Mechanisms of transcription factor evolution in Metazoa.

Transcriptions factors (TFs) are pivotal for the regulation of virtually all cellular processes, including growth and development. Expansions of TF families are causally linked to increases in organismal complexity. Here we study the evolutionary dynamics, genetic causes and functional implications of the five largest metazoan TF families. We find that family expansions dominate across the whole metazoan tree; however, some branches experience exceptional family-specific accelerated expansions. Additionally, we find that such expansions are often predated by modular domain rearrangements, which spur the expansion of a new sub-family by separating it from the rest of the TF family in terms of protein-protein interactions. This separation allows for radical shifts in the functional spectrum of a duplicated TF. We also find functional differentiation inside TF sub-families as changes in expression specificity. Furthermore, accelerated family expansions are facilitated by repeats of sequence motifs such as C2H2 zinc fingers. We quantify whole genome duplications and single gene duplications as sources of TF family expansions, implying that some, but not all, TF duplicates are preferentially retained. We conclude that trans-regulatory changes (domain rearrangements) are instrumental for fundamental functional innovations, that cis-regulatory changes (affecting expression) accomplish wide-spread fine tuning and both jointly contribute to the functional diversification of TFs.

Sexual selection drives evolution and rapid turnover of male gene expression.

The profound and pervasive differences in gene expression observed between males and females, and the unique evolutionary properties of these genes in many species, have led to the widespread assumption that they are the product of sexual selection and sexual conflict. However, we still lack a clear understanding of the connection between sexual selection and transcriptional dimorphism, often termed sex-biased gene expression. Moreover, the relative contribution of sexual selection vs. drift in shaping broad patterns of expression, divergence, and polymorphism remains unknown. To assess the role of sexual selection in shaping these patterns, we assembled transcriptomes from an avian clade representing the full range of sexual dimorphism and sexual selection. We use these species to test the links between sexual selection and sex-biased gene expression evolution in a comparative framework. Through ancestral reconstruction of sex bias, we demonstrate a rapid turnover of sex bias across this clade driven by sexual selection and show it to be primarily the result of expression changes in males. We use phylogenetically controlled comparative methods to demonstrate that phenotypic measures of sexual selection predict the proportion of male-biased but not female-biased gene expression. Although male-biased genes show elevated rates of coding sequence evolution, consistent with previous reports in a range of taxa, there is no association between sexual selection and rates of coding sequence evolution, suggesting that expression changes may be more important than coding sequence in sexual selection. Taken together, our results highlight the power of sexual selection to act on gene expression differences and shape genome evolution.

Magnetic resonance fingerprinting using echo-planar imaging: Joint quantification of T1 and T2∗ relaxation times.

PURPOSE: To develop an implementation of the magnetic resonance fingerprinting (MRF) paradigm for quantitative imaging using echo-planar imaging (EPI) for simultaneous assessment of T1 and T2∗. METHODS: The proposed MRF method (MRF-EPI) is based on the acquisition of 160 gradient-spoiled EPI images with rapid, parallel-imaging accelerated, Cartesian readout and a measurement time of 10 s per slice. Contrast variation is induced using an initial inversion pulse, and varying the flip angles, echo times, and repetition times throughout the sequence. Joint quantification of T1 and T2∗ is performed using dictionary matching with integrated B1+ correction. The quantification accuracy of the method was validated in phantom scans and in vivo in 6 healthy subjects. RESULTS: Joint T1 and T2∗ parameter maps acquired with MRF-EPI in phantoms are in good agreement with reference measurements, showing deviations under 5% and 4% for T1 and T2∗, respectively. In vivo baseline images were visually free of artifacts. In vivo relaxation times are in good agreement with gold-standard techniques (deviation T1 : 4 ± 2%, T2∗: 4 ± 5%). The visual quality was comparable to the in vivo gold standard, despite substantially shortened scan times. CONCLUSION: The proposed MRF-EPI method provides fast and accurate T1 and T2∗ quantification. This approach offers a rapid supplement to the non-Cartesian MRF portfolio, with potentially increased usability and robustness. Magn Reson Med 78:1724-1733, 2017. © 2016 International Society for Magnetic Resonance in Medicine.

Motion-robust cardiac B1+ mapping at 3T using interleaved bloch-siegert shifts.

PURPOSE: To develop and evaluate a robust motion-insensitive Bloch-Siegert shift based B1+ mapping method in the heart. METHODS: Cardiac Bloch-Siegert B1+ mapping was performed with interleaved positive and negative off-resonance shifts and diastolic spoiled gradient echo imaging in 12 heartbeats. Numerical simulations were performed to study the impact of respiratory motion. The method was compared with three-dimensional (3D) actual flip angle imaging (AFI) and two-dimensional (2D) saturated double angle method (SDAM) in phantom scans. Cardiac B1+ maps of three different views were acquired in six healthy volunteers using Bloch-Siegert and SDAM during breath-hold and free breathing. In vivo maps were evaluated for inter-view consistency using the correlation coefficients of the B1+ profiles along the lines of intersection between the views. RESULTS: For the Bloch-Siegert sequence, numerical simulations indicated high similarity between breath-hold and free breathing scans, and phantom results indicated low deviation from the 3D AFI reference (normalized root mean square error [NRMSE] = 2.0%). Increased deviation was observed with 2D SDAM (NRMSE = 5.0%) due to underestimation caused by imperfect excitation slice profiles. Breath-hold and free breathing Bloch-Siegert in vivo B1+ maps were visually comparable with no significant difference in the inter-view consistency (P > 0.36). SDAM showed strongly impaired B1+ map quality during free breathing. Inter-view consistency was significantly lower than with the Bloch-Siegert method (breath-hold: P = 0.014, free breathing: P < 0.0001). CONCLUSION: The proposed interleaved Bloch-Siegert sequence enables cardiac B1+ mapping with improved inter-view consistency and high resilience to respiratory motion. Magn Reson Med 78:670-677, 2017. © 2016 International Society for Magnetic Resonance in Medicine.

Positive Selection Underlies Faster-Z Evolution of Gene Expression in Birds.

The elevated rate of evolution for genes on sex chromosomes compared with autosomes (Fast-X or Fast-Z evolution) can result either from positive selection in the heterogametic sex or from nonadaptive consequences of reduced relative effective population size. Recent work in birds suggests that Fast-Z of coding sequence is primarily due to relaxed purifying selection resulting from reduced relative effective population size. However, gene sequence and gene expression are often subject to distinct evolutionary pressures; therefore, we tested for Fast-Z in gene expression using next-generation RNA-sequencing data from multiple avian species. Similar to studies of Fast-Z in coding sequence, we recover clear signatures of Fast-Z in gene expression; however, in contrast to coding sequence, our data indicate that Fast-Z in expression is due to positive selection acting primarily in females. In the soma, where gene expression is highly correlated between the sexes, we detected Fast-Z in both sexes, although at a higher rate in females, suggesting that many positively selected expression changes in females are also expressed in males. In the gonad, where intersexual correlations in expression are much lower, we detected Fast-Z for female gene expression, but crucially, not males. This suggests that a large amount of expression variation is sex-specific in its effects within the gonad. Taken together, our results indicate that Fast-Z evolution of gene expression is the product of positive selection acting on recessive beneficial alleles in the heterogametic sex. More broadly, our analysis suggests that the adaptive potential of Z chromosome gene expression may be much greater than that of gene sequence, results which have important implications for the role of sex chromosomes in speciation and sexual selection.

N-octanoyl dopamine treatment exerts renoprotective properties in acute kidney injury but not in renal allograft recipients.

BACKGROUND: N-octanoyl dopamine (NOD) treatment improves renal function when applied to brain dead donors and in the setting of warm ischaemia-induced acute kidney injury (AKI). Because it also activates transient receptor potential vanilloid type 1 (TRPV1) channels, we first assessed if NOD conveys its renoprotective properties in warm ischaemia-induced AKI via TRPV1 and secondly, if renal transplant recipients also benefit from NOD treatment. METHODS: We induced warm renal ischaemia in Lewis, wild-type (WT) and TRPV1(-/-) Sprague-Dawley (sd) rats by clamping the left renal artery for 45 min. Transplantations were performed in allogeneic and syngeneic donor-recipient combinations (Fisher to Lewis and Lewis to Lewis) with a cold ischaemia time of 20 h. Treatment was instituted directly after restoration of organ perfusion. Renal function, histology and perfusion were assessed by serum creatinine, microscopy and magnetic resonance imaging (MRI) using arterial spin labelling (ASL). RESULTS: NOD treatment significantly improved renal function in Lewis rats after warm ischaemia-induced AKI. It was, however, not effective after prolonged cold ischaemia. The renoprotective properties of NOD were only observed in Lewis or WT, but not in TRPV1(-/-) sd rats. Renal inflammation was significantly abrogated by NOD. MRI-ASL showed a significantly lower cortical perfusion in ischaemic when compared with non-ischaemic kidneys. No overall differences were observed in renal perfusion between NOD- and NaCl-treated rats. CONCLUSIONS: NOD treatment reduces renal injury in warm ischaemia, but is not effective in renal transplant in our experimental animal models. The salutary effect of NOD appears to be TPRV1-dependent, not involving large changes in renal perfusion.

Pulsed arterial spin labelling at ultra-high field with a B 1 (+) -optimised adiabatic labelling pulse.

OBJECTIVE: Arterial spin labelling (ASL) techniques benefit from the increased signal-to-noise ratio and the longer T 1 relaxation times available at ultra-high field. Previous pulsed ASL studies at 7 T concentrated on the superior regions of the brain because of the larger transmit radiofrequency inhomogeneity experienced at ultra-high field that hinders an adequate inversion of the blood bolus when labelling in the neck. Recently, researchers have proposed to overcome this problem with either the use of dielectric pads, through dedicated transmit labelling coils, or special adiabatic inversion pulses. MATERIALS AND METHODS: We investigate the performance of an optimised time-resampled frequency-offset corrected inversion (TR-FOCI) pulse designed to cause inversion at much lower peak B 1 (+) . In combination with a PICORE labelling, the perfusion signal obtained with this pulse is compared against that obtained with a FOCI pulse, with and without dielectric pads. RESULTS: Mean grey matter perfusion with the TR-FOCI was 52.5 ± 10.3 mL/100 g/min, being significantly higher than the 34.6 ± 2.6 mL/100 g/min obtained with the FOCI pulse. No significant effect of the dielectric pads was observed. CONCLUSION: The usage of the B 1 (+) -optimised TR-FOCI pulse results in a significantly higher perfusion signal. PICORE-ASL is feasible at ultra-high field with no changes to operating conditions.

Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution.

Higher rates of coding sequence evolution have been observed on the Z chromosome relative to the autosomes across a wide range of species. However, despite a considerable body of theory, we lack empirical evidence explaining variation in the strength of the Faster-Z Effect. To assess the magnitude and drivers of Faster-Z Evolution, we assembled six de novo transcriptomes, spanning 90 million years of avian evolution. Our analysis combines expression, sequence and polymorphism data with measures of sperm competition and promiscuity. In doing so, we present the first empirical evidence demonstrating the positive relationship between Faster-Z Effect and measures of promiscuity, and therefore variance in male mating success. Our results from multiple lines of evidence indicate that selection is less effective on the Z chromosome, particularly in promiscuous species, and that Faster-Z Evolution in birds is due primarily to genetic drift. Our results reveal the power of mating system and sexual selection in shaping broad patterns in genome evolution.

The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle.

Leaf-cutter ants are one of the most important herbivorous insects in the Neotropics, harvesting vast quantities of fresh leaf material. The ants use leaves to cultivate a fungus that serves as the colony's primary food source. This obligate ant-fungus mutualism is one of the few occurrences of farming by non-humans and likely facilitated the formation of their massive colonies. Mature leaf-cutter ant colonies contain millions of workers ranging in size from small garden tenders to large soldiers, resulting in one of the most complex polymorphic caste systems within ants. To begin uncovering the genomic underpinnings of this system, we sequenced the genome of Atta cephalotes using 454 pyrosequencing. One prediction from this ant's lifestyle is that it has undergone genetic modifications that reflect its obligate dependence on the fungus for nutrients. Analysis of this genome sequence is consistent with this hypothesis, as we find evidence for reductions in genes related to nutrient acquisition. These include extensive reductions in serine proteases (which are likely unnecessary because proteolysis is not a primary mechanism used to process nutrients obtained from the fungus), a loss of genes involved in arginine biosynthesis (suggesting that this amino acid is obtained from the fungus), and the absence of a hexamerin (which sequesters amino acids during larval development in other insects). Following recent reports of genome sequences from other insects that engage in symbioses with beneficial microbes, the A. cephalotes genome provides new insights into the symbiotic lifestyle of this ant and advances our understanding of host-microbe symbioses.

Deep Learning-based detection of psychiatric attributes from German mental health records.

BACKGROUND: Health care records provide large amounts of data with real-world and longitudinal aspects, which is advantageous for predictive analyses and improvements in personalized medicine. Text-based records are a main source of information in mental health. Therefore, application of text mining to the electronic health records - especially mental state examination - is a key approach for detection of psychiatric disease phenotypes that relate to treatment outcomes. METHODS: We focused on the mental state examination (MSE) in the patients' discharge summaries as the key part of the psychiatric records. We prepared a sample of 150 text documents that we manually annotated for psychiatric attributes and symptoms. These documents were further divided into training and test sets. We designed and implemented a system to detect the psychiatric attributes automatically and linked the pathologically assessed attributes to AMDP terminology. This workflow uses a pre-trained neural network model, which is fine-tuned on the training set, and validated on the independent test set. Furthermore, a traditional NLP and rule-based component linked the recognized mentions to AMDP terminology. In a further step, we applied the system on a larger clinical dataset of 510 patients to extract their symptoms. RESULTS: The system identified the psychiatric attributes as well as their assessment (normal and pathological) and linked these entities to the AMDP terminology with an F1-score of 86% and 91% on an independent test set, respectively. CONCLUSION: The development of the current text mining system and the results highlight the feasibility of text mining methods applied to MSE in electronic mental health care reports. Our findings pave the way for the secondary use of routine data in the field of mental health, facilitating further clinical data analyses.

[The Emergence of Genetic Prenatal Diagnosis from Environmental Research : On a Methodological Shift in Prevention Around 1970]. / Wie aus Umweltforschung die genetische Pränataldiagnostik entstand : Über eine Methodenverschiebung in der Vorsorge um 1970.

The history of genetic prenatal diagnosis has so far been analyzed as a part of the history of human genetics and its reorientation as a clinical and laboratory-based scientific discipline in the second half of the 20th century. Based on new source material, we show in this paper that the interest in prenatal diagnosis also arose within the context of research on mutagenicity (the capacity to induce mutations) that was concerned with environmental dangers to human health. Our analysis of the debates around the establishment of the German Research Foundation's (DFG) research program "Prenatal Diagnosis of Genetic Defects" reveals that amniocentesis was introduced in Western Germany by a group of scientists working on the dangers for the human organism caused by radiation, pharmaceuticals, and other substances and consumer goods. We argue that, in a period of growing environmental concern, the support of prenatal diagnosis aimed to close a perceived gap in the prevention of environmental mutagenicity, i. e. genetic anomalies induced by environmental factors. The expected financing of prenatal diagnosis by health insurance in the course of the reform of abortion rights was used as another argument for the new technology's introduction as a "defensive measure". Only in a second step did changes in research structures, but most importantly experience from gynecological practice lead to a reframing of the technology as a tool for the diagnosis and prevention of mostly genetic or spontaneously occurring anomalies. Eventually, prenatal diagnosis, as it became routinely used in Western Germany from the early 1980s onward, had little to do with "environmental" questions. This case study of the early history of genetic prenatal diagnosis analyzes the still poorly researched relationship between research in human genetics, environmental research and medical practice. Furthermore, we aim to shed new light on a shift in perspective in prevention around 1970 that has so far been described in different contexts.

Quantitative arterial spin labelling perfusion measurements in rat models of renal transplantation and acute kidney injury at 3T.

OBJECTIVES: To employ ASL for the measurement of renal cortical perfusion in particular renal disorders typically associated with graft loss and to investigate its potential to detect and differentiate the related functional deterioration i.e., in a setting of acute kidney injury (AKI) as well as in renal grafts showing acute and chronic transplant rejection. MATERIALS AND METHODS: 14 Lewis rats with unilateral ischaemic AKI and 43 Lewis rats with renal grafts showing acute or chronic rejections were used. All ASL measurements in this study were performed on a 3T MR scanner using a FAIR True-FISP approach to assess renal blood flow (RBF). Perfusion maps were calculated and the cortical blood flow was determined using a region-of-interest based analysis. RBF of healthy and AKI kidneys as well as of both rejection models, were compared. In a subsample of 20 rats, creatinine clearance was measured and correlated with cortical perfusion. RESULTS: RBF differs significantly between healthy and AKI kidneys (P<0.001) with a mean difference of 213±80ml/100g/min. Renal grafts with chronic rejections show a significantly higher (P<0.001) mean cortical perfusion (346±112ml/100g/min) than grafts with acute rejection (240±66ml/100g/min). Both transplantation models have a significantly (P<0.001) lower perfusion than healthy kidneys. Renal creatinine clearance is significantly correlated (R=0.85, P<0.001) with cortical blood flow. CONCLUSION: Perfusion measurements with ASL have the potential to become a valuable diagnostic tool, regarding the detection of renal impairment and the differentiation of disorders that lead to a loss of renal function and that are typically associated with graft loss.

Cerebral Perfusion After Repair of Congenital Diaphragmatic Hernia with Common Carotid Artery Occlusion After ECMO Therapy.

AIM: To prospectively evaluate cerebral perfusion after repair of congenital diaphragmatic hernia (CDH) and right-common-carotid-artery (rCCA) occlusion after extracorporeal membrane oxygenation (ECMO) therapy. PATIENTS AND METHODS: A total of 29 2-year-old-children with a history of CDH repair underwent cerebral magnetic resonance perfusion imaging. In 14 patients, the rCCA was occluded after ECMO therapy. Fifteen patients with CDH without ECMO served as controls. Regional cerebral-blood-flow (rCBF) was measured cortically and subcortically in both hemispheres and compared intra-individually and between both groups. RESULTS: Patients with rCCA-occlusion showed intra-individual side differences between hemispheres, with significantly lower subcortical perfusion of the right hemisphere and reduced cortical perfusion. In one-third of patients with rCCA-occlusion, rCBF of the right-hemisphere was reduced by more than 20% when compared to the left hemisphere. Despite intra-individual side differences, mean rCBF in patients with rCCA occlusion was not reduced compared to controls. CONCLUSION: Beside intra-individual side differences, overall right hemisphere perfusion is sufficient after rCCA-occlusion due to collateral blood supply.

Compensation of Dosage-Sensitive Genes on the Chicken Z Chromosome.

In many diploid species, sex determination is linked to a pair of sex chromosomes that evolved from a pair of autosomes. In these organisms, the degeneration of the sex-limited Y or W chromosome causes a reduction in gene dose in the heterogametic sex for X- or Z-linked genes. Variations in gene dose are detrimental for large chromosomal regions when they span dosage-sensitive genes, and many organisms were thought to evolve complete mechanisms of dosage compensation to mitigate this. However, the recent realization that a wide variety of organisms lack complete mechanisms of sex chromosome dosage compensation has presented a perplexing question: How do organisms with incomplete dosage compensation avoid deleterious effects of gene dose differences between the sexes? Here we use expression data from the chicken (Gallus gallus) to show that ohnologs, duplicated genes known to be dosage-sensitive, are preferentially dosage-compensated on the chicken Z chromosome. Our results indicate that even in the absence of a complete and chromosome wide dosage compensation mechanism, dosage-sensitive genes are effectively dosage compensated on the Z chromosome.

Phylogenetic Analysis Supports a Link between DUF1220 Domain Number and Primate Brain Expansion.

The expansion of DUF1220 domain copy number during human evolution is a dramatic example of rapid and repeated domain duplication. Although patterns of expression, homology, and disease associations suggest a role in cortical development, this hypothesis has not been robustly tested using phylogenetic methods. Here, we estimate DUF1220 domain counts across 12 primate genomes using a nucleotide Hidden Markov Model. We then test a series of hypotheses designed to examine the potential evolutionary significance of DUF1220 copy number expansion. Our results suggest a robust association with brain size, and more specifically neocortex volume. In contradiction to previous hypotheses, we find a strong association with postnatal brain development but not with prenatal brain development. Our results provide further evidence of a conserved association between specific loci and brain size across primates, suggesting that human brain evolution may have occurred through a continuation of existing processes.

Deficit of mitonuclear genes on the human X chromosome predates sex chromosome formation.

Two taxa studied to date, the therian mammals and Caenorhabditis elegans, display underrepresentations of mitonuclear genes (mt-N genes, nuclear genes whose products are imported to and act within the mitochondria) on their X chromosomes. This pattern has been interpreted as the result of sexual conflict driving mt-N genes off of the X chromosome. However, studies in several other species have failed to detect a convergent biased distribution of sex-linked mt-N genes, leading to questions over the generality of the role of sexual conflict in shaping the distribution of mt-N genes. Here we tested whether mt-N genes moved off of the therian X chromosome following sex chromosome formation, consistent with the role of sexual conflict, or whether the paucity of mt-N genes on the therian X is a chance result of an underrepresentation on the ancestral regions that formed the X chromosome. We used a synteny-based approach to identify the ancestral regions in the platypus and chicken genomes that later formed the therian X chromosome. We then quantified the movement of mt-N genes on and off of the X chromosome and the distribution of mt-N genes on the human X and ancestral X regions. We failed to find an excess of mt-N gene movement off of the X. The bias of mt-N genes on ancestral therian X chromosomes was also not significantly different from the biases on the human X. Together our results suggest that, rather than conflict driving mt-N genes off of the mammalian X, random biases on chromosomes that formed the X chromosome could explain the paucity of mt-N genes in the therian lineage.

Conservation of Regional Variation in Sex-Specific Sex Chromosome Regulation.

Regional variation in sex-specific gene regulation has been observed across sex chromosomes in a range of animals and is often a function of sex chromosome age. The avian Z chromosome exhibits substantial regional variation in sex-specific regulation, where older regions show elevated levels of male-biased expression. Distinct sex-specific regulation also has been observed across the male hypermethylated (MHM) region, which has been suggested to be a region of nascent dosage compensation. Intriguingly, MHM region regulatory features have not been observed in distantly related avian species despite the hypothesis that it is situated within the oldest region of the avian Z chromosome and is therefore orthologous across most birds. This situation contrasts with the conservation of other aspects of regional variation in gene expression observed on the avian sex chromosomes but could be the result of sampling bias. We sampled taxa across the Galloanserae, an avian clade spanning 90 million years, to test whether regional variation in sex-specific gene regulation across the Z chromosome is conserved. We show that the MHM region is conserved across a large portion of the avian phylogeny, together with other sex-specific regulatory features of the avian Z chromosome. Our results from multiple lines of evidence suggest that the sex-specific expression pattern of the MHM region is not consistent with nascent dosage compensation.

Functional imaging of acute kidney injury at 3 Tesla: investigating multiple parameters using DCE-MRI and a two-compartment filtration model.

OBJECT: To investigate how MR-based parameters reflect functional changes in kidneys with acute kidney injury (AKI) using dynamic contrast enhanced MRI and a two-compartment renal filtration model. MATERIALS AND METHODS: MRI data of eight male Lewis rats were analyzed retrospectively. Five animals were subjected to AKI, three native rats served as control. All animals underwent perfusion imaging by dynamic contrast-enhanced MRI. Renal blood volume, glomerular filtration rate (GFR) as well as plasma and tubular mean transit times were estimated from regions-of-interest drawn in the renal cortex. Differences between healthy kidneys and kidneys subjected to AKI were analyzed using a paired t-test. RESULTS: Significant differences between ischemic and healthy kidneys could only be detected for the glomerular filtration rate. For all other calculated parameters, differences were present, however not significant. In rats with AKI, average single kidney GFR was 0.66 ± 0.37 ml/min for contralateral and 0.26 ± 0.12 ml/ min for diseased kidneys (P = 0.0254). For the healthy control group, the average GFR was 0.39 ± 0.06 ml/min and 0.41 ± 0.11 ml/min, respectively. Differences between diseased kidneys of AKI rats and ipsilateral kidneys of the healthy control group were significant (P = 0.0381). CONCLUSION: Significant differences of functional parameters reflecting damage of the renal tissue of kidneys with AKI compared to the contralateral, healthy kidneys could only be detected by GFR. GFR might be a useful parameter that allows for a spatially resolved detection of abnormal changes of renal tissue by AKI.

The potential role of sexual conflict and sexual selection in shaping the genomic distribution of Mito-nuclear genes.

Mitochondrial interactions with the nuclear genome represent one of life's most important co-evolved mutualisms. In many organisms, mitochondria are maternally inherited, and in these cases, co-transmission between the mitochondrial and nuclear genes differs across different parts of the nuclear genome, with genes on the X chromosome having two-third probability of co-transmission, compared with one-half for genes on autosomes. These asymmetrical inheritance patterns of mitochondria and different parts of the nuclear genome have the potential to put certain gene combinations in inter-genomic co-adaptation or conflict. Previous work in mammals found strong evidence that the X chromosome has a dearth of genes that interact with the mitochondria (mito-nuclear genes), suggesting that inter-genomic conflict might drive genes off the X onto the autosomes for their male-beneficial effects. Here, we developed this idea to test coadaptation and conflict between mito-nuclear gene combinations across phylogenetically independent sex chromosomes on a far broader scale. We found that, in addition to therian mammals, only Caenorhabditis elegans showed an under-representation of mito-nuclear genes on the sex chromosomes. The remaining species studied showed no overall bias in their distribution of mito-nuclear genes. We discuss possible factors other than inter-genomic conflict that might drive the genomic distribution of mito-nuclear genes.

Renal perfusion in acute kidney injury with DCE-MRI: deconvolution analysis versus two-compartment filtration model.

PURPOSE: To investigate the results of different pharmacokinetic models of a quantitative analysis of renal blood flow (RBF) in acute kidney injury using deconvolution analysis and a two-compartment renal filtration model. MATERIALS AND METHODS: MRI data of ten male Lewis rats were analyzed retrospectively. Six animals were subjected to unilateral acute kidney injury and underwent perfusion imaging by dynamic contrast-enhanced MRI (DCE-MRI). Renal blood flow was estimated from regions-of-interest depicting the cortex in the DCE-MRI perfusion maps. The perfusion models were compared by a paired t-test and Bland-Altman plots. RESULTS: No significant difference was found between the two compartment model and the deconvolution analysis (P=0.2807). Differences between healthy and diseased kidney in the AKI model were significant for both methods (P<0.05). A Bland-Altman plot showed no systematic errors, and values were equally distributed around the mean difference between the methods lying within the range of 1.96 standard deviations. CONCLUSION: Both quantification strategies could detect the kidneys that were impaired by AKI. When just aiming at RBF as a marker, a deconvolution analysis can provide similar values as the 2CFM. If functional parameters beyond RBF like glomerular filtration rate are needed, the 2CFM should be employed.