@article{gremiaux_girard_guerin_lothier_baluska_davies_bonnet_vian_2016, title={Low-amplitude, high-frequency electromagnetic field exposure causes delayed and reduced growth in Rosa hybrida}, volume={190}, ISSN={["1618-1328"]}, DOI={10.1016/j.jplph.2015.11.004}, abstractNote={It is now accepted that plants perceive high-frequency electromagnetic field (HF-EMF). We wondered if the HF-EMF signal is integrated further in planta as a chain of reactions leading to a modification of plant growth. We exposed whole small ligneous plants (rose bush) whose growth could be studied for several weeks. We performed exposures at two different development stages (rooted cuttings bearing an axillary bud and 5-leaf stage plants), using two high frequency (900MHz) field amplitudes (5 and 200Vm(-1)). We achieved a tight control on the experimental conditions using a state-of-the-art stimulation device (Mode Stirred Reverberation Chamber) and specialized culture-chambers. After the exposure, we followed the shoot growth for over a one-month period. We observed no growth modification whatsoever exposure was performed on the 5-leaf stage plants. When the exposure was performed on the rooted cuttings, no growth modification was observed on Axis I (produced from the elongation of the axillary bud). Likewise, no significant modification was noted on Axis II produced at the base of Axis I, that came from pre-formed secondary axillary buds. In contrast, Axis II produced at the top of Axis I, that came from post-formed secondary buds consistently displayed a delayed and significant reduced growth (45%). The measurements of plant energy uptake from HF-EMF in this exposure condition (SAR of 7.2 10(-4)Wkg(-1)) indicated that this biological response is likely not due to thermal effect. These results suggest that exposure to electromagnetic field only affected development of post-formed organs.}, journal={JOURNAL OF PLANT PHYSIOLOGY}, author={Gremiaux, Alexandre and Girard, Sebastien and Guerin, Vincent and Lothier, Jeremy and Baluska, Frantisek and Davies, Eric and Bonnet, Pierre and Vian, Alain}, year={2016}, month={Jan}, pages={44–53} }
 @misc{vian_davies_gendraud_bonnet_2016, title={Plant Responses to High Frequency Electromagnetic Fields}, volume={2016}, ISSN={["2314-6141"]}, DOI={10.1155/2016/1830262}, abstractNote={High frequency nonionizing electromagnetic fields (HF-EMF) that are increasingly present in the environment constitute a genuine environmental stimulus able to evoke specific responses in plants that share many similarities with those observed after a stressful treatment. Plants constitute an outstanding model to study such interactions since their architecture (high surface area to volume ratio) optimizes their interaction with the environment. In the present review, after identifying the main exposure devices (transverse and gigahertz electromagnetic cells, wave guide, and mode stirred reverberating chamber) and general physics laws that govern EMF interactions with plants, we illustrate some of the observed responses after exposure to HF-EMF at the cellular, molecular, and whole plant scale. Indeed, numerous metabolic activities (reactive oxygen species metabolism,α- andβ-amylase, Krebs cycle, pentose phosphate pathway, chlorophyll content, terpene emission, etc.) are modified, gene expression altered (calmodulin, calcium-dependent protein kinase, and proteinase inhibitor), and growth reduced (stem elongation and dry weight) after low power (i.e., nonthermal) HF-EMF exposure. These changes occur not only in the tissues directly exposed but also systemically in distant tissues. While the long-term impact of these metabolic changes remains largely unknown, we propose to consider nonionizing HF-EMF radiation as a noninjurious, genuine environmental factor that readily evokes changes in plant metabolism.}, journal={BIOMED RESEARCH INTERNATIONAL}, author={Vian, Alain and Davies, Eric and Gendraud, Michel and Bonnet, Pierre}, year={2016} }
 @article{davies_2014, title={OMICS applications in crop science foreword}, journal={Omics Applications in Crop Science}, author={Davies, E.}, year={2014}, pages={IX-} }
 @misc{davies_stankovic_vian_wood_2012, title={Where has all the message gone?}, volume={185}, ISSN={["0168-9452"]}, DOI={10.1016/j.plantsci.2011.08.001}, abstractNote={We provide a brief history of polyribosomes, ergosomes, prosomes, informosomes, maternal mRNA, stored mRNA, and RNP particles. Even though most published research focuses on total mRNA rather than polysomal mRNA and often assumes they are synonymous - i.e., if a functional mRNA is present, it must be translated - results from our laboratories comparing polysomal RNA and total mRNA in a range of "normal" issues show that some transcripts are almost totally absent from polysomes while others are almost entirely associated with polysomes. We describe a recent model from yeast showing various destinies for polysomal mRNA once it has been released from polysomes. The main points we want to emphasize are; a) when mRNA leaves polysomes to go to prosomes, P-bodies, stress granules, etc., it is not necessarily destined for degradation - it can be re-utilized; b) "normal" tissue, not just seeds and stressed tissue, contains functional non-polysomal mRNA; c) association of mRNA with different classes of polysomes affects their sub-cellular location and translatability; and d) drawbacks, misinterpretations, and false hopes arise from analysis of total mRNA rather than polysomal mRNA and from presuming that all polysomes are "created equal".}, journal={PLANT SCIENCE}, author={Davies, Eric and Stankovic, Bratislav and Vian, Alain and Wood, Andrew J.}, year={2012}, month={Apr}, pages={23–32} }
 @article{roux_girard_paladian_bonnet_lallechere_gendraud_davies_vian_2011, title={Human Keratinocytes in Culture Exhibit No Response When Exposed to Short Duration, Low Amplitude, High Frequency (900 MHz) Electromagnetic Fields in a Reverberation Chamber}, volume={32}, ISSN={["1521-186X"]}, DOI={10.1002/bem.20641}, abstractNote={We exposed normal human epidermal keratinocytes to short duration, high frequency, and low amplitude electromagnetic fields, similar to that used by mobile phone technologies. We paid particular attention to the control of the characteristics of the electromagnetic environment generated within a mode stirred reverberation chamber (statistical homogeneity and isotropy of the field and SAR distribution). Two non‐thermal exposure conditions were tested on the epidermal cells: 10‐min exposure with a field amplitude of 8 V/m, and 30 min with 41 V/m. Corresponding specific absorption rates ranged from 2.6 to 73 mW/kg (continuous wave, 900 MHz carrier frequency). We collected RNA from cells subjected to these conditions and used it for a large‐scale microarray screening of over 47000 human genes. Under these conditions, exposure of keratinocytes to the electromagnetic field had little effect; only 20 genes displayed significant modulation. The expression ratios were very small (close to 1.5‐fold change), and none of them were shared by the two tested conditions. Furthermore, those assayed using polymerase chain reaction did not display significant expression modulation (overall mean of the exposed samples: 1.20 ± 0.18). In conclusion, the data presented here show that cultured keratinocytes are not significantly affected by EMF exposure. Bioelectromagnetics 32:302–311, 2011. © 2010 Wiley‐Liss, Inc.}, number={4}, journal={BIOELECTROMAGNETICS}, author={Roux, David and Girard, Sebastien and Paladian, Francoise and Bonnet, Pierre and Lallechere, Sebastien and Gendraud, Michel and Davies, Eric and Vian, Alain}, year={2011}, month={May}, pages={302–311} }
 @article{yoneda_davies_morita_abe_2009, title={Immunohistochemical localization of apyrase during initial differentiation and germination of pea seeds}, volume={231}, ISSN={["1432-2048"]}, DOI={10.1007/s00425-009-1025-0}, abstractNote={Localization of the 49-kDa apyrase (ATP diphosphohydrolase, EC3.6.1.5; DDBJ/EMBL/GenBank BAB40230) was investigated during early stages of germination of pea (Pisum sativum L. var. Alaska) at the organ, tissue, cellular, and sub-cellular level using light-microscopical immunohistochemistry. Whole mount tissues were immuno-reacted with anti-APY1 serum, pre-immune serum or anti-actin antibody for control. Antigen to the anti-APY1 serum was not detected until 16 h after sowing (26 h after start of imbibition), when the antigen was detected throughout the tissue, especially in the epidermis and cortex. At 35 h after sowing, the younger regions including the root tip and the tip of the stele were more strongly stained than the control. Both, epidermal and cortical cells of the epicotyl and root tip were stained. The stain was mainly localized in the cytoplasm and around nuclei in the apical meristem and the root tip, while vacuoles and cell walls were not stained. At 62 h, there was major staining in the plumule, hook, and elongating regions of the epicotyl and in the region between cotyledons and the epicotyl. After 84 h, lateral root primordia were stained. The pre-immune serum showed virtually no staining while the anti-actin antibody reacted solely with the cytoplasm. Since the antigen to the anti-APY1 serum was primarily found in the cytoplasm and around nuclei in elongating and differentiating tissues and labeling declined in mature tissues, it is suggested that apyrases may play a role in growth and development of tissues, for example, lateral roots.}, number={1}, journal={PLANTA}, author={Yoneda, Motohito and Davies, Eric and Morita, Eugene Hayato and Abe, Shunnosuke}, year={2009}, month={Dec}, pages={47–56} }
 @article{roux_vian_girard_bonnet_paladian_davies_ledoigt_2008, title={High frequency (900 MHz) low amplitude (5 V m(-1)) electromagnetic field: a genuine environmental stimulus that affects transcription, translation, calcium and energy charge in tomato}, volume={227}, ISSN={["1432-2048"]}, DOI={10.1007/s00425-007-0664-2}, abstractNote={Using an especially-designed facility, the Mode Stirred Reverberation Chamber, we exposed tomato plants (Lycopersicon esculentum Mill. VFN8) to low level (900 MHz, 5 V m(-1)) electromagnetic fields for a short period (10 min) and measured changes in abundance of three specific mRNA soon after exposure. Within minutes of electromagnetic stimulation, stress-related mRNA (calmodulin, calcium-dependent protein kinase and proteinase inhibitor) accumulated in a rapid, large and 3-phase manner typical of an environmental stress response. Accumulation of these transcripts into the polysomal RNA also took place (indicating that the encoded proteins were translated) but was delayed (indicating that newly-synthesized mRNA was not immediately recruited into polysomes). Transcript accumulation was maximal at normal Ca(2+) levels and was depressed at higher Ca(2+), especially for those encoding calcium-binding proteins. Removal of Ca(2+) (by addition of chelating agents or Ca(2+) channel blocker) led to total suppression of mRNA accumulation. Finally, 30 min after the electromagnetic treatment, ATP concentration and adenylate energy charge were transiently decreased, while transcript accumulation was totally prevented by application of the uncoupling reagent, CCCP. These responses occur very soon after exposure, strongly suggesting that they are the direct consequence of application of radio-frequency fields and their similarities to wound responses strongly suggests that this radiation is perceived by plants as an injurious stimulus.}, number={4}, journal={PLANTA}, author={Roux, David and Vian, Alain and Girard, Sebastien and Bonnet, Pierre and Paladian, Francoise and Davies, Eric and Ledoigt, Gerard}, year={2008}, month={Mar}, pages={883–891} }
 @article{beaubois_girard_lallechere_davies_paladian_bonnet_ledoigt_vian_2007, title={Intercellular communication in plants: Evidence for two rapidly transmitted systemic signals generated in response to electromagnetic field stimulation in tomato}, volume={30}, ISSN={["1365-3040"]}, DOI={10.1111/j.1365-3040.2007.01669.x}, abstractNote={ABSTRACT}, number={7}, journal={PLANT CELL AND ENVIRONMENT}, author={Beaubois, Elisabeth and Girard, Sebastien and Lallechere, Sebastien and Davies, Eric and Paladian, Francoise and Bonnet, Pierre and Ledoigt, Gerard and Vian, Alain}, year={2007}, month={Jul}, pages={834–844} }
 @article{arumugam_davies_morita_abe_2007, title={Sequence, expression and tissue localization of a gene encoding a makorin RING zinc-finger protein in germinating rice (Oryza sativa L. ssp Japonica) seeds}, volume={45}, ISSN={["0981-9428"]}, DOI={10.1016/j.plaphy.2007.07.006}, abstractNote={The makorin (MKRN) RING finger protein gene family encodes proteins (makorins) with a characteristic array of zinc-finger motifs and which are present in a wide array of eukaryotes. In the present study, we analyzed the structure and expression of a putative makorin RING finger protein gene in rice (Oryza sativa L. ssp. Japonica cv. Nipponbare). From the analysis of the genomic (AP003543), mRNA (AK120250) and deduced protein (BAD61603) sequences of the putative MKRN gene of rice, obtained from GenBank, we found that it was indeed a bona fide member of the MKRN gene family. The rice MKRN cDNA encoded a protein with four C3H zinc-finger-motifs, one putative Cys-His zinc-finger motif, and one RING zinc-finger motif. The presence of this distinct motif organization and overall amino acid identity clearly indicate that this gene is indeed a true MKRN ortholog. We isolated RNA from embryonic axes of rice seeds at various stages of imbibition and germination and studied the temporal expression profile of MKRN by RT–PCR. This analysis revealed that MKRN transcripts were present at all the time points studied. It was at very low levels in dry seeds, increased slowly during imbibition and germination, and slightly declined in the seedling growth stage. After 6 days of germination, an organ-dependent expression pattern of MKRN was observed: highest in roots and moderate in leaves. Similarly to MKRN transcripts, transcripts of cytoskeletal actin and tubulin were also detected in dry embryos, steadily increased during imbibition and germination and leveled off after 24 h of germination. We studied the spatial expression profile of MKRN in rice tissues, by using a relatively fast, simple and effective non-radioactive mRNA in situ hybridization (NRISH) technique, which provided the first spatial experimental data that hints at the function of a plant makorin. This analysis revealed that MKRN transcripts were expressed in young plumules, lateral root primordia, leaf primordia, leaves and root tissues at many different stages of germination. The presence of MKRN transcripts in dry seeds, its early induction during germination and its continued spatiotemporal expression during early vegetative growth suggest that MKRN has an important role in germination, leaf and lateral root morphogenesis and overall development in rice.}, number={10-11}, journal={PLANT PHYSIOLOGY AND BIOCHEMISTRY}, author={Arumugam, Thangavelu U. and Davies, Eric and Morita, Eugene Hayato and Abe, Shunnosuke}, year={2007}, pages={767–780} }
 @article{roux_vian_girard_bonnet_paladian_davies_ledoigt_2006, title={Electromagnetic fields (900 MHz) evoke consistent molecular responses in tomato plants}, volume={128}, ISSN={["1399-3054"]}, DOI={10.1111/j.1399-3054.2006.00740.x}, abstractNote={Although the effects of high-frequency electromagnetic fields on biological systems have been studied frequently, unequivocal results have rarely been obtained, primarily because suitably controlled experiments could not be performed. In the present work, tomato plants were exposed to a homogeneous and isotropic field (900 MHz) using a mode stirred reverberation chamber, and the stress-related transcripts (calmodulin, protease inhibitor and chloroplast mRNA-binding protein) were assayed by real-time quantitative PCR. Exposure to an electromagnetic field induced a biphasic response, in which the levels of all three transcripts increased four-to six-fold 15 min after the end of electromagnetic stimulation, dropped to close to initial levels by 30 min, and then increased again at 60 min. We deliberately focused on the very early molecular responses to high-frequency electromagnetic fields in order to minimize secondary effects.}, number={2}, journal={PHYSIOLOGIA PLANTARUM}, author={Roux, David and Vian, Alain and Girard, Sebastien and Bonnet, Pierre and Paladian, Francoise and Davies, Eric and Ledoigt, Gerard}, year={2006}, month={Oct}, pages={283–288} }
 @article{coker_vian_davies_2005, title={Identification, accumulation, and functional prediction of novel tomato transcripts systemically upregulated after fire damage}, volume={124}, ISSN={["0031-9317"]}, DOI={10.1111/j.1399-3054.2005.00488.x}, abstractNote={Despite the major impacts of fire on plants, responses to fire damage have not been closely studied on the level of gene expression. Here, we present analyses of novel transcripts from tomato (Lycopersicon esculentum cv. Heinz), which are systemically upregulated in leaves after a distant leaf is wounded by flame. Nine cDNA fragments were isolated from a subtractive cDNA library of leaf tissue 1 h after flaming. Using data mining and polymerase chain reaction (PCR), full‐length open‐reading frames were predicted, amplified, and then sequenced. Real‐time (RT)‐PCR using leaf RNA after flaming confirmed the systemic accumulation of 4 and 7 transcripts within 30 and 60 min, respectively, before returning to basal levels within 3 h. During this same time course, proteinase inhibitor I levels gradually increased over 30‐fold in 6 h. Expression analyses also showed that eight of the transcripts are present in unwounded leaf, stem, and root tissues. The predicted proteins include an acyl carrier, adenylyl sulfate reductase, PS II oxygen‐evolving complex protein 3, anion : sodium symporter, chloroplast‐specific ribosomal protein, a histidine triad family protein, and an unknown wound/stress‐related protein. Homologs of several of these proteins have been associated with other types of wound and stress responses. It appears that, within an hour after being damaged by fire, plants systemically upregulate a variety of genes involved with basic cell metabolism and upkeep, in addition to classic defense genes such as proteinase inhibitors.}, number={3}, journal={PHYSIOLOGIA PLANTARUM}, author={Coker, JS and Vian, A and Davies, E}, year={2005}, month={Jul}, pages={311–322} }
 @article{satoshi_yukio_shiraishi_eric_abe_2004, title={Co-expression of an ethylene receptor gene, ERS1, and ethylene signaling regulator gene, CTR1, in Delphinium during abscission of florets}, volume={42}, ISSN={["0981-9428"]}, DOI={10.1016/j.plaphy.2004.07.006}, abstractNote={We are trying to determine the mechanisms responsible for ethylene-induced floret abscission in cut flowers of Delphinium and recently identified an ethylene receptor gene, ERS1, and studied its response to ethylene treatment. In order to identify additional components of the ethylene response network in Delphinium, we performed 3′ and 5′ rapid amplification of cDNA ends (RACE) using the consensus sequence of the serine/threonine kinase domain of the ethylene signaling regulator gene (CTR1) involved in the constitutive triple response (CTR) to ethylene. The full-length cDNA (2754 nt) encoded a protein of 800 amino acids, which contained the expected serine/threonine kinase domain, the consensus ATP-binding site, and the serine/threonine kinase catalytic site. The protein had quite high (>50%) overall identity to CTR1 from Arabidopsis and tomato, and 70––75% identity in the catalytic site. The amount of mRNA encoding both CTR1 and ERS1 more than doubled within 6 h in cut florets incubated in the presence of exogenous ethylene. Similarly, the amount of ERS1 transcript doubled in florets within 6 d of harvesting, presumably in response to endogenous ethylene, while CTR1 mRNA increased to about 40% over the same period. However, in the presence of silver thiosulfate (STS), an ethylene inhibitor, the level of both transcripts remained essentially unchanged for the first 8 d before declining to very low levels. Florets on the control plants had almost completely abscised by 6 d, but the florets on STS-treated plants had not abscised by 20 d, by which time the flowers were almost dead. The data are consistent with the hypothesis that endogenous ethylene evokes the accumulation of both these transcripts (and their encoded proteins), thereby speeding up abscission and reducing the useful shelf life of the cut flowers.}, number={9}, journal={PLANT PHYSIOLOGY AND BIOCHEMISTRY}, author={Satoshi, KA and Yukio, HB and Shiraishi, M and Eric, DD and Abe, S}, year={2004}, month={Sep}, pages={745–751} }
 @article{coker_davies_2004, title={Identifying adaptor contamination when mining DNA sequence data}, volume={37}, ISSN={["1940-9818"]}, DOI={10.2144/04372BM03}, abstractNote={BioTechniquesVol. 37, No. 2 BenchmarksOpen AccessIdentifying adaptor contamination when mining DNA sequence dataJeffrey Scott Coker & Eric DaviesJeffrey Scott Coker*Address correspondence to: Jeffrey Scott Coker, Elon University, Department of Biology, 2625 Campus Box, Elon, NC, 27244, USA. e-mail: E-mail Address: jeffreycoker@hotmail.comNorth Carolina State University, Raleigh, NC, USASearch for more papers by this author & Eric DaviesNorth Carolina State University, Raleigh, NC, USASearch for more papers by this authorPublished Online:6 Jun 2018https://doi.org/10.2144/04372BM03AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinkedInRedditEmail Analysis of DNA sequences can only be as correct as the sequences themselves, and so contamination in public databases is a major concern for bioinformatics research. Here we describe a simple screen that identified adaptor contamination in over 78,000 eukaryotic sequences in GenBank®. Awareness that over 99% of adaptor contaminants appear near the ends of sequences, are flanked by a vector, or involve adaptor dimerization allows the detection of 99% of these sequences (Figure 1).Figure 1. The path from sequencing a cDNA to an improperly edited sequence.More than 99% of sequences contaminated with adaptors fall into one of the three groups shown at the bottom.A contaminated sequence is defined as “one that does not faithfully represent the genetic information from the biological source organism/organelle because it contains one or more sequence segments of foreign origin” (http://www.ncbi.nlm.nih.gov/VecScreen/contam.html). Sources of contamination for nuclear DNA and cDNA include vector sequence (1–6), plasmid vector insertion sequences (7), impure tissue sources (8), faulty laboratory protocols (9,10), mitochondrial DNA (11), and ribosomal DNA/RNA (12). There is one published account of contamination due to adaptor sequences, where it was shown that commercial adaptor sequences matched the 5′ or 3′ end of 728 GenBank and the European Molecular Biology Laboratory (EMBL) sequences (13). Strategies to decrease contamination in database sequences have emphasized vector sequences (4–6,8) and given little attention to adaptor contamination.An adaptor is a short oligonucleotide that is ligated to the ends of cDNAs for incorporation into a vector cloning site (Figure 1). Usually adaptors consist of several restriction sites, one blunt end (for ligation to cDNA) and one cohesive end (for ligation to a vector). Adaptors are frequently used in the construction of cDNA libraries and in generating cDNA ends using rapid amplification of cDNA ends (RACE) PCR.The presence of adaptor sequences in organismal sequences in public databases has the potential to cause many different errors of interpretation (14,15), which include the following: (i) false hits for others using public databases; (ii) added difficulties in identifying genes and joining contigs; (iii) misconstruction of PCR primers, microarrays, probes, etc.; (iv) incorrect conclusions regarding evolution and differences between organisms; (v) incorrect conclusions about gene structure, mRNA splicing, and mRNA transport; and (vi) incorrect conclusions about protein sequence, structure, transport, and function.To investigate adaptor contamination in public databases, BLASTn searches of GenBank (release 140.0; Feb. 15, 2004) eukaryotic sequences were performed using the search parameters shown in Table 1. The search parameters returned perfect matches (100% identity) with the respective adaptor sequences (Table 1). It should be noted that three separate searches of the expressed sequence tag (EST) databases were performed for ZAP (Stratagene, La Jolla, CA, USA) and P1/PN1 (BD Biosciences Clontech, San Jose, CA, USA) adaptors (human, mouse, and non-human/mouse ESTs were searched separately using the E-values in Table 1) because searching all ESTs simultaneously returned more hits than the server could process. Manual review of individual GenBank entries, literature review, and personal communications were used to investigate several hundred matches further. GenBank entries with adaptor contamination were also screened for vector contamination using VecScreen (www.ncbi.nlm.nih.gov/VecScreen/VecScreen.html), the tool commonly used to screen GenBank submissions.Table 1. Sequences and Search Parameters to Identify Entries in GenBank Contaminated by Seven Commercial Adaptor SequencesThe searches and subsequent analyses identified over 78,000 contaminated sequences in GenBank (Table 1). Most contaminated sequences were found in the GenBank EST database, but the “nr” database (which contains annotated genes, etc.) also contained 4528 false sequences. There were also a large number of shorter matches with adaptors that were not included when using the search parameters in Table 1, making it evident that the actual number of contaminated sequences is much higher than shown in Table 1. Simply increasing the E-value will return these shorter matches.Within the contaminated GenBank sequences, over 99% of adaptors were within 50 bp of an end, connected to vector sequence match as shown by VecScreen, or involved in dimerization (Figure 1). The majority of matches not near the 5′ or 3′ end involved dimerization of the ZAP adaptor as shown in Figure 1. We performed BLASTn searches using the full sequences of many GenBank entries that included putative dimer sequences in the gene or cDNA sequence. These searches typically resulted in some GenBank entries matching the query on one side of the dimer, but had totally different entries matching the other side, suggesting that the query sequences actually contained two unrelated sequences that were joined via dimerization. Obviously, this has the potential to create significant errors, especially since the dimer is often in the middle of sequences where it is more likely to be interpreted as part of the open reading frame.A subset of 210 matches (from the nr database) with BD Biosciences Clontech's Marathon primer adaptors (Table 1) were examined more closely. These adaptors are part of the company's suppression subtractive hybridization procedure (U.S. patents 5,565,340 and 5,759,822) used originally to make cDNA libraries and probes (16,17). Of 210 matches with the Marathon adaptors, at least 82 (39%) are contaminated in regions designated as gene or cDNA sequence, including 11 open reading frames (5%). Through literature review and personal communications, we confirmed that BD Bioscience Clontech protocols had been used. Published literature shows these false sequences appearing in transposons, protein sequences, regions used to join contigs, and other biologically relevant regions. In fact, we found published accounts of (unrecognized) contaminated sequence in most major journals of genetics and molecular biology.Public sequence databases such as GenBank serve as repositories for primary sequence data, and typically sequences are not altered or removed without a submitter's request. Thus, dealing with adapter contamination is more complex than simply removing the false sequences from public databases. Future efforts to reduce adaptor contamination in public databases should include: (i) a discussion of sequence quality control in cDNA library product literature; (ii) greater diligence by researchers; (iii) improved tools for screening database submissions; (iv) checks for adaptor contamination during sequence curation (i.e., GenBank RefSeqs); (v) better communication between those who find mistakes, those who maintenance the databases, and sequence submitters; and (vi) prompt correction by submitters who realize past mistakes.For those mining data, performing searches similar to those in Table 1 (varying parameters as appropriate to return 100% matches with the appropriate adaptors) will uncover possible cases of adaptor contamination. Matches that fall into one of the three classes shown in Figure 1 are almost certainly false sequences. When using many sequences from the same library, it is best to determine what cloning technology was used and search for the appropriate adaptors. If one does not know specific adaptors, another technique is to BLAST the first and/or last 30 bp of all sequences against one another and look for sequences that are overrepresented. Doubts about whether a sequence is an adaptor contaminant can be resolved by finding sequences posted by other laboratories or determining what technology was used to clone and sequence the cDNA.The recognition of adaptor contamination has the potential to resolve many problems in the literature (14,15). It is expected that removing adaptor contamination will clarify many gene sequences as individual laboratories reinterpret their own sequences and will prevent those mining data from amplifying such errors.AcknowledgmentsWe thank the scientists who corresponded with us regarding their GenBank entries, Sophia Clotho for advice, Ron Sederoff for critical review, and staff at National Center for Biotechnology Information (NCBI) for their correspondence.Competing Interests StatementThe authors declare that they have no competing interests.References1. Lamperti, E.D., J.M. Kittelberger, T.F. Smith, and L. Villakomaroff. 1992. Corruption of genomic databases with anomalous sequence. Nucleic Acids Res. 20:2741–2747.Crossref, Medline, CAS, Google Scholar2. Lopez, R., T. Kristensen, and H. Prydz. 1992. Database contamination. Nature 355:211.Crossref, Medline, CAS, Google Scholar3. Reynolds, T.L. 1994. Vector DNA artifacts in the nucleotide-sequence database. 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BioTechniques 23:1084–1086.Link, CAS, Google ScholarFiguresReferencesRelatedDetailsCited ByVecScreen_plus_taxonomy: imposing a tax(onomy) increase on vector contamination screening23 October 2017 | Bioinformatics, Vol. 34, No. 5The Rules of Variation Expanded, Implications for the Research on Compatible Genomics12 May 2011 | Biosemiotics, Vol. 5, No. 1Escaping the Cut by Restriction Enzymes Through Single-Strand Self-Annealing of Host-Edited 12-bp and Longer Synthetic PalindromesDNA and Cell Biology, Vol. 31, No. 2SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read20 January 2010 | BMC Bioinformatics, Vol. 11, No. 1SeqTrim — A Validation and Trimming Tool for All Purpose Sequence ReadsCurrent Awareness on Comparative and Functional GenomicsComparative and Functional Genomics, Vol. 6, No. 1-2 Vol. 37, No. 2 Follow us on social media for the latest updates Metrics Downloaded 571 times History Received 8 April 2004 Accepted 10 May 2004 Published online 6 June 2018 Published in print August 2004 Information© 2004 Author(s)AcknowledgmentsWe thank the scientists who corresponded with us regarding their GenBank entries, Sophia Clotho for advice, Ron Sederoff for critical review, and staff at National Center for Biotechnology Information (NCBI) for their correspondence.Competing Interests StatementThe authors declare that they have no competing interests.PDF download}, number={2}, journal={BIOTECHNIQUES}, author={Coker, JS and Davies, E}, year={2004}, month={Aug}, pages={194-+} }
 @article{davies_2004, title={New functions for electrical signals in plants}, volume={161}, DOI={10.1111/j.1469-8137.2003.01018.x}, abstractNote={Electrical signals in plants have been known for over 100 years, but scientists are still looking for a function. The bulk of the work has focused on heat-wound evoked responses in above-ground parts, but evidence exists for their role in many processes, including transcription, translation and respiration. An additional function elegantly demonstrated in this issue of New Phytologist (Koziolek et al. pp. 713–720) is a transient reduction in photosynthesis. Koziolek et al. measured membrane potential, chlorophyll fluorescence and PSII quantum yield, and showed that the electrical signal preceded the changes in photosynthetic parameters – transport of chemicals in the phloem was far too slow to account for these changes. ‘One of the beauties of this study is that the authors recognize the need to take great care to avoid generating a wound during the act of measurement, and so use techniques imposing little or no stress on the plant’ For many years, the idea of electrical signaling in plants hovered in the research background, a minor interest topic even though Burdon-Sanderson (1873) and Charles Darwin (1875) had demonstrated the existence of electrical signals in insectivorous (‘motorized’) plants. However, by the early 1970s, with the publication of ‘The secret life of plants’ by Tompkins & Bird (1973) the credibility of the area had become severely strained in the research community making it essentially untouchable in the eyes and minds of funding agencies (Box 1). Just over 20 yr ago we presented some research showing that wounding one location on a plant caused very rapid changes in gene expression (translation/polyribosomes) in distant regions (Davies & Schuster, 1981). Joe Varner, a very eminent plant biochemist and molecular biologist, discussed this research with me and suggested that I might be looking at electrical signals. I remember my response: ‘But plants don’t have electrical signals, do they?’. Joe assured me that they did, and arranged for me to work in Barbara Pickard's lab at Washington University in St. Louis. I went there, did my first experiment by taping a plant in place on a styrofoam block, attaching electrodes, hooking them up to recorders, and then cutting the plant. The recorders, in sequence, starting with the one nearest the cut, exhibited a clear transient 70 mV change in membrane potential. I was now a ‘believer’ that electrical signals existed in normal plants, but was unsure whether they actually evoked any important responses. In order to ascertain whether there were any likely functions of electrical signals in plants, I spent a lot of time reviewing the literature until I was convinced that they really did exist, were worth working on, and might, in fact, explain several then inexplicable phenomena (Davies, 1987). Then came the breakthrough – the paper by Wildon et al. (1992) showing that electrical signals are involved in turning on protease inhibitor (PIN) genes in tomato. They showed that a local flame wound evoked rapid changes in membrane potential in distant tissue, while transport of chemical signals in the phloem took an hour or more. The electrical signals arrived in responding tissue much sooner than transcript accumulation began, while transcript accumulation preceded arrival of the chemical signal. The authors (Wildon et al., 1992) claimed, however, that the signal they were monitoring was a ‘genuine’ electrical signal, or action potential (AP). However, we had already worked on tomatoes and knew that a flame wound invariably evoked another type of ‘electrical’ signal known as a variation potential (VP). The AP is described as a ‘genuine’ electrical signal. It can be evoked electrically, it has an all-or-nothing character (below a threshold stimulus there is no response, while above this threshold, there is a maximal response), and it travels with constant velocity and magnitude (Zawadzki et al., 1991). The AP is a self-perpetuating signal based on the activity of voltage-gated channels which respond to (and cause) changes in membrane potential (Davies, 1993). By contrast, the VP cannot be evoked electrically, it varies with the degree of stimulus, and appears to ‘travel’ with decreasing magnitude and velocity away from the site of stimulus. The VP is a nonself-perpetuating signal based on mechano-sensitive (stretch-activated) and/or ligand-activated channels (Davies, 1993; Stankovic et al., 1997). Thus the VP is a local change (in living cells with ion channels) to either a hydraulic surge or chemicals transmitted in the dead xylem. Nevertheless, despite the misunderstandings concerning the different types of electrical signals in plants, this report (Wildon et al., 1992) helped make the study of electrical signals more respectable and closer to mainstream biology. Why do plants have electrical signals? Not only can this involve ‘What plant functions are governed by electrical signals?’, it also concerns ‘Why is there a need for these signals?’ The latter question can also be posed as ‘What properties do electrical signals have that chemical signals do not have?’ The first is ‘rapidity’. The VP in living cells is an almost direct aftermath of a virtually instantaneous loss of tension in the xylem, while the AP is a very rapidly transmitted signal predominantly in the phloem. Why might rapidity be important? In those instances where plants have a movement response, such as in the capture of insects, then speed is essential otherwise the prey would escape. Similarly, when a plant is attacked by insects (especially if they harbor a virus), the plant needs to put up systemic defenses as quickly as possible to prevent spread of the pathogen/herbivore. The second is ‘ubiquity’, insofar as all cells near the xylem will be affected by the VP, and those near the phloem by the AP. Similarly, ubiquity is important in sofar as the entire plant needs to be defended against potentially hostile threats, there may be little point in leaving some regions susceptible while defending others. This underlies the systemic nature of electrical signals as well as the local responses to them. The third property is ‘information’. This is important because the plant may or may not actually ‘recognize’ the exact insult. This is possible for the flame wound, which is the ‘insult’ used in this paper and the one preferred by us to evoke predictable, large, rapid, electrical signals and responses at the level of gene expression. It is conceivable that the plant does, indeed, ‘recognize’ the flame wound for what it is – fire – a very damaging threat which is pervasive throughout many ecosystems. However, it is equally conceivable that the plant does not recognize specifically that the insult is a local flame and so mounts a general stress response. It should be noted here that there is a huge difference between electrical signaling in the animal nervous system compared with that in a plant. In the animal nervous system, the whole point of an AP is to send information from one specific location to another, without affecting the intervening tissue – rather like a telephone system (Davies, 1993). By contrast, both the AP and VP in a plant are designed to inform as much of the plant as quickly as possible so that all the intervening tissue is informed – rather like a megaphone message warning everyone within hearing distance (Davies, 1993). The final property is ‘transience’. Not only is the signal (change in membrane potential) short-lived, but so is the response. After the wounded leaf has informed the rest of the plant, the recipient regions seem to ‘deal with the emergency and then get back to normal business’. Thus transience is important if the signal is merely to warn distant regions of impending disaster, and after receipt of such a warning, the (forewarned) distant tissue regains homeostasis. When studying wounding, great care needs to be taken to avoid generating a wound during the act of measurement, and so noninvasive techniques have to be used. One of the beauties of the study in this issue by Koziolek et al. is that the authors recognize this need, and so used techniques imposing little or no stress on the plant. They used standard techniques including microelectrodes (which impose a very slight puncturing stress) to measure electrical signals, a porometer to measure gas exchange, and autoradiography to estimate time of arrival of an chemical signal. The major feature, however, was their use of a recently developed method involving fluorescence imaging to measure the quantum yield efficiency of photosystem II. These fluorescence images are very persuasive. They show that PSII efficiency is transiently inhibited in the distant leaf beginning within 90 s of the heat pulse, traveling from the base to apex of the leaf (pinna) before returning to normal after about 450 s. The images are magnified to show that the vein region is inhibited initially, implying that the vein is the pathway of transmission, but that the intervein region is affected more massively, implying greater photosynthetic activity in that region. They show that generation and transmission of the electrical signal (variation potential) precedes the changes in stomatal conductance and gas exchange in fixed leaflets, which in turn slightly precedes inhibition of PSII quantum yield. Furthermore, the fact that wound responses tend to be transient adds another facet to the experimental approach. If the techniques require tissue extraction or fixation (as ours mostly do), then very detailed time courses need to be made – which adds to the time and expense of obtaining statistically reliable data. This problem can be circumvented by using ‘real-time’ imaging techniques, where the sample can be assayed repeatedly or even continuously. The authors achieve this, not only with their use of microelectrodes and porometers, both of which give continuous recordings, but especially with chlorophyll fluorescence measurements, which gives beautiful (false)-color images. In this context, it is worth noting that a new, non-invasive technique might have become available to monitor electrical signals. Recently, Hanstein & Felle (2004) described a ‘nanoinfusion’ technique where microelectodes are immersed in liquid infused into the substomatal cavity to measure membrane potential – in a totally non-invasive way – thus circumventing the (minor) damage elicited by micoelectrodes inserted into cells. The bulk of research in the area has focused on responses in above-ground parts and evidence exists for their role in many processes, including transcription (Wildon et al., 1992), translation (Stankovic & Davies, 1997) and respiration (Filek & Koscielniak, 1997), and in all cases the responses are transient. This paper (Koziolek et al.) adds inhibition of photosynthesis to this list, and also shows that PSII efficiency, as well as changes in gas exchange and stomatal aperture, are transient. It is still not known whether the transience of the response is a direct result of the transience of the signal itself (the change in membrane potential and concomitant fluxes of ions) or whether it signifies that the plant has successfully ‘coped with the problem’, or whether both of these are true. Nevertheless, there do seem to be some underlying similarities between the results from several labs working on many different responses to flame- (or heat-pulse-) induced variation potentials. The values shown here for lag times, time of maximum response, and time of return to baseline were roughly 90 s, 240 s, 450 s for PSII inhibition, gas exchange and stomatal conductance. These values are quite similar to, although somewhat slower than, the corresponding times for enhancement of respiration (Filek & Koscielniak, 1997) of 20 s, 80 s, 360 (s). We were also impressed by similarities in the kinetics of response of inhibition of photosynthesis shown in the paper with those from our own work on flame-wound induced changes in gene expression in tomatoes. Here we have measured the level of a putative second messenger, inositol phosphate (IP3) as well as accumulation of the transcript encoding the Rubisco small subunit. As shown in Fig. 1, the systemic increase in IP3 levels shows a lag of 75 s, a maximum at 90 s, and a return to the baseline by 120 s, while the Rubisco SS transcript shows a lag of 90 s, a maximum at 120 s and a return to the baseline by 150 s. There are two main differences between these results on transcript accumulation (Fig. 1) and those on respiration (Filek & Koscielniak, 1997) and photosynthesis (Koziolek et al.). First, our system has the disadvantage that we cannot assay the same tissue over time, but must harvest tissue for each time point. Second, we have an advantage insofar as we have identified a putative local signal (IP3) that could have been evoked by the systemic variation potential, and which could, in turn, evoke transcript accumulation. Three-wk old tomato plants were flame-wounded on leaf 3 and leaf 4, harvested at 15 s intervals, frozen immediately in liquid Nitrogen, and finely pulverized. One aliquot of the frozen powder was extracted to assay IP3 using the release of labeled IP3 from rat brain IP3 receptors. The other aliquot was extracted, electrophoresed, blotted and probed with a Rubisco small subunit probe according to published methods (Vian et al., 1999). Data are from three independent experiments, where the standard deviation was < 12% at all time points (Salinas-Mondragon, Atkinson and Davies, unpublished).}, number={3}, journal={New Phytologist}, author={Davies, E.}, year={2004}, pages={607–610} }
 @article{abe_sakai_yagi_hagino_ochi_shibata_davies_2003, title={A Tudor protein with multiple SNc domains from pea seedlings: cellular localization, partial characterization, sequence analysis, and phylogenetic relationships}, volume={54}, ISSN={["1460-2431"]}, DOI={10.1093/jxb/erg096}, abstractNote={A major high molecular weight protein (HMP) in the cytoskeletal fraction from pea has been purified. A combination of chromatographic techniques and protease fragment analysis also facilitated the isolation of the encoding cDNA, disclosing the sequence of the complete open reading frame. The protein possesses four complete N-terminal Staphylococcal nuclease (SNc) domains, a central Tudor domain and a partial SNc domain at the C-terminus, which may act as a coiled-coil cytoskeleton interaction motif. Cell fractionation studies showed that the protein was abundant in the cytoskeleton fraction in dark-grown pea seedlings, but essentially was absent from the nucleus. Gel filtration column chromatography indicated that the native protein exists as a dimer, while isoelectric focusing suggested that there were at least four HMP isotypes. The protein co-eluted with ribosomes from a heparin affinity column in vitro, consistent with ribosome/polysome interactions in vivo. Significantly, sequence analysis of the C-terminal SNc motif may accurately predict nuclear versus cytoplasmic localization resulting in potentially very different functional roles for this protein family in different organisms. An antibody to HMP from peas was also raised and an HMP with a similar molecular mass was detected in the cytoskeleton fractions and to a lesser extent in the nuclear fraction (250 g pellet) from rice and wheat seedlings.}, number={384}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Abe, S and Sakai, M and Yagi, K and Hagino, T and Ochi, K and Shibata, K and Davies, E}, year={2003}, month={Mar}, pages={971–983} }
 @article{moustafa_yoneda_abe_davies_2003, title={Changes in isotypes and enzyme activity of apyrase during germination of dark-grown pea (Pisum sativum) seedlings}, volume={119}, ISSN={["0031-9317"]}, DOI={10.1034/j.1399-3054.2003.00152.x}, abstractNote={ In the present study we used 2D‐PAGE and Western blotting to investigate the expression of different isotypes of apyrase (EC 3.6.1.5) during imbibition, germination and initial growth of pea (Pisum sativum L. var. Alaska) seedlings in the dark. The 49 kDa apyrase was absent in the 10‐h imbibed embryos, but began to appear after 16 h germination and increased with germination time. By 62 h, there were five isotypes present at pI 5.8, 6.0, 6.3, 6.6 and 6.8, with those at pI 6.0, 6.3, and 6.6 being most abundant and the one at pI 6.3 predominating, whereas the most acidic and basic isotypes were only present in significant amounts in seedlings after 62 h germination. Stems contained all five isotypes and had more pI 6.0, 6.3 and 6.6 isotype than the plumules, whereas in the roots there were very small amounts of all isotypes. Partial amino acid sequencing showed that all isotypes were identical with apy1, not the more recently described apy2. Apyrase activity was absent in imbibed embryos, but increased sharply during germination and reached a maximum after 62 h. Based upon the capability of the enzyme to hydrolyse ATP, CTP, GTP, TTP, UTP, and ADP (but not AMP), its susceptibility to various ATPase inhibitors, and coincidence of expression of the protein and enzyme activity, we estimate that 50–70% of the ATPase activity results from the 49 kDa apyrase. The present results suggest that isotypes of pI 6.0, 6.3, and 6.6 are physiologically important and strongly indicate a crucial role for apyrase in the differentiation and development of pea seedlings. }, number={1}, journal={PHYSIOLOGIA PLANTARUM}, author={Moustafa, MFM and Yoneda, M and Abe, S and Davies, E}, year={2003}, month={Sep}, pages={146–154} }
 @article{coker_jones_davies_2003, title={Identification, conservation, and relative expression of V-ATPase cDNAs in tomato plants}, volume={21}, ISSN={["0735-9640"]}, DOI={10.1007/BF02774241}, number={2}, journal={PLANT MOLECULAR BIOLOGY REPORTER}, author={Coker, JS and Jones, D and Davies, E}, year={2003}, month={Jun}, pages={145–158} }
 @article{azama_abe_sugimoto_davis_2003, title={Lysine-containing proteins in maize endosperm: a major contribution from cytoskeleton-associated carbohydrate-metabolizing enzymes}, volume={217}, ISSN={["1432-2048"]}, DOI={10.1007/s00425-003-1016-5}, abstractNote={We measured fresh weight, dry weight, total protein, and the amounts of several individual proteins during endosperm development in three varieties of maize ( Zea mays L.): W64A wild-type (WT) and opaque-2 (o2), and sweet corn (SW). By 28 days after pollination (DAP), fresh weight was much higher in WT and SW than in o2, but o2 had a higher dry weight and thus a much lower water content. By 28 DAP, protein concentration [mg (g tissue(-1))] was highest in o2 and lowest in WT, while the protein content (microg seed(-1)) was lowest in o2. The storage proteins, alpha- and gamma-zeins, were low initially, but by 28 DAP they comprised over 50% of the total protein in WT and SW, but only about 30% in o2. In all varieties, the cytoskeleton proteins, actin, tubulin and eEF1alpha, sedimented with the protein bodies at 30 g to 27,000 g in tissue homogenized in cytoskeleton-stabilizing buffer. Other cytoskeleton-associated proteins increased during development, including UDP-glucose starch glucosyltransferase (UDP-GSGT, EC 2.4.1.11), sucrose synthase 1 (SuSy-1, EC 2.4.1.13) and fructose-1,6 bisphosphate aldolase (FBA, EC 4.1.2.13). At 28 DAP, these cytoskeleton-associated proteins combined make up 27% (WT), 23% (SW) and 33% (o2) of the total protein. These proteins are all rather high (5-11%) in lysine, and so they contribute about 75% (WT), 67% (o2), and 51% (SW) of the total endosperm lysine. We conclude that efforts to elevate the levels of these proteins could make a significant contribution to the nutritional value of corn.}, number={4}, journal={PLANTA}, author={Azama, K and Abe, S and Sugimoto, H and Davis, E}, year={2003}, month={Aug}, pages={628–638} }
 @article{abe_azama_sugimoto_davies_2003, title={Protein accumulation in the maize endosperm: role of polyribosomes and the cytoskeleton}, volume={41}, ISSN={["0981-9428"]}, DOI={10.1016/S0981-9428(02)00016-5}, abstractNote={We compared fresh weight, dry weight, amounts of several proteins and polyribosome content (putative protein synthesizing potential) in three maize varieties: wild-type (WT), opaque-2 (o2), and sweet corn (SW). All three varieties increased in fresh weight until 28 d after pollination (DAP), but o2 lost large amounts of water during the later stages, thus rendering its dry weight content much higher. Protein content (mg seed–1) was increased similarly in all three varieties, but protein concentration (mg g-tissue–1) was highest in o2 and lowest in WT. WT and SW accumulated about three times as much zein, and three times the amount of protein bodies (PB) as did o2, but only about half the amount of the cytoskeleton proteins, actin, β;-tubulin, and EF1α. Protein synthesizing potential (measured as polysomes and polysomal mRNA) was high in WT, somewhat lower in SW, and much lower in o2. The accumulation of total proteins was similar in all three varieties, the accumulation of zeins was much higher in WT and SW than in o2, but the accumulation of cytoskeleton proteins was higher, and the polysome content was much lower, in o2. This apparent discrepancy (less polysomes, but equal protein accumulation in o2) can be explained by the fact that protein synthesis is dependent not only on the amount of polyribosomes, but also on the cytoskeleton, either in the construction of the cytoskeleton as a scaffold for polysomes·mRNA, or as a provider of factors (EF1α) essential for translation.}, number={2}, journal={PLANT PHYSIOLOGY AND BIOCHEMISTRY}, author={Abe, S and Azama, K and Sugimoto, H and Davies, E}, year={2003}, month={Feb}, pages={125–131} }
 @article{ozeki_chikagawa_kimura_soh_maeda_pornsiriwong_kato_akimoto_oyanagi_fukuda_et al._2003, title={Putative cis-elements in the promoter region of the carrot phenylalanine ammonia-lyase gene induced during anthocyanin synthesis}, volume={116}, ISSN={["0918-9440"]}, DOI={10.1007/s10265-003-0078-6}, abstractNote={Deletion mutants of the carrot phenylalanine ammonia-lyase gene promoter were used to survey cis-elements for their effect on expression of promoter activity by transient expression. Two putative cis-elements were required to give full activity, but a third might be the most important in regulation of the promoter by 2,4-dichlorophenoxyacetic acid.}, number={2}, journal={JOURNAL OF PLANT RESEARCH}, author={Ozeki, Y and Chikagawa, Y and Kimura, S and Soh, H and Maeda, K and Pornsiriwong, W and Kato, M and Akimoto, H and Oyanagi, M and Fukuda, T and et al.}, year={2003}, month={Apr}, pages={155–159} }
 @article{coker_davies_2003, title={Selection of candidate housekeeping controls in tomato plants using EST data}, volume={35}, ISSN={["1940-9818"]}, DOI={10.2144/03354st04}, abstractNote={ Because the expression levels of housekeeping genes are relatively constant in most tissues, they are often useful controls when quantifying gene expression. We present an analytical method for identifying candidate housekeeping controls using expressed sequence tags (ESTs) from The Institute for Genomic Research Tomato Gene Index. We found relative expression levels for a collection of 127 transcripts and calculated the percentage of cDNA libraries that had expression levels (for a given transcript) within 2-fold through 10-fold ranges. When all libraries were considered together, the highest ranked housekeeping controls included transcripts for a DnaJ-like protein, translationally controlled tumor protein, two α-tubulins, cyclophilin, and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). For each organ (leaf, root, fruit, and flower), at least one transcript was found that occurred within a 2-fold range of expression in all respective libraries. These included transcripts for α-tubulin, DnaJ-like proteins, phosphoglycerate kinase, and GAPDH, although different transcripts appear better suited than others for different tissues. This analytical method is useful for identifying candidate housekeeping controls in particular tissues and at particular levels of expression and would be relevant for any species for which significant EST data exist. }, number={4}, journal={BIOTECHNIQUES}, author={Coker, JS and Davies, E}, year={2003}, month={Oct}, pages={740-+} }
 @article{itoh_hasebe_davies_takeda_ozeki_2003, title={Survival of Tdc transposable elements of the En/Spm superfamily in the carrot genome}, volume={269}, ISSN={["1617-4615"]}, DOI={10.1007/s00438-002-0798-7}, abstractNote={Three subfamilies of the En/Spm-type transposable element of carrot, Tdc A, B, and C, were characterized. It was supposed that the Tdc A subfamily may include autonomous elements which can produce transposases. Tdc B elements are defective, but still generate transcripts containing mutant open reading frame (ORF) sequences for transposases. The single member of the Tdc C group recovered seems to be a pseudogene. The sequences of the transposase ORFs of Tdc A and Tdc B elements are more highly conserved than those of the 5; and 3; untranslated regions and introns, as is found in other structural genes that are subject to selection. These observations indicate that the mutations in the nucleotide sequences of the Tdc elements occurred in the host genome. However, the mutations in the 5; and 3; untranslated regions and introns, which may not be sufficient to prevent transposition, accumulated in autonomous elements, which could transpose and produce copies. When the reproduction rate and the rate of disabling mutations reached an equilibrium, that is, when the birth rate of the transposable elements in the genome equalled the death rate, the population of elements achieved a stationary state in the genome, and could thus survive.}, number={1}, journal={MOLECULAR GENETICS AND GENOMICS}, author={Itoh, Y and Hasebe, M and Davies, E and Takeda, J and Ozeki, Y}, year={2003}, month={Apr}, pages={49–59} }
 @article{weidner_fraczek_romanowska_amarowicz_abe_davies_2003, title={The influence of abscisic acid on different polysomal populations in embryonal tissue during pea seeds germination}, volume={25}, ISSN={["0137-5881"]}, DOI={10.1007/s11738-003-0030-3}, number={1}, journal={ACTA PHYSIOLOGIAE PLANTARUM}, author={Weidner, S and Fraczek, E and Romanowska, M and Amarowicz, R and Abe, S and Davies, E}, year={2003}, pages={5–12} }
 @article{yamagata_kato_kuroda_abe_davies_2003, title={Uncleaved legumin in developing maize endosperm: identification, accumulation and putative subcellular localization}, volume={54}, ISSN={["0022-0957"]}, DOI={10.1093/jxb/erg090}, abstractNote={While identifying proteins present in the cytoskeleton and protein body fractions from maize (Zea mays L.) endosperm, a 51 kDa protein was discovered in a fraction containing small (approximately 200 nm in diameter) protein bodies. Based on partial amino acid sequences of V8 protease fragments, degenerate primers were made and fragments of cDNA encoding these partial sequences were cloned. Using 3' and 5' PCR, a full-length cDNA encoding this 51 kDa protein was obtained, which was identified as legumin-1. In other plants, this protein is generally cleaved into 20 and 35 kDa subunits after synthesis. However, SDS-PAGE of both the native and denatured protein indicates that cleavage does not occur in corn endosperm, even though the cleavage site (asparagine) is conserved. The lack of cleavage is presumably because the canonical cleavage sequence downstream from the cleavage site is almost totally absent. levels of transcript and encoded protein were compared in all three varieties and it was shown that both are more abundant in wild-type maize than in opaque-2 or sweet corn. Finally, using TEM, it was shown that the protein apparently occurs in morphologically distinct protein bodies, very similar to the protein bodies in legumes.}, number={384}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Yamagata, T and Kato, H and Kuroda, S and Abe, S and Davies, E}, year={2003}, month={Mar}, pages={913–922} }
 @misc{coker_davies_2002, title={Correspondence re: A. H. Ree et al., expression of a novel factor in human breast cancer cells with metastatic potential. Cancer Res., 59: 4675-4680, 1999}, volume={62}, number={14}, journal={Cancer Research}, author={Coker, J. S. and Davies, E.}, year={2002}, pages={4164–4165} }
 @article{abe_moustafa_shibata_yoneda_davies_2002, title={Purification and characterization of the major isotypes of apyrase from the cytoskeleton fraction in Pisum sativum}, volume={40}, ISSN={["0981-9428"]}, DOI={10.1016/S0981-9428(02)01466-3}, abstractNote={We isolated isotypes of the 49-kDa apyrase from the cytoskeleton fraction of pea (Pisum sativum L. var. Alaska) stems, separated them using heparin affinity and anion exchange column chromatography, and investigated the enzymatic activities of each isotype. When potassium acetate gradients at constant pH were employed, there was poor separation between isotypes. However, when a pH gradient of 6.7–8.5 was used in conjunction with a potassium acetate gradient from 0 to 1 M, five peaks were identifiable, eluting between 0.35 and 0.65 M potassium acetate, and termed P0, P1, P2, P3, and P4. 2D-Polyacrylamide gel electrophoresis showed that each of these peaks was highly enriched for an individual isotype, and the isoelectric points of these isotypes were 5.82, 6.05, 6.30, 6.55, and 6.80 in fractions P0, P1, P2, P3, and P4, respectively. The isotypes of pI 6.05, 6.30, and 6.55 were the most abundant, and the more acidic isotypes had slightly higher molecular mass than other isotypes. Based on their partial amino acid sequences, their capability to hydrolyze both nucleoside tri- and di-phosphates into their respective mono-phosphates, and their similar hydrolyzing activity towards ADP, we presume they are all isotypes of the 49-kDa apyrase (EC 3.6.1.5). Since the calculated isoelectric point of apyrase based upon its amino acid sequence is 7.11, these results indicate that the enzyme is modified in various ways (most likely including phosphorylation) to furnish different isoforms with different activities over different substrates.}, number={12}, journal={PLANT PHYSIOLOGY AND BIOCHEMISTRY}, author={Abe, S and Moustafa, MFM and Shibata, K and Yoneda, M and Davies, E}, year={2002}, month={Dec}, pages={1019–1023} }
 @article{shibata_abe_yoneda_davies_2002, title={Sub-cellular distribution and isotypes of a 49-kDa apyrase from Pisum sativum}, volume={40}, ISSN={["0981-9428"]}, DOI={10.1016/S0981-9428(02)01389-X}, abstractNote={We isolated a 49-kDa protein from various sub-cellular fractions from pea (Pisum sativum L. var. Alaska) stems using heparin affinity and cation exchange column chromatography. The corresponding proteins from all these fractions were identified as apyrase (EC 3.6.1.5) because they hydrolyzed both nucleoside tri- and diphosphates into their respective monophosphates. Using an antibody raised against apyrase, we studied the enzyme’s sub-cellular distribution in isolated fractions and found significant amounts in the cell wall (50%), the supernatant (33%), the cytoskeleton (14%), and the nuclei (3%). Immuno-electron microscopy using gold-labeled antibody confirmed that apyrase was present in cell walls, nuclei, and in filamentous structures in the cytoplasm associated with ribosomes. Even though there is only one gene (with two alleles), for this protein, 2D gels indicated there were at least five isotypes, three being major, and the relative abundance of these isotypes differed in different fractions. Enzymes from all fractions: (a) hydrolyzed nucleoside triphosphates and diphosphates, but not monophosphates, (b) were insensitive to most ATPase inhibitors (azide, fluoride, nitrate, molybdate, ouabain, quercetin), but (c) were all inhibited by vanadium pentoxide at relatively high concentrations. There were, however, some subtle differences between enzymes from different sub-cellular fractions, including different ADP/ATP hydrolysis ratios. These results show that the 49-kDa apyrase is located in various compartments within the cell (cell wall, nuclei, and the cytoskeleton) and that the enzymes from all fractions are basically similar in their apyrase function. We suggest that the enzyme is modified in various ways to furnish different forms with different (non-apyrase) functions in different sub-cellular locations.}, number={5}, journal={PLANT PHYSIOLOGY AND BIOCHEMISTRY}, author={Shibata, K and Abe, S and Yoneda, M and Davies, E}, year={2002}, month={May}, pages={407–415} }
 @misc{davies_stankovic_azama_shibata_abe_2001, title={Novel components of the plant cytoskeleton: a beginning to plant 'cytomics'}, volume={160}, ISSN={["0168-9452"]}, DOI={10.1016/s0168-9452(00)00365-4}, abstractNote={The bulk of our knowledge concerning the plant cytoskeleton has come primarily from the use of techniques and probes derived from animal research. However, in comparison with animal tissues, relatively few plant cytoskeleton proteins have been identified. We presume this is not because the plant cytoskeleton is really made up of such few proteins, but rather that only rarely have attempts been made to identify plant-specific cytoskeleton proteins, using plant-specific methods. Here we outline methods that we have developed both for the isolation and identification of novel cytoskeleton proteins as well as for the visualization of novel filamentous structures in plant cells, and we describe several novel cytoskeleton proteins and two novel cytoskeleton structures, 'nanofilaments' and 'nanotubules'. We postulate that use of such approaches will lead to a rapid expansion of our knowledge of the plant cytoskeleton.}, number={2}, journal={PLANT SCIENCE}, author={Davies, E and Stankovic, B and Azama, K and Shibata, K and Abe, S}, year={2001}, month={Jan}, pages={185–196} }
 @article{heilmann_shin_huang_perera_davies_2001, title={Transient dissociation of polyribosomes and concurrent recruitment of calreticulin and calmodulin transcripts in gravistimulated maize pulvini}, volume={127}, ISSN={["1532-2548"]}, DOI={10.1104/pp.127.3.1193}, abstractNote={In plants, sugars are the main respiratory substrates and important signaling molecules in the regulation of carbon metabolism. Sugar signaling studies suggested that sugar sensing involves several key components, among them hexokinase (HXK). Although the sensing mechanism of HXK is unknown, several experiments support the hypothesis that hexose phosphorylation is a determining factor. Glucose (Glc) analogs transported into cells but not phosphorylated are frequently used to test this hypothesis, among them 3-O-methyl-Glc (3-OMG). The aim of the present work was to investigate the effects and fate of 3-OMG in heterotrophic plant cells. Measurements of respiration rates, protein and metabolite contents, and protease activities and amounts showed that 3-OMG is not a respiratory substrate and does not contribute to biosynthesis. Proteolysis and lipolysis are induced in 3-OMG-fed maize (Zea mays L. cv DEA) roots in the same way as in sugar-starved organs. However, contrary to the generally accepted idea, phosphorous and carbon nuclear magnetic resonance experiments and enzymatic assays prove that 3-OMG is phosphorylated to 3-OMG-6-phosphate, which accumulates in the cells. Insofar as plant HXK is involved in sugar sensing, these findings are discussed on the basis of the kinetic properties because the catalytic efficiency of HXK isolated from maize root tips is five orders of magnitude lower for 3-OMG than for Glc and Man.}, number={3}, journal={PLANT PHYSIOLOGY}, author={Heilmann, I and Shin, J and Huang, J and Perera, IY and Davies, E}, year={2001}, month={Nov}, pages={1193–1203} }
 @article{stankovic_vian_henry-vian_davies_2000, title={Molecular cloning and characterization of a tomato cDNA encoding a systemically wound-inducible bZIP DNA-binding protein}, volume={212}, ISSN={["0032-0935"]}, DOI={10.1007/s004250000362}, abstractNote={Localized wounding of one leaf in intact tomato (Lycopersicon esculentum Mill.) plants triggers rapid systemic transcriptional responses that might be involved in defense. To better understand the mechanism(s) of intercellular signal transmission in wounded tomatoes, and to identify the array of genes systemically up-regulated by wounding, a subtractive cDNA library for wounded tomato leaves was constructed. A novel cDNA clone (designated LebZIP1) encoding a DNA-binding protein was isolated and identified. This clone appears to be encoded by a single gene, and belongs to the family of basic leucine zipper domain (bZIP) transcription factors shown to be up-regulated by cold and dark treatments. Analysis of the mRNA levels suggests that the transcript for LebZIP1 is both organ-specific and up-regulated by wounding. In wounded wild-type tomatoes, the LebZIP1 mRNA levels in distant tissue were maximally up-regulated within only 5 min following localized wounding. Exogenous abscisic acid (ABA) prevented the rapid wound-induced increase in LebZIP1 mRNA levels, while the basal levels of LebZIP1 transcripts were higher in the ABA mutants notabilis (not), sitiens (sit), and flacca (flc), and wound-induced increases were greater in the ABA-deficient mutants. Together, these results suggest that ABA acts to curtail the wound-induced synthesis of LebZIP1 mRNA.}, number={1}, journal={PLANTA}, author={Stankovic, B and Vian, A and Henry-Vian, C and Davies, E}, year={2000}, month={Dec}, pages={60–66} }
 @article{shibata_morita_abe_stankovic_davies_1999, title={Apyrase from pea stems: Isolation, purification, characterization and identification of a NTPase from the cytoskeleton fraction of pea stem tissue}, volume={37}, ISSN={["0981-9428"]}, DOI={10.1016/S0981-9428(99)00102-3}, abstractNote={The cytoskeleton pellet from the first internode of dark-grown pea stems was disintegrated in a high salt buffer, ultracentrifuged to remove ribosomes and the post-ribosomal supernatant was applied to a heparin affinity column. Significant ATPase activity was present in the cytoskeleton fraction and this was eluted from the column at 0.6–0.7 M KOAc, in the same fractions as a 49-kDa protein (which we called B3). B3 was desalted and further purified by cation exchange column chromatography. Purified B3 catalyzed hydrolysis of ATP, CTP, GTP, TTP, UTP and ADP and thus appears to be an apyrase (ATP diphosphohydrolase, EC 3.6.1.5). Partial amino acid sequences of three major fragments were obtained by digestion of B3 by Staphylococcus aureus V8 protease (EC 3.4.21.19), and all these sequences were consistent with the previously reported amino acid sequences for pea nucleoside triphosphatase (NTPase, EC 3.6.1.15) (PIR S48859), which is thought to be an apyrase.}, number={12}, journal={PLANT PHYSIOLOGY AND BIOCHEMISTRY}, author={Shibata, K and Morita, Y and Abe, S and Stankovic, B and Davies, E}, year={1999}, month={Dec}, pages={881–888} }
 @article{stankovic_abe_azama_shibata_ito_weidner_davies_1999, title={Associations of maize protein bodies with cytoskeleton, membranes, and ribosomes in the endosperm of wild type and opaque-2 mutant}, volume={21}, ISSN={["0137-5881"]}, DOI={10.1007/s11738-999-0010-3}, number={4}, journal={ACTA PHYSIOLOGIAE PLANTARUM}, author={Stankovic, B and Abe, S and Azama, K and Shibata, K and Ito, Y and Weidner, S and Davies, E}, year={1999}, pages={383–389} }
 @article{vian_henry-vian_davies_1999, title={Rapid and systemic accumulation of chloroplast mRNA-binding protein transcripts after flame stimulus in tomato}, volume={121}, ISSN={["0032-0889"]}, DOI={10.1104/pp.121.2.517}, abstractNote={Abstract}, number={2}, journal={PLANT PHYSIOLOGY}, author={Vian, A and Henry-Vian, C and Davies, E}, year={1999}, month={Oct}, pages={517–524} }
 @article{stankovic_witters_zawadzki_davies_1998, title={Action potentials and variation potentials in sunflower: An analysis of their relationships and distinguishing characteristics}, volume={103}, ISSN={["1399-3054"]}, DOI={10.1034/j.1399-3054.1998.1030107.x}, abstractNote={Sunflower plants (Helianthus annuus L.) were given an electrical stimulus to the stem or a heat (flame)‐wound to a single leaf or a cotyledon. The resulting electrical activity was monitored with extracellular electrodes. An electrical stimulus applied to the stem frequently evoked an action potential (AP), but never a variation potential (VP). In contrast, a heat‐wound applied to a leaf virtually always elicited a VP, which was often accompanied by one or more superimposed spikes (putative APs). The kinetic parameters of the AP and the VP were investigated. The AP appears to propagate without decrement in velocity or magnitude, whereas the VP parameters decrease significantly with distance. The heat stimulus triggered rapid alterations in stem elongation/contraction, which preceded changes in electrical potential, indicating the transmission of a hydraulic signal. Light‐off and light‐on stimuli evoked negative‐ and positive‐going changes in extracellular electrical potential, respectively, corresponding to de‐ and hyper‐polarization of the plasma membrane. Membrane depolarization (extracellularly manifested as a VP) evoked by both the light‐off and heat‐wounding stimuli was able to trigger one or more APs. We interpret these results to suggest that APs are “genuine” electrical signals involving voltage‐gated ion channels or pumps, which can be evoked directly by electrical stimulation or indirectly by changes in membrane potential occurring during the VP or after the light‐off stimulus. In contrast, VPs appear to be a local (non‐transmissible) electrical consequence of the passage of a rapidly transmitted hydraulic signal in the xylem, presumably acting on mechanosensitive ion channels or pumps in adjacent living cells.}, number={1}, journal={PHYSIOLOGIA PLANTARUM}, author={Stankovic, B and Witters, DL and Zawadzki, T and Davies, E}, year={1998}, month={May}, pages={51–58} }
 @article{stankovic_davies_1998, title={The wound response in tomato involves rapid growth and electrical responses, systemically up-regulated transcription of proteinase inhibitor and calmodulin and down-regulated translation}, volume={39}, ISSN={["0032-0781"]}, DOI={10.1093/oxfordjournals.pcp.a029367}, abstractNote={Localized heat wounding of tomato plants triggered rapid changes in growth and in electrical activity. The growth alterations were manifested as a transient increase in growth (petiole elongation), followed by a massive, long-lasting growth reduction. The electrical potential changes consisted of a wave of depolarization and re-polarization, i.e., a variation potential (VP). The tissue deformation apparently resulted from a pressure surge rapidly transmitted through the xylem, and preceded the changes in electrical potential. Externally-applied pressure mimicked flame wounding by triggering an electrical response resembling a VP. Our findings suggest that the VP results from a pressure surge in the xylem causing change in activity of mechanosensitive ion channels or pumps in adjacent living cells. The ensuing ion fluxes evoke plasma membrane depolarization, monitored extracellularly as a VP. Wounding also evoked a systemic decrease in polysomes, as well as a decrease in their protein synthesizing capacity in vitro. Very little of the newly-synthesized proteinase inhibitor (pin) and calmodulin (cal) mRNA was recruited into polysomes during the first hour following wounding. Since the VP appearance in distant tissue preceded the systemic molecular responses, the VP might be the long-distance signal up-regulating transcription of proteinase inhibitors and calmodulin, and down-regulating translation.}, number={3}, journal={PLANT AND CELL PHYSIOLOGY}, author={Stankovic, B and Davies, E}, year={1998}, month={Mar}, pages={268–274} }
 @article{stankovic_zawadzki_davies_1997, title={Characterization of the variation potential in sunflower}, volume={115}, ISSN={["1532-2548"]}, DOI={10.1104/pp.115.3.1083}, abstractNote={Abstract}, number={3}, journal={PLANT PHYSIOLOGY}, author={Stankovic, B and Zawadzki, T and Davies, E}, year={1997}, month={Nov}, pages={1083–1088} }
 @article{vian_henryvian_schantz_schantz_davies_ledoigt_desbiez_1997, title={Effect of calcium and calcium-counteracting drugs on the response of Bidens pilosa L to wounding}, volume={38}, ISSN={["1471-9053"]}, DOI={10.1093/oxfordjournals.pcp.a029231}, abstractNote={We used calcium counteracting drugs known to reduce the amplitude of wound-induced electric wave of depolarization and we showed that in these conditions, accumulation of the calmodulin mRNA (recently found to be correlated to membrane potential) is strongly reduced. These results bring additional evidence linking membrane potential and calmodulin mRNA accumulation.}, number={6}, journal={PLANT AND CELL PHYSIOLOGY}, author={Vian, A and HenryVian, C and Schantz, R and Schantz, ML and Davies, E and Ledoigt, G and Desbiez, MO}, year={1997}, month={Jun}, pages={751–753} }
 @article{davies_vian_vian_stankovic_1997, title={Rapid systemic up-regulation of genes after heat-wounding and electrical stimulation}, volume={19}, ISSN={["0137-5881"]}, DOI={10.1007/s11738-997-0055-0}, abstractNote={When one leaf of a tomato plant is electrically-stimulated or heat-wounded, proteinase inhibitor genes are rapidly up-regulated in distant leaves. The identity of the systemic wound signal(s) is not yet known, but major candidates include hormones transmitted via the phloem or the xylem, the electrically-stimulated self-propagating electrical signal in the phloem (the action potential, AP), or the heat-wound-induced surge in hydraulic pressure in the xylem evoking a local change in membrane potential in adjacent living cells (the variation potential, VP). In order to discriminate between these signals we have adopted two approaches. The first approach involves applying stimuli that evoke known signals and determining whether these signals have similar effects on the "model" transcripts for proteinase inhibitors (pin) and calmodulin (cal). Here we show that a heat wound almost invariably evokes a VP, while an electrical stimulation occasionally evokes an AP, and both of these signals induce accumulation of transcripts encoding proteinase inhibitors. The second approach involves identifying the array of genes turned on by heat-wounding. To this end, we have constructed a subtractive library for heat-wounded tissue, isolated over 800 putatively up-regulated clones, and shown that all but two of the fifty that we have analyzed by Northern hybridization are, indeed, up-regulated. Here we show the early kinetics of up-regulation of three of these transcripts in the terminal (4th) leaf in response to heat-wounding the 3rd leaf, about 5 cm away. Even though these transcripts show somewhat different time courses of induction, with one peaking at 30 min, another at 15 min, and another at 5 min after flaming of a distant leaf, they all exhibit a similar pattern, i.e., a transient period of transcript accumulation preceding a period of transcript decrease, followed by a second period of transcript accumulation.}, number={4}, journal={ACTA PHYSIOLOGIAE PLANTARUM}, author={Davies, E and Vian, A and Vian, C and Stankovic, B}, year={1997}, pages={571–576} }
 @article{ozeki_davies_takeda_1997, title={Somatic variation during long term subculturing of plant cells caused by insertion of a transposable element in a phenylalanine ammonia-lyase (PAL) gene}, volume={254}, ISSN={["0026-8925"]}, DOI={10.1007/s004380050433}, abstractNote={We have identified a new En/Spm-like transposable element, Tdc1, in the 5' flanking region of a phenylalanine ammonia-lyase gene (gDcPAL1) that is normally induced by transferring cells of carrot suspension cultures to fresh liquid medium (transfer or dilution effect). The initial integration into gDcPAL1 occurred more than 4 years after culture initiation. Tdc1 was first detected in gDcPAL1 genomic clones of a genomic library made from cells of the same cultured cell line 7 years after its initiation and thus following repeated subculturing. Twelve years after initiation, about 5-10% of the cells had Tdc1 inserted into the gDcPAL1 gene, indicating that Tdc1 insertion into gDcPAL1 occurred in one (or more) cell(s) during the first 4-7 years of subculturing. These mutant cells did not disappear during numerous passages; instead the proportion of cells having this Tdc1 inserted into gDcPAL1 has been increasing over the last 5 years. The promoter activity and the inducibility by transfer/dilution of the gDcPAL1 gene harboring Tdc1 is reduced relative to wild type. Finally, we show that insertion of a transposable element is one of the mechanisms that can cause variation of plant cell cultures during repeated subculture.}, number={4}, journal={MOLECULAR & GENERAL GENETICS}, author={Ozeki, Y and Davies, E and Takeda, J}, year={1997}, month={Apr}, pages={407–416} }