One billion years of bZIP transcription factor evolution: conservation and change in dimerization and DNA-binding site specificity.

The genomic era has revealed that the large repertoire of observed animal phenotypes is dependent on changes in the expression patterns of a finite number of genes, which are mediated by a plethora of transcription factors (TFs) with distinct specificities. The dimerization of TFs can also increase the complexity of a genetic regulatory network manifold, by combining a small number of monomers into dimers with distinct functions. Therefore, studying the evolution of these dimerizing TFs is vital for understanding how complexity increased during animal evolution. We focus on the second largest family of dimerizing TFs, the basic-region leucine zipper (bZIP), and infer when it expanded and how bZIP DNA-binding and dimerization functions evolved during the major phases of animal evolution. Specifically, we classify the metazoan bZIPs into 19 families and confirm the ancient nature of at least 13 of these families, predating the split of the cnidaria. We observe fixation of a core dimerization network in the last common ancestor of protostomes-deuterostomes. This was followed by an expansion of the number of proteins in the network, but no major dimerization changes in interaction partners, during the emergence of vertebrates. In conclusion, the bZIPs are an excellent model with which to understand how DNA binding and protein interactions of TFs evolved during animal evolution.

Mismatch of arterial and central venous blood gas analysis during haemorrhage.

BACKGROUND AND OBJECTIVE: Arterial base excess and lactate levels are key parameters in the assessment of critically ill patients. The use of venous blood gas analysis may be of clinical interest when no arterial blood is available initially. METHODS: Twenty-four pigs underwent progressive normovolaemic haemodilution and subsequent progressive haemorrhage until the death of the animal. Base excess and lactate levels were determined from arterial and central venous blood after each step. In addition, base excess was calculated by the Van Slyke equation modified by Zander (BE(z)). Continuous variables were summarized as mean +/- SD and represent all measurements (n = 195). RESULTS: Base excess according to National Committee for Clinical Laboratory Standards for arterial blood was 2.27 +/- 4.12 versus 2.48 +/- 4.33 mmol(-l) for central venous blood (P = 0.099) with a strong correlation (r(2) = 0.960, P < 0.001). Standard deviation of the differences between these parameters (SD-DIFBE) did not increase (P = 0.355) during haemorrhage as compared with haemodilution. Arterial lactate was 2.66 +/- 3.23 versus 2.71 +/- 2.80 mmol(-l) in central venous blood (P = 0.330) with a strong correlation (r(2) = 0.983, P < 0.001). SD-DIFLAC increased (P < 0.001) during haemorrhage. BE(z) for central venous blood was 2.22 +/- 4.62 mmol(-l) (P = 0.006 versus arterial base excess according to National Committee for Clinical Laboratory Standards) with strong correlation (r(2) = 0.942, P < 0.001). SD-DIFBE(z)/base excess increased (P < 0.024) during haemorrhage. CONCLUSION: Central venous blood gas analysis is a good predictor for base excess and lactate in arterial blood in steady-state conditions. However, the variation between arterial and central venous lactate increases during haemorrhage. The modification of the Van Slyke equation by Zander did not improve the agreement between central venous and arterial base excess.

Seasonal changes in 24-h and basal energy expenditures in rural Gambian men as measured in a respiration chamber.

Adaptation of 24-h energy expenditure (24-h EE) to seasonal variations in food availability was studied, by using a respiration chamber, in 18 rural Gambian men on three occasions: period 1--at the end of the rainy season, which is characterized by low food availability; period 2--during the nutritionally favorable dry season; and period 3--at the onset of the following rainy season. From periods 1 to 2 body weight increased by 2.8 +/- 0.4 kg, and a rise in 24-h EE was observed (from 8556 +/- 212 kJ/d to 9166 +/- 224 kJ/d), which was correlated to weight change (r = 0.73, P less than 0.001). During period 3, 24-h EE averaged 8740 +/- 194 kJ/d. Diet-induced thermogenesis increased significantly from periods 1 to 2 (5.9 +/- 0.5% to 8.2 +/- 0.8%) and subsequently decreased to 3.6 +/- 0.6% during period 3. In rural Gambian men, metabolic adaptations in response to seasonal changes in food availability are reflected by a decrease in body weight, mainly manifested by a loss of fat-free mass accompanied by a decreased 24-h EE and a lowered diet-induced thermogenesis.

Hundreds of variants clustered in genomic loci and biological pathways affect human height.

Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P < 0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.

Free-living energy expenditure measured by two independent techniques in pregnant and nonpregnant Gambian women.

Free-living energy expenditure (EE) was assessed in 37 young pregnant Gambian women at the 12th (n = 11, 53.5 +/- 1.7 kg), 24th (n = 14, 54.7 +/- 2.1 kg), and 36th (n = 12, 65.0 +/- 2.6 kg) wk of pregnancy and was compared with nonpregnant nonlactating (NPNL) control women (n = 12, 50.3 +/- 1.6 kg). The following two methods were used to assess EE: 1) the heart rate (HR) method using individual regression lines (HR vs EE) established at different activity levels in a respiration chamber and 2) the doubly labeled water (2H2(18)O) method in a subgroup of 25 pregnant and 7 control women. With the HR method the EE during the agricultural rainy season was found to be 2,408 +/- 87, 2,293 +/- 122, and 2,782 +/- 130 kcal/day at 12, 24, and 36 wk of gestation and were not significantly different from the control group (2,502 +/- 133 kcal/day). These findings were confirmed by the 2H2(18)O measurements, which failed to show any effect of pregnancy on EE. Expressed per unit body weight, the free-living EE was found to be lower (P less than 0.01 with 2H2(18)O method) at 36 wk of gestation than in the NPNL group. It is concluded that, in these Gambian women, energy-sparing mechanisms that contribute to meet the additional energy stress of gestation are operating during pregnancy (e.g., diminished spontaneous physical activity).

Irritability in pre-clinical Huntington's disease.

Irritability, together with depression and anxiety, form three salient clinical features of pre-symptomatic Huntington's disease (HD). To date, the understanding of irritability in HD suffers from a paucity of experimental data and is largely based on questionnaires or clinical anecdotes. Factor analysis suggests that irritability is related to impulsivity and aggression and is likely to engage the same neuronal circuits as these behaviours, including areas such as medial orbitofrontal cortex (OFC) and amygdala. 16 pre-symptomatic gene carriers (PSCs) and 15 of their companions were asked to indicate the larger of two squares consecutively shown on a screen while undergoing functional magnetic resonance imaging (fMRI). Despite correct identification of the larger square, participants were often told that they or their partner had given the wrong answer. Size differences were subtle to make negative feedback credible but detectable. Although task performance, baseline irritability, and reported task-induced irritation were the same for both groups, fMRI revealed distinct neuronal processing in those who will later develop HD. In controls but not PSCs, task-induced irritation correlated positively with amygdala activation and negatively with OFC activation. Repetitive negative feedback induced greater amygdala activations in controls than PSCs. In addition, the inverse functional coupling between amygdala and OFC was significantly weaker in PSCs compared to controls. Our results argue that normal emotion processing circuits are disrupted in PSCs via attenuated modulation of emotional status by external or internal indicators. At later stages, this dysfunction may increase the risk for developing recognised, HD-associated, psychiatric symptoms such as irritability.

A pipeline approach with spatial information for segmenting multiple sclerosis lesions on brain magnetic resonance imaging

Background: Conventional magnetic resonance imaging (MRI) techniques are highly sensitive to detect multiple sclerosis (MS) plaques, enabling a quantitative assessment of inflammatory activity and lesion load. In quantitative analyses of focal lesions, manual or semi-automated segmentations have been widely used to compute the total number of lesions and the total lesion volume. These techniques, however, are both challenging and time-consuming, being also prone to intra-observer and inter-observer variability.Aim: To develop an automated approach to segment brain tissues and MS lesions from brain MRI images. The goal is to reduce the user interaction and to provide an objective tool that eliminates the inter- and intra-observer variability.Methods: Based on the recent methods developed by Souplet et al. and de Boer et al., we propose a novel pipeline which includes the following steps: bias correction, skull stripping, atlas registration, tissue classification, and lesion segmentation. After the initial pre-processing steps, a MRI scan is automatically segmented into 4 classes: white matter (WM), grey matter (GM), cerebrospinal fluid (CSF) and partial volume. An expectation maximisation method which fits a multivariate Gaussian mixture model to T1-w, T2-w and PD-w images is used for this purpose. Based on the obtained tissue masks and using the estimated GM mean and variance, we apply an intensity threshold to the FLAIR image, which provides the lesion segmentation. With the aim of improving this initial result, spatial information coming from the neighbouring tissue labels is used to refine the final lesion segmentation.Results:The experimental evaluation was performed using real data sets of 1.5T and the corresponding ground truth annotations provided by expert radiologists. The following values were obtained: 64% of true positive (TP) fraction, 80% of false positive (FP) fraction, and an average surface distance of 7.89 mm. The results of our approach were quantitatively compared to our implementations of the works of Souplet et al. and de Boer et al., obtaining higher TP and lower FP values.Conclusion: Promising MS lesion segmentation results have been obtained in terms of TP. However, the high number of FP which is still a well-known problem of all the automated MS lesion segmentation approaches has to be improved in order to use them for the standard clinical practice. Our future work will focus on tackling this issue.

A review of atlas-based segmentation for magnetic resonance brain images.

Normal and abnormal brains can be segmented by registering the target image with an atlas. Here, an atlas is defined as the combination of an intensity image (template) and its segmented image (the atlas labels). After registering the atlas template and the target image, the atlas labels are propagated to the target image. We define this process as atlas-based segmentation. In recent years, researchers have investigated registration algorithms to match atlases to query subjects and also strategies for atlas construction. In this paper we present a review of the automated approaches for atlas-based segmentation of magnetic resonance brain images. We aim to point out the strengths and weaknesses of atlas-based methods and suggest new research directions. We use two different criteria to present the methods. First, we refer to the algorithms according to their atlas-based strategy: label propagation, multi-atlas methods, and probabilistic techniques. Subsequently, we classify the methods according to their medical target: the brain and its internal structures, tissue segmentation in healthy subjects, tissue segmentation in fetus, neonates and elderly subjects, and segmentation of damaged brains. A quantitative comparison of the results reported in the literature is also presented.

Transcription factor PROX1 induces colon cancer progression by promoting the transition from benign to highly dysplastic phenotype.

The Drosophila transcription factor Prospero functions as a tumor suppressor, and it has been suggested that the human counterpart of Prospero, PROX1, acts similarly in human cancers. However, we show here that PROX1 promotes dysplasia in colonic adenomas and colorectal cancer progression. PROX1 expression marks the transition from benign colon adenoma to carcinoma in situ, and its loss inhibits growth of human colorectal tumor xenografts and intestinal adenomas in Apc(min/+) mice, while its transgenic overexpression promotes colorectal tumorigenesis. Furthermore, in intestinal tumors PROX1 is a direct and dose-dependent target of the beta-catenin/TCF signaling pathway, responsible for the neoplastic transformation. Our data underscore the complexity of cancer pathogenesis and implicate PROX1 in malignant tumor progression through the regulation of cell polarity and adhesion.

Evidence of energy sparing in Gambian women during pregnancy: a longitudinal study using whole-body calorimetry.

Components of daily energy expenditure were measured serially by whole-body calorimetry in Gambian women before pregnancy and at 6, 12, 18, 24, 30, and 36 wk gestation. Weight gain was (mean +/- SD) 6.8 +/- 2.8 kg, fat deposition was 2.0 +/- 2.5 kg and lean tissue deposition was 5.0 +/- 2.5 kg. Basal metabolic rate (BMR) was depressed during the first 18 wk of gestation, causing total cumulative maintenance costs by week 36 to be 8.4 MJ. Individual responses to pregnancy correlated with changes in body mass (36 wk: delta BMR vs delta weight; r = 0.60, P < 0.01 delta BMR vs delta LBM; r = 0.62, P < 0.01). There was no significant increase in the cost of treadmill exercise (0% slope: F = 0.71, P = 0.64; 5% slope: F = 1.97, P = 0.10), 24-h energy expenditure (F = 0.72, P = 0.64), activity or diet-induced thermogenesis (F = 1.02, P = 0.43), during pregnancy in spite of body weight gain. Total metabolic costs over 36 wk were 144 MJ (fetus 43 MJ, fat deposition 92 MJ, cumulative maintenance costs 8.4 MJ). These were far lower than reported for well-nourished Western populations.

A whole body transportable indirect calorimeter for human use in the tropics.

A transportable, whole body indirect calorimeter, designed for use in the tropics, is described. The calorimeter was built to study energy expenditure of people having chronically or acutely low levels of food intake, and it will help to determine energy adaptations made by individuals with restricted food intake. The calorimeter comprises two units: a 27 m3 ventilated chamber connected to an office housing control and monitoring equipment. The system also allows the experimenter to assess the rate of energy expenditure by means of a ventilated hood or a baby respiration chamber. The incoming air flow rate is variable and is typically set at approximately 30 l/min. Carbon dioxide production (VCO2) and oxygen consumption (VO2) are continuously monitored by means of differential gas analysers via a computerized data acquisition unit. Gas production/consumption rates are measured with a delay of 80 s, the complete response to step changes in VCO2 or VO2 consumption being calculated over 15 min using the rate of change terms in the gas exchange equations. The total electrical power required for the whole system is 12 kW. The calorimeter has been functioning for nearly 4 years in a rural village of The Gambia during which ambient temperatures have ranged from 16 to 44 degrees C and dewpoints from -8 to 24 degrees C. The performance and accuracy of the calorimeter were tested using 20 per cent CO2 in N2 infusion and butane burning. Agreement between the theoretical and the measured values was found to be 99 per cent for VO2 and 100 per cent for VCO2 with a precision for both gases of +/- 10 ml/min over a 1-h period.

Postprandial thermogenesis in lactating and non-lactating women from The Gambia.

Postprandial thermogenesis was assessed by indirect calorimetry in 32 Gambian women classified into three groups as follows: 12 non-pregnant non-lactating and 10 lactating women studied during the dry season and 10 lactating women studied during the rainy season. The test meal consisted of a typical Gambian breakfast and its energy content corresponded to 30% of the individual's resting metabolic rate (RMR)/24 h. During the dry season, the postprandial thermogenesis of the lactating women averaged 6.0 +/- 0.4% of the test meal energy content and was similar to that observed in the non-pregnant non-lactating women studied during the same season (5.8 +/- 0.3%). In contrast, the postprandial thermogenesis of lactating women studied during the rainy, nutritionally unfavourable season was found to be significantly lower (4.9 +/- 0.5%). There was no significant difference in the pre- and postprandial respiratory quotients among groups. This leads to the conclusion that lactation does not alter the thermogenic response to food and that the reduction in postprandial thermogenesis observed in lactating women during the wet season constitutes an adaptive response to energy deficit allowing a saving of energy in periods of food restriction.

Comparative analysis of the transcriptome across distant species.

The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.

How Reliable Is Ki-67 Immunohistochemistry in Grade 2 Breast Carcinomas? A QA Study of the Swiss Working Group of Breast- and Gynecopathologists.

Adjuvant chemotherapy decisions in breast cancer are increasingly based on the pathologist's assessment of tumor proliferation. The Swiss Working Group of Gyneco- and Breast Pathologists has surveyed inter- and intraobserver consistency of Ki-67-based proliferative fraction in breast carcinomas. METHODS: Five pathologists evaluated MIB-1-labeling index (LI) in ten breast carcinomas (G1, G2, G3) by counting and eyeballing. In the same way, 15 pathologists all over Switzerland then assessed MIB-1-LI on three G2 carcinomas, in self-selected or pre-defined areas of the tumors, comparing centrally immunostained slides with slides immunostained in the different laboratoires. To study intra-observer variability, the same tumors were re-examined 4 months later. RESULTS: The Kappa values for the first series of ten carcinomas of various degrees of differentiation showed good to very good agreement for MIB-1-LI (Kappa 0.56-0.72). However, we found very high inter-observer variabilities (Kappa 0.04-0.14) in the read-outs of the G2 carcinomas. It was not possible to explain the inconsistencies exclusively by any of the following factors: (i) pathologists' divergent definitions of what counts as a positive nucleus (ii) the mode of assessment (counting vs. eyeballing), (iii) immunostaining technique, and (iv) the selection of the tumor area in which to count. Despite intensive confrontation of all participating pathologists with the problem, inter-observer agreement did not improve when the same slides were re-examined 4 months later (Kappa 0.01-0.04) and intra-observer agreement was likewise poor (Kappa 0.00-0.35). CONCLUSION: Assessment of mid-range Ki-67-LI suffers from high inter- and intra-observer variability. Oncologists should be aware of this caveat when using Ki-67-LI as a basis for treatment decisions in moderately differentiated breast carcinomas.