Browsing by Subject "identification"

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Adaptive Expansion of the Maize Maternally Expressed Gene (Meg) Family involves Changes in Expression Patterns and Protein Secondary Structures of its Members
(2014-08) Xiong, Yuqing; Mei, Wenbin; Kim, Eun-Deok; Mukherjee, Krishanu; Hassanein, Hatem; Barbazuk, William Brad; Sung, Sibum; Kolaczkowski, Bryan; Kang, Byung-Ho; Kim, Eun-Deok; Sung, Sibum
The Maternally expressed gene (Meg) family is a locally-duplicated gene family of maize which encodes cysteine-rich proteins (CRPs). The founding member of the family, Meg1, is required for normal development of the basal endosperm transfer cell layer (BETL) and is involved in the allocation of maternal nutrients to growing seeds. Despite the important roles of Meg1 in maize seed development, the evolutionary history of the Meg cluster and the activities of the duplicate genes are not understood. Results: In maize, the Meg gene cluster resides in a 2.3 Mb-long genomic region that exhibits many features of non-centromeric heterochromatin. Using phylogenetic reconstruction and syntenic alignments, we identified the pedigree of the Meg family, in which 11 of its 13 members arose in maize after allotetraploidization similar to 4.8 mya. Phylogenetic and population-genetic analyses identified possible signatures suggesting recent positive selection in Meg homologs. Structural analyses of the Meg proteins indicated potentially adaptive changes in secondary structure from alpha-helix to beta-strand during the expansion. Transcriptomic analysis of the maize endosperm indicated that 6 Meg genes are selectively activated in the BETL, and younger Meg genes are more active than older ones. In endosperms from B73 by Mo17 reciprocal crosses, most Meg genes did not display parent-specific expression patterns. Conclusions: Recently-duplicated Meg genes have different protein secondary structures, and their expressions in the BETL dominate over those of older members. Together with the signs of positive selections in the young Meg genes, these results suggest that the expansion of the Meg family involves potentially adaptive transitions in which new members with novel functions prevailed over older members.
Crystallographic Study Of The Phosphoethanolamine Transferase EptC required For Polymyxin Resistance And Motility In Campylobacter jejuni
(2014-10) Fage, Christopher D.; Brown, Dusty B.; Boll, Joseph M.; Keatinge-Clay, Adrian T.; Trent, M. Stephen; Fage, Christopher D.; Brown, Dusty B.; Boll, Joseph M.; Keatinge-Clay, Adrian T.; Trent, M. Stephen
The foodborne enteric pathogen Campylobacter jejuni decorates a variety of its cell-surface structures with phosphoethanolamine (pEtN). Modifying lipid A with pEtN promotes cationic antimicrobial peptide resistance, whereas post-translationally modifying the flagellar rod protein FlgG with pEtN promotes flagellar assembly and motility, which are processes that are important for intestinal colonization. EptC, the pEtN transferase required for all known pEtN cell-surface modifications in C. jejuni, is a predicted inner-membrane metalloenzyme with a five-helix N-terminal transmembrane domain followed by a soluble sulfatase-like catalytic domain in the periplasm. The atomic structure of the catalytic domain of EptC (cEptC) was crystallized and solved to a resolution of 2.40 angstrom. cEptC adopts the alpha/beta/alpha fold of the sulfatase protein family and harbors a zinc-binding site. A phosphorylated Thr266 residue was observed that was hypothesized to mimic a covalent pEtN-enzyme intermediate. The requirement for Thr266 as well as the nearby residues Asn308, Ser309, His358 and His440 was ascertained via in vivo activity assays on mutant strains. The results establish a basis for the design of pEtN transferase inhibitors.
Detection Of High-Degree Prograde Sectoral Mode Sequences In The A-Star Kic 8054146?
(2013-08) Breger, Michel; Lenz, P.; Pamyatnykh, A. A.; Breger, Michel
This paper examines the 46 frequencies found in the delta Sct star KIC 8054146 involving a frequency spacing of exactly 2.814 cycles day(-1) (32.57 mu Hz), which is also a dominant low-frequency peak near or equal to the rotational frequency. These 46 frequencies range up to 146 cycles day(-1). Three years of Kepler data reveal distinct sequences of these equidistantly spaced frequencies, including the basic sequence and side lobes associated with other dominant modes (i.e., small amplitude modulations). The amplitudes of the basic sequence show a high-low pattern. The basic sequence follows the equation f(m) = 2.8519 + m * 2.81421 cycles day(-1) with m ranging from 25 to 35. The zero-point offset and the lack of low-order harmonics eliminate an interpretation in terms of a Fourier series of a non-sinusoidal light curve. The exactness of the spacing eliminates high-order asymptotic pulsation. The frequency pattern is not compatible with simple hypotheses involving single or multiple spots, even with differential rotation. The basic high-frequency sequence is interpreted in terms of prograde sectoral modes. These can be marginally unstable, while their corresponding low-degree counterparts are stable due to stronger damping. The measured projected rotation velocity (300 km s(-1)) indicates that the star rotates with greater than or similar to 70% of the Keplerian break-up velocity. This suggests a near equator-on view. We qualitatively examine the visibility of prograde sectoral high-degree g-modes in integrated photometric light in such a geometrical configuration and find that prograde sectoral modes can reproduce the frequencies and the odd-even amplitude pattern of the high-frequency sequence.
Development Of An Engineered Bioluminescent Reporter Phage For Detection Of Bacterial Blight Of Crucifers
(2012-05) Schofield, David A.; Bull, Carolee T.; Rubio, Isael; Wechter, W. Patrick; Westwater, Caroline; Molineux, Ian J.; Molineux, Ian J.
Bacterial blight, caused by the phytopathogen Pseudomonas cannabina pv. alisalensis, is an emerging disease afflicting important members of the Brassicaceae family. The disease is often misdiagnosed as pepper spot, a much less severe disease caused by the related pathogen Pseudomonas syringae pv. maculicola. We have developed a phage-based diagnostic that can both identify and detect the causative agent of bacterial blight and differentiate the two pathogens. A recombinant >light>-tagged reporter phage was generated by integrating bacterial luxAB genes encoding luciferase into the genome of P. cannabina pv. alisalensis phage PBSPCA1. The PBSPCA1::luxAB reporter phage is viable and stable and retains properties similar to those of the wildtype phage. PBSPCA1::luxAB rapidly and sensitively detects P. cannabina pv. alisalensis by conferring a bioluminescent signal response to cultured cells. Detection is dependent on cell viability. Other bacterial pathogens of Brassica species such as P. syringae pv. maculicola, Pseudomonas marginalis, Pectobacterium carotovorum, Xanthomonas campestris pv. campestris, and X. campestris pv. raphani either do not produce a response or produce significantly attenuated signals with the reporter phage. Importantly, the reporter phage detects P. cannabina pv. alisalensis on diseased plant specimens, indicating its potential for disease diagnosis.
Development Of Caspofungin Resistance Following Prolonged Therapy For Invasive Candidiasis Secondary To Candida Glabrata Infection
(2008-10) Thompson, George R.; Wiederhold, Nathan P.; Vallor, Ana C.; Villareal, Nyria C.; Lewis, James S.; Patterson, Thomas F.; Wiederhold, Nathan P.
We report a case of Candida glabrata invasive candidiasis that developed reduced susceptibility to caspofungin during prolonged therapy. Pre- and posttreatment isolates were confirmed to be isogenic, and sequencing of hot spots known to confer echinocandin resistance revealed an F659V substitution within the FKS2 region of the glucan synthase complex.
Discovery Of Ethanol-Responsive Small Rnas In Zymomonas Mobilis
(2014-07) Cho, Seung Hee; Lei, Roy; Henninger, Trey D.; Contreras, Lydia M.; Cho, Seung Hee; Lei, Roy; Henninger, Trey D.; Contreras, Lydia M.
Zymomonas mobilis is a bacterium that can produce ethanol by fermentation. Due to its unique metabolism and efficient ethanol production, Z. mobilis has attracted special interest for biofuel energy applications; an important area of study is the regulation of those specific metabolic pathways. Small RNAs (sRNAs) have been studied as molecules that function as transcriptional regulators in response to cellular stresses. While sRNAs have been discovered in various organisms by computational prediction and experimental approaches, their discovery in Z. mobilis has not yet been reported. In this study, we have applied transcriptome analysis and computational predictions to facilitate identification and validation of 15 novel sRNAs in Z. mobilis. We furthermore characterized their expression in the context of high and low levels of intracellular ethanol. Here, we report that 3 of the sRNAs (Zms2, Zms4, and Zms6) are differentially expressed under aerobic and anaerobic conditions, when low and high ethanol productions are observed, respectively. Importantly, when we tested the effect of ethanol stress on the expression of sRNAs in Z. mobilis, Zms2, Zms6, and Zms18 showed differential expression under 5% ethanol stress conditions. These data suggest that in this organism regulatory RNAs can be associated with metabolic functions involved in ethanol stress responses.
Effects Of Signal Level And Spectral Contrast On Vowel Formant Discrimination For Normal-Hearing And Hearing-Impaired Listeners
(2013-06) Woodall, Ashley; Liu, Chang; Woodall, Ashley; Liu, Chang
Purpose: The aim of this study was to determine whether increasing the overall speech level or the individual spectral contrasts of vowel sounds can improve vowel formant discrimination for listeners both with and without normal hearing. Method: Thresholds of vowel formant discrimination were examined for the F2 frequencies of 3 American English vowels for listeners with and without normal hearing. Spectral contrasts of the F2 were enhanced by 3, 6, and 9 dB. Vowel stimuli were presented at 70 and 90 dB SPL. Results: The thresholds of listeners with hearing impairment were reduced significantly after spectral enhancement was implemented, especially at 90 dB SPL, whereas normal-hearing listeners did not benefit from spectral enhancement. Conclusion: These results indicate that a combination of spectral enhancement of F2 and high speech level is most beneficial to improve vowel formant discrimination for listeners with hearing impairment.
Empirical Determination Of Convection Parameters In White Dwarfs. I. Whole Earth Telescope Observations Of EC14012-1446
(2012-06) Provencal, J. L.; Montgomery, Michael H.; Kanaan, A.; Thompson, Susan E.; Dalessio, J.; Shipman, H. L.; Childers, D.; Clemens, J. Christopher; Rosen, R.; Henrique, P.; Bischoff-Kim, Agnes; Strickland, W.; Chandler, Dean; Walter, B.; Watson, T. K.; Castanheira, B.; Wang, S.; Handler, G.; Wood, M.; Vennes, S.; Nemeth, P.; Kepler, S. O.; Reed, M.; Nitta, Atsuko; Kleinman, S. J.; Brown, T.; Kim, S. L.; Sullivan, D.; Chen, W. P.; Yang, M.; Shih, C. Y.; Jiang, X. J.; Sergeev, A. V.; Maksim, A.; Janulis, R.; Baliyan, K. S.; Vats, H. O.; Zola, S.; Baran, A.; Winiarski, M.; Ogloza, W.; Paparo, M.; Bognar, Z.; Papics, P.; Kilkenny, D.; Sefako, R.; Buckley, D.; Loaring, N.; Kniazev, A.; Silvotti, R.; Galleti, S.; Nagel, T.; Vauclair, G.; Dolez, N.; Fremy, J. R.; Perez, J.; Almenara, J. M.; Fraga, L.; Montgomery, Michael H.; Wang, S.
We report on an analysis of 308.3 hr of high-speed photometry targeting the pulsating DA white dwarf EC14012-1446. The data were acquired with the Whole Earth Telescope during the 2008 international observing run XCOV26. The Fourier transform of the light curve contains 19 independent frequencies and numerous combination frequencies. The dominant peaks are 1633.907, 1887.404, and 2504.897 mu Hz. Our analysis of the combination amplitudes reveals that the parent frequencies are consistent with modes of spherical degree l = 1. The combination amplitudes also provide m identifications for the largest amplitude parent frequencies. Our seismology analysis, which includes 2004-2007 archival data, confirms these identifications, provides constraints on additional frequencies, and finds an average period spacing of 41 s. Building on this foundation, we present nonlinear fits to high signal-to-noise light curves from the SOAR 4.1 m, McDonald 2.1 m, and KPNO 2 m telescopes. The fits indicate a time-averaged convective response timescale of tau(0) = 99.4 +/- 17 s, a temperature exponent N = 85 +/- 6.2, and an inclination angle of theta(i) = 32 degrees.9 +/- 3 degrees.2. We present our current empirical map of the convective response timescale across the DA instability strip.
Identifying Structural Variation in Haploid Microbial Genomes from Short-Read Resequencing Data Using Breseq
(2014-11) Barrick, Jeffrey E.; Colburn, Geoffrey; Deatherage, Daniel E.; Traverse, Charles C.; Strand, Matthew D.; Borges, Jordan J.; Knoester, David B.; Reba, Aaron; Meyer, Austin G.; Barrick, Jeffrey E.; Colburn, Geoffrey; Deatherage, Daniel E.; Traverse, Charles C.; Strand, Matthew D.; Borges, Jordan J.; Reba, Aaron; Meyer, Austin G.
Mutations that alter chromosomal structure play critical roles in evolution and disease, including in the origin of new lifestyles and pathogenic traits in microbes. Large-scale rearrangements in genomes are often mediated by recombination events involving new or existing copies of mobile genetic elements, recently duplicated genes, or other repetitive sequences. Most current software programs for predicting structural variation from short-read DNA resequencing data are intended primarily for use on human genomes. They typically disregard information in reads mapping to repeat sequences, and significant post-processing and manual examination of their output is often required to rule out false-positive predictions and precisely describe mutational events. Results: We have implemented an algorithm for identifying structural variation from DNA resequencing data as part of the breseq computational pipeline for predicting mutations in haploid microbial genomes. Our method evaluates the support for new sequence junctions present in a clonal sample from split-read alignments to a reference genome, including matches to repeat sequences. Then, it uses a statistical model of read coverage evenness to accept or reject these predictions. Finally, breseq combines predictions of new junctions and deleted chromosomal regions to output biologically relevant descriptions of mutations and their effects on genes. We demonstrate the performance of breseq on simulated Escherichia coli genomes with deletions generating unique breakpoint sequences, new insertions of mobile genetic elements, and deletions mediated by mobile elements. Then, we reanalyze data from an E. coli K-12 mutation accumulation evolution experiment in which structural variation was not previously identified. Transposon insertions and large-scale chromosomal changes detected by breseq account for similar to 25% of spontaneous mutations in this strain. In all cases, we find that breseq is able to reliably predict structural variation with modest read-depth coverage of the reference genome (>40-fold). Conclusions: Using breseq to predict structural variation should be useful for studies of microbial epidemiology, experimental evolution, synthetic biology, and genetics when a reference genome for a closely related strain is available. In these cases, breseq can discover mutations that may be responsible for important or unintended changes in genomes that might otherwise go undetected.
Indole Production Promotes Escherichia Coli Mixed-Culture Growth With Pseudomonas Aeruginosa By Inhibiting Quorum Signaling
(2012-01) Chu, Weihua; Zere, Tesfalem R.; Weber, Mary M.; Wood, Thomas K.; Whiteley, Marvin; Hidalgo-Romano, Benjamin; Valenzuela, Ernesto; McLean, Robert J. C.; Whiteley, Marvin
Indole production by Escherichia coli, discovered in the early 20th century, has been used as a diagnostic marker for distinguishing E. coli from other enteric bacteria. By using transcriptional profiling and competition studies with defined mutants, we show that cyclic AMP (cAMP)-regulated indole formation is a major factor that enables E. coli growth in mixed biofilm and planktonic populations with Pseudomonas aeruginosa. Mutants deficient in cAMP production (cyaA) or the cAMP receptor gene (crp), as well as indole production (tnaA), were not competitive in coculture with P. aeruginosa but could be restored to wild-type competitiveness by supplementation with a physiologically relevant indole concentration. E. coli sdiA mutants, which lacked the receptor for both indole and N-acyl-homoserine lactones (AHLs), showed no change in competitive fitness, suggesting that indole acted directly on P. aeruginosa. An E. coli tnaA mutant strain regained wild-type competiveness if grown with P. aeruginosa AHL synthase (rhlI and rhlI lasI) mutants. In contrast to the wild type, P. aeruginosa AHL synthase mutants were unable to degrade indole. Indole produced during mixed-culture growth inhibited pyocyanin production and other AHL-regulated virulence factors in P. aeruginosa. Mixed-culture growth with P. aeruginosa stimulated indole formation in E. coli cpdA, which is unable to regulate cAMP levels, suggesting the potential for mixed-culture gene activation via cAMP. These findings illustrate how indole, an early described feature of E. coli central metabolism, can play a significant role in mixed-culture survival by inhibiting quorum-regulated competition factors in P. aeruginosa.
Large Methyl Halide Emissions from South Texas Salt Marshes
(2014) Rhew, R. C.; Whelan, M. E.; Min, D. H.; Min, D. H.
Coastal salt marshes are natural sources of methyl chloride (CH3Cl) and methyl bromide (CH3Br) to the atmosphere, but measured emission rates vary widely by geography. Here we report large methyl halide fluxes from subtropical salt marshes of south Texas. Sites with the halophytic plant, Batis maritima, emitted methyl halides at rates that are orders of magnitude greater than sites containing other vascular plants or macroalgae. B. maritima emissions were generally highest at midday; however, diurnal variability was more pronounced for CH3Br than CH3Cl, and surprisingly high nighttime CH3Cl fluxes were observed in July. Seasonal and intra-site variability were large, even taking into account biomass differences. Overall, these subtropical salt marsh sites show much higher emission rates than temperate salt marshes at similar times of the year, supporting the contention that low-latitude salt marshes are significant sources of CH3Cl and CH3Br.
Letter to C.I. Alexander from H.B. Stenzel on 1940-02-07
(1940-02-07) Stenzel, Henryk B.
Letter to Chester Stock from H.B. Stenzel on 1946-02-11
(1946-02-11) Stenzel, Henryk B.
Letter to E.Wallace Moore from H.B. Stenzel on 1941-05-29
(1941-05-29) Stenzel, H.B.
Letter to Fred T. Moseley from H.B. Stenzel on 1942-01-15
(1942-01-15) Stenzel, H.B.
Letter to Gayle Scott from H.B. Stenzel on 1942-09-11
(1942-09-11) Stenzel, Henryk B.
Letter to H. B. Stenzel from M. N. Broughton on 1938-06-23
(1938-06-23) Broughton, M. N.
Letter to H.A. Pilsbry from H.B. Stenzel on 1940-08-14
(1940-08-14) Stenzel, H.B.
Letter to H.B. Parks from H.B. Stenzel on 1935-05-29
(1935-05-29) Stenzel, H.B.
Letter to H.B. Parks from H.B. Stenzel on 1935-06-11
(1935-06-11) Stenzel, H.B.