A key challenge in genetics is identifying the functional roles of genes in pathways. Numerous functional genomics techniques (e.g. machine learning) that predict protein function have been developed to address this question. These methods generally build from existing annotations of genes to pathways and thus are often unable to identify additional genes participating in processes that are not already well studied. Many of these processes are well studied in some organism, but not necessarily in an investigator's organism of interest. Sequence-based search methods (e.g. BLAST) have been used to transfer such annotation information between organisms. We demonstrate that functional genomics can complement traditional sequence similarity to improve the transfer of gene annotations between organisms. Our method transfers annotations only when functionally appropriate as determined by genomic data and can be used with any prediction algorithm to combine transferred gene function knowledge with organism-specific high-throughput data to enable accurate function prediction.
We show that diverse state-of-art machine learning algorithms leveraging functional knowledge transfer (FKT) dramatically improve their accuracy in predicting gene-pathway membership, particularly for processes with little experimental knowledge in an organism. We also show that our method compares favorably to annotation transfer by sequence similarity. Next, we deploy FKT with state-of-the-art SVM classifier to predict novel genes to 11,000 biological processes across six diverse organisms and expand the coverage of accurate function predictions to processes that are often ignored because of a dearth of annotated genes in an organism. Finally, we perform in vivo experimental investigation in Danio rerio and confirm the regulatory role of our top predicted novel gene, wnt5b, in leftward cell migration during heart development. FKT is immediately applicable to many bioinformatics techniques and will help biologists systematically integrate prior knowledge from diverse systems to direct targeted experiments in their organism of study.
Due to technical and ethical challenges many human diseases or biological processes are studied in model organisms. Discoveries in these organisms are then transferred back to human or other model organisms. Traditional methods for transferring novel gene function annotations have relied on finding genes with high sequence similarity believed to share evolutionary ancestry. However, sequence similarity does not guarantee a shared functional role in molecular pathways. In this study, we show that functional genomics can complement traditional sequence similarity measures to improve the transfer of gene annotations between organisms. We coupled our knowledge transfer method with current state-of-the-art machine learning algorithms and predicted gene function for 11,000 biological processes across six organisms. We experimentally validated our prediction of wnt5b's involvement in the determination of left-right heart asymmetry in zebrafish. Our results show that functional knowledge transfer can improve the coverage and accuracy of machine learning methods used for gene function prediction in a diverse set of organisms. Such an approach can be applied to additional organisms, and will be especially beneficial in organisms that have high-throughput genomic data with sparse annotations.
Integrated analyses of functional genomics data have enormous potential for identifying phenotype-associated genes. Tissue-specificity is an important aspect of many genetic diseases, reflecting the potentially different roles of proteins and pathways in diverse cell lineages. Accounting for tissue specificity in global integration of functional genomics data is challenging, as “functionality” and “functional relationships” are often not resolved for specific tissue types. We address this challenge by generating tissue-specific functional networks, which can effectively represent the diversity of protein function for more accurate identification of phenotype-associated genes in the laboratory mouse. Specifically, we created 107 tissue-specific functional relationship networks through integration of genomic data utilizing knowledge of tissue-specific gene expression patterns. Cross-network comparison revealed significantly changed genes enriched for functions related to specific tissue development. We then utilized these tissue-specific networks to predict genes associated with different phenotypes. Our results demonstrate that prediction performance is significantly improved through using the tissue-specific networks as compared to the global functional network. We used a testis-specific functional relationship network to predict genes associated with male fertility and spermatogenesis phenotypes, and experimentally confirmed one top prediction, Mbyl1. We then focused on a less-common genetic disease, ataxia, and identified candidates uniquely predicted by the cerebellum network, which are supported by both literature and experimental evidence. Our systems-level, tissue-specific scheme advances over traditional global integration and analyses and establishes a prototype to address the tissue-specific effects of genetic perturbations, diseases and drugs.
Tissue specificity is an important aspect of many genetic diseases, reflecting the potentially different roles of proteins and pathways in diverse cell lineages. We propose an effective strategy to model tissue-specific functional relationship networks in the laboratory mouse. We integrated large scale genomics datasets as well as low-throughput tissue-specific expression profiles to estimate the probability that two proteins are co-functioning in the tissue under study. These networks can accurately reflect the diversity of protein functions across different organs and tissue compartments. By computationally exploring the tissue-specific networks, we can accurately predict novel phenotype-related gene candidates. We experimentally confirmed a top candidate gene, Mybl1, to affect several male fertility phenotypes, predicted based on male-reproductive system-specific networks and we predicted candidates related to a rare genetic disease ataxia, which are supported by experimental and literature evidence. The above results demonstrate the power of modeling tissue-specific dynamics of co-functionality through computational approaches.
A major goal in the study of motor learning is to improve the extent to which subjects adapt their movements in response to errors. Recent attention has focused on the gradual-adaptation paradigm, in which an adaptive stimulus is introduced incrementally, rather than all at once as in conventional adaptation paradigms. However, there is disagreement – even among studies involving the same sensorimotor-learning task – as to the robustness of this approach. In particular, although all studies confirm that retention of learning is improved, not all agree that exposure to a gradual-adaptation paradigm can improve the extent of adaptation that takes place. Also, the paradigm has not previously been studied with saccadic eye movements, which are unique in that they typically lack online error feedback during each movement. To determine the effectiveness of gradual adaptation in this system, we compared saccadic adaptation performed with gradual and conventional adaptation paradigms. We find evidence consistent with more robust adaptation – in the sense of greater extent of adaptation as well as greater retention of learning (larger aftereffects) – in response to a gradual adaptation stimulus. The results suggest the need to develop alternative models of motor learning, as current error-based modeling efforts are unable to account for the increased extent of adaptation when subjects are only exposed to the full adaptive stimulus for a brief time.
gradual adaptation; saccades; motor learning
Integrative multi-species prediction (IMP) is an interactive web server that enables molecular biologists to interpret experimental results and to generate hypotheses in the context of a large cross-organism compendium of functional predictions and networks. The system provides a framework for biologists to analyze their candidate gene sets in the context of functional networks, as they expand or focus these sets by mining functional relationships predicted from integrated high-throughput data. IMP integrates prior knowledge and data collections from multiple organisms in its analyses. Through flexible and interactive visualizations, researchers can compare functional contexts and interpret the behavior of their gene sets across organisms. Additionally, IMP identifies homologs with conserved functional roles for knowledge transfer, allowing for accurate function predictions even for biological processes that have very few experimental annotations in a given organism. IMP currently supports seven organisms (Homo sapiens, Mus musculus, Rattus novegicus, Drosophila melanogaster, Danio rerio, Caenorhabditis elegans and Saccharomyces cerevisiae), does not require any registration or installation and is freely available for use at http://imp.princeton.edu.
The maintenance of movement accuracy uses prior performance errors to correct future motor plans; this motor-learning process ensures that movements remain quick and accurate. The control of predictive saccades, in which anticipatory movements are made to future targets before visual stimulus information becomes available, serves as an ideal paradigm to analyze how the motor system utilizes prior errors to drive movements to a desired goal. Predictive saccades constitute a stationary process (the mean and to a rough approximation the variability of the data do not vary over time, unlike a typical motor adaptation paradigm). This enables us to study inter-trial correlations, both on a trial-by-trial basis and across long blocks of trials. Saccade errors are found to be corrected on a trial-by-trial basis in a direction-specific manner (the next saccade made in the same direction will reflect a correction for errors made on the current saccade). Additionally, there is evidence for a second, modulating process that exhibits long memory. That is, performance information, as measured via inter-trial correlations, is strongly retained across a large number of saccades (about 100 trials). Together, this evidence indicates that the dynamics of motor learning exhibit complexities that must be carefully considered, as they cannot be fully described with current state-space (ARMA) modeling efforts.
Musladin-Lueke Syndrome (MLS) is a hereditary disorder affecting Beagle dogs that manifests with extensive fibrosis of the skin and joints. In this respect, it resembles human stiff skin syndrome and the Tight skin mouse, each of which is caused by gene defects affecting fibrillin-1, a major component of tissue microfibrils. The objective of this work was to determine the genetic basis of MLS and the molecular consequence of the identified mutation.
Methodology and Principal Findings
We mapped the locus for MLS by genome-wide association to a 3.05 Mb haplotype on canine chromosome 9 (CFA9 (50.11–54.26; praw <10−7)), which was homozygous and identical-by-descent among all affected dogs, consistent with recessive inheritance of a founder mutation. Sequence analysis of a candidate gene at this locus, ADAMTSL2, which is responsible for the human TGFβ dysregulation syndrome, Geleophysic Dysplasia (GD), uncovered a mutation in exon 7 (c.660C>T; p.R221C) perfectly associated with MLS (p-value = 10−12). Murine ADAMTSL2 containing the p.R221C mutation formed anomalous disulfide-bonded dimers when transiently expressed in COS-1, HEK293F and CHO cells, and was present in the medium of these cells at lower levels than wild-type ADAMTSL2 expressed in parallel.
The genetic basis of MLS is a founder mutation in ADAMTSL2, previously shown to interact with latent TGF-β binding protein, which binds fibrillin-1. The molecular effect of the founder mutation on ADAMTSL2 is formation of disulfide-bonded dimers. Although caused by a distinct mutation, and having a milder phenotype than human GD, MLS nevertheless offers a new animal model for study of GD, and for prospective insights on mechanisms and pathways of skin fibrosis and joint contractures.
Saccadic eye movements rapidly orient the line of sight towards the object of interest. Pre-motor burst neurons (BNs) controlling saccades receive excitation from superior colliculus and cerebellum, but inhibition by omnipause neurons (OPNs) prevents saccades. When the OPNs pause, BNs begin to fire. It has been presumed that part of the BN burst comes from post-inhibitory rebound (PIR). We hypothesized that in the absence of prior inhibition from OPNs there would be no PIR, and thus the increase in initial firing rate of BNs would be reduced. Consequently, saccade acceleration would be reduced. We measured eye movements and showed that sustained eye closure, which inhibits the activity of OPNs and thus hypothetically should weaken PIR, reduced the peak velocity, acceleration, and deceleration of saccades in healthy human subjects. Saccades under closed eyelids also had irregular trajectories; the frequency of the oscillations underlying this irregularity was similar to that of high-frequency ocular flutter (back-to-back saccades) often seen in normal subjects during attempted fixation at straight ahead while eyes are closed. Saccades and quick phases of nystagmus are generated by the same pre-motor neurons, and we found that the quick-phase velocity of nystagmus was also reduced by lid closure. These changes were not due to a mechanical hindrance to the eyes, because lid closure did not affect the peak velocities or accelerations of the eyes in the “slow-phase” response to rapid head movements of comparable speeds to those of saccades. These results indicate a role for OPNs in generating the abrupt onset and high velocities of saccades. We hypothesize that the mechanism involved is PIR in pre-motor burst neurons.
Omnipause neurons; Burst neurons; Oscillations; Ballistic movement; Post-inhibitory rebound
Coat color and type are essential characteristics of domestic dog breeds. Although the genetic basis of coat color has been well characterized, relatively little is known about the genes influencing coat growth pattern, length, and curl. We performed genome-wide association studies of more than 1000 dogs from 80 domestic breeds to identify genes associated with canine fur phenotypes. Taking advantage of both inter- and intrabreed variability, we identified distinct mutations in three genes, RSPO2, FGF5, and KRT71 (encoding R-spondin–2, fibroblast growth factor–5, and keratin-71, respectively), that together account for most coat phenotypes in purebred dogs in the United States. Thus, an array of varied and seemingly complex phenotypes can be reduced to the combinatorial effects of only a few genes.
AMPK (AMP-activated protein kinase) is a heterotrimetric enzyme that is expressed in many tissues, including the heart and vasculature, and plays a central role in the regulation of energy homoeostasis. It is activated in response to stresses that lead to an increase in the cellular AMP/ATP ratio caused either by inhibition of ATP production (i.e. anoxia or ischaemia) or by accelerating ATP consumption (i.e. muscle contraction or fasting). In the heart, AMPK activity increases during ischaemia and functions to sustain ATP, cardiac function and myocardial viability. There is increasing evidence that AMPK is implicated in the pathophysiology of cardiovascular and metabolic diseases. A principle mode of AMPK activation is phosphorylation by upstream kinases [e.g. LKB1 and CaMK (Ca2+/calmodulin-dependent protein kinase], which leads to direct effects on tissues and phosphorylation of various downstream kinases [e.g. eEF2 (eukaryotic elongation factor 2) kinase and p70 S6 kinase]. These upstream and downstream kinases of AMPK have fundamental roles in glucose metabolism, fatty acid oxidation, protein synthesis and tumour suppression; consequently, they have been implicated in cardiac ischaemia, arrhythmias and hypertrophy. Recent mechanistic studies have shown that AMPK has an important role in the mechanism of action of MF (metformin), TDZs (thiazolinediones) and statins. Increased understanding of the beneficial effects of AMPK activation provides the rationale for targeting AMPK in the development of new therapeutic strategies for cardiometabolic disease.
5-amino-4-imidazolecarboxamide riboside-1-β-D-ribofuranoside (AICAR); AMP-activated protein kinase (AMPK); cardiovascular disease; insulin resistance; metformin; obesity; ACC, acetyl-CoA carboxylase; AICAR, 5-amino-4-imidazolecarboxamide riboside-1-β-D-ribofuranoside; AMPK, AMP-activated protein kinase; CaMK, Ca2+/calmodulin-dependent protein kinase; CPT-1, carnitine palmitoyltransferase-1; CVD, cardiovascular disease; eEF2, eukaryotic elongation factor 2; eNOS, endothelial NO synthase; GLUT-4, glucose transporter-4; HF, heart failure; CHF, chronic HF; HMG-CoA, 3-hydroxy-3-methyl-CoA; IL-6, interleukin-6; LV, left ventricular; MF, metformin; MI, myocardial infarction; MO25, mouse protein 25; mTOR, mammalian target of rapamycin; NEFA, non-esterified fatty acid (‘free fatty acid’); p70RSK, p70 ribosomal protein S6 kinase; PDH, pyruvate dehydrogenase; PFK-2, phosphofructokinase-2; PPAR-γ, peroxisome-proliferator-activated receptor-γ; PROactive, PROspective pioglitAzone Clinical Trial In macroVascular Events; STRAD, Ste20-related adaptor; TNF-α, tumour necrosis factor-α; TZD, thiazolinedione
Coronary artery spasm is common during percutaneous coronary intervention and is easily relieved by intracoronary administration of vasodilators. We report the case of a patient who had severe, protracted, generalized spasm of the entire left coronary artery system during coronary artery stenting. The spasm, which was unresponsive to intracoronary vasodilators administered via guiding catheter, resulted in pulmonary edema and cardiogenic shock. Local injection of nitroglycerin via a transit catheter in the coronary artery eventually resolved the spasm and reversed the cardiogenic shock. To our knowledge, this is the 1st report of such a case in the English-language medical literature.
Angina pectoris/etiology; angioplasty, percutaneous coronary/adverse effects; cardiogenic shock; coronary vasospasm; coronary stenting; heart catheterization/adverse effects; nitroglycerin/therapeutic use; vasoconstriction
Coronary artery bypass grafting in patients with porcelain aorta and calcified great vessels is associated with a high risk of systemic embolism. Various techniques have been suggested to minimize that risk. We describe the case of a patient with left main coronary disease and a severely calcified ascending aorta, who could not undergo cardiopulmonary bypass. To the best of our knowledge, this is the 1st reported use of a congenital coronary–pulmonary arteriovenous fistula as a proximal anastomotic site for saphenous vein grafts, to achieve optimal revascularization in a patient with porcelain aorta. (Tex Heart Inst J 2003;30:143–5)
Aorta, thoracic; cerebrovascular disorders/prevention & control; fistula; intraoperative complications; saphenous vein/transplantation