The cognitive mechanisms of optimal sampling

How can animals learn the prey densities available in an environment that changes unpredictably from day to day, and how much effort should they devote to doing so, rather than exploiting what they already know? Using a two-armed bandit situation, we simulated several processes that might explain the trade-off between exploring and exploiting. They included an optimising model, dynamic backward sampling; a dynamic version of the matching law; the Rescorla-Wagner model; a neural network model; and ?-greedy and rule of thumb models derived from the study of reinforcement learning in artificial intelligence. Under conditions like those used in published studies of birds’ performance under two-armed bandit conditions, all models usually identified the more profitable source of reward, and did so more quickly when the reward probability differential was greater. Only the dynamic programming model switched from exploring to exploiting more quickly when available time in the situation was less. With sessions of equal length presented in blocks, a session-length effect was induced in some of the models by allowing motivational, but not memory, carry-over from one session to the next. The rule of thumb model was the most successful overall, though the neural network model also performed better than the remaining models.     

Increased expression of HIF-1alpha, nNOS, and VEGF in the cerebral cortex of anemic rats

This study tested the hypothesis that specific hypoxic molecules, including hypoxia-inducible factor-1alpha (HIF-1alpha), neuronal nitric oxide synthase (nNOS), and vascular endothelial growth factor (VEGF), are upregulated within the cerebral cortex of acutely anemic rats. Isoflurane-anesthetized rats underwent acute hemodilution by exchanging 50% of their blood volume with pentastarch. Following hemodilution, mean arterial pressure and arterial Pa(O(2)) values did not differ between control and anemic rats while the hemoglobin concentration decreased to 57 +/- 2 g/l. In anemic rats, cerebral cortical HIF-1alpha protein levels were increased, relative to controls (1.7 +/- 0.5-fold, P < 0.05). This increase was associated with an increase in mRNA levels for VEGF, erythropoietin, CXCR4, iNOS, and nNOS (P < 0.05 for all), but not endothelial NOS. Cerebral cortical nNOS and VEGF protein levels were increased in anemic rats, relative to controls (2.0 +/- 0.2- and 1.5 +/- 0.4-fold, respectively, P < 0.05 for both). Immunohistochemistry demonstrated increased HIF-1alpha and VEGF staining in perivascular regions of the anemic cerebral cortex and an increase in the number of nNOS-positive cerebral cortical cells (3.2 +/- 1.0-fold, P < 0.001). The nNOS-positive cells costained with the neuronal marker, Neu-N, but not with the astrocytic marker glial fibrillary acidic protein (GFAP). These nNOS-positive neurons frequently sent axonal projections toward cerebral blood vessels. Conversely, VEGF immunostaining colocalized with both neuronal (NeuN) and astrocytic markers (GFAP). In conclusion, acute normotensive, normoxemic hemodilution increased the levels of HIF-1alpha protein and mRNA for HIF-1-responsive molecules. nNOS and VEGF protein levels were also increased within the cerebral cortex of anemic rats at clinically relevant hemoglobin concentrations.     

Polygenic in vivo validation of cancer mutations using transposons

The in vivo validation of cancer mutations and genes identified in cancer genomics is resource-intensive because of the low throughput of animal experiments. We describe a mouse model that allows multiple cancer mutations to be validated in each animal line. Animal lines are generated with multiple candidate cancer mutations using transposons. The candidate cancer genes are tagged and randomly expressed in somatic cells, allowing easy identification of the cancer genes involved in the generated tumours. This system presents a useful, generalised and efficient means for animal validation of cancer genes.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0455-6) contains supplementary material, which is available to authorized users.     

Ergosterol concentration and variability in genotype-by-pathogen interaction for grain mold resistance in sorghum

A lack of understanding of host-by-pathogen relations can hinder the success of breeding for resistance to a major disease. Fungal strain pathogenicity has to be understood from the virulence it can cause on susceptible genotypes and host resistance indicates which genotypes have resistance genes. Where the two worlds meet lies the place where researchers match the prevalent pathogen in the area of production with resistant varieties. This paper uses ergosterol concentration analysis as a measure of fungal biomass accumulation to assess levels of resistance in host genotypes. 11 sorghum genotypes were inoculated with 5 strains of fungi that are known to be associated with grain mold disease of sorghum. The resulting interaction was analyzed using GGE Biplot analysis and Cluster analysis which showed that none of the genotypes were resistant to Phoma sorghina and Curvularia lunata. Three genotypes were resistant to Fusarium thapsinum. One fungal strain (Alternaria alternata) does not contribute any significant damage in the grain mold disease. Fusarium graminearum causes very little grain mold disease. There was no correlation between the fungal strains. Visual scoring did not correlate with ergosterol accumulation. Resistance to grain mold in sorghum is shown to be due to vertical or specific resistance genes. Sorghum breeders should, therefore, identify predominant fungal strains in their localities and then locate and tag these resistance genes in their germplasm and pyramid them in commercial varieties.     

OCP3 is an important modulator of NPR1-mediated jasmonic acid-dependent induced defenses in <Emphasis Type="Italic">Arabidopsis</Emphasis>

Background  

Upon appropriate stimulation, plants increase their level of resistance against future pathogen attack. This phenomenon, known as induced resistance, presents an adaptive advantage due to its reduced fitness costs and its systemic and broad-spectrum nature. In Arabidopsis, different types of induced resistance have been defined based on the signaling pathways involved, particularly those dependent on salicylic acid (SA) and/or jasmonic acid (JA).     

Generation Challenge Programme (GCP): standards for crop data

The Generation Challenge Programme (GCP) is an international research consortium striving to apply molecular biological advances to crop improvement for developing countries. Central to its activities is the creation of a next generation global crop information platform and network to share genetic resources, genomics, and crop improvement information. This system is being designed based on a comprehensive scientific domain object model and associated shared ontology. This model covers germplasm, genotype, phenotype, functional genomics, and geographical information data types needed in GCP research. This paper provides an overview of this modeling effort.     

利用双标图分析作物区试数据

品种区试中品种的基因型和环境存在着交互作用（G×E）,使区试数据的分析比较棘手．主效可加和互作可乘模型（简称AMMI模型）是分析区试数据的一新类模型,与常规的方差分析模型和线性回归模型相比,这一方法应用范围广而且更有效．而双标图（biplot）不仅是解释AMMI分析结果的直观有效的工具,而且可以帮助我们选择分析数据的合适模型．本文以95年南方水稻区试单季晚粳组数据为例,对AMMI模型及双标图作一扼要介绍,给出双标图的一些新的性质和用途,和一种可用于产量预测的双标图.     

Pluripotential stem cells derived from migrating primordial germ cells

Pluripotent stem cells termed embryonic germ cells (EGCs) have earlier been derived from pre- and post-migrating mouse primordial germ cells (PGCs). We have recently obtained four EGC lines from migrating PGCs of 9.5 days post coitum (dpc) embryos. All lines were male with normal karyotype and showed properties that are similar to previously established EGC lines, including colony morphology, expression of alkaline phosphatase (AP), and expression of SSEA-1 antigen. The developmental potency of two of these lines was tested in vivo. They contributed to a range of tissues in fetal chimeras including heart, lung, kidney, intestine, muscle, brain and skin. We also examined the methylation status of the imprinted genes: Igf2r, p57Kip2, Lit1, H19 and Igf2. Igf2r, p57Kip2 and Lit1 were unmethylated in all analysed EGC lines, whereas H19 and Igf2 showed significant hypo-methylation in the 9.5 dpc EGC-1 line when compared to previously derived 11.5 dpc male EGC lines. This suggests that imprint erasure in the male germ line occurs prior to 9.5 dpc for all imprinted genes examined.     

Investigating the feasibility of spatially offset Raman spectroscopy for in‐vivo monitoring of bone healing in rat calvarial defect models

A wide range of biomaterials and tissue‐engineered scaffolds are being investigated to support and stimulate bone healing in animal models. Using phantoms and rat cadavers, we investigated the feasibility of using spatially offset Raman spectroscopy (SORS) to monitor changes in collagen concentration at levels similar to those expected to occur in vivo during bone regeneration (0‐0.84 g/cm³). A partial least squares (PLS) regression model was developed to quantify collagen concentration in plugs consisting of mixtures or collagen and hydroxyapatite (predictive power of ±0.16 g/cm³). The PLS model was then applied on SORS spectra acquired from rat cadavers after implanting the collagen: hydroxyapatite plugs in drilled skull defects. The PLS model successfully predicting the profile of collagen concentration, but with an increased predictive error of ±0.30 g/cm³. These results demonstrate the potential of SORS to quantify collagen concentrations, in the range relevant to those occurring during new bone formation.