Improving the analysis of designed studies by combining statistical modelling with study design information

Background  

In the fields of life sciences, so-called designed studies are used for studying complex biological systems. The data derived from these studies comply with a study design aimed at generating relevant information while diminishing unwanted variation (noise). Knowledge about the study design can be used to decompose the total data into data blocks that are associated with specific effects. Subsequent statistical analysis can be improved by this decomposition if these are applied on selected combinations of effects.     

Effects of cyanobacterial extracellular products and gibberellic acid on salinity tolerance in Oryza sativa L

The XI International Rotifer Symposium was held during 11–18 March, 2006 at the National Autonomous University of Mexico Campus Iztacala located at the North Mexico City (Mexico). These triennial international meetings, first organized in Austria by Late Ruttner-Kolisko in September 1976, are gradually becoming the focal point of discussion and collaboration from rotifer workers across the world. The present XI symposium was attended by 125 participants from 20 nations. During this meeting, different themes of rotifer research from morphology to molecular biology were considered. In addition, there were four invited lectures and four workshops covering different themes of the symposium. During the last 30 years, rotifer research has witnessed gradual shift from the conventional morphological taxonomy to molecular and evolutionary systematics. While the basic rotifer ecological studies continue today, applied areas such as ecotoxicology and aquaculture have taken key roles in the recent meetings. The international rotifer meetings provide ample opportunities not only for exchange of ideas and recent research, but also for material and in establishing inter-personal relationships. Over the last 30 years, the number of participants attending the rotifer meetings has increased.     

土壤中棉花黄萎病菌SYBR Green Ⅰ荧光RT-PCR定量检测技术研究

为实现田间土壤棉花黄萎病菌的早期检测,建立了土壤中棉花黄萎病菌的SYBR GreenⅠ荧光定量PCR检测方法.以含342bp PCR扩增产物的阳性质粒为参考,构建了标准曲线,并对该曲线的特异性、敏感性、可重复性进行了评价.结果表明,该方法具有快速、特异性强、敏感度高等特点.检测范围在3.8×103-3.8×108cop...     

RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations

Visualization and analysis of molecular networks are both central to systems biology. However, there still exists a large technological gap between them, especially when assessing multiple network levels or hierarchies. Here we present RedeR, an R/Bioconductor package combined with a Java core engine for representing modular networks. The functionality of RedeR is demonstrated in two different scenarios: hierarchical and modular organization in gene co-expression networks and nested structures in time-course gene expression subnetworks. Our results demonstrate RedeR as a new framework to deal with the multiple network levels that are inherent to complex biological systems. RedeR is available from http://bioconductor.org/packages/release/bioc/html/RedeR.html.     

Nitrogen in global animal production and management options for improving nitrogen use efficiency

Animal production systems convert plant protein into animal protein. Depending on animal species, ration and management, between 5% and 45 % of the nitrogen (N) in plant protein is converted to and deposited in animal protein. The other 55%-95% is excreted via urine and feces, and can be used as nutrient source for plant (= often animal feed) production. The estimated global amount of N voided by animals ranges between 80 and 130 Tg N per year, and is as large as or larger than the global annual N fertilizer consumption. Cattle (60%), sheep (12%) and pigs (6%) have the largest share in animal manure N production. The conversion of plant N into animal N is on average more efficient in poultry and pork production than in dairy production, which is higher than in beef and sheep production. However, differences within a type of animal production system can be as large as differences between types of animal production systems, due to large effects of the genetic potential of animals, animal feed and management. The management of animals and animal feed, together with the genetic potential of the animals, are key factors to a high efficiency of conversion of plant protein into animal protein. The efficiency of the conversion of N from animal manure, following application to land, into plant protein ranges between 0 and 60%, while the estimated global mean is about 15%. The other 40%-100% is lost to the wider environment via NH3 volatilization, denitrification, leaching and run-off in pastures or during storage and/or following application of the animal manure to land. On a global scale, only 40%-50% of the amount of N voided is collected in barns, stables and paddocks, and only half of this amount is recycled to crop land. The N losses from animal manure collected in barns, stables and paddocks depend on the animal manure management system. Relative large losses occur in confined animal feeding operations, as these often lack the land base to utilize the N from animal manure effectively. Losses will be relatively low when all manure are collected rapidly in water-tight and covered basins, and when they are subsequently applied to the land in proper amounts and at the proper time, and using the proper method (low-emission techniques). There is opportunity for improving the N conversion in animal production systems by improving the genetic production potential of the herd, the composition of the animal feed, and the management of the animal manure. Coupling of crop and animal production systems, at least at a regional scale, is one way to high N use efficiency in the whole system. Clustering of confined animal production systems with other intensive agricultural production systems on the basis of concepts from industrial ecology with manure processing is another possible way to improve N use efficiency.     

Effect of Modification of the N-Terminal Region of Semax on the Expression of Nootropic Effect of Semax Analogs

A comparative study of nootropic activity of semax (MEHFPGP), an analog of ACTH_4–10, and some of its derivatives, in which the N-terminal methionine was modified or substituted with other amino acid residues, was performed. The effect of these peptides on learning of albino rats in tests with positive (food) and negative (pain) reinforcement was studied. In the case of modification of methionine by attachment of the gluconic-acid residue or substitution of methionine with lysine, the nootropic effect of the peptide was retained. The substitution of methionine with tryptophan or serine resulted in a decrease in the nootropic activity. The substitution of methionine with glycine, threonine, or alanine caused a complete loss of the nootropic activity of the peptide. Therefore, the amino acid residue located at position 1 of the heptapeptide analog semax, plays a key role in retaining the nootropic effects of the peptide and determines the degree of their expression.__________Translated from Izvestiya Akademii Nauk, Seriya Biologicheskaya, No. 4, 2005, pp. 460–466.Original Russian Text Copyright © 2005 by Glazova, Sebentsova, Levitskaya, Andreeva, Alfeeva, Kamenskii, Myasoedov.     

Participation of Catecholamines and Nitric Oxide in Regulation of Apoptosis in Nonapeptidergic Neurons of the Rat Hypothalamus

The goal of this work was to study effects of blockade of catecholamine (CA) synthesis on activation of neuronal NO synthase (nNOS) and to elucidate the role of NO in activation of pro- and anti-apoptotic signal proteins in nonapeptidergic neurons of supraoptic (SON) and paraventricular (PVN) nuclei of hypothalamus. The experiment was carried out on adult male Wistar rats. Dehydration for 5 days was used as an apoptosis-activating factor in vasopressinergic neurosecretory cells of SON and PVN of hypothalamus in adult rats. To find out the role of CA, a part of the animals subjected to dehydration were administered intraperitoneally, for the last 3 consecutive experimental days, with an inhibitor of CA synthesis, -methyl-p-tyrosine (-MT) at a dose of 200 mg/kg body weight. A marker of the programmed cell death initiation, pro-apoptotic protein caspase-9, as well as anti-apoptotic protein bcl-2 and nNOS, were revealed using an immunohistochemical technique. Evaluation of immunopositive substance (nNOS, caspase-9, and bcl-2) in neurosecretory cells of SON and PVN were carried out quantitatively by determination of optical density of the stained material in perikarya, using a computerized digital television image analyzer and software PhotoM. On comparing the nNOS amount with the level of pro- and anti-apoptotic protein expression, we have come to the conclusion that a decrease of the brain CA level increases the nNOS and caspase-9 expression. This allows suggesting that an increased level of NO mediates activation of the pro-apoptotic protein caspase-9 and initiates apoptosis in neurons of SON and PVN of hypothalamus. The lack of neuronal loss in SON under conditions of decrease CA synthesis on the background of dehydration might be due to increased expression of the anti-apoptotic protein bcl-2, whose increased elevated level seems to prevent the further rise of the caspase-9 level and, thereby, protects cells from death. An increased level of bcl-2 in neurons of PVN correlated with high amounts of nNOS and caspase-9, but there also was observed no cell loss. It is suggested that suppression of apoptosis in PVN is due either to the bcl-2 effects at later stages of apoptosis, or to other mechanisms that inhibit active caspases.