scholarly journals Gene Transcript Abundance Profiles Distinguish Kawasaki Disease from Adenovirus Infection

2009 ◽  
Vol 200 (4) ◽  
pp. 657-666 ◽  
Author(s):  
Stephen J. Popper ◽  
Virginia E. Watson ◽  
Chisato Shimizu ◽  
John T. Kanegaye ◽  
Jane C. Burns ◽  
...  
BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shuhua Zhan ◽  
Cortland Griswold ◽  
Lewis Lukens

Abstract Background Genetic variation for gene expression is a source of phenotypic variation for natural and agricultural species. The common approach to map and to quantify gene expression from genetically distinct individuals is to assign their RNA-seq reads to a single reference genome. However, RNA-seq reads from alleles dissimilar to this reference genome may fail to map correctly, causing transcript levels to be underestimated. Presently, the extent of this mapping problem is not clear, particularly in highly diverse species. We investigated if mapping bias occurred and if chromosomal features associated with mapping bias. Zea mays presents a model species to assess these questions, given it has genotypically distinct and well-studied genetic lines. Results In Zea mays, the inbred B73 genome is the standard reference genome and template for RNA-seq read assignments. In the absence of mapping bias, B73 and a second inbred line, Mo17, would each have an approximately equal number of regulatory alleles that increase gene expression. Remarkably, Mo17 had 2–4 times fewer such positively acting alleles than did B73 when RNA-seq reads were aligned to the B73 reference genome. Reciprocally, over one-half of the B73 alleles that increased gene expression were not detected when reads were aligned to the Mo17 genome template. Genes at dissimilar chromosomal ends were strongly affected by mapping bias, and genes at more similar pericentromeric regions were less affected. Biased transcript estimates were higher in untranslated regions and lower in splice junctions. Bias occurred across software and alignment parameters. Conclusions Mapping bias very strongly affects gene transcript abundance estimates in maize, and bias varies across chromosomal features. Individual genome or transcriptome templates are likely necessary for accurate transcript estimation across genetically variable individuals in maize and other species.


2000 ◽  
Vol 6 (9) ◽  
pp. 750-765 ◽  
Author(s):  
Ann-Marie Martoglio ◽  
Brian D. M. Tom ◽  
Michael Starkey ◽  
Anthony N. Corps ◽  
D. Stephen Charnock-Jones ◽  
...  

2020 ◽  
Vol 65 (1) ◽  
pp. 373-389 ◽  
Author(s):  
David S. Saunders

Whole-animal experiments devised to investigate possible association between photoperiodic time measurement and the circadian system (Bünning's hypothesis) are compared with more recent molecular investigations of circadian clock genes. In Sarcophaga argyrostoma and some other species, experimental cycles of light and darkness revealed a photoperiodic oscillator, set to constant phase at dusk and measuring night length repeatedly during extended periods of darkness. In some species, however, extreme dampening revealed an unrepetitive (i.e., hourglass-like) response. Rhythms of clock gene transcript abundance may also show similar phase relationships to the light cycle, and gene silencing of important clock genes indicates that they play a crucial role in photoperiodism either alone or in concert. However, the multiplicity of peripheral oscillators in the insect circadian system indicates that more complex mechanisms might also be important.


2010 ◽  
Vol 18 (1) ◽  
pp. 89-99 ◽  
Author(s):  
Nerea Bartolomé ◽  
Patricia Aspichueta ◽  
María J Martínez ◽  
Mercedes Vázquez-Chantada ◽  
María L Martínez-Chantar ◽  
...  

Dyslipidemia and hepatic overproduction of very low density lipoprotein (VLDL) are hallmarks of the septic response, yet the underlying mechanisms are not fully defined. We evaluated the lipoprotein subclasses profile and hepatic VLDL assembly machinery over 24 h in fasted LPS-treated rats. The response of serum non-esterified fatty acids (NEFA) and glucose to endotoxin was biphasic, with increased levels of NEFA and hypoglycemia in the first 12 h-phase, and low NEFA and high glucose in the second 12 h-phase. Hypertriglyceridemia was more marked in the first 12 h (6.8-fold), when triglyceride abundance increased in all lipoprotein subclasses, and preferentially in large VLDL. The abundance of medium-sized VLDL and the increase in the number of VLDL particles was higher in the second phase (10-fold vs 5-fold in the first phase); however, apoB gene transcript abundance increased only in the second phase. Analysis of putative pre-translational mechanisms revealed that neither increased Apob transcription rate nor increased transcript binding to mRNA stabilizing HuR (Hu antigen R) protein paralleled the increase in apoB transcripts. In conclusion, endotoxin challenge induces increases in plasma NEFA and large, triglyceride-rich VLDL. After approximately 12 h, the triglyceride-rich VLDLs are replaced by medium-sized, triglyceride-poor VLDL particles. Hepatic apoB mRNA abundance also increases during the second period, suggesting a role for apoB protein expression in the acute reaction against sepsis.


1994 ◽  
Vol 4 (3) ◽  
pp. 299-305 ◽  
Author(s):  
Douglas C. Doehlert ◽  
Leslie J. Smith ◽  
Edwin R. Duke

AbstractRelationships have been investigated between gene transcript abundance, enzyme activities and storage product accumulation in developing maize (Zea maysL.) kernels from 10 to 55 days postpollination (DPP). At the early stages of kernel development, there was very little increase in dry weight but kernels accumulated high concentrations of sugars and amino acids. At the end of this ‘lag’ phase (at 15 DPP), many transcripts appeared with little evidence of their translation. The initiation of the kernel-fill period at 20 DPP was characterized by a sudden rise in total RNA, increases in enzyme activities, and the initiation of storage product accumulation. Zein accumulation during this phase was highly correlated with α-zein transcript abundance. Starch accumulation was correlated with both the activity of ADP-GIc pyrophosphorylase and the abundance of gene transcripts encoding this enzyme (Shrunken-2andBrittle-2). DNA content of kernels increased linearly up to 30 DPP as a result of endoreplication, but had no apparent relationship to gene expression. DNA may accumulate as a storage product. Kernel-fill terminated when the moisture content fell below 36% and was marked by a decline of transcripts and a reduction of enzyme activities.


2013 ◽  
Vol 79 (12) ◽  
pp. 3716-3723 ◽  
Author(s):  
Christopher A. Gulvik ◽  
Alison Buchan

ABSTRACTPlant-derived aromatic compounds are important components of the dissolved organic carbon pool in coastal salt marshes, and their mineralization by resident bacteria contributes to carbon cycling in these systems. Members of the roseobacter lineage of marine bacteria are abundant in coastal salt marshes, and several characterized strains, includingSagittula stellataE-37, utilize aromatic compounds as primary growth substrates. The genome sequence ofS. stellatacontains multiple, potentially competing, aerobic ring-cleaving pathways. Preferential hierarchies in substrate utilization and complex transcriptional regulation have been demonstrated to be the norm in many soil bacteria that also contain multiple ring-cleaving pathways. The purpose of this study was to ascertain whether substrate preference exists inS. stellatawhen the organism is provided a mixture of aromatic compounds that proceed through different ring-cleaving pathways. We focused on the protocatechuate (pca) and the aerobic benzoyl coenzyme A (box) pathways and the substrates known to proceed through them,p-hydroxybenzoate (POB) and benzoate, respectively. When these two substrates were provided at nonlimiting carbon concentrations, temporal patterns of cell density, gene transcript abundance, enzyme activity, and substrate concentrations indicated thatS. stellatasimultaneously catabolized both substrates. Furthermore, enhanced growth rates were observed whenS. stellatawas provided both compounds simultaneously compared to the rates of cells grown singly with an equimolar concentration of either substrate alone. This simultaneous-catabolism phenotype was also demonstrated in another lineage member,Ruegeria pomeroyiDSS-3. These findings challenge the paradigm of sequential aromatic catabolism reported for soil bacteria and contribute to the growing body of physiological evidence demonstrating the metabolic versatility of roseobacters.


2009 ◽  
Vol 22 (3) ◽  
pp. 362-368 ◽  
Author(s):  
Benjamin P. Millett ◽  
Dimitre S. Mollov ◽  
Massimo Iorizzo ◽  
Domenico Carputo ◽  
James M. Bradeen

Foliar late blight is one of the most important diseases of potato. Foliar blight resistance has been shown to change as a plant ages. In other pathosystems, resistance (R) gene transcript levels appear to be correlated to disease resistance. The cloning of the broad-spectrum, foliar blight resistance gene RB provided the opportunity to explore how foliar blight resistance and R-gene transcript levels vary with plant age. Plants of Solanum bulbocastanum PT29, from which RB, including the native promoter and other flanking regions, was cloned, and S. tuberosum cv. Dark Red Norland (nontransformed and RB-transformed) representing three different developmental stages were screened for resistance to late blight and RB transcript levels. Preflowering plants of all genotypes exhibited the highest levels of resistance, followed by postflowering and near-senescing plants. The RB transgene significantly affected resistance, enhancing resistance levels of all RB-containing lines, especially in younger plants. RB transgene transcripts were detected at all plant ages, despite weak correlation with disease resistance. Consistent transcript levels in plants of different physiological ages with variable levels of disease resistance demonstrate that changes in disease-resistance phenotypes associated with plant age cannot be attributed to changes in R-gene transcript abundance.


2012 ◽  
Vol 79 (3) ◽  
pp. 901-907 ◽  
Author(s):  
Jessica A. Smith ◽  
Derek R. Lovley ◽  
Pier-Luc Tremblay

ABSTRACTGeobacterspecies are important Fe(III) reducers in a diversity of soils and sediments. Mechanisms for Fe(III) oxide reduction have been studied in detail inGeobacter sulfurreducens, but a number of the most thoroughly studied outer surface components ofG. sulfurreducens, particularlyc-type cytochromes, are not well conserved amongGeobacterspecies. In order to identify cellular components potentially important for Fe(III) oxide reduction inGeobacter metallireducens, gene transcript abundance was compared in cells grown on Fe(III) oxide or soluble Fe(III) citrate with whole-genome microarrays. Outer-surface cytochromes were also identified. Deletion of genes forc-type cytochromes that had higher transcript abundance during growth on Fe(III) oxides and/or were detected in the outer-surface protein fraction identified sixc-type cytochrome genes, that when deleted removed the capacity for Fe(III) oxide reduction. Several of thec-type cytochromes which were essential for Fe(III) oxide reduction inG. metallireducenshave homologs inG. sulfurreducensthat are not important for Fe(III) oxide reduction. Other genes essential for Fe(III) oxide reduction included a gene predicted to encode an NHL (Ncl-1–HT2A–Lin-41) repeat-containing protein and a gene potentially involved in pili glycosylation. Genes associated with flagellum-based motility, chemotaxis, and pili had higher transcript abundance during growth on Fe(III) oxide, consistent with the previously proposed importance of these components in Fe(III) oxide reduction. These results demonstrate that there are similarities in extracellular electron transfer betweenG. metallireducensandG. sulfurreducensbut the outer-surfacec-type cytochromes involved in Fe(III) oxide reduction are different.


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