Integrating gene expression and GO classification for PCA by preclustering

Background  

Gene expression data can be analyzed by summarizing groups of individual gene expression profiles based on GO annotation information. The mean expression profile per group can then be used to identify interesting GO categories in relation to the experimental settings. However, the expression profiles present in GO classes are often heterogeneous, i.e., there are several different expression profiles within one class. As a result, important experimental findings can be obscured because the summarizing profile does not seem to be of interest. We propose to tackle this problem by finding homogeneous subclasses within GO categories: preclustering.     

Ultrasound imaging in an experimental model of fatty liver disease and cirrhosis in rats

Background

Atypical scrapie was first identified in Norwegian sheep in 1998 and has subsequently been identified in many countries. Retrospective studies have identified cases predating the initial identification of this form of scrapie, and epidemiological studies have indicated that it does not conform to the behaviour of an infectious disease, giving rise to the hypothesis that it represents spontaneous disease. However, atypical scrapie isolates have been shown to be infectious experimentally, through intracerebral inoculation in transgenic mice and sheep. The first successful challenge of a sheep with 'field' atypical scrapie from an homologous donor sheep was reported in 2007.

Results

This study demonstrates that atypical scrapie has distinct clinical, pathological and biochemical characteristics which are maintained on transmission and sub-passage, and which are distinct from other strains of transmissible spongiform encephalopathies in the same host genotype.

Conclusions

Atypical scrapie is consistently transmissible within AHQ homozygous sheep, and the disease phenotype is preserved on sub-passage.     

The threat of rebellion: claiming entitled personhood in Central Africa

A recent anthropological literature on arms‐carrying and violence has sought to understand these undertakings as modes of labour and work. In contrast, I focus on threats, specifically threats made in conjunction with rebellion in the Central African Republic (CAR). Doing so show what the violence/labour approach has missed. Far from seeking to adapt to the exigencies of flexible, uncertain labour circumstances, these men seek to leverage the interests of international interveners in Central African conflicts and revive a statist, entitlement‐centred system in which getting paid indicates status, not work produced. As such, their threats are a critique of their expendability, and a critique of violence, at the same time as they perpetuate the importance of a capacity for violence as a political and personal asset.     

The rate of chromosome breakage is age dependent in lymphocytes of adult controls

Summary Chromosome breaks and chromatid-type lesions from a prospective study of more than 1000 lymphocyte karyotypes from each of six controls were analysed. These lesions were more frequent in older (75 years old on average) than in younger (29 years old on average) controls, especially after 72h cultures. All controls were found to be carriers of fragile sites. The most frequent were 3p14.3 and 16q23, especially in older controls. At least one fra(X)(q27) mitosis was found in each control. Most deletions occurred after breakage in heterochromatin or in late-replicating euchromatin. As almost all radials were either mitotic chiasmata or triradials (branched chromosomes), it is concluded that chromatid exchanges between non-homologous segments are very rare, and indicate chromosomal instability syndrome or recent exposure to a mutagen.     

Evaluation of laser-Doppler flowmetry as a measure of tissue blood flow

In this study the technique of laser-Doppler flowmetry was evaluated for the measurement of tissue blood flow by comparing laser-Doppler flow (LDF) signal in the renal cortex, gracilis muscle, and cremaster muscle of anesthetized rats to whole-organ blood flow measured with an electromagnetic flowmeter or radioactive microspheres. In vitro, LDF signal was closely correlated (r = 0.99) to changes in erythrocyte velocity generated with a rotating wheel. Although individual LDF readings varied in situ, mean LDF signal calculated from multiple readings on the tissue surface were significantly correlated (r = 0.74-0.95) with tissue blood flows measured at various perfusion pressures. However, significant differences in the slope of the LDF signal vs. blood flow relationship were observed in different tissues and with different methods of measurement in the same tissue. This study indicates that mean laser-Doppler flow signal provides a good estimate of tissue blood flow, provided a sufficient number of points is scanned. However, there appears to be no universal calibration factor for the method.     

Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

Metagenomics approaches represent an important way to acquire information on the microbial communities present in complex environments like soil. However, to what extent do these approaches provide us with a true picture of soil microbial diversity? Soil is a challenging environment to work with. Its physicochemical properties affect microbial distributions inside the soil matrix, metagenome extraction and its subsequent analyses. To better understand the bias inherent to soil metagenome 'processing', we focus on soil physicochemical properties and their effects on the perceived bacterial distribution. In the light of this information, each step of soil metagenome processing is then discussed, with an emphasis on strategies for optimal soil sampling. Then, the interaction of cells and DNA with the soil matrix and the consequences for microbial DNA extraction are examined. Soil DNA extraction methods are compared and the veracity of the microbial profiles obtained is discussed. Finally, soil metagenomic sequence analysis and exploitation methods are reviewed.     

Evidence for neuropeptide FF (FLFQRFamide) in rat dorsal root ganglia.

By using specific antibodies and radioimmunological and immunohistochemical methods, we here show that neuropeptide FF (NPFF) occurs in cervical and lumbar dorsal root ganglia cells. Levels in the ganglia were low because they were detectable only after colchicine treatment or after unilateral dorsal rhizotomy. Similar high-performance liquid chromatography profiles were obtained from dorsal root ganglia and spinal cord extracts, indicating that the NPFF-immunoreactivity in the dorsal root ganglia represented similar molecular forms to that in the spinal cord. Immunocytochemistry localized NPFF-immunoreactivity in small- and medium-sized cells. These data suggest that low levels of NPFF present in fine diameter primary afferent fibers could be involved in the treatment of nociceptive information from fore- or hindlimb.     

Molecular phylogenetics at the population/species interface in cave spiders of the southern Appalachians (Araneae:Nesticidae:Nesticus)

This paper focuses on the relationship between population genetic structure and speciation mechanisms in a monophyletic species group of Appalachian cave spiders (Nesticus). Using mtDNA sequence data gathered from 256 individuals, I analyzed patterns of genetic variation within and between populations for three pairs of closely related sister species. Each sister-pair comparison involves taxa with differing distributional and ecological attributes; if these ecological attributes are reflected in basic demographic differences, then speciation might proceed differently across these sister taxa comparisons. Both frequency-based and gene tree analyses reveal that the genetic structure of the Nesticus species studied is characterized by similar and essentially complete population subdivision, regardless of differences in general ecology. These findings contrast with results of prior genetic studies of cave-dwelling arthropods that have typically revealed variation in population structure corresponding to differences in general ecology. Species fragmentation through both extrinsic and intrinsic evolutionary forces has resulted in discrete, perhaps independent, populations within morphologically defined species. Large sequence divergence values observed between populations suggest that this independence may extend well into the past. These patterns of mtDNA genealogical structure and divergence imply that species as morphological lineages are currently more inclusive than basal evolutionary or phylogenetic units, a suggestion that has important implications for the study of speciation mechanisms.      

Chromosome-banding study in Gerbillinae (Rodentia). I. Comparative analysis of Gerbillus poecilops, G. henleyi and G. nanus

An analysis was made of the R- and C-banding of chromosomes of the following Gerbillus species (Rodentia, Gerbillidae): G. poecilops (Taif, Saudi Arabia), G. henleyi (Oursi, Burkina Faso; Kairouan, Tunisia), and G. nanus (Taif and Hofuf, Saudi Arabia; Sind desert, Pakistan). Their karyotypes show the same chromosome number (2n = 52), but a different N.F.a. (number of autosomal arms), ranging from 58 to 62 in the species overall, and from 58 to 60 among G. nanus forms, due to pericentric inversions involving chromosomes 1 and 4. Moreover, large inter-individual variations of heterochromatin segments of chromosomes 25, X, and Y were found. Considering morphology and karyotype, G. poecilops and G. henleyi appear to be rather monomorphous species, whereas G. nanus produces a series of forms as a consequence of speciation, in which both chromosomal and morphological differentiations occur that do not correlate.