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.     

Effects Silver Nanoparticles and Magnetic Field on Growth of Fodder Maize (Zea mays L.)

Two experiments were done in 2008 and 2009 to study the effects of magnetic field and silver nanoparticles on fodder maize (Zea mays L.). These experiments were done with seven treatments based on a randomized complete block design in four replications. The treatments were as follows: magnetic field and silver nanoparticles?+?Kemira fertilizer (T1), magnetic field and silver nanoparticles?+?Humax fertilizer (T2), magnetic field and silver nanoparticles (T3), Kemira fertilizer (T4), Librel fertilizer (T5), Humax fertilizer (T6), and a control (T7). Results showed that fresh yield was higher in treatments T3 and T4. Treatments T3 and T4 had increased maize fresh yields of 35 and 17.5?% in comparison to the control, respectively. The dry matter yield of those plants exposed to magnetic field and silver nanoparticles was significantly higher than that from any of the other treatments. Magnetic field and silver nanoparticle treatments (T3 and T1) showed higher percentages for ears, and the lowest percentages were found in treatments T7 and T5. In general, the soil conditions for crop growth were more favorable in 2009 than in 2008, which caused the maize to respond better to treatments tested in the study; therefore, treatments had more significant effects on studied traits in 2008 than in 2009.     

Efficacy of yeasts in the management of root-knot nematode Meloidogyne incognita,in Flame Seedless grape vines and the consequent effect on the productivity of the vines

Twenty-two yeast strains were screened for their efficacy in suppression of root-knot nematode Meloidogyne incognita on Flame Seedless grapevines. The most effective seven strains were chosen to study their effect on nematode population in vitro and in vivo as well as their impact on crop productivity and fruit quality. Data showed that all treatments significantly reduced the number of juveniles in vitro after 24 and 48 h. The highest percentage of nematode mortality was achieved by the application of Pichia gluilliermondii Moh10, Pachytrichospora transvaalensis Y-1240, Candida albicans Moh Y-5 and Geotichum terrestre Y 2162. Similarly, under greenhouse conditions, all treatments significantly reduced the number of juveniles and disease index compared to the untreated plants during both incubation periods (30 and 50 days). Under field conditions, the tested yeast strains as well as Nemacour (nematocide) resulted in a significant reduction (P<0.05) of populations of Meloidogyne incognita compared to the control in two successive seasons tested. The beneficial impact of application of yeast strains was reflected in crop productivity on Flame Seedless grapevines as well as fruit quality. Percentages of vegetative buds, flower buds, shoot length and leaf number were significantly enhanced as a result of application of the different yeast strains and Nemacour. Bunch weight, berry weight and berry numbers were significantly increased by Pachytrichospora transvaalensis Y-1240, Geotichum terrestre Y-2162 and Candida albicans Moh Y-5. Nemacour and other yeast strains did not show any significant differences compared to the infected vines. Percentage of total soluble solids (TSS%) increased by applying all yeast strains, whereas Nemacour treatment gave the highest value of both TSS percent and percentage of acidity and increased anthocyanins in the skin of berries.     

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.     

Posthypoxic ventilatory decline during NREM sleep: influence of sleep apnea.

We wished to determine the severity of posthypoxic ventilatory decline in patients with sleep apnea relative to normal subjects during sleep. We studied 11 men with sleep apnea/hypopnea syndrome and 11 normal men during non-rapid eye movement sleep. We measured EEG, electrooculogram, arterial O(2) saturation, and end-tidal P(CO2). To maintain upper airway patency in patients with sleep apnea, nasal continuous positive pressure was applied at a level sufficient to eliminate apneas and hypopneas. We compared the prehypoxic control (C) with posthypoxic recovery breaths. Nadir minute ventilation in normal subjects was 6.3 +/- 0.5 l/min (83.8 +/- 5.7% of room air control) vs. 6.7 +/- 0.9 l/min, 69.1 +/- 8.5% of room air control in obstructive sleep apnea (OSA) patients; nadir minute ventilation (% of control) was lower in patients with OSA relative to normal subjects (P < 0.05). Nadir tidal volume was 0.55 +/- 0.05 liter (80.0 +/- 6.6% of room air control) in OSA patients vs. 0.42 +/- 0.03 liter, 86.5 +/- 5.2% of room air control in normal subjects. In addition, prolongation of expiratory time (Te) occurred in the recovery period. There was a significant difference in Te prolongation between normal subjects (2.61 +/- 0.3 s, 120 +/- 11.2% of C) and OSA patients (5.6 +/- 1.5 s, 292 +/- 127.6% of C) (P < 0.006). In conclusion, 1) posthypoxic ventilatory decline occurred after termination of hypocapnic hypoxia in normal subjects and patients with sleep apnea and manifested as decreased tidal volume and prolongation of Te; and 2) posthypoxic ventilatory prolongation of Te was more pronounced in patients with sleep apnea relative to normal subjects.     

Identification of the human ortholog of the t-complex-encoded protein TCTE3 and evaluation as a candidate gene for primary ciliary dyskinesia

Primary ciliary dyskinesia (PCD) is a heterogeneous autosomal recessive disease that is caused by impaired ciliary and flagellar functions. About 50% of PCD patients show situs inversus, denoted as Kartagener syndrome. In most cases, axonemal defects in cilia and sperm tails can be demonstrated by electron microscopy, i.e. PCD patients often lack inner and/or outer dynein arms in their sperm tails and cilia, supporting the hypothesis that mutations in dynein genes may cause PCD. In order to identify novel PCD genes we have isolated the human ortholog of the murine TCTE3 gene. The human TCTE3 gene encodes a dynein light chain and shares high similarity to dynein light chains of other species. The TCTE3 gene is expressed in tissues containing cilia or flagella, it is composed of four exons and located on chromosome 6q25-->q27. To elucidate the role of TCTE3 as a candidate gene for PCD a mutational analysis of thirty-six PCD patients was performed. We detected five polymorphisms in the coding sequence and in the 5' UTR of the TCTE3 gene. In one patient a heterozygous nucleotide exchange was identified resulting in an arginine to isoleucine substitution at the amino acid level. However, this exchange was also detected in one control DNA. Our results indicate that mutations in the TCTE3 gene are not a main cause of primary ciliary dyskinesia.     

Identification of a new gene locus for adolescent nephronophthisis, on chromosome 3q22 in a large Venezuelan pedigree

Nephronophthisis, an autosomal-recessive cystic kidney disease, is the most frequent monogenic cause for renal failure in childhood. Infantile and juvenile forms of nephronophthisis are known to originate from separate gene loci. We describe here a new disease form, adolescent nephronophthisis, that is clearly distinct by clinical and genetic findings. In a large, 340-member consanguineous Venezuelan kindred, clinical symptoms and renal pathology were evaluated. Onset of terminal renal failure was compared with that in a historical sample of juvenile nephronophthisis. Onset of terminal renal failure in adolescent nephronophthisis occurred significantly later (median age 19 years, quartile borders 16.0 and 25.0 years) than in juvenile nephronophthisis (median age 13.1 years, quartile borders 11.3 and 17.3 years; Wilcoxon test P=.0069). A total-genome scan of linkage analysis was conducted and evaluated by LOD score and total-genome haplotype analyses. A gene locus for adolescent nephronophthisis was localized to a region of homozygosity by descent, on chromosome 3q22, within a critical genetic interval of 2. 4 cM between flanking markers D3S1292 and D3S1238. The maximum LOD score for D3S1273 was 5.90 (maximum recombination fraction.035). This locus is different than that identified for juvenile nephronophthisis. These findings will have implications for diagnosis and genetic counseling in hereditary chronic renal failure and provide the basis for identification of the responsible gene.     

Light Quality Affects Protocorm-Like Body (PLB) Formation,Growth and Development of In Vitro Plantlets of Phalaenopsis pulcherrima

Biology Bulletin - Light-emitting diodes (LEDs) can be used as a useful alternative to the in vitro culture of various plant species, which not only accelerates plantlet growth and development but...