A statistical method for revealing form-function relations in biological networks

Over the past decade, a number of researchers in systems biology have sought to relate the function of biological systems to their network-level descriptions -- lists of the most important players and the pairwise interactions between them. Both for large networks (in which statistical analysis is often framed in terms of the abundance of repeated small subgraphs) and for small networks which can be analyzed in greater detail (or even synthesized in vivo and subjected to experiment), revealing the relationship between the topology of small subgraphs and their biological function has been a central goal. We here seek to pose this revelation as a statistical task, illustrated using a particular setup which has been constructed experimentally and for which parameterized models of transcriptional regulation have been studied extensively. The question "how does function follow form" is here mathematized by identifying which topological attributes correlate with the diverse possible information-processing tasks which a transcriptional regulatory network can realize. The resulting method reveals one form-function relationship which had earlier been predicted based on analytic results, and reveals a second for which we can provide an analytic interpretation. Resulting source code is distributed via http://formfunction.sourceforge.net.Comment: To appear in Proc. Natl. Acad. Sci. USA. 17 pages, 9 figures, 2 table

Determination of minerals, vitamins, antinutrient and amino acid profile of pumpkin pie produced pumpkin (cucurbeta spp) puree and wheat (tritium aestivum) flour supplemented with spices and butter

Pumpkin (Cucurbita spp.), is one of the most popular vegetables consumed in the world, has been recently recognized as a functional food. Traditional crops including the pumpkins, which are rich in micronutrients, are not consumed widely by smallholder farmers in Africa. However, the cultivation of high yielding, nutrient-rich, multipurpose crops-like pumpkin is important in solving the problems of malnutrition and contributing to food security in Africa including Nigeria. Objectives: Therefore, this work aimed at producing Pumpkin pie from Pumpkin puree and wheat supplemented with some indigenous spices alongside butter. Methodology: Formulations into various formed were made using Pearson's method. The formulations were assayed for mineral, vitamin, antinutrient and amino acid composition using standard laboratory methods. A significant (P<0.05) difference was observed in Zn and Ca content of all the samples, with sample D recording the highest value for Zn (1.30±0.01) mg/g and Ca (0.47±0.01) mg/g. However, samples A and D had the least values for Na and Fe. An increasing and decreasing pattern was observed in all the vitamin contents(B 1, B 2 , B 6 , B12 and C), moving from samples A through to D. Vitamin contents of samples B1 and B6 and higher than he RDA, while B2 , B12 and C were below RDA. The overall antinutrient contents observed were generally low, with sample A having the lowest values for Phytate, Oxalate and tannins. The B, C and D are more enhanced in terms of essential amino acids compared to the control group (sample A). Conclusion: Pumpkin pie can be produced from pumpkin and its supplementation of the spices can boost the pie with essential amino acids, minerals, and vitamin composition. This shows the potential of using pumpkin pie as snacks in-between meals for the prevention of Protein Energy Malnutrition (PEM).&nbsp

Dynamics of epigenetic regulation at the single-cell level

Chromatin regulators play a major role in establishing and maintaining gene expression states. Yet how they control gene expression in single cells, quantitatively and over time, remains unclear. We used time-lapse microscopy to analyze the dynamic effects of four silencers associated with diverse modifications: DNA methylation, histone deacetylation, and histone methylation. For all regulators, silencing and reactivation occurred in all-or-none events, enabling the regulators to modulate the fraction of cells silenced rather than the amount of gene expression. These dynamics could be described by a three-state model involving stochastic transitions between active, reversibly silent, and irreversibly silent states. Through their individual transition rates, these regulators operate over different time scales and generate distinct types of epigenetic memory. Our results provide a framework for understanding and engineering mammalian chromatin regulation and epigenetic memory

Studies on the glycemic response of wheat at various level of processing fed to normal healthy rats

In this study, glycemic response was studied using wheat at various forms of processing. The study was aimed at estimating the glycemic index of various processing effect subjected to wheat, in normal rats using white bread as standard (control). Twenty rats were separated into four groups of five rats: one control group and three experimental groups. Group one was given durum wheat spaghetti, group two was given whole wheat, group three was given dehulled wheat and group four was given white bread (control). For the purpose of consistency, the samples were ground into flour and made into viscous paste using flour and water in a ratio of 1:3 respectively. Blood samples were collected from the tip of rats' tails at fasting and also at 30, 60, 90 and 120 minutes post feed respectively. Blood glucose level was determined using Accu-Chek glucometer and test strips. Dehulled wheat showed the highest blood glucose level at 30 minutes and 60 minutes post feeding, while whole wheat showed the highest blood glucose level at 90 minutes. Durum wheat showed the lowest blood glucose level at 30 minutes, 60 minutes, 90 minutes and 120 minutes. In conclusion, the study revealed that dehulled wheat has the highest glycemic response while durum wheat spaghetti has the lowest glycemic response

Quality of Life in Hormone Receptor–Positive HER-2+ Metastatic Breast Cancer Patients During Treatment with Letrozole Alone or in Combination with Lapatinib

This paper presents analyses evaluating quality of life in patients with hormone receptor–positive human epidermal growth factor receptor 2–positive tumors receiving letrozole alone or in combination with lapatinib in clinical trial EGF30008

Production and evaluation of chemical composition, tanin, in vitro protein digestibility and microbiological studies of fermented local variety of sorghum, fortified with cowpea and ground nut

*Corresponding author The fermented sorghum (yafi moro) based cereal/legume blend was produced from 70 parts of fermented local sorghum flour, 20 parts of dehulled cowpea and 10 parts of roasted ground paste (FSCG). The chemical composition, mineral elements, in vitro protein digestibility and microbiological was determined using standard methods. The result showed that the protein of the samples (FSCG), raw and fermented sorghum were 12.46%, 8.65 and 9.5% respectively. The Moisture content 4.0%, 3.6%, 3.8%; Ash content was 2.0%, 2.2% and 1.5% while Carbohydrate 70.1%, 74.3% and 68.54%. The calculated energy value is 351Kcal, 332.8Kcal and 353.2 Kcal respectively. A significant decreased (p≥0.05) in the level of phytate, mineral element levels with a concomitant increased in in vitro digestibility in both fermented and fermented fortified blend compared to the unprocessed samples. The microorganism isolated and characterized were lactic acid bacteria. It can thus be concluded that; processing methods such as fermentation and subsequent fortification of the fermented samples with legume has greatly enhanced its nutritional value as reported in this study

Combinatorial Signal Perception in the BMP Pathway

The bone morphogenetic protein (BMP) signaling pathway comprises multiple ligands and receptors that interact promiscuously with one another and typically appear in combinations. This feature is often explained in terms of redundancy and regulatory flexibility, but it has remained unclear what signal-processing capabilities it provides. Here, we show that the BMP pathway processes multi-ligand inputs using a specific repertoire of computations, including ratiometric sensing, balance detection, and imbalance detection. These computations operate on the relative levels of different ligands and can arise directly from competitive receptor-ligand interactions. Furthermore, cells can select different computations to perform on the same ligand combination through expression of alternative sets of receptor variants. These results provide a direct signal-processing role for promiscuous receptor-ligand interactions and establish operational principles for quantitatively controlling cells with BMP ligands. Similar principles could apply to other promiscuous signaling pathways

Combinatorial Signal Perception in the BMP Pathway

The bone morphogenetic protein (BMP) signaling pathway comprises multiple ligands and receptors that interact promiscuously with one another and typically appear in combinations. This feature is often explained in terms of redundancy and regulatory flexibility, but it has remained unclear what signal-processing capabilities it provides. Here, we show that the BMP pathway processes multi-ligand inputs using a specific repertoire of computations, including ratiometric sensing, balance detection, and imbalance detection. These computations operate on the relative levels of different ligands and can arise directly from competitive receptor-ligand interactions. Furthermore, cells can select different computations to perform on the same ligand combination through expression of alternative sets of receptor variants. These results provide a direct signal-processing role for promiscuous receptor-ligand interactions and establish operational principles for quantitatively controlling cells with BMP ligands. Similar principles could apply to other promiscuous signaling pathways

Effect of promoter architecture on the cell-to-cell variability in gene expression

According to recent experimental evidence, the architecture of a promoter, defined as the number, strength and regulatory role of the operators that control the promoter, plays a major role in determining the level of cell-to-cell variability in gene expression. These quantitative experiments call for a corresponding modeling effort that addresses the question of how changes in promoter architecture affect noise in gene expression in a systematic rather than case-by-case fashion. In this article, we make such a systematic investigation, based on a simple microscopic model of gene regulation that incorporates stochastic effects. In particular, we show how operator strength and operator multiplicity affect this variability. We examine different modes of transcription factor binding to complex promoters (cooperative, independent, simultaneous) and how each of these affects the level of variability in transcription product from cell-to-cell. We propose that direct comparison between in vivo single-cell experiments and theoretical predictions for the moments of the probability distribution of mRNA number per cell can discriminate between different kinetic models of gene regulation.Comment: 35 pages, 6 figures, Submitte