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1.  Enhancing Terpene Yield from Sugars via Novel Routes to 1-Deoxy-d-Xylulose 5-Phosphate 
Terpene synthesis in the majority of bacterial species, together with plant plastids, takes place via the 1-deoxy-d-xylulose 5-phosphate (DXP) pathway. The first step of this pathway involves the condensation of pyruvate and glyceraldehyde 3-phosphate by DXP synthase (Dxs), with one-sixth of the carbon lost as CO2. A hypothetical novel route from a pentose phosphate to DXP (nDXP) could enable a more direct pathway from C5 sugars to terpenes and also circumvent regulatory mechanisms that control Dxs, but there is no enzyme known that can convert a sugar into its 1-deoxy equivalent. Employing a selection for complementation of a dxs deletion in Escherichia coli grown on xylose as the sole carbon source, we uncovered two candidate nDXP genes. Complementation was achieved either via overexpression of the wild-type E. coli yajO gene, annotated as a putative xylose reductase, or via various mutations in the native ribB gene. In vitro analysis performed with purified YajO and mutant RibB proteins revealed that DXP was synthesized in both cases from ribulose 5-phosphate (Ru5P). We demonstrate the utility of these genes for microbial terpene biosynthesis by engineering the DXP pathway in E. coli for production of the sesquiterpene bisabolene, a candidate biodiesel. To further improve flux into the pathway from Ru5P, nDXP enzymes were expressed as fusions to DXP reductase (Dxr), the second enzyme in the DXP pathway. Expression of a Dxr-RibB(G108S) fusion improved bisabolene titers more than 4-fold and alleviated accumulation of intracellular DXP.
PMCID: PMC4272731  PMID: 25326299
2.  The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat 
Genomes were obtained for three closely related strains of Synechococcus that are representative of putative ecotypes (PEs) that predominate at different depths in the 1 mm-thick, upper-green layer in the 60°C mat of Mushroom Spring, Yellowstone National Park, and exhibit different light adaptation and acclimation responses. The genomes were compared to the published genome of a previously obtained, closely related strain from a neighboring spring, and differences in both gene content and orthologous gene alleles between high-light-adapted and low-light-adapted strains were identified. Evidence of genetic differences that relate to adaptation to light intensity and/or quality, CO2uptake, nitrogen metabolism, organic carbon metabolism, and uptake of other nutrients were found between strains of the different putative ecotypes. In situ diel transcription patterns of genes, including genes unique to either low-light-adapted or high-light-adapted strains and different alleles of an orthologous photosystem gene, revealed that expression is fine-tuned to the different light environments experienced by ecotypes prevalent at various depths in the mat. This study suggests that strains of closely related PEs have different genomic adaptations that enable them to inhabit distinct ecological niches while living in close proximity within a microbial community.
PMCID: PMC4477158  PMID: 26157428
comparative genomics; microbial species; thermophilic Synechococcus; microbial mats; adaptation
3.  Complete Genome Sequence of Sulfolobus solfataricus Strain 98/2 and Evolved Derivatives 
Genome Announcements  2015;3(3):e00549-15.
Sulfolobus solfataricus is a thermoacidophilic crenarcheote with a 3.0-Mb genome. Here, we report the genome sequence of S. solfataricus strain 98/2, along with several evolved derivatives generated through experimental microbial evolution for enhanced thermoacidophily.
PMCID: PMC4447912  PMID: 26021927
4.  Complete Genome Sequence of an Evolved Thermotoga maritima Isolate 
Genome Announcements  2015;3(3):e00557-15.
Thermotoga maritima is a hyperthermophilic bacterium with a small genome (1.86 Mbp). Genome resequencing of Tma200, a derivative produced by experimental microbial evolution, revealed the occurrence of deletions and substitution mutations. Their identification contributes to a better understanding of genome instability in this organism.
PMCID: PMC4447916  PMID: 26021931
5.  Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype 
BMC Genomics  2015;16(1):326.
Trichoderma reesei is the main industrial source of cellulases and hemicellulases required for the hydrolysis of biomass to simple sugars, which can then be used in the production of biofuels and biorefineries. The highly productive strains in use today were generated by classical mutagenesis. As byproducts of this procedure, mutants were generated that turned out to be unable to produce cellulases. In order to identify the mutations responsible for this inability, we sequenced the genome of one of these strains, QM9136, and compared it to that of its progenitor T. reesei QM6a.
In QM9136, we detected a surprisingly low number of mutagenic events in the promoter and coding regions of genes, i.e. only eight indels and six single nucleotide variants. One of these indels led to a frame-shift in the Zn2Cys6 transcription factor XYR1, the general regulator of cellulase and xylanase expression, and resulted in its C-terminal truncation by 140 amino acids. Retransformation of strain QM9136 with the wild-type xyr1 allele fully recovered the ability to produce cellulases, and is thus the reason for the cellulase-negative phenotype. Introduction of an engineered xyr1 allele containing the truncating point mutation into the moderate producer T. reesei QM9414 rendered this strain also cellulase-negative. The correspondingly truncated XYR1 protein was still able to enter the nucleus, but failed to be expressed over the basal constitutive level.
The missing 140 C-terminal amino acids of XYR1 are therefore responsible for its previously observed auto-regulation which is essential for cellulases to be expressed. Our data present a working example of the use of genome sequencing leading to a functional explanation of the QM9136 cellulase-negative phenotype.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1526-0) contains supplementary material, which is available to authorized users.
PMCID: PMC4409711  PMID: 25909478
Single nucleotide polymorphism; SNP; Indel; Comparative genomics; Classical mutant; XYR1; Transcription factor shuttling; Cellulases; Trichoderma reesei; QM9136
6.  Draft Genome Sequence of Neurospora crassa Strain FGSC 73 
Genome Announcements  2015;3(2):e00074-15.
We report the elucidation of the complete genome of the Neurospora crassa (Shear and Dodge) strain FGSC 73, a mat-a, trp-3 mutant strain. The genome sequence around the idiotypic mating type locus represents the only publicly available sequence for a mat-a strain. 40.42 Megabases are assembled into 358 scaffolds carrying 11,978 gene models.
PMCID: PMC4384475  PMID: 25838471
7.  Database queries for hospitalizations for acute congestive heart failure: flexible methods and validation based on set theory 
Background and objective
Electronic health records databases are increasingly used for identifying cohort populations, covariates, or outcomes, but discerning such clinical ‘phenotypes’ accurately is an ongoing challenge. We developed a flexible method using overlapping (Venn diagram) queries. Here we describe this approach to find patients hospitalized with acute congestive heart failure (CHF), a sampling strategy for one-by-one ‘gold standard’ chart review, and calculation of positive predictive value (PPV) and sensitivities, with SEs, across different definitions.
Materials and methods
We used retrospective queries of hospitalizations (2002–2011) in the Indiana Network for Patient Care with any CHF ICD-9 diagnoses, a primary diagnosis, an echocardiogram performed, a B-natriuretic peptide (BNP) drawn, or BNP >500 pg/mL. We used a hybrid between proportional sampling by Venn zone and over-sampling non-overlapping zones. The acute CHF (presence/absence) outcome was based on expert chart review using a priori criteria.
Among 79 091 hospitalizations, we reviewed 908. A query for any ICD-9 code for CHF had PPV 42.8% (SE 1.5%) for acute CHF and sensitivity 94.3% (1.3%). Primary diagnosis of 428 and BNP >500 pg/mL had PPV 90.4% (SE 2.4%) and sensitivity 28.8% (1.1%). PPV was <10% when there was no echocardiogram, no BNP, and no primary diagnosis. ‘False positive’ hospitalizations were for other heart disease, lung disease, or other reasons.
This novel method successfully allowed flexible application and validation of queries for patients hospitalized with acute CHF.
PMCID: PMC3932461  PMID: 24113802
Phenotypes; Electronic Health Records; Heart Failure; Predictive Value of Tests; Algorithms; Validation Studies
8.  Detecting Outbreaks in Time-Series Data with RecentMax 
PMCID: PMC4512360
aberration detection; algorithm; outbreak detection; surveillance; situational awareness
9.  High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus 
BMC Genomics  2015;16(1):24.
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.
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.
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.
PMCID: PMC4307895  PMID: 25613058
QTL cloning; Association genetics; Cell wall recalcitrance; Lignin; Cellulose; Hemicellulose
10.  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.
PMCID: PMC4202335  PMID: 25364804
bioenergy; genomics; transcriptomics; environmental stress
11.  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
12.  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.
PMCID: PMC4064684  PMID: 23742067
finger pressing; motor commands; optimization; motor variability
13.  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.
PMCID: PMC4038874  PMID: 24874669
14.  DADAR: A New Situational Awareness Platform for Data Analysis, Detection and Response 
PMCID: PMC4050864
surveillance; situational awareness; data fusion; outbreak detection; informatics
15.  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.
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.
PMCID: PMC3939492  PMID: 24596148
DNA repair; ionizing radiation; evolution; extremophile; mutation; E. coli
16.  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 
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.
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.
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.
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.
PMCID: PMC3609902  PMID: 23219762
MRI; carpal tunnel syndrome; moment arm; flexor digitorum profundus
17.  Population Level Analysis of Evolved Mutations Underlying Improvements in Plant Hemicellulose and Cellulose Fermentation by Clostridium phytofermentans 
PLoS ONE  2014;9(1):e86731.
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.
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.
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.
PMCID: PMC3899296  PMID: 24466216
18.  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 
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.
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).
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.
Moment arms of the flexor digitorum superficialis change due to both changes in joint angle and muscle activation; they scale with various anthropometric measures.
PMCID: PMC3328664  PMID: 22192658
MRI; moment arm; flexor digitorum superficialis; finger interaction
19.  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.
PMCID: PMC3510577  PMID: 23209255
20.  À la Recherche du Temps Perdu: extracting temporal relations from medical text in the 2012 i2b2 NLP challenge 
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.
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.
PMCID: PMC3756270  PMID: 23523875
information extraction; temporal reasoning; natural language processing; relation extraction; clinical text
21.  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.
PMCID: PMC3554632  PMID: 23357949
22.  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.
PMCID: PMC3538342  PMID: 23316438
wheat (Triticum aestivum); copy number variation; histone H3 transduplication; ToxA; ToxB; anastomosis
23.  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.
PMCID: PMC3492765  PMID: 23145324
Cerataspis monstrosa; Decapoda; DNA barcoding; larval–adult linkage; phylogenetics
24.  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.
PMCID: PMC3366947  PMID: 22675544
25.  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

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