Thesaurus-based disambiguation of gene symbols

Background  

Massive text mining of the biological literature holds great promise of relating disparate information and discovering new knowledge. However, disambiguation of gene symbols is a major bottleneck.     

Functional studies of signaling pathways in peri-implantation development of the mouse embryo by RNAi

Background

Studies of gene function in the mouse have relied mainly on gene targeting via homologous recombination. However, this approach is difficult to apply in specific windows of time, and to simultaneously knock-down multiple genes. Here we report an efficient method for dsRNA-mediated gene silencing in late cleavage-stage mouse embryos that permits examination of phenotypes at post-implantation stages.

Results

We show that introduction of Bmp4 dsRNA into intact blastocysts by electroporation recapitulates the genetic Bmp4 null phenotype at gastrulation. It also reveals a novel role for Bmp4 in the regulation the anterior visceral endoderm specific gene expression and its positioning. We also show that RNAi can be used to simultaneously target several genes. When applied to the three murine isoforms of Dishevelled, it leads to earlier defects than previously observed in double knock-outs. These include severe delays in post-implantation development and defects in the anterior midline and neural folds at headfold stages.

Conclusion

Our results indicate that the BMP4 signalling pathway contributes to the development of the anterior visceral endoderm, and reveal an early functional redundancy between the products of the murine Dishevelled genes. The proposed approach constitutes a powerful tool to screen the functions of genes that govern the development of the mouse embryo.     

Changing Global Climate: Historical Carbon and Nitrogen Budgets and Projected Responses of Ohio’s Cropland Ecosystems

As the evidence of global climate change continues to mount, its consequences for cropland productivity assume particular significance. Against the backdrop of past agricultural practices, simulation models offer a glimpse into the future, showing the effect of temperature changes on crop production. In this study, we first quantified the carbon (C) and nitrogen (N) budgets of Ohios cropland ecosystems using inventory yield data of corn for grain, oat, and all wheat for the period 1866–1996 and soybean for the period 1924–96. Then we explored the responses of Ohios continuous soybean croplands to changes in temperature, carbon dioxide (CO₂) concentration, initial soil organic C and N (SOC-N) pools, soil texture, and management practices by developing a simple cropland ecosystem model (CEM) and performing a long-term sensitivity analysis. Finally, CEM simulations were evaluated against independent observations of SOC values (0–19 cm) averaged over 470 northwest Ohio sites between 1954 and 1987 under conventional tillage and rotations of corn–soybean–winter wheat by using the historical yield data (r ² = 0.8). The C contents per hectare of crop harvests increased by 178% for oats, 300% for corn for grain, and 652% for all wheat between 1866 and 1996 and by 305% for soybean between 1924 and 1996. Ohio croplands acted as C–N sources, releasing average net ecosystem emissions (NEE), including the removal of harvested C–N, of 4,598 kg CO₂ ha^–1 and 141 kg N ha^–1 in 1886 and 205 kg CO₂ ha^–1 (except for the corn-for-grain cropland) and 39 kg N ha^–1 in 1996. The continuous corn croplands continued to become a C sink, sequestering 255 kg C ha^–1 in 1996. Results of the sensitivity analysis for Ohios continuous soybean croplands revealed that the SOC pool increased by 6.9% and decreased by 7.5% in response to a doubled CO₂ concentration and a temperature increase of 2.8°C over 100 years, respectively. The sequestration potential of the SOC pool increased by 6.5% at a rate of 24.6 kg C ha^–1 y^–1 for the same period with finer soil texture (loam to silty clay loam). The shift from conventional to conservation residue practice led to an 11% increase in the steady-state SOC storage at a rate of 42 kg C ha^–1 y^–1 for 100 years.     

Behavioural and physiological consequences of acute social defeat in growing gilts: effects of the social environment

Endocrine, behavioural and immunologic processes, together with body growth, were evaluated in gilts that were defeated at 10 weeks of age in resident-intruder tests. Immediately after defeat, gilts were either separated from or reunited with a familiar conspecific (litter-mate; always a barrow). Gilts were assigned to one of four treatments: (a) DI: defeat, followed by isolation (separation from original litter-mate; n=8); (b) I: no defeat, isolation (control group; n=9); (c) DP; defeat, followed by pair-housing (reunion with original litter-mate; n=8); and (d) P: no defeat, pair-housing (control group; n=8). The following general conclusions were derived: (1) social defeat caused pronounced short-term elevations in hypothalamic-pituitary-adrenal (HPA) and sympathetic-adrenal medullary activities, and of prolactin levels. Moreover, as soon as 1h after defeat, percentages of blood lymphocytes and neutrophilic granulocytes were, respectively, decreased and increased; (2) social defeat had some long-lasting influence on behaviour and physiology, but isolation predominantly determined responses in the longer term. Defeat, as well as isolation, resulted in increased cardiovascular activities compared to P controls, as observed in a novel object test (NOT: +7 days) and an aversion test (AVT: +14 days). Moreover, defeated as well as isolated gilts did not habituate to a repeated novel environment test (NET: -7, +2 and +7 days) in terms of frequencies of vocalising, whereas P controls did. Isolation, through the separation from any other pig, was responsible for the other observed long-term characteristics, which developed progressively. Isolated gilts showed high mobilities and high cortisol responses in the repeated NET (+7 days), not being habituated. This contrasted the reactions of pair-housed gilts, which were much reduced. In addition to their high cardiovascular activities in the NOT and the AVT, isolated gilts also displayed higher heart rates in the repeated NET and during human presence following the NOT, compared to pair-housed gilts. Finally, isolated gilts were more inhibited to approach a novel object (in the NOT) than pair-housed pigs; and (3) stress responses of defeated gilts were modulated by the subsequent social environment. Stimulation of the HPA-axis (plasma- and salivary cortisol) was prolonged in those defeated gilts which were isolated (observed in the first hour). Changes in leucocyte subsets were still observed after 3 days in DI, but were 'normalised' within 1 day in DP gilts. Two days after defeat, habituation to the repeated NET in terms of mobility and salivary cortisol responses occurred in control and DP gilts, but not in DI gilts. We argue that these effects of the social environment shortly after defeat were related to a stress-reducing effect of a stable social relationship, i.e. social support.     

Effect of anaesthetics on calcium-induced luminescence of aequorin

The effect of some general and local anaesthetics on the calcium-induced luminescence of aequorin was studied in vitro using a photomultiplier tube and recording technique. Purified aequorin (0.1 microliter) was injected into a 500 micron diameter porous cellulose acetate capillary tube containing 0.5 M KC1, 20 mM phosphate (pH 7.2) and calcium-EGTA buffers. The trapped aequorin was superfused with buffer solutions which sometimes contained anaesthetic (test) solutions. The results showed that some anaesthetics, e.g. urethane, etomidate and lignocaine, increased whereas others, e.g. methohexitone, thiopentone, decreased the light output (luminescence) of aequorin in constant ionized calcium and EGTA buffers. Similar results were produced by some non-anaesthetic drugs, e.g. glycerol, TEA, caffeine, etc. Concentration-response curves for calcium-dependent and -independent luminescence of aequorin showed that anaesthetics variously affected the aequorin response. Some anaesthetics, e.g. lignocaine, increased the maximum response while others, e.g. etomidate, increased the affinity (i.e. decreased EC50s) of aequorin to calcium ions without altering the slope, which remained at about 2. It was concluded that anaesthetics can either excite or depress aequorin luminescence, the effect being dependent on the type and the concentration used.     

Heparin increases the infectivity of Human Papillomavirus Type 16 independent of cell surface proteoglycans and induces L1 epitope exposure

Human Papillomaviruses (HPVs) are the etiological agents of cervical cancer, and HPV‐16 is the most prevalent type. Several HPVs require heparan sulfate proteoglycans (HSPGs) for cell binding. Here, we analyse the phenomenon that preincubation of HPV‐16 with increasing concentrations of heparin results in partial restoration rather than more efficient inhibition of infection. While corroborating that the HSPGs are cell‐binding receptors for HPV‐16, heparin‐preincubated virus bound to the extracellular matrix (ECM) via laminin‐332. Furthermore, the interaction of virions with heparin, a representative of the highly sulfated S‐domains of heparan sulfate (HS) chains of HSPGs, allowed HPV‐16 infection in the absence of cell surface HSPGs. Therefore, we concluded that specific glycan moieties but not specific HSPG protein backbones are required for infection. The increased binding of an epitope‐specific antibody to the viral capsid after heparin binding suggested that initial conformational changes in the HPV‐16 virion occur during infection by interaction with‘heparin‐like’ domains of cellular HSPGs. We propose that HS sequences with specific sulfation patterns are required to facilitate HPV‐16 infection.     

Genetic polymorphims of estrogen receptor alpha −397 PvuII (T>C) and −351 XbaI (A>G) in a portuguese population: prevalence and relation with breast cancer susceptibility

Estrogen receptor alpha (ERα), that mediates the biologic effects of estrogen in estrogen-sensitive tissues like breast, is genetically polymorphic. To evaluate the association between ?397 PvuII (T>C) and ?351 XbaI (A>G) restriction fragment length polymorphisms (RFLPs) in intron 1 of ERα gene and susceptibility of breast cancer, we undertook a case–control study in BRCA1 185delAG and 5382insC/BRCA2 6174delT negative Portuguese women. The study population consisted of 107 patients with histological diagnosis of breast cancer and 121 women with no history of breast cancer. Genomic DNA was extracted from blood samples and genotyping analyses were performed by PCR–RFLP. XbaI polymorphism was associated with a significant reduced risk of breast cancer for carriers of the x allele in homozygozity (OR 0.178; 95 % CI 0.070–0.456; P < 0.001) or heterozigozity (OR 0.223; 95 % CI 0.089–0.561; P = 0.001). The PvuII polymorphism was associated with a non-significantly reduced risk. The combined analysis of PvuII and XbaI polymorphisms revealed none synergistic effect of the two genotypes, except for simultaneous carriers of pp and xx genotypes, that have a reduced risk of breast cancer (OR 0.226; 95 % CI 0.049–1.035; P = 0.044). The combination of PvuII and XbaI genotypes into haplotypes showed that carriers of two copies of the px (ppxx) haplotype had a reduced risk of breast cancer (OR 0.405; 95 % CI 0.194–0.843; P = 0.014), compared with PX (PPXX + PPXx + PpXX + PpXx) haplotypes. PvuII and XbaI polymorphisms were in linkage disequilibrium both in cases (D = 0.044, r² = 0.049, X² = 5.216, P = 0.022) and controls (D = 0.090, r² = 0.139, X² = 16.819, P < 0.001), but not in the entire sample population analyzed as a whole (D = 0.087, r² = 0.0076, X² = 1.733, P = 0.188). In conclusion, in this case–control study we found that ERα gene XbaI polymorphism may modify individual susceptibility for breast cancer in this population.     

THE COMBINED USE OF WHOLE CUPHEA SEEDS CONTAINING MEDIUM CHAIN FATTY ACIDS AND AN EXOGENOUS LIPASE IN PIGLET NUTRITION

In search for an alternative for nutritional antimicrobials in piglet feeding, the effects of adding whole Cuphea seeds, as a natural source of medium chain fatty acids (MCFA), with known antimicrobial effects, and an exogenous lipase to a weaner diet were studied. The foregut flora, the gut morphology, some digestive parameters and the zootechnical performance of weaned piglets were investigated. Thirty newly weaned piglets, initial weight 7.0 ± 0.4 kg, were divided according to litter, sex and weight in two groups (control diet; Cuphea+lipase diet). The Cuphea seeds (lanceolata and ignea) (50 g kg^?1) were substituted for soybean oil (15 g kg^?1), Alphacell (25 g kg^?1) and soy protein isolate (10 g kg^?1) in the control diet. Also 500 mg kg^?1 microbial lipase was added to the Cuphea diet. The piglets were weighted individually on days 0, 3, 7, 14 and 16. Feed intake was recorded per pen during days 0 to 3, 3 to 7, 7 to 14 and 14 to 16. On day 7 five piglets of each experimental group were euthanized for counting the gastric and small intestinal gut flora and for gut morphology at two sites of the small intestine (proximal, distal). The results indicate a trend towards improved performances parameters by feeding Cuphea + lipase. The enzymic released MCFA (1.7 g kg^?1 fresh gastric contents) tended to decrease the number of Coliforms in the proximal small intestine, but increased the number in the stomach and distal small intestine. With Cuphea, the number of Streptococci was significantly lower in small intestine, but not in the stomach, while the number of Lactobacilli was significantly lower in the distal small intestine and tended to be lower in the stomach and proximal small intestine. No differences between the diets were noted for the total anaerobic microbial load in the stomach or in the gut. Feeding Cuphea+lipase resulted in a significantly greater villus height (distal small intestine) and a lesser crypt depth (proximal and distal small intestine) and greater villus/crypt ratio depth (proximal and distal small intestine). The intra-epithelial lymphocyte (IEL) counts per 100 enterocytes were significantly decreased in the proximal small intestine and tended to decrease in the distal small intestine by feeding the Cuphea+lipase diet. Both phenomena are indicative for a more healthy and better functional state of the mucosa. Present results are in line with foregoing research, showing that manipulation of the gut ecosystem by the enzymic in situ released MCFA in the stomach and foregut can result in improved performances of the piglets, which makes the concept a potential alternative for in-feed nutritional antibiotics.     

Fluxes and retention of sediment and nutrients in valley bottom fish and rice farms and wetlands: impacts on surface water

This study compares nutrient and sediment retention among rice and fish farms and wetlands in valley bottoms in southern Rwanda. Small-scale wetland, rice and fishpond experimental systems were established to measure sediment, nitrogen (N) and phosphorus (P) fluxes during a 9-month period. There were significant differences in the processes contributing to sediment, N and P retention in the three systems related to system characteristics, management practices, and seasons. Overall nutrient retention was higher in the rice and fish systems, but these systems had higher inputs and outputs of sediment and nutrients. In rice plots, resuspension and discharge of sediment and nutrients to the outflow were caused by ploughing and weeding during the first 3 months of the culture period. In fishponds, nutrients and sediment discharge were associated with water renewal and sediment removal during the last 5 months of the farming period. The undisturbed wetland plots had the lowest outflows of sediment and nutrients. Nutrient uptake and accumulation in biomass was much higher in rice and wetland vegetation than in fish biomass. In fishponds and wetlands, nutrients accumulated in soil, whereas rice plots showed a decrease or depletion in nutrient storage. To increase nutrient utilization at the plot level, sediment and nutrient discharge from land preparation and rice transplanting should be reduced by better farm practices. Within a catchment, nutrient flows can be integrated by using fishpond sediments for crop farming, by incorporating natural wetlands in crop rotations or using them as buffer zones.