Roderick Jensen - Academia.edu (original) (raw)

Papers by Roderick Jensen

Cellular glucan metabolism related genes differentially expressed in early stages of seed develop... more Cellular glucan metabolism related genes differentially expressed in early stages of seed development. The genes up-regulated in 3mlpa mutant in both stages are indicated by asterisk (*) symbol. The genes differentially expressed only in stage 1 and stage 2 are indicated by section sign (§) and double dagger (‡) symbols, respectively. The non-significant adjusted P-values are indicated by dash (-). The genes down-regulated in 3mlpa mutant are indicated by negative values of log2 ratio. Zero read count (no gene expression) in 3MWT, resulting in infinite value for FC and log2 ratio indicated by infinite sign (∞). (XLSX 59 kb)

Photosynthesis related genes differentially expressed in late stages of seed development. (XLSX 4... more Photosynthesis related genes differentially expressed in late stages of seed development. (XLSX 49Â kb)

Defense related genes differentially expressed in early stages of seed development. Column â Sâ r... more Defense related genes differentially expressed in early stages of seed development. Column â Sâ reports the stages of development in which the gene is differentially expressed. Genes down-regulated in 3mlpa mutant are indicated by negative values of log 2 ratio. Adjusted P-values are only reported for the stages in which the gene is differentially expressed. (XLSX 60Â kb)

ABSTRACTPantoea stewartiisubsp.stewartii, a Gram-negative proteobacterium, causes Stewart’s wilt ... more ABSTRACTPantoea stewartiisubsp.stewartii, a Gram-negative proteobacterium, causes Stewart’s wilt disease in corn. Bacterial transmission to plants occurs primarily via the corn flea beetle insect vector, which is native to North America.P. stewartiiDC283 is the wild-type reference strain most used to study pathogenesis. Previously the complete genome ofP. stewartiiwas released. Here, the method whereby the genome was assembled is described in greater detail. Data from a matepair library preparation with 3.5 kilobase insert size and high-throughput sequencing from the MiSeq Illumina platform, together with the available incomplete genome sequence of AHIE00000000.1 (containing 65 contigs) was used. This work resulted in the complete assembly of one circular chromosome, ten circular plasmids and one linear phage fromP. stewartiiDC283. A high number of sequences encoding repetitive transposases (> 400) were found in the complete genome. The separation of plasmids from genomic DNA rev...

Physical Review E, 2002

We present exact, explicit, convergent periodic-orbit expansions for individual energy levels of ... more We present exact, explicit, convergent periodic-orbit expansions for individual energy levels of regular quantum graphs in the paper. One simple application is the energy levels of a particle in a piecewise constant potential. Since the classical ray trajectories ͑including ray splitting͒ in such systems are strongly chaotic, this result provides an explicit quantization of a classically chaotic system.

... (1996) Nat Biotechnol, 14, 1675-1680. 8. Hsiao, L., Yoshida, T., Hong, R., Jensen, R., Dangon... more ... (1996) Nat Biotechnol, 14, 1675-1680. 8. Hsiao, L., Yoshida, T., Hong, R., Jensen, R., Dangond, F., Misra, J., Haverty, P., Weng, Z., Mutter, G., Milford, EL et al. (Accepted) Physiological Genomics. 9. Visual Mining, I. (2001). 3.7 ed, Rockville. 10. ...

BMC genomics, Jan 18, 2015

Low phytic acid (lpa) crops are potentially eco-friendly alternative to conventional normal phyti... more Low phytic acid (lpa) crops are potentially eco-friendly alternative to conventional normal phytic acid (PA) crops, improving mineral bioavailability in monogastric animals as well as decreasing phosphate pollution. The lpa crops developed to date carry mutations that are directly or indirectly associated with PA biosynthesis and accumulation during seed development. These lpa crops typically exhibit altered carbohydrate profiles, increased free phosphate, and lower seedling emergence, the latter of which reduces overall crop yield, hence limiting their large-scale cultivation. Improving lpa crop yield requires an understanding of the downstream effects of the lpa genotype on seed development. Towards that end, we present a comprehensive comparison of gene-expression profiles between lpa and normal PA soybean lines (Glycine max) at five stages of seed development using RNA-Seq approaches. The lpa line used in this study carries single point mutations in a myo-inositol phosphate synt...

Microbiology Resource Announcements, 2020

We report the complete genome of clinical strain Pseudomonas aeruginosa CMC-115, which was isolat... more We report the complete genome of clinical strain Pseudomonas aeruginosa CMC-115, which was isolated from an acute ventilator-associated pneumonia patient. Illumina sequencing reads were assembled using Geneious to yield a 6,375,262-bp circular chromosome that exhibited an unusual ferrichrome receptor in the pyoverdine synthesis locus and the absence of type 3 secretion system genes. ABSTRACT We report the complete genome of clinical strain Pseudomonas aeruginosa CMC-115, which was isolated from an acute ventilator-associated pneumonia patient. Illumina sequencing reads were assembled using Geneious to yield a 6,375,262-bp circular chromosome that exhibited an unusual ferrichrome receptor in the pyoverdine synthesis locus and the absence of type 3 secretion system genes.

Journal of Experimental and Theoretical Physics Letters, 2001

We present quantum graphs with remarkably regular spectral characteristics. We call them regular ... more We present quantum graphs with remarkably regular spectral characteristics. We call them regular quantum graphs. Although regular quantum graphs are strongly chaotic in the classical limit, their quantum spectra are explicitly solvable in terms of periodic orbits. We present analytical solutions for the spectrum of regular quantum graphs in the form of explicit and exact periodic orbit expansions for each individual energy level.

Genome Announcements

The phytopathogen Pantoea stewartii subsp. stewartii DC283 causes Stewart’s wilt disease in corn ... more The phytopathogen Pantoea stewartii subsp. stewartii DC283 causes Stewart’s wilt disease in corn after transmission from the corn flea beetle insect vector. Here, we report that the complete annotated genome of P. stewartii DC283 has been fully assembled into one circular chromosome, 10 circular plasmids, and one linear phage.

Cancers

Sex differences in incidence, prognosis, and treatment response have been described for many canc... more Sex differences in incidence, prognosis, and treatment response have been described for many cancers. In malignant pleural mesothelioma (MPM), a lethal disease associated with asbestos exposure, men outnumber women 4 to 1, but women consistently live longer than men following surgery-based therapy. This study investigated whether tumor expression of genes associated with estrogen signaling could potentially explain observed survival differences. Two microarray datasets of MPM tumors were analyzed to discover estrogen-related genes associated with survival. A validation cohort of MPM tumors was selected to balance the numbers of men and women and control for competing prognostic influences. The RAS like estrogen regulated growth inhibitor (RERG) gene was identified as the most differentially-expressed estrogen-related gene in these tumors and predicted prognosis in discovery datasets. In the sex-matched validation cohort, low RERG expression was significantly associated with increase...

Molecular plant pathology, Jan 26, 2018

The bacterium Pantoea stewartii ssp. stewartii causes Stewart's wilt disease in corn. Pantoea... more The bacterium Pantoea stewartii ssp. stewartii causes Stewart's wilt disease in corn. Pantoea stewartii is transmitted to plants via corn flea beetles, where it first colonizes the apoplast causing water-soaked lesions, and then migrates to the xylem and forms a biofilm that blocks water transport. Bacterial quorum sensing ensures that the exopolysaccharide production necessary for biofilm formation occurs only at high cell density. A genomic-level transposon sequencing (Tn-Seq) analysis was performed to identify additional bacterial genes essential for survival in planta and to provide insights into the plant-microbe interactions occurring during wilt disease. A mariner transposon library of approximately 40 000 mutants was constructed and used to inoculate corn seedlings through a xylem infection model. Cultures of the library grown in Luria-Bertani (LB) broth served as the in vitro pre-inoculation control. Tn-Seq analysis showed that the number of transposon mutations was red...

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Frontiers in microbiology, 2018

Skin symbiotic bacteria on amphibians can play a role in protecting their host against pathogens.... more Skin symbiotic bacteria on amphibians can play a role in protecting their host against pathogens. Chytridiomycosis, the disease caused by, Bd, has caused dramatic population declines and extinctions of amphibians worldwide. Anti-Bd bacteria from amphibian skin have been cultured, and skin bacterial communities have been described through 16S rRNA gene amplicon sequencing. Here, we present a shotgun metagenomic analysis of skin bacterial communities from a Neotropical frog,. We sequenced the metagenome of six frogs from two different sites in Panamá: three frogs from Soberanía (Sob), a Bd-endemic site, and three frogs from Serranía del Sapo (Sapo), a Bd-naïve site. We described the taxonomic composition of skin microbiomes and found thatwas a major component of these communities. We also identified that Sob communities were enriched in Actinobacteria while Sapo communities were enriched in Gammaproteobacteria. We described gene abundances within the main functional classes and found ...

Genomics, proteomics & bioinformatics, Dec 1, 2017

The differential expression of two closelyassociated cyclooxygenase isozymes, COX-1 and COX-2, ex... more The differential expression of two closelyassociated cyclooxygenase isozymes, COX-1 and COX-2, exhibited functions beyond eicosanoid metabolism. We hypothesized that COX-1 or COX-2 knockout lung fibroblasts may display altered protein profiles which may allow us to further differentiate the functional roles of these isozymes at the molecular level. Proteomic analysis shows constitutive production of macrophage migration inhibitory factor (MIF) in lung fibroblasts derived from COX-2-/- but not wild-type (WT) or COX-1-/- mice. MIF was spontaneously released in high levels into the extracellular milieu of COX2-/- fibroblasts seemingly from the preformed intracellular stores, with no change in the basal gene expression of MIF. The secretion and regulation of MIF in COX-2-/- was "prostaglandin-independent." GO analysis showed that concurrent with upregulation of MIF, there is a significant surge in expression of genes related to fibroblast growth, FK506 binding proteins, and is...

Toxins

Toxin-antitoxin (TA) systems are key regulators of bacterial persistence, a multidrug-tolerant st... more Toxin-antitoxin (TA) systems are key regulators of bacterial persistence, a multidrug-tolerant state found in bacterial species that is a major contributing factor to the growing human health crisis of antibiotic resistance. Type II TA systems consist of two proteins, a toxin and an antitoxin; the toxin is neutralized when they form a complex. The ratio of antitoxin to toxin is significantly greater than 1.0 in the susceptible population (non-persister state), but this ratio is expected to become smaller during persistence. Analysis of multiple datasets (RNA-seq, ribosome profiling) and results from translation initiation rate calculators reveal multiple mechanisms that ensure a high antitoxin-to-toxin ratio in the non-persister state. The regulation mechanisms include both translational and transcriptional regulation. We classified E. coli type II TA systems into four distinct classes based on the mechanism of differential protein production between toxin and antitoxin. We find that the most common regulation mechanism is translational regulation. This classification scheme further refines our understanding of one of the fundamental mechanisms underlying bacterial persistence, especially regarding maintenance of the antitoxin-to-toxin ratio.

Physical Review A

The geometric-optics theory for the Dirac equation is derived using a procedure developed for the... more The geometric-optics theory for the Dirac equation is derived using a procedure developed for the description of electromagnetic waves in inhomogeneous plasmas. This semiclassical description of relativistic electrons permits simple estimates of the magnitude and relevance of quantum corrections to the classical particle dynamics which can be used to assess the validity of the classical treatment of relativistic electron beams in a variety of applications. Moreover, these results correct several errors in the literature and are presented in a form which is easily solved, numerically, using stl a1ghtfolward modlf1catlons of exlstlng ray-tracing codes fol electr omagnet1c radlat1on.