Transcriptome changes in the phenylpropanoid pathway of Glycine max in response to Pseudomonas syringae infection

BACKGROUND: Reports of plant molecular responses to pathogenic infections have pinpointed increases in activity of several genes of the phenylpropanoid pathway leading to the synthesis of lignin and flavonoids. The majority of those findings were derived from single gene studies and more recently from several global gene expression analyses. We undertook a global transcriptional analysis focused on the response of genes of the multiple branches of the phenylpropanoid pathway to infection by the Pseudomonas syringae pv. glycinea with or without the avirulence gene avrB to characterize more broadly the contribution of the multiple branches of the pathway to the resistance response in soybean. Transcript abundance in leaves was determined from analysis of soybean cDNA microarray data and hybridizations to RNA blots with specific gene probes. RESULTS: The majority of the genes surveyed presented patterns of increased transcript accumulation. Some increased rapidly, 2 and 4 hours after inoculation, while others started to accumulate slowly by 8 – 12 hours. In contrast, transcripts of a few genes decreased in abundance 2 hours post inoculation. Most interestingly was the opposite temporal fluctuation in transcript abundance between early responsive genes in defense (CHS and IFS1) and F3H, the gene encoding a pivotal enzyme in the synthesis of anthocyanins, proanthocyanidins and flavonols. F3H transcripts decreased rapidly 2 hours post inoculation and increased during periods when CHS and IFS transcripts decreased. It was also determined that all but one (CHS4) family member genes (CHS1, CHS2, CHS3, CHS5, CHS6 and CHS7/8) accumulated higher transcript levels during the defense response provoked by the avirulent pathogen challenge. CONCLUSION: Based on the mRNA profiles, these results show the strong bias that soybean has towards increasing the synthesis of isoflavonoid phytoalexins concomitant with the down regulation of genes required for the synthesis of anthocyanins and proanthocyanins. Although proanthocyanins are known to be toxic compounds, the cells in the soybean leaves seem to be programmed to prioritize the synthesis and accumulation of isoflavonoid and pterocarpan phytoalexins during the resistance response. It was known that CHS transcripts accumulate in great abundance rapidly after inoculation of the soybean plants but our results have demonstrated that all but one (CHS4) member of the gene family member genes accumulated higher transcript levels during the defense response

Chemical analysis of flotsam ambergris

The natural product ambergris is only found rarely on beaches, as jetsam. Even more scarce, or even absent, are accounts of flotsam ambergris. Here, we report the chemical analysis of a rare, large piece (\u3e100kg) of flotsam found in the Atlantic in 2019. About 95% of subsamples from the outside of the coprolith was soluble in dichloromethane. Of this, FTIR spectroscopy, APCI-MS and GC-MS indicated the presence of ambrein. Radiocarbon dating indicated that the sample was post 1950s in age. The 13C/12C isotope ratio (−22.5 ‰) was typical of those reported to date for whale ‘body’ ambergris. Metals of ambergris have hardly been reported previously. The distribution found here for the flotsam, was dominated by copper and zinc, which is similar to that of several squid species. This is also consistent with the presence of squid beaks in the coprolith. Squid are a major prey species of sperm whales

Two Colors, One Species: The Case of Melissodes nigroaenea (Apidae: Eucerini), an Important Pollinator of Cotton Fields in Brazil

Accurate taxonomic delimitation in ecological research is absolutely critical as studies that seek to evaluate levels of biodiversity and qualify human effects on the environment are rapidly undertaken. Coloration is a widely used morphological character for species identification through dichotomous keys. However, taxonomic identification based upon coloration is often unreliable because this character can exhibit high degree of intraspecific variation. In this study, we use a DNA barcoding approach to investigate the interpretation of two color morphs (yellow or dark) in the eucerine bee Melissodes nigroaenea. Our hypothesis is that if significant genetic divergence exists between each morphotype of M. nigroaenea, coloration reflects two distinct evolutionary lineages within this species, which may require taxonomic revision. Our alternative hypothesis is that, if genetic divergence is low between each morphotype of M. nigroaenea, we can attribute this variation to color polymorphism. Our Bayesian phylogenetic reconstruction revealed that both yellow and black individuals clustered together in a highly supported phylogenetic group. Additionally, pairwise genetic distances between M. nigroaenea color morphotypes were lower than 3%. These results indicate that both mesosome color morphs correspond to intraspecific variability within the same evolutionary unit. Together, our results indicate that mesosome coloration is not a reliable character for taxonomic differentiation of these Melissodes species, and that the incorporation of DNA barcoding approaches to taxonomic classification can help resolve some of the problems that originate while relying on purely morphological taxonomy

Two Colors, One Species: The Case of Melissodes nigroaenea (Apidae: Eucerini), an Important Pollinator of Cotton Fields in Brazil

Accurate taxonomic delimitation in ecological research is absolutely critical as studies that seek to evaluate levels of biodiversity and qualify human effects on the environment are rapidly undertaken. Coloration is a widely used morphological character for species identification through dichotomous keys. However, taxonomic identification based upon coloration is often unreliable because this character can exhibit high degree of intraspecific variation. In this study, we use a DNA barcoding approach to investigate the interpretation of two color morphs (yellow or dark) in the eucerine bee Melissodes nigroaenea. Our hypothesis is that if significant genetic divergence exists between each morphotype of M. nigroaenea, coloration reflects two distinct evolutionary lineages within this species, which may require taxonomic revision. Our alternative hypothesis is that, if genetic divergence is low between each morphotype of M. nigroaenea, we can attribute this variation to color polymorphism. Our Bayesian phylogenetic reconstruction revealed that both yellow and black individuals clustered together in a highly supported phylogenetic group. Additionally, pairwise genetic distances between M. nigroaenea color morphotypes were lower than 3%. These results indicate that both mesosome color morphs correspond to intraspecific variability within the same evolutionary unit. Together, our results indicate that mesosome coloration is not a reliable character for taxonomic differentiation of these Melissodes species, and that the incorporation of DNA barcoding approaches to taxonomic classification can help resolve some of the problems that originate while relying on purely morphological taxonomy

Diatraea saccharalis history of colonization in the Americas: The case for human-mediated dispersal

The sugarcane borer moth, Diatraea saccharalis, is one of the most important pests of sugarcane and maize crops in the Western Hemisphere. The pest is widespread throughout South and Central America, the Caribbean region and the southern United States. One of the most intriguing features of D. saccharalis population dynamics is the high rate of range expansion reported in recent years. To shed light on the history of colonization of D. saccharalis, we investigated the genetic structure and diversity in American populations using single nucleotide polymorphism (SNPs) markers throughout the genome and sequences of the mitochondrial gene cytochrome oxidase (COI). Our primary goal was to propose possible dispersal routes from the putative center of origin that can explain the spatial pattern of genetic diversity. Our findings showed a clear correspondence between genetic structure and the geographical distributions of this pest insect on the American continents. The clustering analyses indicated three distinct groups: one composed of Brazilian populations, a second group composed of populations from El Salvador, Mexico, Texas and Louisiana and a third group composed of the Florida population. The predicted time of divergence predates the agriculture expansion period, but the pattern of distribution of haplotype diversity suggests that human-mediated movement was most likely the factor responsible for the widespread distribution in the Americas. The study of the early history of D. saccharalis promotes a better understanding of range expansion, the history of invasion, and demographic patterns of pest populations in the Americas.Fil: Francischini, Fabricio J. B.. Universidade Estadual de Campinas. Instituto de Biología; BrasilFil: Cordeiro, Erick M. G.. Universidade do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz; BrasilFil: Campos, Jaqueline B. de. Universidade Estadual de Campinas. Instituto de Biología; BrasilFil: Alves Pereira, Alessandro. Universidade Estadual de Campinas; BrasilFil: Gomes Viana, João Paulo. Universidade Estadual de Campinas. Instituto de Biología; BrasilFil: Wu, Xing. University of Illinois; Estados UnidosFil: Wei, Wei. University of Illinois; Estados UnidosFil: Brown, Patrick. University of Illinois; Estados UnidosFil: Joyce, Andrea. University of California; Estados UnidosFil: Murúa, María Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Tecnología Agroindustrial del Noroeste Argentino. Provincia de Tucumán. Ministerio de Desarrollo Productivo. Estación Experimental Agroindustrial "Obispo Colombres" (p). Instituto de Tecnología Agroindustrial del Noroeste Argentino; ArgentinaFil: Fogliata, Sofia Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Tecnología Agroindustrial del Noroeste Argentino. Provincia de Tucumán. Ministerio de Desarrollo Productivo. Estación Experimental Agroindustrial "Obispo Colombres" (p). Instituto de Tecnología Agroindustrial del Noroeste Argentino; ArgentinaFil: Clough, Steven J.. University of Illinois; Estados Unidos. United States Department of Agriculture; Estados UnidosFil: Zucchi, María Inmaculada. Universidade Estadual de Campinas; Brasi

Lateral organic carbon supply to the deep Canada Basin

Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 35 (2008): L11607, doi:10.1029/2008GL034271.Understanding the processes driving the carbon cycle in the Arctic Ocean is important for assessing the impacts of the predicted rapid and amplified climate change in this region. We analyzed settling particle samples intercepted by a time-series sediment trap deployed in the abyssal Canada Basin (at 3067 m) in order to examine carbon export to the deep Arctic Ocean. Strikingly old radiocarbon ages (apparent mean 14C age = ∼1900 years) of the organic carbon, abundant lithogenic material (∼80%), and mass flux variations temporally decoupled from the cycle of primary productivity in overlying surface waters together suggest that, unlike other ocean basins, the majority of the particulate organic carbon entering the deep Canada Basin is supplied from the surrounding margins.This research was funded by the NSF Ocean Sciences Division (Chemical Oceanography program) and NSF Office of Polar Programs, Office of Naval Research, as well as the Ocean and Climate Change Institute and Arctic Research Initiative at the Woods Hole Oceanographic Institution

Alteration of the bZIP60/IRE1 Pathway Affects Plant Response to ER Stress in Arabidopsis thaliana

The Unfolded Protein Response (UPR) is elicited under cellular and environmental stress conditions that disrupt protein folding in the endoplasmic reticulum (ER). Through the transcriptional induction of genes encoding ER resident chaperones and proteins involved in folding, the pathway contributes to alleviating ER stress by increasing the folding capacity in the ER. Similarly to other eukaryotic systems, one arm of the UPR in Arabidopsis is set off by a non-conventional splicing event mediated by ribonuclease kinase IRE1b. The enzyme specifically targets mature bZIP60 RNA for cleavage, which results in a novel splice variant encoding a nuclear localized transcription factor. Although it is clear that this molecular switch widely affects the transcriptome, its exact role in overall plant response to stress has not been established and mutant approaches have not provided much insight. In this study, we took a transgenic approach to manipulate the pathway in positive and negative fashions. Our data show that the ER-resident chaperone BiP accumulates differentially depending on the level of activation of the pathway. In addition, phenotypes of the transgenic lines suggest that BiP accumulation is positively correlated with plant tolerance to chronic ER stress

The Orphan Gene ybjN Conveys Pleiotropic Effects on Multicellular Behavior and Survival of Escherichia coli

YbjN, encoding an enterobacteria-specific protein, is a multicopy suppressor of temperature sensitivity in the ts9 mutant strain of Escherichia coli. In this study, we further explored the role(s) of ybjN. First, we demonstrated that the ybjN transcript was about 10-fold lower in the ts9 strain compared to that of E. coli strain BW25113 (BW). Introduction of multiple copies of ybjN in the ts9 strain resulted in over-expression of ybjN by about 10-fold as compared to that of BW. These results suggested that temperature sensitivity of the ts9 mutant of E. coli may be related to expression levels of ybjN. Characterization of E. coli ybjN mutant revealed that ybjN mutation resulted in pleiotropic phenotypes, including increased motility, fimbriation (auto-aggregation), exopolysaccharide production, and biofilm formation. In contrast, over-expression of ybjN (in terms of multiple copies) resulted in reduced motility, fimbriation, exopolysaccharide production, biofilm formation and acid resistance. In addition, our results indicate that a ybjN-homolog gene from Erwinia amylovora, a plant enterobacterial pathogen, is functionally conserved with that of E. coli, suggesting similar evolution of the YbjN family proteins in enterobacteria. A microarray study revealed that the expression level of ybjN was inversely correlated with the expression of flagellar, fimbrial and acid resistance genes. Over-expression of ybjN significantly down-regulated genes involved in citric acid cycle, glycolysis, the glyoxylate shunt, oxidative phosphorylation, amino acid and nucleotide metabolism. Furthermore, over-expression of ybjN up-regulated toxin-antitoxin modules, the SOS response pathway, cold shock and starvation induced transporter genes. Collectively, these results suggest that YbjN may play important roles in regulating bacterial multicellular behavior, metabolism, and survival under stress conditions in E. coli. These results also suggest that ybjN over-expression-related temperature rescue of the ts9 mutant may be due to down-regulation of metabolic activity and activation of stress response genes in the ts9 mutant