Le SY et al. (2003) Proc IEEE Comput Soc Bioinform Conf "Statistical inference for well-ordered structures in nucleotide sequences."

Maize JV, Le SY, Chen JH

[Proc IEEE Comput Soc Bioinform Conf, 2003]

Distinct, local structures are frequently correlated with functional RNA elements involved in post-transcriptional regulation of gene expression. Discovery of microRNAs (miRNAs) suggests that there are a large class of small non-coding RNAs in eukaryotic genomes. These miRNAs have the potential to form distinct fold-back stem-loop structures. The prediction of those well-ordered folding sequences (WFS) in genomic sequences is very helpful for our understanding of RNA-based gene regulation and the determination of local RNA elements with structure-dependent functions. In this study, we describe a novel method for discovering the local WFS in a nucleotide sequence by Monte Carlo simulation and RNA folding. In the approach the quality of a local WFS is assessed by the energy difference (E(diff)) between the optimal structure folded in the local segment and its corresponding optimal, restrained structure where all the previous base pairings formed in the optimal structure are prohibited. Distinct WFS can be discovered by scanning successive segments along a sequence for evaluating the difference between E(diff) of the natural sequence and those computed from randomly shuffled sequences. Our results indicate that the statistically significant WFS detected in the genomic sequences of Caenorhabditis elegans (C.elegans) F49E12, T07C5, T07D1, T10H9, Y56A3A and Y71G12B are coincident with known fold-back stem-loops found in miRNA precursors. The potential and implications of our method in searching for miRNAs in genomes is discussed.

Hoss S et al. (2011) Sci Total Environ "Assessing the risk posed to free-living soil nematodes by a genetically modified maize expressing the insecticidal Cry3Bb1 protein."

Jehle JA, Tebbe CC, Pagel-Wieder S, Traunspurger W, Miethling-Graf R, Nguyen HT, Menzel R, Hoss S

[Sci Total Environ, 2011]

Before pest-resistant genetically modified maize can be grown commercially, the risks for soil-beneficial, non-target organisms must be determined. Here, a tiered approach was used to assess the risk to free-living soil nematodes posed by maize genetically modified to express the insecticidal Cry3Bb1 protein (event Mon88017), which confers resistance towards western corn rootworm (Diabrotica virgifera; Coleoptera). The toxicity of purified Cry3Bb1 for the nematode Caenorhabditis elegans was determined using a bioassay and gene expression analysis. In addition, a soil toxicity test was used to assess the effects on C. elegans of rhizosphere soil obtained from plots of an experimental field grown with Mon88017, the near-isogenic cultivar, or either of two conventional cultivars. Finally, the indigenous nematode communities from the experimental field site with Mon88017 and from the control cultivars were analyzed. The results showed a dose-dependent inhibitory effect of Cry3Bb1 on the growth and reproduction of C. elegans, with EC50 values of 22.3 mg l and 7.9 mg l, respectively. Moreover, Cry-protein-specific defense genes were found to be up-regulated in the presence of either Cry1Ab or Cry3Bb1. However, C. elegans was not affected by rhizosphere soils from Mon88017 compared to the control plots, due to the very low Cry3Bb1 concentrations, as indicated by quantitative analyses (< 1 ng g soil). Nematode abundance and diversity were essentially the same between the various maize cultivars. At the last sampling date, nematode genus composition in Bt-maize plots differed significantly from that in two of the three non-Bt cultivars, including the near-isogenic maize, but the shift in genus composition did not influence the composition of functional guilds within the nematode communities. In conclusion, the risk to free-living soil nematodes posed by Mon88017 cultivation can be regarded as low, as long as Cry3Bb1 concentrations in soil remain four orders of magnitude below the toxicity threshold.

Muller B et al. (2010) J Proteomics "Model organisms--A historical perspective."

Muller B, Grossniklaus U

[J Proteomics, 2010]

Much of our knowledge on heredity, development, physiology and the underlying cellular and molecular processes is derived from the studies of model, or reference, organisms. Despite the great variety of life, a common base of shared principles could be extracted by studying a few life forms, selected based on their amenability to experimental studies. Very briefly, the origins of a few model organisms are described, including E. coli, yeast, C. elegans, Drosophila, Xenopus, zebrafish, mouse, maize and Arabidopsis. These model organisms were chosen because of their importance and wide use, which made them systems of choice for genome-wide studies. Many of their genomes were between the first to be fully sequenced, opening unprecedented opportunities for large-scale transcriptomics and proteomics studies.

Chattopadhyay D et al. (2018) Mech Ageing Dev "Longevity promoting efficacies of different plant extracts in lower model organisms."

Thirumurugan K, Chattopadhyay D

[Mech Ageing Dev, 2018]

Past investigations have shown that various plant extracts are capable of promoting longevity in lower model organisms like Caenorhabditis elegans, Drosophila melanogaster, Saccharomyces cerevisiae, Bombyx mori etc. Longevity studies on such organisms provide a foundation to explore anti-aging efficacies of such plant extracts in higher organisms. Plant extracts of acai palm, apple, asparagus, blueberry, cinnamon, cocoa, Damnacanthus, maize, mistletoe, peach, pomegranate, Rhodiola, rose, Sasa, turmeric, and Withania have extended lifespan in lower model organisms via diverse mechanisms like insulin like growth factor (IGF) signaling pathway, and antioxidant defense mechanisms. Knowledge of pathways altered by the extracts can be investigated as potential drug-targets for natural anti-aging interventions. Thus, the aim of the review is to scrutinize longevity promoting efficacies of various plant extracts in lower model organisms.

Hoss S et al. (2013) Environ Pollut "Effects of insecticidal crystal proteins (Cry proteins) produced by genetically modified maize (Bt maize) on the nematode Caenorhabditis elegans."

Menzel R, Hoss S, Nguyen HT, Gessler F, Jehle JA, Traunspurger W

[Environ Pollut, 2013]

The genetically modified maize MON89034xMON88017 expresses different crystal (Cry) proteins with pesticidal activity against the European corn borer (Cry1.105; Cry2Ab2) and the Western corn root worm (Cry3Bb1). Non-target organisms, such as soil nematodes, might be exposed to the Cry proteins that enter the soil in course of crop growing. Therefore, the risk of those proteins for nematodes was assessed by testing their toxic effects on Caenorhabditis elegans. All three insecticidal Cry proteins showed dose-dependent inhibitory effects on C.elegans reproduction (EC50: 0.12-0.38molL(-1)), however, at concentrations that were far above the expected soil concentrations. Moreover, a reduced toxicity was observed when Cry proteins were added jointly. A C.elegans mutant strain deficient for receptors for the nematicidal Cry5B was also resistant against Cry1.105 and Cry2Ab2, suggesting that these Cry proteins bound to the same or similar receptors as nematicidal Cry proteins and thereby affect the reproduction of C.elegans.

Jeff Harford (2004) East Coast Worm Meeting "High Throughput TILLING, Ecotilling, Genotyping, and Sequencing Instrumentation"

Jeff Harford

[East Coast Worm Meeting, 2004]

Targeting Induced Local Lesions In Genomes, or TILLING R , is a novel high throughput technology for reverse genetics. TILLING uses chemical mutagenesis to yield a traditional allelic series of point mutations for virtually all genes. TILLING is of particular value for essential genes where sublethal alleles are required for phenotypic analysis. TILLING has become an established technique on many model organisms, including C. Elegans, Arabidopsis, Zebrafish, Maize, Rice, and others. A variation on TILLING is called Ecotilling, in which high throughput SNP discovery is performed by locating natural variations throughout the genome. LI-COR Biosciences is a manufacturer of DNA Analysis Instrumentation for high throughput TILLING and Ecotilling, as well as for DNA Sequencing, AFLP R , and Microsatellite analysis. LI-COR also manufactures instrumentation for infrared fluorescent protein imaging, offering superior quantification over standard chemiluminescence. Stop by our booth to pick up the latest literature and publications on our products. TILLING is a registered trademark of Anawah, Inc. AFLP is a registered trademark of KeyGene, N.V.

Kuzmin EV et al. (2004) J Biol Chem "Mitochondrial respiratory deficiencies signal up-regulation of genes for heat shock proteins."

Karpova OV, Elthon TE, Kuzmin EV, Newton KJ

[J Biol Chem, 2004]

The consequences of mitochondrial dysfunction are not limited to the development of oxidative stress or initiation of apoptosis but can result in the establishment of stress tolerance. Using maize mitochondrial mutants, we show that permanent mitochondrial deficiencies trigger novel Ca2+-independent signaling pathways, leading to constitutive expression of genes for molecular chaperones, heat shock proteins (HSPs) of different classes. The signaling to activate hsp genes appears to originate from a reduced mitochondrial transmembrane potential. Upon depolarization of mitochondrial membranes in transient assays, gene induction for mitochondrial HSPs occurred more rapidly than that for cytosolic HSPs. We also demonstrate that in the nematode Caenorhabditis elegans transcription of hsp genes can be induced by RNA interference of nuclear respiratory genes. In both organisms, activation of hsp genes in response to mitochondrial impairment is distinct from their responses to heat shock and is not associated with oxidative stress. Thus, mitochondria-to-nucleus signaling to express a hsp gene network is apparently a widespread retrograde mechanism to facilitate cell defense

Zhang Z et al. (2016) Food Funct "The novel dipeptide Tyr-Ala (TA) significantly enhances the lifespan and healthspan of Caenorhabditis elegans."

Xu L, Zhao B, Zhao Y, Guo Y, Zhang Z, Lin R, Zhang Y, Wang X, Ma H

[Food Funct, 2016]

Food-derived bioactive peptides may have various physiological modulatory and regulatory functions and are now being studied extensively. Recently, the novel dipeptide Tyr-Ala was isolated from hydrolyzed maize protein. Tyr-Ala significantly prolonged the lifespan of wild-type Caenorhabditis elegans and extended the nematode healthspan and lifespan during heat/oxidative stress. Compared with its constituent amino acids, Tyr-Ala was more efficient in enhancing stress resistance. Further studies demonstrated that the significant longevity-extending effects of Tyr-Ala on Caenorhabditis elegans were attributed to its in vitro and in vivo free radical-scavenging effects, in addition to its ability to up-regulate stress resistance-related proteins, such as SOD (Superoxide Dismutase)-3 and HSP (Heat Shock Protein)-16.2. Real-time PCR results showed that the up-regulation of aging-associated genes, such as daf-16, sod-3, hsp-16.2 and skn-1, also contributed to the stress-resistance effect of Tyr-Ala. These results indicate that the novel dipeptide Tyr-Ala can protect against external stress and thus extend the lifespan and healthspan of Caenorhabditis elegans. Thereby, Tyr-Ala could be used as a potential medicine in anti-aging research.

Ruvolo VR et al. (1991) International C. elegans Meeting "SEQUENCE ANALYSIS OF THE TRANSPOSABLE ELEMENT Tc2."

Levitt A, Ruvolo VR

[International C. elegans Meeting, 1991]

We have sequenced a transposed copy of the transposable element Tc2. The Tc2 element is 2074 base pairs in length and has perfect inverted terminal repeats of 24 base pairs. m e structure of the transposon suggests that it may have the capacity to code for a transposase protein and/or for regulatory functions. Tc2 contains nine potential open reading frames of 75 codons or longer, six on one strand and three on the other. Three open reading frames on one strand show non- random codon usage an,d may be exons in a single message. The first of these coding regions is preceded by a potential CAAT box, TATA box, and consensus heat shock sequence. In addition to its inverted terminal repeats, TC2 has an unusual structural feature: subterminal degenerate direct repeats that are arranged in an irregular overlapping pattern. The Spm elements of maize also have a subtermunal repetitive region, which is believed to be required for transpcsition (Masson et al., 1987. Genetics 177: 117- 137). However, unlike the subterminal repeats of Tc2, the Spm repeats are present in discrete units and are oriented in both directions. We found that the 12 base pair motif of the Spm repeats is similar at seven positions to a 10 base pair motif in Tc2. Using GoG profile analysis to ccmpare amino acid sequences, we determined that TC2 is not a member of the Tcl-like y.-oup of transpc60ns, which includes some elements of nematodes and fruit flies (Brezinsky et al., 1990. NAR 18: 20s3-2059). m e Tcl-like elements are shorter than Tc2 by about 500 base pairs, and they have one large open reading frame which specifies a protein of about 270 amino acids. The multi-codon structure of Tc2 is more similar to the Ac and Spm elements of maize and the P elements of Drosophila. What some of the Tcl-like elements do have in ccmmon with Tc2 is the generation of a target site duplication of the dinucleotide TA. We examined the insertion sites of two transposed elements which were identified as the cause of restriction fragment length polymorphisms. Except for the TA dinucleotide, the two sites were not similar to each other. One element was located in a highly repetitive chromosomal region. The other had inaertel inside the inverted terminal repeat of a Tcl element, splitting it into two unequal parts.

Carta LK (2000) J Nematol "Bacterial-Feeding Nematode Growth and Preference for Biocontrol Isolates of the Bacterium Burkholderia cepacia."

Carta LK

[J Nematol, 2000]

The potential of different bacterial-feeding Rhabditida to consume isolates of Burkholderia cepacia with known agricultural biocontrol ability was examined. Caenorhabditis elegans, Diploscapter sp., Oscheius myriophila, Pelodera strongyloides, Pristionchus pacificus, Zeldia punctata, Panagrellus redivivus, and Distolabrellus veechi were tested for growth on and preference for Escherichia coli OP50 or B. cepacia maize soil isolates J82, BcF, M36, Bc2, and PHQM100. Considerable growth and preference variations occurred between nematode taxa on individual bacterial isolates, and between different bacterial isolates on a given nematode. Populations of Diploscapter sp. and P. redivivus were most strongly suppressed. Only Z. punctata and P. pacificus grew well on all isolates, though Z. punctata preferentially accumulated on all isolates and P. pacificus had no preference. Oscheius myriophila preferentially accumulated on growth-supportive Bc2 and M36, and avoided less supportive J82 and PHQM100. Isolates with plant-parasitic nematicidal properties and poor fungicidal properties supported the best growth of three members of the Rhabditidae, C. elegans, O. myriophila, and P. strongyloides. Distolabrellus veechi avoided commercial nematicide M36 more strongly than fungicide J82.