Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana

BACKGROUND: The central role of transcription factors (TFs) in higher eukaryotes has led to much interest in deciphering transcriptional regulatory interactions. Even in the best case, experimental identification of TF target genes is error prone, and has been shown to be improved by considering additional forms of evidence such as expression data. Previous expression based methods have not explicitly tried to associate TFs with their targets and therefore largely ignored the treatment specific and time dependent nature of transcription regulation. RESULTS: In this study we introduce CERMT, Covariance based Extraction of Regulatory targets using Multiple Time series. Using simulated and real data we show that using multiple expression time series, selecting treatments in which the TF responds, allowing time shifts between TFs and their targets and using covariance to identify highly responding genes appear to be a good strategy. We applied our method to published TF - target gene relationships determined using expression profiling on TF mutants and show that in most cases we obtain significant target gene enrichment and in half of the cases this is sufficient to deliver a usable list of high-confidence target genes. CONCLUSION: CERMT could be immediately useful in refining possible target genes of candidate TFs using publicly available data, particularly for organisms lacking comprehensive TF binding data. In the future, we believe its incorporation with other forms of evidence may improve integrative genome-wide predictions of transcriptional networks

Grazing in a porous environment. 2. Nematode community structure

The influence of soil matrix potential on nematode community composition and grazing associations were examined. Undisturbed cores (5 cm diameter, 10 cm depth) were collected in an old field dominated by perennial grasses on a Hinckley sandy loam at Peckham Farm near Kingston, Rhode Island. Ten pairs of cores were incubated at -3, -10, -20 and -50 kPa matric potential after saturation for 21-28 or 42-58 days. Nematodes were extracted using Cobb\u27s decanting and sieving method followed by sucrose centrifugal-flotation and identified to family or genus. Collembola and enchytraeids present were also enumerated because they are grazers that reside in air-filled spaces. Direct counts of bacteria and fungi were made to estimate biovolume using fluorescein isothiocyanate and fluorescein diacetate stains, respectively. Trophic diversity and maturity indices were calculated for nematode communities. Three patterns of matric potential effect were observed for nematode taxa. One, there was a consistent effect of matric potential for all season for Alaimus, Monhysteridae, Prismatolaimus, Paraxonchium and Dorylaimoides. Two, some effects of matric potential were consistent among seasons and other effects were inconsistent for Aphelenchoides, Aphelenchus, Cephalobidae, Coomansus, Eudorylaimus, Huntaphelenchoides, Panagrolaimide, Paraphelenchus, Sectonema, and Tripyla. Third, effects of matric potential were always inconsistent among seasons for Aphanolaimus, Aporcelaimellus, Bunonema, Rhabditidae, and Tylencholaimus. As predicted, fungal and bacterial biomass responded oppositely to matric potential. Total bacterial biomass was greater at -3 kPa than -10, -20 and -50 kPa (P=0.0095). Total fungal biomass was greater at -50, -20 and -10 kPa than -3 kPa (P=0.0095). Neither bacterial-feeding, fungal-feeding nor predacious nematodes correlated significantly with bacterial or fungal biomass. Omnivorous and predacious nematodes correlated positively with number of bacterial-feeding nematodes; predacious nematodes also correlated positively with fungal-feeding nematodes. Numbers of Collembola and enchytraeids were more often correlated positively with microbial-grazing nematode numbers in drier than moist soils. From this study, we propose two mechanisms that may explain nematode community structure changes with matric potential: differential anhydrobiosis and/or enclosure hypotheses. The later suggests that drying of soil generates pockets of moisture in aggregates that become isolated from one another enclosing nematodes and their food in relatively high concentrations creating patches of activity separated by larger areas of inactivity

Grazing in a porous environment: 1. The effect of soil pore structure on C and N mineralization. Plant Soil 212

Abstract The porous soil environment constrains grazing of microorganisms by microbivorous nematodes. In particular, at matric potentials at which water-filled pore spaces have capillary diameters less than nematode body diameters the effect of grazing, e.g. enhanced mineralization, should be reduced ('exclusion hypothesis') because nematodes cannot access their microbial forage. We examined C and N mineralization, microbial biomass C (by fumigationextraction), the metabolic quotient (C mineralization per unit biomass C), nematode abundance, and soil water content in intact soil cores from an old field as a function of soil matric potential (−3 to −50 kPa). We expected, in accordance with the exclusion hypothesis, that nematode abundance, N and C mineralization would be reduced as matric potential decreased, i.e. as soils became drier. N mineralization was significantly greater than zero for −3 kPa but not for −10, −20 and −50 kPa. Microbial biomass C was less at −50 kPa than at −10 kPa, but not significantly different from biomass C at −3 and −20 kPa. The metabolic quotient was greatest at −50 kPa than any of the other matric potentials. From the exclusion hypothesis we expected significantly fewer nematodes to be present at −50 and −20 kPa representing water-filled capillary pore sizes less than 6 and 15 µm, respectively, than at −3 and −10 kPa. Microbivorous (fungivorous+bacterivorous) nematode abundance per unit mass of soil was not significantly different among matric potentials. Body diameters of nematodes ranged from 9 µm to 40 µm. We discuss several alternatives to the exclusion hypothesis, such as the 'enclosure hypothesis' which states that nematodes may become trapped in large water-filled pore spaces even when capillary pore diameters (as computed from matric potential) are smaller than body diameters. One of the expected outcomes of grazing in enclosures is the acceleration of nutrient cycling

Материалы к познанию Ostracoda Чёрного моря

Increased geographical mobility, improved medical treatment, and prolonged life expectancy have changed the way of life for older persons and their next of kin. This chapter discusses intergenerational care, mainly from the next of kin’s point of view, when an older family member and the next of kin live far from each other. The study is based on my—the author’s—autoethnographic account of the experience after my father suffered a stroke a few years ago. Inspired by Ellis et al. (2011, p. 392), who stated that autoethnography may ‘analyse personal experience in order to understand cultural experience’, I use my father’s and my own experiences to analyse how geographical distance and serious illness impact intergenerational care and kinship. While I argue that intergenerational care across geographical distance creates certain vulnerabilities, this specific situation also enables and enacts kinship relations. The study focused on practical support, emotional relations, and communication technologies, and their limitations when illness hits and life changes. It also adds to our understanding of aging, illness, and care across vast geographical distances. I claim that the autoethnographic approach accommodates the subjectivity, emotions and first-hand experiences between the older person and the next of kin. This geography of intergenerational care provides new knowledge about an experience, influencing the later years, for an increasing number of individuals and service-providing municipalities, especially in regions marked by outmigration and high youth mobility