C. Most of the dormancy was released after 5 weeks of prechilling, with nearly 70% of the seeds germinating at 15°C, and dormancy was fully released after 11 weeks of prechilling. Most of the seed desiccation tolerance, measured as the final germination percentage for dried seeds, was lost between 11 and 13 weeks of prechilling. A further decline in desiccation tolerance was recorded from 13 to 19 weeks, with a moderate recovery after 26 weeks. Germination was compared with the expression of a previously described abscisic-acid-responsive GRPF1 mRNA for a glycine-rich protein inF. sylvatica. There was a clear decline in accumulation of the transcript in seeds during prechilling, but not during the warm pretreatment. The amount of GRPF1 expression correlated significantly (P< 0.001) with dormancy status.
Smoke exposure alters endogenous gibberellin and abscisic acid pools and gibberellin sensitivity while eliciting germination in the post-fire annual, Nicotiana attenuata
Authors: Schwachtje Jens , Baldwin Ian T.
Published: May 2008

Exposure to smoke is required for the germination of seeds from dormant genotypes ofNicotiana attenuata, a post-fire annual of the Great Basin Desert. Germination can be elicited by GA1,3,4,7treatments and inhibited by the GA biosynthesis inhibitor, paclobutrazol (PAC), abscisic acid (ABA) and terpenes leached from unburned litter of the plant’s natural habitat. We analysed the endogenous GA and ABA dynamics during the 22 h after imbibition, when smoke-treated dormant seeds commit to germination. Extractable GA1+3pools decreased in all seeds, but the decrease was more dramatic within 2 h of smoke exposure, which was followed by an increase between hours 2 and 4. Extractable ABA pools increased shortly after imbibition and remained stable in control, water-treated seeds, but decreased sharply in smoke-treated seeds. PAC completely inhibited smoke-induced germination when seeds were treated for 12 h after smoke exposure, consistent with the requirement ofde novoGA synthesis for germination. Smoke treatment in the dark did not result in germination, whereas GA3treatment did, a result consistent with phytochrome-mediated GA biosynthesis. Smoke exposure dramatically increased the sensitivity of seeds to exogenous GA3treatments in both the light and dark, and light exposure increased this sensitivity an additional tenfold. Taken together, these results suggest that while germination requires endogenous GA synthesis, the effects of smoke treatment increase GA sensitivity, which is correlated with a decrease in endogenous ABA pools.
Spatial variation of post-dispersal seed removal by rodents in highland microhabitats of Spain and Switzerland
Authors: García-Castaño Juan Luis , Kollmann Johannes , Jordano Pedro
Published: May 2008

Few data are available and little is known about spatial variation in post-dispersal seed removal at different levels throughout the geographic range of a plant species. Here, we compare post-dispersal seed removal by rodents within and among sites in two distinct regions, the south-eastern Spanish Mediterranean highlands and the Swiss Jura. Seed removal was assessed experimentally for four fleshy-fruited species (Berberis vulgaris,Crataegus monogyna,Rosaspp. andTaxus baccata) in heterogeneous sites with distinct microhabitats. A factorial general linear model (GLM) analysis was used to evaluate the relative influence of species-specific seed traits on removal at three spatial levels (microhabitat, site and region). In both highland ecosystems, live trapping revealed that rodents were the main seed removers:Apodemus sylvaticuswas observed in both regions, whereasA. flavicollisandClethrionomys glareolusoccurred only at the Swiss sites. There was a significant difference in seed removal between regions, and the preferences of the rodents varied among plant species and microhabitats. Variation in rodent presence explained some differences in seed removal between regions and among microhabitats. Finally, the effect of rodent presence on seed removal differs due to both regional and microhabitat effects.
Physical dormancy in the endemic Australian genus Stylobasium, a first report for the family Surianaceae (Fabales)
Authors: Baskin Jerry M. , Baskin Carol C. , Dixon Kingsley W.
Published: May 2008

The intact germination unit [seed+endocarp, (‘seed’)] of the two species of the Australian endemic genus Stylobasium (Surianaceae, Fabales) is water impermeable. Thus, the seed does not imbibe water or germinate until the integrity of the endocarp, which contains an outer layer of palisade cells, is disrupted. In this study, intact seeds of S. australe and of S. spathulatum, incubated on a moist substrate (for up to 2 years), did not imbibe water, whereas those that were mechanically scarified (both species), or dipped in boiling water for 30 s (S. spathulatum), imbibed and germinated. Thus, seeds of Stylobasium species have physical dormancy (PY). This is the first report of PY in Surianaceae, making it only the sixteenth family of angiosperms (no gymnosperms) in which this class of seed dormancy has been identified.
In Cultured Oligodendrocytes the A/B-type hnRNP CBF-A Accompanies MBP mRNA Bound to mRNA Trafficking Sequences
Authors: Raju Chandrasekhar S. , Göritz Christian , Nord Ylva , Hermanson Ola , López-Iglesias Carmen , Visa Neus , Castelo-Branco Goncalo , Percipalle Piergiorgio
Published: May 2008

Heterogeneous ribonucleoproteins (hnRNPs) have key roles in RNA biogenesis, including pre-mRNP assembly, transport and cytoplasmic localization. Here we show by biochemical fractionation of nuclear extracts and protein–protein interaction assays that the A/B-type hnRNP CBF-A is in a multiprotein complex with hnRNP A2 and A3 and hnRNP U. Using RNA affinity chromatography and gel retardation assays, CBF-A was found to bind directly to RNA trafficking sequences in the 3′-UTR of the myelin basic protein (MBP) mRNA. In primary oligodendrocytes, astrocytes, neurons, and mouse forebrain sections, CBF-A revealed a characteristic granular cytoplasmic distribution. In mouse forebrain CBF-A–positive granules were preferentially found in regions with loosely bundled myelin fibers. In cultured oligodendrocytes, CBF-A was found to be specifically associated with endogenous MBP mRNA and CBF-A gene silencing resulted in the retention of MBP granules in the cell body. Finally, immunoelectron microscopy in differentiating oligodendrocytes showed that CBF-A is located in cytoplasmic granules that are often associated with the cytoskeleton. The results suggest that CBF-A is a novel transacting factor required for cytoplasmic mRNA transport and localization.
Ubiquitination of Fibroblast Growth Factor Receptor 1 Is Required for Its Intracellular Sorting but Not for Its Endocytosis
Authors: Haugsten Ellen Margrethe , Małecki Jędrzej , Bjørklund Sunniva Maria Stordal , Olsnes Sjur , Wesche Jørgen
Published: May 2008

Endocytosis and targeting of growth factor receptors for lysosomal degradation have been associated with ubiquitination of the intracellular part of the receptors. To elucidate the role of receptor ubiquitination in internalization and sorting of fibroblast growth factor receptor (FGFR), we constructed several mutants of FGFR1 in which lysines, potential ubiquitination sites, were substituted for arginines. Substitution of all lysine residues in the intracellular part of FGFR1 resulted in inactivation of the tyrosine kinase domain of the receptor. However, several multilysine FGFR1 mutants, where up to 26 of 29 lysines in the intracellular part of the receptor were mutated, retained tyrosine kinase activity. The active multilysine mutants were poorly ubiquitinated, but internalized normally, indicating that ubiquitination of the receptor is not required for endocytosis. In contrast, degradation of the multilysine mutants was dramatically reduced as the mutants were inefficiently transported to lysosomes but rather sorted to recycling endosomes. The altered sorting resulted in sustained signaling. The duration of FGFR1 signaling seems to be tightly regulated by receptor ubiquitination and subsequent sorting to the lysosomes for degradation.
The Sac1 Phosphoinositide Phosphatase Regulates Golgi Membrane Morphology and Mitotic Spindle Organization in Mammals
Authors: Liu Yang , Boukhelifa Malika , Tribble Emily , Morin-Kensicki Elizabeth , Uetrecht Andrea , Bear James E. , Bankaitis Vytas A.
Published: May 2008

Phosphoinositides (PIPs) are ubiquitous regulators of signal transduction events in eukaryotic cells. PIPs are degraded by various enzymes, including PIP phosphatases. The integral membrane Sac1 phosphatases represent a major class of such enzymes. The central role of lipid phosphatases in regulating PIP homeostasis notwithstanding, the biological functions of Sac1-phosphatases remain poorly characterized. Herein, we demonstrate that functional ablation of the single murine Sac1 results in preimplantation lethality in the mouse and that Sac1 insufficiencies result in disorganization of mammalian Golgi membranes and mitotic defects characterized by multiple mechanically active spindles. Complementation experiments demonstrate mutant mammalian Sac1 proteins individually defective in either phosphoinositide phosphatase activity, or in recycling of the enzyme from the Golgi system back to the endoplasmic reticulum, are nonfunctional proteins in vivo. The data indicate Sac1 executes an essential household function in mammals that involves organization of both Golgi membranes and mitotic spindles and that both enzymatic activity and endoplasmic reticulum localization are important Sac1 functional properties.
Protein Phosphatase Type 1 Directs Chitin Synthesis at the Bud Neck inSaccharomyces cerevisiae
Authors: Larson Jennifer R. , Bharucha Jennifer P. , Ceaser Shantelle , Salamon Joanna , Richardson Charles J. , Rivera Segalit M. , Tatchell Kelly
Published: May 2008

Yeast chitin synthase III (CSIII) is targeted to the bud neck, where it is thought to be tethered by the septin-associated protein Bni4. Bni4 also associates with the yeast protein phosphatase (PP1) catalytic subunit, Glc7. To identify regions of Bni4 necessary for its targeting functions, we created a collection of 23 deletion mutants throughout the length of Bni4. Among the deletion variants that retain the ability to associate with the bud neck, only those deficient in Glc7 binding fail to target CSIII to the neck. A chimeric protein composed of the septin Cdc10 and the C-terminal Glc7-binding domain of Bni4 complements the defects of a bni4Δ mutant, indicating that the C-terminus of Bni4 is necessary and sufficient to target Glc7 and CSIII to the bud neck. A Cdc10-Glc7 chimera fails to target CSIII to the bud neck but is functional in the presence of the C-terminal Glc7-binding domain of Bni4. The conserved C-terminal PP1-binding domain of mammalian Phactr-1 can functionally substitute for the C-terminus of Bni4. These results suggest that the essential role of Bni4 is to target Glc7 to the neck and activate it toward substrates necessary for CSIII recruitment and synthesis of chitin at the bud neck.
Computing chemical organizations in biological networks
Authors: Centler Florian , Kaleta Christoph , di Fenizio Pietro Speroni , Dittrich Peter
Published: May 2008

Motivation: Novel techniques are required to analyze computational models of intracellular processes as they increase steadily in size and complexity. The theory of chemical organizations has recently been introduced as such a technique that links the topology of biochemical reaction network models to their dynamical repertoire. The network is decomposed into algebraically closed and self-maintaining subnetworks called organizations. They form a hierarchy representing all feasible system states including all steady states.

Results: We present three algorithms to compute the hierarchy of organizations for network models provided in SBML format. Two of them compute the complete organization hierarchy, while the third one uses heuristics to obtain a subset of all organizations for large models. While the constructive approach computes the hierarchy starting from the smallest organization in a bottom-up fashion, the flux-based approach employs self-maintaining flux distributions to determine organizations. A runtime comparison on 16 different network models of natural systems showed that none of the two exhaustive algorithms is superior in all cases. Studying a ‘genome-scale’ network model with 762 species and 1193 reactions, we demonstrate how the organization hierarchy helps to uncover the model structure and allows to evaluate the model's quality, for example by detecting components and subsystems of the model whose maintenance is not explained by the model.

Availability: All data and a Java implementation that plugs into the Systems Biology Workbench is available from http://www.minet.uni-jena.de/csb/prj/ot/tools.

Contact:  dittrich@minet.uni-jena.de

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Are silica defences in grasses driving vole population cycles?
Authors: Massey F.P , Smith M.J , Lambin X , Hartley S.E
Published: May 2008

Understanding the factors that drive species population dynamics is fundamental to biology. Cyclic populations of microtine rodents have been the most intensively studied to date, yet there remains great uncertainty over the mechanisms determining the dynamics of most of these populations. For one such population, we present preliminary evidence for a novel mechanism by which herbivore-induced reductions in plant quality alter herbivore life-history parameters and subsequent population growth. We tested the effect of high silica levels on the population growth and individual performance of voles (
Microtus agrestis
) reared on their winter food plant (
Deschampsia caespitosa
). In sites where the vole population density was high, silica levels in
D. caespitosa
leaves collected several months later were also high and vole populations subsequently declined; in sites where the vole densities were low, levels of silica were low and population density increased. High silica levels in their food reduced vole body mass by 0.5% a day. We argue that silica-based defences in grasses may play a key role in driving vole population cycles.
Caecilian jaw-closing mechanics: integrating two muscle systems
Authors: Kleinteich Thomas , Haas Alexander , Summers Adam P
Published: May 2008

Caecilians (Lissamphibia: Gymnophiona) are unique among vertebrates in having two sets of jaw-closing muscles, one on either side of the jaw joint. Using data from high-resolution X-ray radiation computed tomography scans, we modelled the effect of these two muscle groups (
mm. levatores mandibulae
and
m. interhyoideus posterior
) on bite force over a range of gape angles, employing a simplified lever arm mechanism that takes into account muscle cross-sectional area and fibre angle. Measurements of lever arm lengths, muscle fibre orientations and physiological cross-sectional area of cranial muscles were available from three caecilian species:
Ichthyophis
cf.
kohtaoensis
;
Siphonops annulatus
; and
Typhlonectes natans
. The maximal gape of caecilians is restricted by a critical gape angle above which the
mm. levatores mandibulae
will open the jaw and destabilize the mandibular joint. The presence of destabilizing forces in the caecilian jaw mechanism may be compensated for by a mandibular joint in that the fossa is wrapped around the condyle to resist dislocation. The caecilian skull is streptostylic; the quadrate–squamosal complex moves with respect to the rest of the skull. This increases the leverage of the jaw-closing muscles. We also demonstrate that the unusual jaw joint requires streptostyly because there is a dorsolateral movement of the quadrate–squamosal complex when the jaw closes. The combination of the two jaw-closing systems results in high bite forces over a wide range of gape angles, an important advantage for generalist feeders such as caecilians. The relative sizes and leverage mechanics of the two closing systems allow one to exert more force when the other has a poor mechanical advantage. This effect is seen in all three species we examined. In the aquatic
T. natans
, with its less well-roofed skull, there is a larger contribution of the
mm. levatores mandibulae
to total bite force than in the terrestrial
I
. cf.
kohtaoensis
and
S. annulatus
.
PP2B and PP1α cooperatively disrupt 7SK snRNP to release P-TEFb for transcription in response to Ca2+signaling
Authors: Chen Ruichuan , Liu Min , Li Huan , Xue Yuhua , Ramey Wanichaya N. , He Nanhai , Ai Nanping , Luo Haohong , Zhu Ying , Zhou Nan , Zhou Qiang
Published: May 2008

The positive transcription elongation factor b (P-TEFb), consisting of Cdk9 and cyclin T, stimulates RNA polymerase II elongation and cotranscriptional pre-mRNA processing. To accommodate different growth conditions and transcriptional demands, a reservoir of P-TEFb is kept in an inactive state in the multisubunit 7SK snRNP. Under certain stress or disease conditions, P-TEFb is released to activate transcription, although the signaling pathway(s) that controls this is largely unknown. Here, through analyzing the UV- or hexamethylene bisacetamide (HMBA)-induced release of P-TEFb from 7SK snRNP, an essential role for the calcium ion (Ca2+)–calmodulin–protein phosphatase 2B (PP2B) signaling pathway is revealed. However, Ca2+signaling alone is insufficient, and PP2B must act sequentially and cooperatively with protein phosphatase 1α (PP1α) to disrupt 7SK snRNP. Activated by UV/HMBA and facilitated by a PP2B-induced conformational change in 7SK snRNP, PP1α releases P-TEFb through dephosphorylating phospho-Thr186 in the Cdk9 T-loop. This event is also necessary for the subsequent recruitment of P-TEFb by the bromodomain protein Brd4 to the preinitiation complex, where Cdk9 remains unphosphorylated and inactive until after the synthesis of a short RNA. Thus, through cooperatively dephosphorylating Cdk9 in response to Ca2+signaling, PP2B and PP1α alter the P-TEFb functional equilibrium through releasing P-TEFb from 7SK snRNP for transcription.
Role of platelet-derived growth factors in physiology and medicine
Authors: Andrae Johanna , Gallini Radiosa , Betsholtz Christer
Published: May 2008

Platelet-derived growth factors (PDGFs) and their receptors (PDGFRs) have served as prototypes for growth factor and receptor tyrosine kinase function for more than 25 years. Studies of PDGFs and PDGFRs in animal development have revealed roles for PDGFR-α signaling in gastrulation and in the development of the cranial and cardiac neural crest, gonads, lung, intestine, skin, CNS, and skeleton. Similarly, roles for PDGFR-β signaling have been established in blood vessel formation and early hematopoiesis. PDGF signaling is implicated in a range of diseases. Autocrine activation of PDGF signaling pathways is involved in certain gliomas, sarcomas, and leukemias. Paracrine PDGF signaling is commonly observed in epithelial cancers, where it triggers stromal recruitment and may be involved in epithelial–mesenchymal transition, thereby affecting tumor growth, angiogenesis, invasion, and metastasis. PDGFs drive pathological mesenchymal responses in vascular disorders such as atherosclerosis, restenosis, pulmonary hypertension, and retinal diseases, as well as in fibrotic diseases, including pulmonary fibrosis, liver cirrhosis, scleroderma, glomerulosclerosis, and cardiac fibrosis. We review basic aspects of the PDGF ligands and receptors, their developmental and pathological functions, principles of their pharmacological inhibition, and results using PDGF pathway-inhibitory or stimulatory drugs in preclinical and clinical contexts.