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1.  High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus 
BMC Genomics  2015;16(1):24.
Background
QTL cloning for the discovery of genes underlying polygenic traits has historically been cumbersome in long-lived perennial plants like Populus. Linkage disequilibrium-based association mapping has been proposed as a cloning tool, and recent advances in high-throughput genotyping and whole-genome resequencing enable marker saturation to levels sufficient for association mapping with no a priori candidate gene selection. Here, multiyear and multienvironment evaluation of cell wall phenotypes was conducted in an interspecific P. trichocarpa x P. deltoides pseudo-backcross mapping pedigree and two partially overlapping populations of unrelated P. trichocarpa genotypes using pyrolysis molecular beam mass spectrometry, saccharification, and/ or traditional wet chemistry. QTL mapping was conducted using a high-density genetic map with 3,568 SNP markers. As a fine-mapping approach, chromosome-wide association mapping targeting a QTL hot-spot on linkage group XIV was performed in the two P. trichocarpa populations. Both populations were genotyped using the 34 K Populus Infinium SNP array and whole-genome resequencing of one of the populations facilitated marker-saturation of candidate intervals for gene identification.
Results
Five QTLs ranging in size from 0.6 to 1.8 Mb were mapped on linkage group XIV for lignin content, syringyl to guaiacyl (S/G) ratio, 5- and 6-carbon sugars using the mapping pedigree. Six candidate loci exhibiting significant associations with phenotypes were identified within QTL intervals. These associations were reproducible across multiple environments, two independent genotyping platforms, and different plant growth stages. cDNA sequencing for allelic variants of three of the six loci identified polymorphisms leading to variable length poly glutamine (PolyQ) stretch in a transcription factor annotated as an ANGUSTIFOLIA C-terminus Binding Protein (CtBP) and premature stop codons in a KANADI transcription factor as well as a protein kinase. Results from protoplast transient expression assays suggested that each of the polymorphisms conferred allelic differences in the activation of cellulose, hemicelluloses, and lignin pathway marker genes.
Conclusion
This study illustrates the utility of complementary QTL and association mapping as tools for gene discovery with no a priori candidate gene selection. This proof of concept in a perennial organism opens up opportunities for discovery of novel genetic determinants of economically important but complex traits in plants.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1215-z) contains supplementary material, which is available to authorized users.
doi:10.1186/s12864-015-1215-z
PMCID: PMC4307895  PMID: 25613058
QTL cloning; Association genetics; Cell wall recalcitrance; Lignin; Cellulose; Hemicellulose
2.  Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production 
Genome Biology and Evolution  2014;6(9):2557-2566.
Lignocellulosic plant material is a viable source of biomass to produce alternative energy including ethanol and other biofuels. However, several factors—including toxic byproducts from biomass pretreatment and poor fermentation of xylose and other pentose sugars—currently limit the efficiency of microbial biofuel production. To begin to understand the genetic basis of desirable traits, we characterized three strains of Saccharomyces cerevisiae with robust growth in a pretreated lignocellulosic hydrolysate or tolerance to stress conditions relevant to industrial biofuel production, through genome and transcriptome sequencing analysis. All stress resistant strains were highly mosaic, suggesting that genetic admixture may contribute to novel allele combinations underlying these phenotypes. Strain-specific gene sets not found in the lab strain were functionally linked to the tolerances of particular strains. Furthermore, genes with signatures of evolutionary selection were enriched for functional categories important for stress resistance and included stress-responsive signaling factors. Comparison of the strains’ transcriptomic responses to heat and ethanol treatment—two stresses relevant to industrial bioethanol production—pointed to physiological processes that were related to particular stress resistance profiles. Many of the genotype-by-environment expression responses occurred at targets of transcription factors with signatures of positive selection, suggesting that these strains have undergone positive selection for stress tolerance. Our results generate new insights into potential mechanisms of tolerance to stresses relevant to biofuel production, including ethanol and heat, present a backdrop for further engineering, and provide glimpses into the natural variation of stress tolerance in wild yeast strains.
doi:10.1093/gbe/evu199
PMCID: PMC4202335  PMID: 25364804
bioenergy; genomics; transcriptomics; environmental stress
3.  Comparison of Inter-Finger Connection Matrix Computation Techniques 
Journal of applied biomechanics  2012;29(5):525-534.
A hypothesis was proposed that the central nervous system controls force production by the fingers through hypothetical neural commands (NCs). The NCs are scaled between values of 0 to 1, indicating no intentional force production or maximal voluntary contraction (MVC) force production, respectively. A matrix of finger inter-connections, [IFC], transforms NCs into finger forces. Two methods have been proposed to compute the [IFC]. The first method uses only single finger MVC trials and multiplies the [IFC] by a gain factor. The second method uses a neural network (NN) model based on experimental data. The performance of the two methods was compared on the MVC data and on a data set of sub-maximal forces, collected over a range of total forces and moments of force. The methods were compared in terms of: 1) ability to predict finger forces; 2) accuracy of NC reconstruction; and 3) preserved planarity of force data for sub-maximal force production task. Both methods did a reasonable job of predicting the total force in multi-finger MVC trials; however, the NN model performed better in regards to all other criteria. Overall, the results indicate that for modeling multi-finger interaction the NN method is preferable.
PMCID: PMC4064683  PMID: 23183029
finger interaction; neural network; mode commands
4.  Optimization and variability of motor behavior in multi-finger tasks: What variables does the brain use? 
Journal of motor behavior  2013;45(4):289-305.
The neural control of movement has been described using different sets of elemental variables. Two possible sets of elemental variables have been suggested for finger pressing tasks: the forces of individual fingers and the finger commands (also called “finger modes” or “central commands”). In this study we analyze which of the two sets of the elemental variables is more likely used in the optimization of the finger force sharing and which set is used for the stabilization of performance. We used two recently developed techniques – the analytical inverse optimization (ANIO) and the uncontrolled manifold (UCM) analysis – to evaluate each set of elemental variables with respect to both aspects of performance. The results of the UCM analysis favored the finger commands as the elemental variables used for performance stabilization, while ANIO worked equally well on both sets of elemental variables. A simple scheme is suggested as to how the CNS could optimize a cost function dependent on the finger forces, but for the sake of facilitation of the feed-forward control it substitutes the original cost function by a cost function, which is convenient to optimize in the space of finger commands.
doi:10.1080/00222895.2013.792234
PMCID: PMC4064684  PMID: 23742067
finger pressing; motor commands; optimization; motor variability
5.  Draft Genome Sequence of Enterobacter cloacae Strain JD6301 
Genome Announcements  2014;2(3):e00381-14.
Enterobacter cloacae strain JD6301 was isolated from a mixed culture with wastewater collected from a municipal treatment facility and oleaginous microorganisms. A draft genome sequence of this organism indicates that it has a genome size of 4,772,910 bp, an average G+C content of 53%, and 4,509 protein-coding genes.
doi:10.1128/genomeA.00381-14
PMCID: PMC4038874  PMID: 24874669
6.  DADAR: A New Situational Awareness Platform for Data Analysis, Detection and Response 
doi:10.5210/ojphi.v6i1.5065
PMCID: PMC4050864
surveillance; situational awareness; data fusion; outbreak detection; informatics
7.  Evolution of extreme resistance to ionizing radiation via genetic adaptation of DNA repair 
eLife  2014;3:e01322.
By directed evolution in the laboratory, we previously generated populations of Escherichia coli that exhibit a complex new phenotype, extreme resistance to ionizing radiation (IR). The molecular basis of this extremophile phenotype, involving strain isolates with a 3-4 order of magnitude increase in IR resistance at 3000 Gy, is now addressed. Of 69 mutations identified in one of our most highly adapted isolates, functional experiments demonstrate that the IR resistance phenotype is almost entirely accounted for by only three of these nucleotide changes, in the DNA metabolism genes recA, dnaB, and yfjK. Four additional genetic changes make small but measurable contributions. Whereas multiple contributions to IR resistance are evident in this study, our results highlight a particular adaptation mechanism not adequately considered in studies to date: Genetic innovations involving pre-existing DNA repair functions can play a predominant role in the acquisition of an IR resistance phenotype.
DOI: http://dx.doi.org/10.7554/eLife.01322.001
eLife digest
X-rays and other forms of ionizing radiation can damage DNA and proteins inside cells. The radiation interacts with aqueous solutions to produce reactive forms of oxygen, which then cause the damage. A range of mechanisms exist to moderate and/or repair this damage, with certain species being able to tolerate extraordinary levels of radiation. The bacterium D. radiodurans, for example, can survive radiation levels that are over 1000 times higher than the levels that can kill human cells.
The molecular basis of high-level resistance to ionizing radiation is not well understood, and several mechanisms have been proposed. Recent work has focused on passive mechanisms that are based on changes in cellular levels of certain small molecules that prevent damage by reactive forms of oxygen molecules.
Now, based on experiments on E. coli, Byrne et al. demonstrate that active mechanisms, involving adaptations in the cellular DNA repair systems, can bring about dramatic increases in radiation resistance. The experiments were performed on populations of E. coli cells that had been subjected to an evolutionary selection for extremely high resistance to ionizing radiation. This involved exposing the E. coli cells to ionizing radiation that killed most of the population, and then growing up the survivors. Many repetitions of this process led to a population of cells with a resistance that was comparable to that of the bacterium D. radiodurans. The same evolution experiment was carried out four times, generating four separate populations of bacteria that were resistant to ionizing radiation.
Byrne et al. sequenced the genomes of the E. coli after 20, 40 or 50 rounds of the selection process, and compared mutations found in the four separate evolved populations. This showed that nine genes were particularly prone to mutations. Together, these genes had roles in repairing and copying DNA sequences, in decreasing damage caused by reactive forms of oxygen, and in manufacturing the molecular wall that shields cells.
To assess the importance of the mutations in the nine genes, Byrne et al. took Founder cells from the initial population of E. coli cells–which were not resistant to ionizing radiation–and introduced the very same mutations, one at a time. Then the mutations that had the largest positive effects on resistance to ionizing radiation were combined. Introducing particular mutations into three DNA repair genes resulted in the highest aggregate levels of resistance. Finally, evolved E. coli cells that were already resistant were made more sensitive to radiation by repairing the same individual mutations. Again, the biggest change was observed with the DNA repair genes. Indeed, repairing the mutations in just the three DNA repair genes completely removed the radiation resistance.
The next step is to determine how the properties of the mutated proteins change, and how those changes lead to radiation resistance. Also, there are clues in the work that suggest the presence of additional ways for cells to become radiation resistant, and these remain to be explored.
DOI: http://dx.doi.org/10.7554/eLife.01322.002
doi:10.7554/eLife.01322
PMCID: PMC3939492  PMID: 24596148
DNA repair; ionizing radiation; evolution; extremophile; mutation; E. coli
8.  Changes in the Flexor Digitorum Profundus Tendon Geometry in the Carpal Tunnel Due to Force Production and Posture of Metacarpophalangeal Joint of the Index Finger: an MRI Study 
Background
Carpal tunnel syndrome is a disorder caused by increased pressure in the carpal tunnel associated with repetitive, stereotypical finger actions. Little is known about in vivo geometrical changes in the carpal tunnel caused by motion at the finger joints and exerting a fingertip force.
Methods
The hands and forearms of five subjects were scanned using a 3.0T magnetic resonance imaging scanner. The metacarpophalangeal joint of the index finger was placed in: flexion, neutral and extension. For each joint posture subjects either produced no active force (passive condition) or exerted a flexion force to resist a load (~4.0 N) at the fingertip (active condition). Changes in the radii of curvature, position and transverse plane area of the flexor digitorum profundus tendons at the carpal tunnel level were measured.
Results
The radius of curvature of the flexor digitorum profundus tendons, at the carpal tunnel level, was significantly affected by posture of the index finger metacarpophalangeal joint (p<0.05) and the radii was significantly different between fingers (p<0.05). Actively producing force caused a significant shift (p<0.05) in the flexor digitorum profundus tendons in the ventral (palmar) direction. No significant change in the area of an ellipse containing the flexor digitorum profundus tendons was observed between conditions.
Interpretation
The results show that relatively small changes in the posture and force production of a single finger can lead to significant changes in the geometry of all the flexor digitorum profundus tendons in the carpal tunnel. Additionally, voluntary force production at the fingertip increases the moment arm of the FDP tendons about the wrist joint.
doi:10.1016/j.clinbiomech.2012.11.004
PMCID: PMC3609902  PMID: 23219762
MRI; carpal tunnel syndrome; moment arm; flexor digitorum profundus
9.  Population Level Analysis of Evolved Mutations Underlying Improvements in Plant Hemicellulose and Cellulose Fermentation by Clostridium phytofermentans 
PLoS ONE  2014;9(1):e86731.
Background
The complexity of plant cell walls creates many challenges for microbial decomposition. Clostridium phytofermentans, an anaerobic bacterium isolated from forest soil, directly breaks down and utilizes many plant cell wall carbohydrates. The objective of this research is to understand constraints on rates of plant decomposition by Clostridium phytofermentans and identify molecular mechanisms that may overcome these limitations.
Results
Experimental evolution via repeated serial transfers during exponential growth was used to select for C. phytofermentans genotypes that grow more rapidly on cellobiose, cellulose and xylan. To identify the underlying mutations an average of 13,600,000 paired-end reads were generated per population resulting in ∼300 fold coverage of each site in the genome. Mutations with allele frequencies of 5% or greater could be identified with statistical confidence. Many mutations are in carbohydrate-related genes including the promoter regions of glycoside hydrolases and amino acid substitutions in ABC transport proteins involved in carbohydrate uptake, signal transduction sensors that detect specific carbohydrates, proteins that affect the export of extracellular enzymes, and regulators of unknown specificity. Structural modeling of the ABC transporter complex proteins suggests that mutations in these genes may alter the recognition of carbohydrates by substrate-binding proteins and communication between the intercellular face of the transmembrane and the ATPase binding proteins.
Conclusions
Experimental evolution was effective in identifying molecular constraints on the rate of hemicellulose and cellulose fermentation and selected for putative gain of function mutations that do not typically appear in traditional molecular genetic screens. The results reveal new strategies for evolving and engineering microorganisms for faster growth on plant carbohydrates.
doi:10.1371/journal.pone.0086731
PMCID: PMC3899296  PMID: 24466216
10.  Effects of the Index Finger Position and Force Production on the Flexor Digitorum Superficialis Moment Arms at the Metacarpophalangeal Joints- an Magnetic Resonance Imaging Study 
Background
The purpose of this study was to use magnetic resonance imaging to measure the moment arm of the flexor digitorum superficialis tendon about the metacarpophalangeal joint of the index, middle, ring, and little fingers when the position and force production level of the index finger was altered. A secondary goal was to create regression models using anthropometric data to predict moment arms of the flexor digitorum superficialis about the metacarpophalangeal joint of each finger.
Methods
The hands of subjects were scanned using a 3.0T magnetic resonance imaging scanner. The metacarpophalangeal joint of the index finger was placed in: flexion, neutral, and extension. For each joint configuration subjects produced no active force (passive condition) and exerted a flexion force to resist a load at the fingertip (active condition).
Results
The following was found: (1) The moment arm of the flexor digitorum superficialis at the metacarpophalangeal joint of the index finger (a) increased with the joint flexion and stayed unchanged with finger extension; and (b) decreased with the increase of force at the neutral and extended finger postures and did not change at the flexed posture. (2) The moment arms of the flexor digitorum superficialis tendon of the middle, ring, and little fingers (a) did not change when the index metacarpophalangeal joint position changed (p > 0.20); and (b) The moment arms of the middle and little fingers increased when the index finger actively produced force at the flexed metacarpophalangeal joint posture. (4) The moment arms showed a high correlation with anthropometric measurements.
Interpretation
Moment arms of the flexor digitorum superficialis change due to both changes in joint angle and muscle activation; they scale with various anthropometric measures.
doi:10.1016/j.clinbiomech.2011.11.008
PMCID: PMC3328664  PMID: 22192658
MRI; moment arm; flexor digitorum superficialis; finger interaction
11.  Revised Sequence and Annotation of the Rhodobacter sphaeroides 2.4.1 Genome 
Journal of Bacteriology  2012;194(24):7016-7017.
The DNA sequences of chromosomes I and II of Rhodobacter sphaeroides strain 2.4.1 have been revised, and the annotation of the entire genomic sequence, including both chromosomes and the five plasmids, has been updated. Errors in the originally published sequence have been corrected, and ∼11% of the coding regions in the original sequence have been affected by the revised annotation.
doi:10.1128/JB.01214-12
PMCID: PMC3510577  PMID: 23209255
12.  À la Recherche du Temps Perdu: extracting temporal relations from medical text in the 2012 i2b2 NLP challenge 
Objective
An analysis of the timing of events is critical for a deeper understanding of the course of events within a patient record. The 2012 i2b2 NLP challenge focused on the extraction of temporal relationships between concepts within textual hospital discharge summaries.
Materials and methods
The team from the National Research Council Canada (NRC) submitted three system runs to the second track of the challenge: typifying the time-relationship between pre-annotated entities. The NRC system was designed around four specialist modules containing statistical machine learning classifiers. Each specialist targeted distinct sets of relationships: local relationships, ‘sectime’-type relationships, non-local overlap-type relationships, and non-local causal relationships.
Results
The best NRC submission achieved a precision of 0.7499, a recall of 0.6431, and an F1 score of 0.6924, resulting in a statistical tie for first place. Post hoc improvements led to a precision of 0.7537, a recall of 0.6455, and an F1 score of 0.6954, giving the highest scores reported on this task to date.
Discussion and conclusions
Methods for general relation extraction extended well to temporal relations, and gave top-ranked state-of-the-art results. Careful ordering of predictions within result sets proved critical to this success.
doi:10.1136/amiajnl-2013-001624
PMCID: PMC3756270  PMID: 23523875
information extraction; temporal reasoning; natural language processing; relation extraction; clinical text
13.  Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens 
PLoS Genetics  2013;9(1):e1003233.
The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five percent of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25× higher than those between inbred lines and 50× lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP–encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.
Author Summary
The filamentous ascomycete genus Cochliobolus includes highly aggressive necrotrophic and hemibiotrophic pathogens with particular specificity to their host plants, often associated with production of host selective toxins (HST) that allow necrotrophs to trigger host cell death. Hemibiotrophs must keep their hosts alive during initial infection stages and rely on subverting host defenses by secreting small protein effectors. Many Cochliobolus species have emerged rapidly as devastating pathogens due to HSTs. The genomes of Cochliobolus and related pathogens that differ in host preference, host specificity, and virulence strategies have been sequenced. Our comparative results, at the whole-genome level, and with a spotlight on core genes for secondary metabolism and small secreted proteins, touch on how pathogens develop and hone these tools, according to host or lifestyle. We suggest that, while necrotrophs and hemibiotrophs employ fundamentally contrasting mechanisms of promoting disease, the tools they utilize (HSTs and protein effectors) overlap. The suites of secondary metabolite and SSP genes that each possesses reflect astounding diversity among species, hinting that gene products, particularly those associated with unique genomic regions, are candidates for pathogenic lifestyle differences. Manipulations of strain-unique secondary metabolite genes associated with host-specific virulence provide tangible examples.
doi:10.1371/journal.pgen.1003233
PMCID: PMC3554632  PMID: 23357949
14.  Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence 
G3: Genes|Genomes|Genetics  2013;3(1):41-63.
Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes.
doi:10.1534/g3.112.004044
PMCID: PMC3538342  PMID: 23316438
wheat (Triticum aestivum); copy number variation; histone H3 transduplication; ToxA; ToxB; anastomosis
15.  Phylogenetics links monster larva to deep-sea shrimp 
Ecology and Evolution  2012;2(10):2367-2373.
Mid-water plankton collections commonly include bizarre and mysterious developmental stages that differ conspicuously from their adult counterparts in morphology and habitat. Unaware of the existence of planktonic larval stages, early zoologists often misidentified these unique morphologies as independent adult lineages. Many such mistakes have since been corrected by collecting larvae, raising them in the lab, and identifying the adult forms. However, challenges arise when the larva is remarkably rare in nature and relatively inaccessible due to its changing habitats over the course of ontogeny. The mid-water marine species Cerataspis monstrosa (Gray 1828) is an armored crustacean larva whose adult identity has remained a mystery for over 180 years. Our phylogenetic analyses, based in part on recent collections from the Gulf of Mexico, provide definitive evidence that the rare, yet broadly distributed larva, C. monstrosa, is an early developmental stage of the globally distributed deepwater aristeid shrimp, Plesiopenaeus armatus. Divergence estimates and phylogenetic relationships across five genes confirm the larva and adult are the same species. Our work demonstrates the diagnostic power of molecular systematics in instances where larval rearing seldom succeeds and morphology and habitat are not indicative of identity. Larval–adult linkages not only aid in our understanding of biodiversity, they provide insights into the life history, distribution, and ecology of an organism.
doi:10.1002/ece3.347
PMCID: PMC3492765  PMID: 23145324
Cerataspis monstrosa; Decapoda; DNA barcoding; larval–adult linkage; phylogenetics
16.  Fine Mapping of the Bsr1 Barley Stripe Mosaic Virus Resistance Gene in the Model Grass Brachypodium distachyon 
PLoS ONE  2012;7(6):e38333.
The ND18 strain of Barley stripe mosaic virus (BSMV) infects several lines of Brachypodium distachyon, a recently developed model system for genomics research in cereals. Among the inbred lines tested, Bd3-1 is highly resistant at 20 to 25°C, whereas Bd21 is susceptible and infection results in an intense mosaic phenotype accompanied by high levels of replicating virus. We generated an F6∶7 recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21 and used the RILs, and an F2 population of a second Bd21 × Bd3-1 cross to evaluate the inheritance of resistance. The results indicate that resistance segregates as expected for a single dominant gene, which we have designated Barley stripe mosaic virus resistance 1 (Bsr1). We constructed a genetic linkage map of the RIL population using SNP markers to map this gene to within 705 Kb of the distal end of the top of chromosome 3. Additional CAPS and Indel markers were used to fine map Bsr1 to a 23 Kb interval containing five putative genes. Our study demonstrates the power of using RILs to rapidly map the genetic determinants of BSMV resistance in Brachypodium. Moreover, the RILs and their associated genetic map, when combined with the complete genomic sequence of Brachypodium, provide new resources for genetic analyses of many other traits.
doi:10.1371/journal.pone.0038333
PMCID: PMC3366947  PMID: 22675544
17.  Coordination of Contact Forces During Multifinger Static Prehension 
This study investigated the effects of modifying contact finger forces in one direction—normal or tangential—on the entire set of the contact forces, while statically holding an object. Subjects grasped a handle instrumented with finger force-moment sensors, maintained it at rest in the air, and then slowly: (1) increased the grasping force, (2) tried to spread fingers apart, and (3) tried to squeeze fingers together. Analysis was mostly performed at the virtual finger (VF) level (the VF is an imaginable finger that generates the same force and moment as the four fingers combined). For all three tasks there were statistically significant changes in the VF normal and tangential forces. For finger spreading/squeezing the tangential force neutral point was located between the index and middle fingers. We conclude that the internal forces are regulated as a whole, including adjustments in both normal and tangential force, instead of only a subset of forces (normal or tangential). The effects of such factors as EFFORT and TORQUE were additive; their interaction was not statistically significant, thus supporting the principle of superposition in human prehension.
PMCID: PMC3235002  PMID: 21576716
prehension; grasping; motor control; occupational therapy
18.  Complete genome sequence of Paenibacillus sp. strain JDR-2 
Paenibacillus sp. strain JDR-2, an aggressively xylanolytic bacterium isolated from sweetgum (Liquidambar styraciflua) wood, is able to efficiently depolymerize, assimilate and metabolize 4-O-methylglucuronoxylan, the predominant structural component of hardwood hemicelluloses. A basis for this capability was first supported by the identification of genes and characterization of encoded enzymes and has been further defined by the sequencing and annotation of the complete genome, which we describe. In addition to genes implicated in the utilization of β-1,4-xylan, genes have also been identified for the utilization of other hemicellulosic polysaccharides. The genome of Paenibacillus sp. JDR-2 contains 7,184,930 bp in a single replicon with 6,288 protein-coding and 122 RNA genes. Uniquely prominent are 874 genes encoding proteins involved in carbohydrate transport and metabolism. The prevalence and organization of these genes support a metabolic potential for bioprocessing of hemicellulose fractions derived from lignocellulosic resources.
doi:10.4056/sigs.2374349
PMCID: PMC3368403  PMID: 22675593
aerobic; mesophile; Gram-positive; Paenibacillus; xylanolytic; xylan
19.  Binding and neutralization of vascular endothelial growth factor (VEGF) and related ligands by VEGF Trap, ranibizumab and bevacizumab 
Angiogenesis  2012;15(2):171-185.
Pharmacological inhibition of VEGF-A has proven to be effective in inhibiting angiogenesis and vascular leak associated with cancers and various eye diseases. However, little information is currently available on the binding kinetics and relative biological activity of various VEGF inhibitors. Therefore, we have evaluated the binding kinetics of two anti-VEGF antibodies, ranibizumab and bevacizumab, and VEGF Trap (also known as aflibercept), a novel type of soluble decoy receptor, with substantially higher affinity than conventional soluble VEGF receptors. VEGF Trap bound to all isoforms of human VEGF-A tested with subpicomolar affinity. Ranibizumab and bevacizumab also bound human VEGF-A, but with markedly lower affinity. The association rate for VEGF Trap binding to VEGF-A was orders of magnitude faster than that measured for bevacizumab and ranibizumab. Similarly, in cell-based bioassays, VEGF Trap inhibited the activation of VEGFR1 and VEGFR2, as well as VEGF-A induced calcium mobilization and migration in human endothelial cells more potently than ranibizumab or bevacizumab. Only VEGF Trap bound human PlGF and VEGF-B, and inhibited VEGFR1 activation and HUVEC migration induced by PlGF. These data differentiate VEGF Trap from ranibizumab and bevacizumab in terms of its markedly higher affinity for VEGF-A, as well as its ability to bind VEGF-B and PlGF.
Electronic supplementary material
The online version of this article (doi:10.1007/s10456-011-9249-6) contains supplementary material, which is available to authorized users.
doi:10.1007/s10456-011-9249-6
PMCID: PMC3338918  PMID: 22302382
VEGF receptor; Aflibercept; Affinity; Age-related macular degeneration; Placental growth factor; Biomedicine; Cardiology; Biomedicine general; Ophthalmology; Cancer Research; Cell Biology; Oncology
22.  Rediscovery by Whole Genome Sequencing: Classical Mutations and Genome Polymorphisms in Neurospora crassa 
G3: Genes|Genomes|Genetics  2011;1(4):303-316.
Classical forward genetics has been foundational to modern biology, and has been the paradigm for characterizing the role of genes in shaping phenotypes for decades. In recent years, reverse genetics has been used to identify the functions of genes, via the intentional introduction of variation and subsequent evaluation in physiological, molecular, and even population contexts. These approaches are complementary and whole genome analysis serves as a bridge between the two. We report in this article the whole genome sequencing of eighteen classical mutant strains of Neurospora crassa and the putative identification of the mutations associated with corresponding mutant phenotypes. Although some strains carry multiple unique nonsynonymous, nonsense, or frameshift mutations, the combined power of limiting the scope of the search based on genetic markers and of using a comparative analysis among the eighteen genomes provides strong support for the association between mutation and phenotype. For ten of the mutants, the mutant phenotype is recapitulated in classical or gene deletion mutants in Neurospora or other filamentous fungi. From thirteen to 137 nonsense mutations are present in each strain and indel sizes are shown to be highly skewed in gene coding sequence. Significant additional genetic variation was found in the eighteen mutant strains, and this variability defines multiple alleles of many genes. These alleles may be useful in further genetic and molecular analysis of known and yet-to-be-discovered functions and they invite new interpretations of molecular and genetic interactions in classical mutant strains.
doi:10.1534/g3.111.000307
PMCID: PMC3276140  PMID: 22384341
single nucleotide polymorphism; SNP; indel; comparative genomics; classical mutant
23.  Machine-learned solutions for three stages of clinical information extraction: the state of the art at i2b2 2010 
Objective
As clinical text mining continues to mature, its potential as an enabling technology for innovations in patient care and clinical research is becoming a reality. A critical part of that process is rigid benchmark testing of natural language processing methods on realistic clinical narrative. In this paper, the authors describe the design and performance of three state-of-the-art text-mining applications from the National Research Council of Canada on evaluations within the 2010 i2b2 challenge.
Design
The three systems perform three key steps in clinical information extraction: (1) extraction of medical problems, tests, and treatments, from discharge summaries and progress notes; (2) classification of assertions made on the medical problems; (3) classification of relations between medical concepts. Machine learning systems performed these tasks using large-dimensional bags of features, as derived from both the text itself and from external sources: UMLS, cTAKES, and Medline.
Measurements
Performance was measured per subtask, using micro-averaged F-scores, as calculated by comparing system annotations with ground-truth annotations on a test set.
Results
The systems ranked high among all submitted systems in the competition, with the following F-scores: concept extraction 0.8523 (ranked first); assertion detection 0.9362 (ranked first); relationship detection 0.7313 (ranked second).
Conclusion
For all tasks, we found that the introduction of a wide range of features was crucial to success. Importantly, our choice of machine learning algorithms allowed us to be versatile in our feature design, and to introduce a large number of features without overfitting and without encountering computing-resource bottlenecks.
doi:10.1136/amiajnl-2011-000150
PMCID: PMC3168309  PMID: 21565856
natural language processing; semantics; classification/*methods; computerized medical records systems; patient discharge/*statistics & numerical data; text mining; concept detection; relation extraction; document coding; machine learning; modeling physiologic and disease processes; linking the genotype and phenotype; identifying genome and protein structure and function; visualization of data and knowledge
24.  ExaCT: automatic extraction of clinical trial characteristics from journal publications 
Background
Clinical trials are one of the most important sources of evidence for guiding evidence-based practice and the design of new trials. However, most of this information is available only in free text - e.g., in journal publications - which is labour intensive to process for systematic reviews, meta-analyses, and other evidence synthesis studies. This paper presents an automatic information extraction system, called ExaCT, that assists users with locating and extracting key trial characteristics (e.g., eligibility criteria, sample size, drug dosage, primary outcomes) from full-text journal articles reporting on randomized controlled trials (RCTs).
Methods
ExaCT consists of two parts: an information extraction (IE) engine that searches the article for text fragments that best describe the trial characteristics, and a web browser-based user interface that allows human reviewers to assess and modify the suggested selections. The IE engine uses a statistical text classifier to locate those sentences that have the highest probability of describing a trial characteristic. Then, the IE engine's second stage applies simple rules to these sentences to extract text fragments containing the target answer. The same approach is used for all 21 trial characteristics selected for this study.
Results
We evaluated ExaCT using 50 previously unseen articles describing RCTs. The text classifier (first stage) was able to recover 88% of relevant sentences among its top five candidates (top5 recall) with the topmost candidate being relevant in 80% of cases (top1 precision). Precision and recall of the extraction rules (second stage) were 93% and 91%, respectively. Together, the two stages of the extraction engine were able to provide (partially) correct solutions in 992 out of 1050 test tasks (94%), with a majority of these (696) representing fully correct and complete answers.
Conclusions
Our experiments confirmed the applicability and efficacy of ExaCT. Furthermore, they demonstrated that combining a statistical method with 'weak' extraction rules can identify a variety of study characteristics. The system is flexible and can be extended to handle other characteristics and document types (e.g., study protocols).
doi:10.1186/1472-6947-10-56
PMCID: PMC2954855  PMID: 20920176
25.  De-identification of primary care electronic medical records free-text data in Ontario, Canada 
Background
Electronic medical records (EMRs) represent a potentially rich source of health information for research but the free-text in EMRs often contains identifying information. While de-identification tools have been developed for free-text, none have been developed or tested for the full range of primary care EMR data
Methods
We used deid open source de-identification software and modified it for an Ontario context for use on primary care EMR data. We developed the modified program on a training set of 1000 free-text records from one group practice and then tested it on two validation sets from a random sample of 700 free-text EMR records from 17 different physicians from 7 different practices in 5 different cities and 500 free-text records from a group practice that was in a different city than the group practice that was used for the training set. We measured the sensitivity/recall, precision, specificity, accuracy and F-measure of the modified tool against manually tagged free-text records to remove patient and physician names, locations, addresses, medical record, health card and telephone numbers.
Results
We found that the modified training program performed with a sensitivity of 88.3%, specificity of 91.4%, precision of 91.3%, accuracy of 89.9% and F-measure of 0.90. The validations sets had sensitivities of 86.7% and 80.2%, specificities of 91.4% and 87.7%, precisions of 91.1% and 87.4%, accuracies of 89.0% and 83.8% and F-measures of 0.89 and 0.84 for the first and second validation sets respectively.
Conclusion
The deid program can be modified to reasonably accurately de-identify free-text primary care EMR records while preserving clinical content.
doi:10.1186/1472-6947-10-35
PMCID: PMC2907300  PMID: 20565894

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