Collapse of the inner mitochondrial transmembrane potential is not required for apoptosis of HL60 cells.

Apoptotic cell death involves a series of morphological and biochemical changes orchestrated by activated proteases belonging to the caspase family. Recent studies have suggested that the activation of this process of execution is dependent upon events associated with the loss of mitochondrial inner transmembrane potential (Deltapsi(m)), as a consequence of the formation of the permeability transition (PT) pore. This has led to the proposal that mitochondrial depolarization represents a central irreversible checkpoint in the apoptotic program. Here, we present evidence that HL-60 cells undergo apoptosis in response to the cytotoxic insults of actinomycin-D, etoposide, and staurosporine without showing significant changes in Deltapsi(m). Instead, the loss of Deltapsi(m) could be detected only later in the cell death pathway. In addition, the uncoupling agent CCCP produced an early mitochondrial depolarization in HL-60s but these cells showed few signs of apoptosis up to 8 h after the insult. Furthermore, examination of these cells in response to staurosporine revealed the release of mitochondrial cytochrome c into the cytosol over time, corresponding to caspase activation irrespective of mitochondrial depolarization. In summary, our data suggest that the collapse of Deltapsi(m) as a consequence of PT is not a universal early marker for apoptosis and, moreover, it is not part of the central apoptotic machinery.     

Quality determination and the repair of poor quality spots in array experiments

Background  

A common feature of microarray experiments is the occurence of missing gene expression data. These missing values occur for a variety of reasons, in particular, because of the filtering of poor quality spots and the removal of undefined values when a logarithmic transformation is applied to negative background-corrected intensities. The efficiency and power of an analysis performed can be substantially reduced by having an incomplete matrix of gene intensities. Additionally, most statistical methods require a complete intensity matrix. Furthermore, biases may be introduced into analyses through missing information on some genes. Thus methods for appropriately replacing (imputing) missing data and/or weighting poor quality spots are required.     

A Taxonomic Search Engine: Federating taxonomic databases using web services

Background  

The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism.     

Radiographic joint damage in rheumatoid arthritis is associated with differences in cartilage turnover and can be predicted by serum biomarkers: an evaluation from 1 to 4 years after diagnosis

Introduction  

The objective of this study was to determine whether serum biomarkers for degradation and synthesis of the extracellular matrix of cartilage are associated with, and can predict, radiographic damage in patients with rheumatoid arthritis (RA).     

A model of the respiratory pump

The interaction of forces that produce chest wall motion and lung volume change is complex and incompletely understood. To aid understanding we have developed a simple model that allows prediction of the effect on chest wall motion of changes in applied forces. The model is a lever system on which the forces generated actively by the respiratory muscles and passively by impedances of rib cage, lungs, abdomen, and diaphragm act at fixed sites. A change in forces results in translational and/or rotational motion of the lever; motion represents volume change. The distribution and magnitude of passive relative to active forces determine the locus and degree of rotation and therefore the effect of an applied force on motion of the chest wall, allowing the interaction of diaphragm, rib cage, and abdomen to be modeled. Analysis of moments allow equations to be derived that express the effect on chest wall motion of the active component in terms of the passive components. These equations may be used to test the model by comparing predicted with empirical behavior. The model is simple, appears valid for a variety of respiratory maneuvers, is useful in interpreting relative motion of rib cage and abdomen and may be useful in quantifying the effective forces acting on the rib cage.     

tigaR: integrative significance analysis of temporal differential gene expression induced by genomic abnormalities

Background

To determine which changes in the host cell genome are crucial for cervical carcinogenesis, a longitudinal in vitro model system of HPV-transformed keratinocytes was profiled in a genome-wide manner. Four cell lines affected with either HPV16 or HPV18 were assayed at 8 sequential time points for gene expression (mRNA) and gene copy number (DNA) using high-resolution microarrays. Available methods for temporal differential expression analysis are not designed for integrative genomic studies.

Results

Here, we present a method that allows for the identification of differential gene expression associated with DNA copy number changes over time. The temporal variation in gene expression is described by a generalized linear mixed model employing low-rank thin-plate splines. Model parameters are estimated with an empirical Bayes procedure, which exploits integrated nested Laplace approximation for fast computation. Iteratively, posteriors of hyperparameters and model parameters are estimated. The empirical Bayes procedure shrinks multiple dispersion-related parameters. Shrinkage leads to more stable estimates of the model parameters, better control of false positives and improvement of reproducibility. In addition, to make estimates of the DNA copy number more stable, model parameters are also estimated in a multivariate way using triplets of features, imposing a spatial prior for the copy number effect.

Conclusion

With the proposed method for analysis of time-course multilevel molecular data, more profound insight may be gained through the identification of temporal differential expression induced by DNA copy number abnormalities. In particular, in the analysis of an integrative oncogenomics study with a time-course set-up our method finds genes previously reported to be involved in cervical carcinogenesis. Furthermore, the proposed method yields improvements in sensitivity, specificity and reproducibility compared to existing methods. Finally, the proposed method is able to handle count (RNAseq) data from time course experiments as is shown on a real data set.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-327) contains supplementary material, which is available to authorized users.     

A Taxonomic Signature of Obesity in the Microbiome? Getting to the Guts of the Matter

Obesity is an important and intractable public health problem. In addition to the well-known risk factors of behavior, diet, and genetics, gut microbial communities were recently identified as another possible source of risk and a potential therapeutic target. However, human and animal-model studies have yielded conflicting results about the precise nature of associations between microbiome composition and obesity. In this paper, we use publicly available data from the Human Microbiome Project (HMP) and MetaHIT, both surveys of healthy adults that include obese individuals, plus two smaller studies that specifically examined lean versus obese adults. We find that inter-study variability in the taxonomic composition of stool microbiomes far exceeds differences between lean and obese individuals within studies. Our analyses further reveal a high degree of variability in stool microbiome composition and diversity across individuals. While we confirm the previously published small, but statistically significant, differences in phylum-level taxonomic composition between lean and obese individuals in several cohorts, we find no association between BMI and taxonomic composition of stool microbiomes in the larger HMP and MetaHIT datasets. We explore a range of different statistical techniques and show that this result is robust to the choice of methodology. Differences between studies are likely due to a combination of technical and clinical factors. We conclude that there is no simple taxonomic signature of obesity in the microbiota of the human gut.     

Efficiency of the normal human diaphragm with hyperinflation.

We evaluated an index of diaphragm efficiency (Eff(di)), diaphragm power output (Wdi) relative to electrical activation, in five healthy adults during tidal breathing at usual end-expiratory lung volume (EELV) and diaphragm length (L(di ee)) and at shorter L(di ee) during hyperinflation with expiratory positive airway pressure (EPAP). Measurements were repeated with an inspiratory threshold (7.5 cmH(2)O) plus resistive (6.5 cmH(2)O.l(-1).s) load. Wdi was the product of mean inspiratory transdiaphragmatic pressure (DeltaPdi(mean)), diaphragm volume displacement measured fluoroscopically, and 1/inspiratory duration (Ti(-1)). Diaphragm activation, measured with esophageal electrodes, was quantified by computing root-mean-square values (RMS(di)). With EPAP, 1) EELV increased [mean r(2) = 0.91 (SD 0.01)]; 2) in four subjects, L(di ee) decreased [mean r(2) = 0.85 (SD 0.07)] and mean Eff(di) decreased 34% per 10% decrease in L(di ee) (P < 0.001); and 3) in one subject, gastric pressure at EELV increased two- to threefold, L(di ee) was unchanged or increased, and Eff(di) increased at two of four levels of EPAP (P < or = 0.006, ANOVA). Inspiratory loading increased Wdi (P = 0.003) and RMS(di) (P = 0.004) with no change in Eff(di) (P = 0.63) or its relationship with L(di ee). Eff(di) was more accurate in defining changes in L(di ee) [(true positives + true negatives)/total = 0.78 (SD 0.13)] than DeltaPdi(mean).RMS(di)(-1), RMS(di), or DeltaPdi(mean).Ti (all <0.7, P < or = 0.05, without load). Thus Eff(di) was principally a function of L(di ee) independent of inspiratory loading, behavior consistent with muscle force-length-velocity properties. We conclude that Eff(di), measured during tidal breathing and in the absence of expiratory muscle activity at EELV, is a valid and accurate measure of diaphragm contractile function.     

Trophy heads from Nawinpukio, Perú: physical and chemical analysis of Huarpa-era modified human remains

Rescue excavations at the site of Nawinpukio in Perú's Ayacucho Valley exposed a cache of fragmented skulls dating to the Huarpa-era, about AD 400-700. Physical analysis of these remains revealed that they belonged to individuals of both sexes and a range of ages (MNI = 8), and that four crania had been modified through drilling, cutting, and scraping. The occipital and parietal bones of one cranium had been modified to form a shallow basin. Carbon stable isotope analysis of these remains revealed that five individuals had isotopic signatures consistent with maize consumption and one individual exhibited a carbon isotope value indicative of a C(3) plant based diet. Such a nonmaize diet distinguishes this individual from all other prehistoric humans analyzed from the Ayacucho Valley and is consistent with an origin a different ecozone of the valley. On the basis of their physical properties it is argued that these remains represent trophies obtained during raiding. Drawing on the formal properties of the specimens as well as ethnographic and archaeological analogies, it is suggested that the cranial basin served as a vessel for liquid.