Functional genomics of arbuscular mycorrhiza: decoding the symbiotic cell programme

2004 ◽  
Vol 82 (8) ◽  
pp. 1228-1234 ◽  
Author(s):  
Vivienne Gianinazzi-Pearson ◽  
Laurent Brechenmacher
Keyword(s):  
Functional Genomics ◽  
Arbuscular Mycorrhiza ◽  
Gene Networks ◽  
Large Scale ◽  
Subtractive Hybridization ◽  
Suppressive Subtractive Hybridization ◽  
Rna Expression ◽  
Plant Genes ◽  
Fungal Interactions ◽  
Insight Into

More extensive insight into plant genes involved in the symbiotic programme of arbuscular mycorrhiza is presently being achieved by global approaches that aim to discover novel genes or subsets of genes that are essential to cell programmes in the different steps of plant–fungal interactions. The strategy of functional genomics based on large-scale differential RNA expression analyses (differential-display reverse transcriptase - PCR), electronic Northerns, suppressive subtractive hybridization, DNA chips) is presented, with a focus on arbuscular mycorrhiza in Pisum sativum and Medicago truncatula. The most recent knowledge about gene networks that are modulated in roots during arbuscular establishment and functioning is discussed.Key words: arbuscular mycorrhiza, symbiotic programme, gene expression, pea, annual alfalfa.

scholarly journals Molecular Characterization of Brucella abortus Chromosome II Recombination

2003 ◽  
Vol 185 (20) ◽  
pp. 6130-6136 ◽  
Author(s):  
Georgios Tsoktouridis ◽  
Christian A. Merz ◽  
Simon P. Manning ◽  
Renée Giovagnoli-Kurtz ◽  
Leanne E. Williams ◽  
...  
Keyword(s):  
Brucella Abortus ◽  
Large Scale ◽  
Brucella Melitensis ◽  
Subtractive Hybridization ◽  
Open Reading Frames ◽  
Suppressive Subtractive Hybridization ◽  
Recombination Mechanism ◽  
Chromosome Ii ◽  
Reading Frames

ABSTRACT Large-scale genomic rearrangements including inversions, deletions, and duplications are significant in bacterial evolution. The recently completed Brucella melitensis 16M and Brucella suis 1330 genomes have facilitated the investigation of such events in the Brucella spp. Suppressive subtractive hybridization (SSH) was employed in identifying genomic differences between B. melitensis 16M and Brucella abortus 2308. Analysis of 45 SSH clones revealed several deletions on chromosomes of B. abortus and B. melitensis that encoded proteins of various metabolic pathways. A 640-kb inversion on chromosome II of B. abortus has been reported previously (S. Michaux Charachon, G. Bourg, E. Jumas Bilak, P. Guigue Talet, A. Allardet Servent, D. O'Callaghan, and M. Ramuz, J. Bacteriol. 179:3244-3249, 1997) and is further described in this study. One end of the inverted region is located on a deleted TATGC site between open reading frames BMEII0292 and BMEII0293. The other end inserted at a GTGTC site of the cyclic-di-GMP phosphodiesterase A (PDEA) gene (BMEII1009), dividing PDEA into two unequal DNA segments of 160 and 977 bp. As a consequence of inversion, the 160-bp segment that encodes the N-terminal region of PDEA was relocated at the opposite end of the inverted chromosomal region. The splitting of the PDEA gene most likely inactivated the function of this enzyme. A recombination mechanism responsible for this inversion is proposed.

scholarly journals Host Genes Involved in Nodulation Preference in Common Bean (Phaseolus vulgaris)–Rhizobium etli Symbiosis Revealed by Suppressive Subtractive Hybridization

2008 ◽  
Vol 21 (4) ◽  
pp. 459-468 ◽  
Author(s):  
Eitel Peltzer Meschini ◽  
Flavio Antonio Blanco ◽  
María Eugenia Zanetti ◽  
María Pía Beker ◽  
Helge Küster ◽  
...  
Keyword(s):  
Common Bean ◽  
Transcript Abundance ◽  
Subtractive Hybridization ◽  
Suppressive Subtractive Hybridization ◽  
Specific Response ◽  
Rhizobium Etli ◽  
Symbiotic Interaction ◽  
Consensus Sequences ◽  
Bean Plants ◽  
Plant Genes

Common bean cultivars are nodulated preferentially by Rhizobium etli lineages from the same center of host diversification. Nodulation was found to be earlier and numerous in bean plants inoculated with the cognate strain. We predicted that analysis of transcripts at early stages of the interaction between host and rhizobium would identify plant genes that are most likely to be involved in this preferential nodulation. Therefore, we applied a suppressive subtractive hybridization approach in which cDNA from a Mesoamerican cultivar inoculated with either the more- or less-efficient strain of R. etli was used as the driver and the tester, respectively. Forty-one independent tentative consensus sequences (TCs) were obtained and classified into different functional categories. Of 11 selected TCs, 9 were confirmed by quantitative reverse-transcriptase polymerase chain reaction. Two genes show high homology to previously characterized plant receptors. Two other upregulated genes encode for Rab11, a member of the small GTP-binding protein family, and HAP5, a subunit of the heterotrimeric CCAAT-transcription factor. Interestingly, one of the TCs encodes for an isoflavone reductase, which may lead to earlier Nod factor production by specific strains of rhizobia. The transcript abundance of selected cDNAs also was found to be higher in mature nodules of the more efficient interaction. Small or no differences were observed when an Andean bean cultivar was inoculated with a cognate strain, suggesting involvement of these genes in the strain-specific response. The potential role of these genes in the early preferential symbiotic interaction is discussed.

scholarly journals Geo-Spatial Analysis of Population Density and Annual Income to Identify Large-Scale Socio-Demographic Disparities

2021 ◽  
Vol 10 (7) ◽  
pp. 432
Author(s):  
Nicolai Moos ◽  
Carsten Juergens ◽  
Andreas P. Redecker
Keyword(s):  
Population Density ◽  
Large Scale ◽  
Methodological Approach ◽  
Spatial Relationship ◽  
Postal Code ◽  
Annual Income ◽  
Choropleth Maps ◽  
Clustering Approach ◽  
Relationship Of ◽  
Insight Into

This paper describes a methodological approach that is able to analyse socio-demographic and -economic data in large-scale spatial detail. Based on the two variables, population density and annual income, one investigates the spatial relationship of these variables to identify locations of imbalance or disparities assisted by bivariate choropleth maps. The aim is to gain a deeper insight into spatial components of socioeconomic nexuses, such as the relationships between the two variables, especially for high-resolution spatial units. The used methodology is able to assist political decision-making, target group advertising in the field of geo-marketing and for the site searches of new shop locations, as well as further socioeconomic research and urban planning. The developed methodology was tested in a national case study in Germany and is easily transferrable to other countries with comparable datasets. The analysis was carried out utilising data about population density and average annual income linked to spatially referenced polygons of postal codes. These were disaggregated initially via a readapted three-class dasymetric mapping approach and allocated to large-scale city block polygons. Univariate and bivariate choropleth maps generated from the resulting datasets were then used to identify and compare spatial economic disparities for a study area in North Rhine-Westphalia (NRW), Germany. Subsequently, based on these variables, a multivariate clustering approach was conducted for a demonstration area in Dortmund. In the result, it was obvious that the spatially disaggregated data allow more detailed insight into spatial patterns of socioeconomic attributes than the coarser data related to postal code polygons.

scholarly journals Using protein turnover to expand the applications of transcriptomics

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marissa A. Smail ◽  
James K. Reigle ◽  
Robert E. McCullumsmith
Keyword(s):  
Protein Turnover ◽  
Half Life ◽  
Rna Expression ◽  
Protein Abundance ◽  
Life Data ◽  
Research Fields ◽  
Extended Application ◽  
Functional Implications ◽  
Transcriptomics Data ◽  
Insight Into

AbstractRNA expression and protein abundance are often at odds when measured in parallel, raising questions about the functional implications of transcriptomics data. Here, we present the concept of persistence, which attempts to address this challenge by combining protein half-life data with RNA expression into a single metric that approximates protein abundance. The longer a protein’s half-life, the more influence it can have on its surroundings. This data offers a valuable opportunity to gain deeper insight into the functional meaning of transcriptome changes. We demonstrate the application of persistence using schizophrenia (SCZ) datasets, where it greatly improved our ability to predict protein abundance from RNA expression. Furthermore, this approach successfully identified persistent genes and pathways known to have impactful changes in SCZ. These results suggest that persistence is a valuable metric for improving the functional insight offered by transcriptomics data, and extended application of this concept could advance numerous research fields.

scholarly journals Metachronal waves in magnetic micro-robotic paddles for artificial cilia

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Matthew T. Bryan ◽  
Elizabeth L. Martin ◽  
Aleksandra Pac ◽  
Andrew D. Gilbert ◽  
Feodor Y. Ogrin
Keyword(s):  
Large Scale ◽  
Point Of Care ◽  
Hydrodynamic Response ◽  
Flow Speeds ◽  
Break Time ◽  
Large Scale Manufacture ◽  
Fresh Insight ◽  
Metachronal Waves ◽  
Insight Into ◽  
Phase Differences

AbstractBiological cilia generate fluid movement within viscosity-dominated environments using beating motions that break time-reversal symmetry. This creates a metachronal wave, which enhances flow efficiency. Artificially mimicking this behaviour could improve microfluidic point-of-care devices, since viscosity-dominated fluid dynamics impede fluid flow and mixing of reagents, limiting potential for multiplexing diagnostic tests. However, current biomimicry schemes require either variation in the hydrodynamic response across a cilia array or a complex magnetic anisotropy configuration to synchronise the actuation sequence with the driving field. Here, we show that simple modifications to the structural design introduce phase differences between individual actuators, leading to the spontaneous formation of metachronal waves. This generates flow speeds of up to 16 μm/s as far as 675 μm above the actuator plane. By introducing metachronal waves through lithographic structuring, large scale manufacture becomes feasible. Additionally, by demonstrating that metachronal waves emerge from non-uniformity in internal structural mechanics, we offer fresh insight into the mechanics of cilia coordination.

scholarly journals Meeting Highlights: Genome Sequencing and Biology 2001

2001 ◽  
Vol 2 (4) ◽  
pp. 243-251
Author(s):  
Jo Wixon
Keyword(s):  
Comparative Genomics ◽  
Functional Genomics ◽  
Genome Sequencing ◽  
Large Scale ◽  
Model Organism

We bring you a report from the CSHL Genome Sequencing and Biology Meeting, which has a long and prestigious history. This year there were sessions on large-scale sequencing and analysis, polymorphisms (covering discovery and technologies and mapping and analysis), comparative genomics of mammalian and model organism genomes, functional genomics and bioinformatics.

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