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Jerry D Cohen

Publications and source records attributed to Jerry D Cohen.

16 recordsLinked to original sources
PubMed2006

Analysis of four-way two-dimensional liquid chromatography-diode array data: application to metabolomics.

Two-dimensional liquid chromatography (2D-LC) is rapidly gaining popularity for the analysis of very complex mixtures, including proteomic and metabolomic samples. It provides an effective strategy for separating such samples, because the resolving power of 2D-LC is far superior to that of traditional single-dimension separations. The present work focuses on the development of data analysis methods for the extremely large data sets, on the order of 10 million data points, generated by 2D-LC with diode-array detection (DAD). Specifically, we have applied and adapted chemometric methods to the analysis of maize seedling digests, focusing on compounds related to the biosynthetic pathways of indole-3-acetic acid, the primary growth regulator in plants. The chemometric techniques of window target testing factor analysis (WTTFA), along with parallel factor analysis - alternating least squares (PARAFAC-ALS) were used to analyze 2D-LC-DAD chromatograms of a sample composed of 26 indolic standards, 2 extracts of mutant orange pericarp maize seedlings, 2 extracts of wild-type maize seedlings, and a blank sample. The indolic compounds studied belonged to six spectrally unique groups, and WTTFA was able to specifically identify the presence or absence of any of the 26 indolic standards in the mutant and wild-type samples. A PARAFAC-ALS algorithm and an ALS algorithm with flexible constraints were successfully applied to resolve the spectrally rank deficient data and to demonstrate the quantitative potential of multivariate curve resolution methods. Using this procedure, 95 total peaks were resolved in the data set analyzed. Of those 95 peaks, 45 were found in both the mutant and wild-type maize samples, 16 peaks were unique to the mutant maize samples, 13 peaks were unique to the wild-type maize samples, and 15 peaks were unique to the standard chromatograms. Of the 26 standards included in the data set, several indole acetic acid conjugates were identified and quantified in the maize samples at levels of approximately 0.3-2 microg/g plant material.

Algorithms↗
PubMed2006

Fast, comprehensive online two-dimensional high performance liquid chromatography through the use of high temperature ultra-fast gradient elution reversed-phase liquid chromatography.

A new approach to high speed, comprehensive online dual gradient elution 2DLC (LCxLC) based on the use of ultra-fast, high temperature gradient elution reversed phase chromatography is described. Entirely conventional gradient elution instrumentation and columns are assembled in a system which develops a total peak capacity of about 900 in 25 min; this is equivalent to roughly one peak/2 s. Each second dimension gradient is done in a cycle time of 21 s and the peak retention times measured for a set of twenty six indole-3-acetic acid (IAA) derivatives are reproducible to 0.2 s. Each peak eluting from the first dimension column is sampled at least twice across its width, as the corresponding peaks on the second dimension column appear in two or three consecutive second dimension chromatograms, clearly indicating that there is little loss in the resolution gained in the first dimension separation. Application to the separation of the low molecular weight components of wild-type and mutant maize seedlings indicates the presence of about 100 peaks on a timescale of 25 min. Compelling illustrations of the analytical potential of fast, high temperature 2DLC are evident in the clear presence of nine distinct peaks in a single second dimension chromatogram from a single quite narrow first dimension peak, and the great power of 2DLC to solve the "analytic dynamic range" problem inherent in the measurement of small peaks that are neighbors to a gigantic peak.

Chromatography, High Pressure Liquid↗
PubMed2006

Strawberry fruit protein with a novel indole-acyl modification.

Achenes and receptacle tissue of Fragaria vesca, L. cultivar Yellow Wonder were shown to contain conjugated indole-3-acetic acid (IAA) that was not soluble in organic solvents and yielded IAA after strong alkaline hydrolysis, suggestive of IAA attached to plant proteins. This solvent insoluble conjugated IAA accounted for between 0.4 and 4 ng of IAA per gram fresh weight of tissue in both achenes and receptacles. To investigate this strawberry conjugate class further, a polyclonal antibody was produced to IAA-glycine attached to BSA that detected neutral indole acid esters, monocarboxylic-amino acid IAA conjugates and IAA proteins. Using immunoblotting, both achenes and receptacles of strawberry were shown to have primarily an immuno-detectable band at 76 kDa. Two-dimensional polyacrylamide gel electrophoresis yielded a wide band that was analyzed by LC-MS/MS analysis following in-gel trypsin digestion. Peptides derived from the immuno-detectable band were tentatively identified by peptide fragment analysis as being from either a chaperonin related to the hsp60 class of proteins or, alternatively, an ATP synthase. This is one of the first reports of an IAA modified protein in fruit tissue.

Fragaria↗
PubMed2006

The effect of temperature, photoperiod, and light quality on gluconasturtiin concentration in watercress (Nasturtium officinale R. Br.).

The effects of different growth regimes on gluconasturtiin concentration in watercress (Nasturtium officinale R. Br.) were investigated. Watercress plantlets at the 5th mature leaf stage (ca. 2 weeks old) were exposed to different day and night temperatures, to long (16 h) or short (8 h) days, to red (R) or far-red (FR) light given during the main long day photoperiod, and finally to R or FR light given at the end of the main photoperiod. Watercress plants grown under long days contained a 30-40% higher gluconasturtiin concentration and had a higher fresh weight than watercress plants grown under short days. Watercress plants grown under long days and temperatures of 15 or 10 degrees C had at least a 50% higher gluconasturtiin concentration, but a lower fresh weight, than that of plants grown at 20 or 25 degrees C. Watercress plants grown under metal halide light enriched with R light had approximately a 25-40% higher concentration of gluconasturtiin as compared to the FR-enriched plants. Likewise, a brief R light exposure at the end of the main photoperiod resulted in approximately a 25% or higher concentration of gluconasturtiin as compared to a FR end-of-day exposure. These data indicate that the concentration of gluconasturtiin in watercress can be significantly increased by growing plants at lower temperatures, under long days, and by exposure to R light.

Chromatography, High Pressure Liquid↗
PubMed2005

Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation.

Pollination in flowering plants requires that anthers release pollen when the gynoecium is competent to support fertilization. We show that in Arabidopsis thaliana, two paralogous auxin response transcription factors, ARF6 and ARF8, regulate both stamen and gynoecium maturation. arf6 arf8 double-null mutant flowers arrested as infertile closed buds with short petals, short stamen filaments, undehisced anthers that did not release pollen and immature gynoecia. Numerous developmentally regulated genes failed to be induced. ARF6 and ARF8 thus coordinate the transition from immature to mature fertile flowers. Jasmonic acid (JA) measurements and JA feeding experiments showed that decreased jasmonate production caused the block in pollen release, but not the gynoecium arrest. The double mutant had altered auxin responsive gene expression. However, whole flower auxin levels did not change during flower maturation, suggesting that auxin might regulate flower maturation only under specific environmental conditions, or in localized organs or tissues of flowers. arf6 and arf8 single mutants and sesquimutants (homozygous for one mutation and heterozygous for the other) had delayed stamen development and decreased fecundity, indicating that ARF6 and ARF8 gene dosage affects timing of flower maturation quantitatively.

Arabidopsis↗
PubMed2005

Aminoethyl-substituted indole-3-acetic acids for the preparation of tagged and carrier-linked auxin.

Indole-3-acetic acid is an indispensable hormone (auxin) in plants and an important metabolite in humans, animals, and microorganisms. Here we introduce its 5- and 6-(2-aminoethyl)-derivatives for use in the design of novel research tools, such as immobilized and carrier-linked forms of indole-3-acetic acid and its conjugates with biochemical tags or biocompatible molecular probes. The aliphatic nitrogens of 5- and 6-(2-aminoethyl)indole were acetylated and the products were converted to the corresponding 3-(N,N-dimethylamino)methyl derivatives (gramines). These were reacted with cyanide. Saponification of the resulting acetonitriles was accompanied by N-deprotection to yield 5- and 6-(2-aminoethyl)indole-3-acetic acids. The latter were chemically stable and could be linked, via their amino groups, and without prior protection of their carboxyl moieties, to bovine serum albumin and to biotin, including appropriate spacer modules. One of the protein conjugates was used to elicit the formation of monoclonal antibodies, which were evaluated using the biotin conjugates in an enzyme-linked immunosorbent assay employing streptavidin-coupled alkaline phosphatase, and thus shown to recognize predominantly the indole-3-acetic acid moiety.

Animals↗
PubMed2004

Long-term inhibition by auxin of leaf blade expansion in bean and Arabidopsis.

The role of auxin in controlling leaf expansion remains unclear. Experimental increases to normal auxin levels in expanding leaves have shown conflicting results, with both increases and decreases in leaf growth having been measured. Therefore, the effects of both auxin application and adjustment of endogenous leaf auxin levels on midrib elongation and final leaf size (fresh weight and area) were examined in attached primary monofoliate leaves of the common bean (Phaseolus vulgaris) and in early Arabidopsis rosette leaves. Aqueous auxin application inhibited long-term leaf blade elongation. Bean leaves, initially 40 to 50 mm in length, treated once with alpha-naphthalene acetic acid (1.0 mm), were, after 6 d, approximately 80% the length and weight of controls. When applied at 1.0 and 0.1 mm, alpha-naphthalene acetic acid significantly inhibited long-term leaf growth. The weak auxin, beta-naphthalene acetic acid, was effective at 1.0 mm; and a weak acid control, benzoic acid, was ineffective. Indole-3-acetic acid (1 microm, 10 microm, 0.1 mm, and 1 mm) required daily application to be effective at any concentration. Application of the auxin transport inhibitor, 1-N-naphthylphthalamic acid (1% [w/w] in lanolin), to petioles also inhibited long-term leaf growth. This treatment also was found to lead to a sustained elevation of leaf free indole-3-acetic acid content relative to untreated control leaves. Auxin-induced inhibition of leaf growth appeared not to be mediated by auxin-induced ethylene synthesis because growth inhibition was not rescued by inhibition of ethylene synthesis. Also, petiole treatment of Arabidopsis with 1-N-naphthylphthalamic acid similarly inhibited leaf growth of both wild-type plants and ethylene-insensitive ein4 mutants.

Arabidopsis↗
PubMed2004

His-404 and His-405 are essential for enzyme catalytic activities of a bacterial indole-3-acetyl-L-aspartic acid hydrolase.

Bacterial indole-3-acetyl-l-aspartic acid (IAA-Asp) hydrolase has shown very high substrate specificity compared with similar IAA-amino acid hydrolase enzymes found in Arabidopsis thaliana. The IAA-Asp hydrolase also exhibits, relative to the Arabidopsis thaliana-derived enzymes, a very high Vmax (fast reaction rate) and a higher Km (lower substrate affinity). These two characteristics indicate that there are fundamental differences in the catalytic activity between this bacterial enzyme and the Arabidopsis enzymes. By employing a computer simulation approach, a catalytic residue, His-385, from a non-sequence-related zinc-dependent exopeptidase of Pseudomonas was found to structurally match His-405 of IAA-Asp hydrolase. The His-405 residue is conserved in all related sequences of bacteria and Arabidopsis. Point mutation experiments of this His-405 to seven different amino acids resulted in complete elimination of enzyme activity. However, point mutation on the neighboring His-404 to eight other residues resulted in reduction, to various degrees, of enzyme activity. Amino acid substitutions for His-404 also showed that this residue influenced the minor activity of the IAA-Asp hydrolase for the substrates IAA-Gly, IAA-Ala, IAA-Ser, IAA-Glu and IAA-Asn. These results show the value and potential of structural modeling for predicting target residues for further study and for directing bioengineering of enzyme structure and function.

Amino Acid Sequence↗
PubMed2003

Two genetically discrete pathways convert tryptophan to auxin: more redundancy in auxin biosynthesis.

The answer to the simple question of how plants make auxin has proven to be inordinately complex. Recent in planta studies in Arabidopsis have uncovered additional complexity in auxin biosynthesis. Two distinct pathways from tryptophan to the intermediate indoleacetaldoxime were identified. Genic, as well as functional redundancy, appear to be characteristic for auxin biosynthesis and plants might have evolved many different solutions for making and regulating auxin.

Arabidopsis↗
PubMed2002

A gene encoding a protein modified by the phytohormone indoleacetic acid.

We show that the expression of an indole-3-acetic acid (IAA)-modified protein from bean seed, IAP1, is correlated to the developmental period of rapid growth during seed development. Moreover, this protein undergoes rapid degradation during germination. The gene for IAP1, the most abundant protein covalently modified by IAA (iap1, GenBank accession no. ) was isolated and cloned from bush bean (Phaseolus vulgaris) seeds. The 957-bp sequence encodes a 35-kDa polypeptide. IAA-modified proteins represent a distinct class of conjugated phytohormones and appear in bean to be the major form of auxin in seeds. IAA proteins also are found at other stages of development in bean plants. Our immunological and analytical data suggest that auxin modification of a small class of proteins may be a feature common to many plants.

Amino Acid Sequence↗
PubMed2002

An auxin surge following fertilization in carrots: a mechanism for regulating plant totipotency.

All plants exhibit the property of cellular totipotency, whereby individual cells can regenerate into an entire organism. However little is known about the underlying mechanisms regulating totipotency. Using a preparative microtechnique, we report an 80-fold surge in the concentration of free auxin that is correlated with the initial stages of zygotic embryogenesis in carrots. The concentration of free IAA increases from a basal level of ca. 25 ng/g FW in unfertilized ovules to ca. 2.000 ng/g FW in the late globular and early heart stages, then back to the basal level in the torpedo stage. This initial increase in IAA levels is diagnostic of the activity of the tryptophan-mediated pathway for IAA biosynthesis, while the maintenance of the basal levels is attributed to the tryptophan-independent pathway for IAA biosynthesis. Our observations are consistent with the hypothesis that the sequential activation of alternative IAA biosynthetic pathways is a critical mechanism for regulating carrot (Daucus carota L. cv. Danvers 126) embryogenesis and other instances of plant totipotency.

Daucus carota↗
PubMed2002

Identification and quantification of three active auxins in different tissues of Tropaeolum majus.

Indole-3-acetic acid (IAA), indole-3-butyric acid (IBA) and phenylacetic acid (PAA) were identified as endogenous compounds with auxin activity in nasturtium (Tropaeolum majus L.) by full scan gas chromatography-mass spectrometry. The endogenous concentrations of the three auxins were measured by GC-selected ion monitoring-MS and isotope dilution analysis using stable labelled isotopes. PAA was present at concentrations about 10- to 100-fold lower than IAA, whereas IBA was found to be in the same concentration range as IAA. Free IAA was highest in roots followed by young leaves. IBA was also highest in the roots, and relatively high concentrations were found in young leaves and flowers. The distribution of PAA was quite different from that found for IBA. No PAA could be detected in young leaves and flowers, and in all other tissues studied the concentrations were well below those of the other two auxin compounds. The presence of a nitrilase gene family and nitrilase activity in extracts from T. majus suggests that PAA might be synthesized by the nitrilase pathway using benzylglucosinolate as precursor.

Journal Article↗
PubMed2002

Indole-3-acetic acid metabolism in Lemna gibba undergoes dynamic changes in response to growth temperature.

Auxin is the mobile signal controlling the rate of growth and specific aspects of the development of plants. It has been known for over a century that auxins act as the messenger linking plant development to specific environmental changes. An often overlooked aspect of how this is accomplished is the effect of the environment on metabolism of the major plant auxin, indole-3-acetic acid (IAA). We have studied the metabolism of IAA in relation to one environmental variable, growth temperature. The model system used was an inbred line of the aquatic monocot Lemna gibba G-3, 3F7-11 grown at temperatures ranging from 5 degrees C to 35 degrees C. IAA levels, the rate of IAA turnover, and the patterns of label incorporation from IAA precursors were measured using stable isotope-mass spectrometric techniques and were evaluated relative to growth at the experimental temperatures. IAA levels exhibited unusually high variability in plants grown at 15 degrees C and 20 degrees C. Turnover rates were quite rapid throughout the range of experimental temperatures except at 25 degrees C, where IAA turnover was notably slower. These results suggest that a transition occurred over these temperatures for some aspect of IAA metabolism. Analysis of [(15)N]anthranilate and [(2)H(5)]tryptophan (Trp) incorporation into IAA showed that Trp-dependent biosynthesis predominated at 15 degrees C; however, Trp-independent biosynthesis of IAA was the major route to IAA at 30 degrees C. The effects of growth temperature on auxin levels have been reported previously, but no prior studies correlated these effects with which pathway becomes the primary one for IAA production.

Carbon Radioisotopes↗
PubMedDate not supplied

Evolutionary patterns in auxin action.

This review represents the first effort ever to survey the entire literature on auxin (indole-3-acetic acid, IAA) action in all plants, with special emphasis on the green plant lineage, including charophytes (the green alga group closest to the land plants), bryophytes (the most basal land plants), pteridophytes (vascular non-seed plants), and seed plants. What emerges from this survey is the surprising perspective that the physiological mechanisms for regulating IAA levels and many IAA-mediated responses found in seed plants are also present in charophytes and bryophytes, at least in nascent forms. For example, the available evidence suggests that the apical regions of both charophytes and liverworts synthesize IAA via a tryptophan-independent pathway, with IAA levels being regulated via the balance between the rates of IAA biosynthesis and IAA degradation. The apical regions of all the other land plants utilize the same class of biosynthetic pathway, but they have the potential to utilize IAA conjugation and conjugate hydrolysis reactions to achieve more precise spatial and temporal control of IAA levels. The thallus tips of charophytes exhibit saturable IAA influx and efflux carriers, which are apparently not sensitive to polar IAA transport inhibitors. By contrast, two divisions of bryophyte gametophytes and moss sporophytes are reported to carry out polar IAA transport, but these groups exhibit differing sensitivities to those inhibitors. Although the IAA regulation of charophyte development has received almost no research attention, the bryophytes manifest a wide range of developmental responses, including tropisms, apical dominance, and rhizoid initiation, which are subject to IAA regulation that resembles the hormonal control over corresponding responses in seed plants. In pteridophytes, IAA regulates root initiation and vascular tissue differentiation in a manner also very similar to its effects on those processes in seed plants. Thus, it is concluded that the seed plants did not evolve de novo mechanisms for mediating IAA responses, but have rather modified pre-existing mechanisms already operating in the early land plants. Finally, this paper discusses the encouraging prospects for investigating the molecular evolution of auxin action.

Biological Evolution↗