Relative and absolute test-retest reliabilities of biomechanical risk factors for knee osteoarthritis progression: benchmarks for meaningful change.

OBJECTIVE: Biomechanical factors are important treatment targets in knee osteoarthritis. The knee adduction (KAM) and flexion (KFM) moments, quadriceps strength and power, load frequency, and body mass index (BMI) all have the potential to affect knee articular cartilage integrity by modulating forces across the joint. To identify clinically meaningful change, however, these measurements must be reliable and sensitive to change. This study estimated relative and absolute test-retest reliabilities over long periods of biomechanical risk factors for knee osteoarthritis progression. METHOD: Data from a longitudinal, observational study were analyzed for knee osteoarthritis patients with data at baseline, 6-month and 24-month follow-ups. Gait kinematics and kinetics, quadriceps strength and power, daily load frequency and BMI were collected. Relative and absolute test-retest reliabilities of these measures were estimated using intraclass correlation coefficients (ICCs) and standard errors of measurement (SEMs), respectively. Minimal detectable change at the 95% confidence level (MDC95) was also calculated. RESULTS: Data from 46 participants [36 women; age 61.0 (6.6) years] were included. Good-to-excellent relative reliabilities (ICC ≥ 0.80) indicated that KAM peak and impulse, quadriceps strength and power, and BMI had a strong ability to discriminate amongst participants. Absolute reliabilities were high for quadriceps strength and BMI, which demonstrated reasonable within-participant variability (SEMs ≤ 11% of the mean). The MDC95 values supported use of clinical interventions effective in reducing BMI and KAM, and increasing quadriceps strength. CONCLUSION: These data are useful in interpreting findings from interventional or longitudinal investigations by determining whether observed changes are beyond measurement error and interpretable as true change.

T1 and T2* mapping of the human quadriceps and patellar tendons using ultra-short echo-time (UTE) imaging and bivariate relaxation parameter-based volumetric visualization.

Quantification of magnetic resonance (MR)-based relaxation parameters of tendons and ligaments is challenging due to their very short transverse relaxation times, requiring application of ultra-short echo-time (UTE) imaging sequences. We quantify both T1 and T2* in the quadriceps and patellar tendons of healthy volunteers at a field strength of 3 T and visualize the results based on 3D segmentation by using bivariate histogram analysis. We applied a 3D ultra-short echo-time imaging sequence with either variable repetition times (VTR) or variable flip angles (VFA) for T1 quantification in combination with multi-echo acquisition for extracting T2*. The values of both relaxation parameters were subsequently binned for bivariate histogram analysis and corresponding cluster identification, which were subsequently visualized. Based on manually-drawn regions of interest in the tendons on the relaxation parameter maps, T1 and T2* boundaries were selected in the bivariate histogram to segment the quadriceps and patellar tendons and visualize the relaxation times by 3D volumetric rendering. Segmentation of bone marrow, fat, muscle and tendons was successfully performed based on the bivariate histogram analysis. Based on the segmentation results mean T2* relaxation times, over the entire tendon volumes averaged over all subjects, were 1.8 ms ±â€¯0.1 ms and 1.4 ms ±â€¯0.2 ms for the patellar and quadriceps tendons, respectively. The mean T1 value of the patellar tendon, averaged over all subjects, was 527 ms ±â€¯42 ms and 476 ms ±â€¯40 ms for the VFA and VTR acquisitions, respectively. The quadriceps tendon had higher mean T1 values of 662 ms ±â€¯97 ms (VFA method) and 637 ms ±â€¯40 ms (VTR method) compared to the patellar tendon. 3D volumetric visualization of the relaxation times revealed that T1 values are not constant over the volume of both tendons, but vary locally. This work provided additional data to build upon the scarce literature available on relaxation times in the quadriceps and patellar tendons. We were able to segment both tendons and to visualize the relaxation parameter distributions over the entire tendon volumes.

Creation of a Metabolic Sink for Tryptophan Alters the Phenylpropanoid Pathway and the Susceptibility of Potato to Phytophthora infestans.

The creation of artificial metabolic sinks in plants by genetic engineering of key branch points may have serious consequences for the metabolic pathways being modified. The introduction into potato of a gene encoding tryptophan decarboxylase (TDC) isolated from Catharanthus roseus drastically altered the balance of key substrate and product pools involved in the shikimate and phenylpropanoid pathways. Transgenic potato tubers expressing the TDC gene accumulated tryptamine, the immediate decarboxylation product of the TDC reaction. The redirection of tryptophan into tryptamine also resulted in a dramatic decrease in the levels of tryptophan, phenylalanine, and phenylalanine-derived phenolic compounds in transgenic tubers compared with nontransformed controls. In particular, wound-induced accumulation of chlorogenic acid, the major soluble phenolic ester in potato tubers, was found to be two- to threefold lower in transgenic tubers. Thus, the synthesis of polyphenolic compounds, such as lignin, was reduced due to the limited availability of phenolic monomers. Treatment of tuber discs with arachidonic acid, an elicitor of the defense response, led to a dramatic accumulation of soluble and cell wall-bound phenolics in tubers of untransformed potato plants but not in transgenic tubers. The transgenic tubers were also more susceptible to infection after inoculation with zoospores of Phytophthora infestans, which could be attributed to the modified cell wall of these plants. This study provides strong evidence that the synthesis and accumulation of phenolic compounds, including lignin, could be regulated by altering substrate availability through the introduction of a single gene outside the pathway involved in substrate supply. This study also indicates that phenolics, such as chlorogenic acid, play a critical role in defense responses of plants to fungal attack.

The Activation of the Potato PR-10a Gene Requires the Phosphorylation of the Nuclear Factor PBF-1.

The pathogenesis-related gene PR-10a (formerly STH[middot]2) is induced in various organs of potato after wounding, elicitor treatment, or infection by Phytophthora infestans. Deletion analysis of the promoter of the PR-10a gene enabled us to identify a 50-bp region, located between positions -155 and -105, necessary for the elicitor responsiveness of the [beta]-glucuronidase reporter gene in transgenic potato plants. Within this region, a 30-bp sequence, located between positions -135 and -105, was necessary for the activation of the promoter by the elicitor. However, strong promoter activity after elicitor treatment required the presence of a 20-bp sequence located between positions -155 and -135. The region between -135 and -105 was specifically recognized by two nuclear factors, PBF-1 (PR-10a Binding Factor 1) and PBF-2, and binding of PBF-1 was coordinated with the accumulation of the PR-10a mRNA. Gel shift assays using nuclear extracts pretreated with sodium deoxycholate or alkaline phosphatase suggested that PBF-1 is a multimeric factor in which at least one of the constituent proteins can be phosphorylated. Treatment with alkaline phosphatase also indicated that binding of PBF-1 is positively regulated by phosphorylation and that it is phosphorylated only in tissues in which PR-10a is expressed. The use of protein phosphatase and kinase inhibitors in vivo provided additional evidence that wounding and elicitor treatment induce the phosphorylation of PBF-1 and that this phosphorylation is associated with gene activation.

Direct visualization of protein interactions in plant cells.

The protein NPR1/NIM1 is required for the induction of systemic acquired resistance (SAR) in plants and has been shown to interact with members of the TGA/OBF family of basic leucine zipper (bZIP) transcription factors. However, to date, there is no method available to monitor such interactions in plant cells. We report here an in vivo protein fragment complementation assay (PCA), based on association of reconstituted murine dihydrofolate reductase (mDHFR) with a fluorescent probe to detect protein-protein interaction in planta. We demonstrate that the interaction between Arabidopsis NPR1/NIM1 and the bZIP factor TGA2 is induced by the regulators of SAR, salicylic acid (SA), and its analog 2,6-dichloroisonicotinic acid (INA) with distinct species-specific responses. Furthermore, the induced interaction is localized predominantly in the nucleus. Protein fragment complementation assays could be of value to agricultural research by providing a system for high-throughput biochemical pathway mapping and for screening of small molecules that modulate protein interactions.

Long term prospective of the Seine River system: confronting climatic and direct anthropogenic changes.

To explore the evolution of a human impacted river, the Seine (France), over the 21st century, three driving factors were examined: climate, agriculture, and point source inputs of domestic and industrial origin. Three future scenarios were constructed, by modification of a baseline representative of recent conditions. A climate change scenario, based on simulations by a general circulation model driven by the SRES-A2 scenario of radiative forcing, accounts for an average warming of +3.3 degrees C over the watershed and marked winter increase and summer decrease in precipitation. To illustrate a possible reduction in nitrate pollution from agricultural origin, a scenario of good agricultural practices was considered, introducing catch crops and a 20% decrease in nitrogen fertilisation. Future point source pollution was estimated following the assumptions embedded in scenario SRES-A2 regarding demographic, economic and technologic changes, leading to reductions of 30 to 75% compared to 2000, depending on the pollutants. Four models, addressing separate components of the river system (agronomical model, hydrogeological model, land surface model and water quality model), were used to analyse the relative impact of these scenarios on water quality, in light of their impact on hydrology and crop production. The first-order driving factor of water quality over the 21st century is the projected reduction of point source pollution, inducing a noticeable decrease in eutrophication and oxygen deficits downstream from Paris. The impact of climate change on these terms is driven by the warming of the water column. It enhances algal growth in spring and the loss factors responsible for phytoplankton mortality in late summer (grazers and viruses). In contrast, increased seasonal contrasts in river discharge have a negligible impact on river water quality, as do the changes in riverine nitrate concentration, which never gets limiting. The latter changes have a similar magnitude under the three scenarios. Under climate change, riverine and groundwater nitrate concentrations increase and crop production is advantaged with reduced growing cycles and increased yields. In contrast, nitrate concentrations decrease under the good agricultural practices scenario, with a limited decrease in crop production. When these two scenarios are combined, the changes in nitrate concentrations balance each other and crop yields increase. The results of this numerical exercise indicate that the potential changes to the Seine River system during the 21st century will not lead to severely degraded water quality.

Streptomycin-induced conformational changes in the 70-S bacterial ribosome.

Conformational alterations induced by streptomycin in the bacterial ribosome have been investigated using as probes, ethidium bromide, N-[14C]ethylmaleimide and a spin label nitroxide analog of N-ethylmaleimide. 1. The binding of the antibiotic to the ribosome does not affect the reactivity of sulfhydryl groups towards N-ethylmaleimide. 2. The motional freedom of spin labels bound to ribosomal proteins S1 and S18 is increased but it is hardly affected at other labeled sites. This observation suggests that the binding of streptomycin causes a local loosening of the ribosomal structure. 3. Ribosomes are found to bind less ethidium bromide in the presence of streptomycin, which suggests that the binding of streptomycin decreases the degree of organization of ribosomal RNA.

Regulation of the expression of leghaemoglobin genes in effective and ineffective root nodules of soybean.

The expression of leghaemoglobin genes in effective and ineffective (unable to fix nitrogen) root nodules of soybean developed by Rhizobium japonicum strains 61A76, 61A24 and SM5 was measured by using a cDNA probe or a cloned leghaemoglobin sequence and in vitro translation of Lb-mRNA. Hybridization of the poly(A)-containing nodule polysomal RNA from 3-week-old nodules with a kinetically purified Lb-cDNA or with plasmid (pLbl) containing a leghaemoglobin sequence showed that Lb-mRNA is present in ineffective nodules formed by strains SM5 and 61A24 at reduced levels. Of the two major classes of electrophoretically distinguishable leghaemoglobins in soybean, LbS was not synthesized in 3-week-old strain 61A24-induced nodules while both sorts of leghaemoglobin were synthesized and accumulated in ineffective nodules formed by strain SM5 of Rhizobium. Ineffective nodules formed by strain 61A24 are green inside and do not appear to accumulate leghaemoglobin as measured by the haemochromogen assay, although low levels of apoleghaemoglobin were detected using leghaemoglobin antibodies. SM5-induced nodules were found to have about half as much as leghaemoglobin of the of effective (61A76-induced) nodules. This study demonstrates that while the appearance of leghaemoglobin is independent of nitrogenase activity in bacteroids, its synthesis is influenced to different degrees both by a mutation (SM5) and incompatibility (61A24) of Rhizobium. The primary regulation appears to be at the level of transcription or processing of mRNA since ineffective nodules contain Lb-mRNA approximately in proportion to the amount of apoleghaemoglobin present in these nodules.

Cloning, expression, and sequence conservation of pathogenesis-related gene transcripts of potato.

Treatment of potato tuber disks with arachidonic acid elicits the accumulation of several mRNAs. cDNA clones corresponding to two of these mRNAs were isolated and characterized. Nucleotide sequence analysis reveals that both clones (pSTH-2 and pSTH-21) contain an open-reading frame coding for a 155-amino acid polypeptide. The polypeptides encoded by the two clones differ by only six amino acids and show a high degree of similarity with PR protein sequences from pea (approximately 42%) and parsley (approximately 37%). mRNAs corresponding to the two potato cDNA clones also accumulate in Solanum chacoense and in tomato following elicitor treatment. Maximum accumulation of the mRNAs corresponding to the two cDNA clones is reached 24 hr after elicitor treatment of the tuber disks. pSTH-2-related mRNAs also accumulate in tubers after wounding or treatment with eicosapentaenoic acid and are detected in potato and tomato leaves treated with a Phytophthora infestans mycelium homogenate. The presence of these conserved genes in species from three plant families and the similarity of their induction pattern suggest an important function during the plant defense response.

Nucleotide sequence of the dihydrofolate-reductase gene borne by the plasmid R67 and conferring methotrexate resistance.

The complete nucleotide sequence of the methotrexate-resistant dihydrofolate reductase (DHFR) gene borne by the plasmid R67 was determined. The gene is 234 bp long and codes for 78 amino acids. The polypeptide deduced from the DNA sequence is in perfect agreement with the previously published amino acid sequence. Comparison of the nucleotide sequence with the one determined for the R388-encoded DHFR indicates that 75% of the nucleotides are conserved in the two genes. The 3' end of the R67 gene can be modified without altering significantly the activity of the enzyme.

The organization of a nuclear DNA sequence from a higher plant: molecular cloning and characterization of soybean ribosomal DNA.

The recombinant DNA vector, lambda Charon 4A, was used to construct a library of DNA sequences from the genomic DNA of soybean (Glycine max). To define the organization of ribosomal DNA (rDNA) in the soybean genome, clones containing sequences complementary to both 17S and 25S rRNA have been isolated from this library and used in conjunction with Southern blot hybridization. The rRNA genes are tandemly reiterated with a relatively small unit repeat length of 7.8 kb. There is no heterogeneity in the length of the rDNA repeat units although they display limited differences in either base sequence or pattern of methylation. The cloned rDNA sequences are shown to comprise the entire repeat unit and have been used to obtain a detailed restriction map as well as an approximate transcription map of soybean rRNA genes. The cloning of rDNA from soybean suggests that recombinant DNA techniques can be successfully applied to the genomic DNA of higher plants despite the high degree of methylation exhibited by plant DNA.

Robustness and precision of an automatic marker detection algorithm for online prostate daily targeting using a standard V-EPID.

An algorithm for the daily localization of the prostate using implanted markers and a standard video-based electronic portal imaging device (V-EPID) has been tested. Prior to planning, three gold markers were implanted in the prostate of seven patients. The clinical images were acquired with a BeamViewPlus 2.1 V-EPID for each field during the normal course radiotherapy treatment and are used off-line to determine the ability of the automatic marker detection algorithm to adequately and consistently detect the markers. Clinical images were obtained with various dose levels from ranging 2.5 to 75 MU. The algorithm is based on marker attenuation characterization in the portal image and spatial distribution. A total of 1182 clinical images were taken. The results show an average efficiency of 93% for the markers detected individually and 85% for the group of markers. This algorithm accomplishes the detection and validation in 0.20-0.40 s. When the center of mass of the group of implanted markers is used, then all displacements can be corrected to within 1.0 mm in 84% of the cases and within 1.5 mm in 97% of cases. The standard video-based EPID tested provides excellent marker detection capability even with low dose levels. The V-EPID can be used successfully with radiopaque markers and the automatic detection algorithm to track and correct the daily setup deviations due to organ motions.

Changes in time of sowing, flowering and maturity of cereals in Europe under climate change.

The phenological development of cereal crops from emergence through flowering to maturity is largely controlled by temperature, but also affected by day length and potential physiological stresses. Responses may vary between species and varieties. Climate change will affect the timing of cereal crop development, but exact changes will also depend on changes in varieties as affected by plant breeding and variety choices. This study aimed to assess changes in timing of major phenological stages of cereal crops in Northern and Central Europe under climate change. Records on dates of sowing, flowering, and maturity of wheat, oats and maize were collected from field experiments conducted during the period 1985-2009. Data for spring wheat and spring oats covered latitudes from 46 to 64°N, winter wheat from 46 to 61°N, and maize from 47 to 58°N. The number of observations (site-year-variety combinations) varied with phenological phase, but exceeded 2190, 227, 2076 and 1506 for winter wheat, spring wheat, spring oats and maize, respectively. The data were used to fit simple crop development models, assuming that the duration of the period until flowering depends on temperature and day length for wheat and oats, and on temperature for maize, and that the duration of the period from flowering to maturity in all species depends on temperature only. Species-specific base temperatures were used. Sowing date of spring cereals was estimated using a threshold temperature for the mean air temperature during 10 days prior to sowing. The mean estimated temperature thresholds for sowing were 6.1, 7.1 and 10.1°C for oats, wheat and maize, respectively. For spring oats and wheat the temperature threshold increased with latitude. The effective temperature sums required for both flowering and maturity increased with increasing mean annual temperature of the location, indicating that varieties are well adapted to given conditions. The responses of wheat and oats were largest for the period from flowering to maturity. Changes in timing of cereal phenology by 2040 were assessed for two climate model projections according to the observed dependencies on temperature and day length. The results showed advancements of sowing date of spring cereals by 1-3 weeks depending on climate model and region within Europe. The changes were largest in Northern Europe. Timing of flowering and maturity were projected to advance by 1-3 weeks. The changes were largest for grain maize and smallest for winter wheat, and they were generally largest in the western and northern part of the domain. There were considerable differences in predicted timing of sowing, flowering and maturity between the two climate model projections applied.

Repression of the defense gene PR-10a by the single-stranded DNA binding protein SEBF.

The potato pathogenesis-related gene PR-10a is transcriptionally activated in response to pathogen infection or elicitor treatment. Characterization of the cis-acting elements of the PR-10a promoter revealed the presence of a silencing element between residues -52 and -27 that contributes to transcriptional regulation. In this study, we have isolated a silencing element binding factor (SEBF) from potato tuber nuclei that binds to the coding strand of the silencing element in a sequence-specific manner. The consensus binding site of SEBF, PyTGTCNC, is present in a number of PR genes and shows striking similarity to the auxin response element. Mutational analysis of the PR-10a promoter revealed an inverse correlation between the in vitro binding of SEBF and the expression of PR-10a. SEBF was purified to homogeneity from potato tubers, and sequencing of the N terminus of the protein led to the isolation of a cDNA clone. Sequence analysis revealed that SEBF is homologous with chloroplast RNA binding proteins that possess consensus sequence-type RNA binding domains characteristic of heterogeneous nuclear ribonucleoproteins (hnRNPs). Overexpression of SEBF in protoplasts repressed the activity of a PR-10a reporter construct in a silencing element-dependent manner, confirming the role of SEBF as a transcriptional repressor.

The defense-related STH-2 gene product of potato shows race-specific accumulation after inoculation with low concentrations of Phytophthora infestans zoospores.

The defense-related STH-2 gene is rapidly activated following infection or elicitor treatment of potato (Solanum tuberosum L.) tubers. However, its physiological or biochemical function is unknown. To study the STH-2 gene product and its accumulation during the defense response, we raised antibodies to a ß-galactosidase-STH-2 fusion protein in Escherichia coli. The antiserum specifically recognized a protein of the predicted 17-kDa size in extracts of elicited tuber disks when analyzed by Western blot. In control extracts this band was not detected. The accumulation of STH-2 protein in response to incompatible and compatible zoospores of Phytophthora infestans (Mont.) de Bary depended on the inoculum density applied. Whereas a low concentration of spores induced accumulation of STH-2 protein faster in the incompatible than the compatible interaction, this difference in timing was less pronounced at higher inoculum densities. Inoculation with a high concentration of compatible spores also resulted in the disappearance of STH-2 protein late during the infection. In both control and induced tuber tissue the antibody strongly reacted with an unknown protein of 18 kDa. This protein was present constitutively in tubers, but in leaves its accumulation was stimulated by inoculation with P. infestans.

Evidence for a conformational change in tRNAPhe upon aminoacylation.

A conformational difference between the structure of tRNAPhe and Cbz-Phe-tRNAPhe from Escherichia coli was detected using the spin label method. A comparison of the respective rotational correlation time (tau c) values of three differently located spin labels, indicates that upon aminoacylation of tRNAPhe, the 4-thiouridine residue region and the miniloop region become more flexible, while the environment of the anticodon loop is not affected. These observations suggest that the main difference in structure between charged and uncharged tRNA resides in the release and exposure of the TpsiC loop for eventual binding to the ribosomes.

A functional homolog of mammalian protein kinase C participates in the elicitor-induced defense response in potato.

The elicitor-induced activation of the potato pathogenesis-related gene PR-10a is positively controlled by a protein kinase(s) that affects the binding of the nuclear factors PBF-1 (for PR-10a binding factor-1) and PBR-2 to an elicitor response element (ERE). In this study, we have identified a kinase that has properties similar to the conventional isoenzymes of the mammalian protein kinase C (PKC) family. the treatment of potato tuber discs with specific inhibitors of PKC abolished the elicitor-induced binding of the nuclear factor PBF-2 to the ERE. This correlated with a reduction in the accumulation of the PR-10a protein. In contrast, treatment of the tuber discs with 12-O-tetradecanoylphorbol 13-acetate (TPA), an activator of PKC, led to an increase in binding of PBF-2 to the ERE and the corresponding increase in the level of the PR-10a protein, mimicking the effect seen with the elicitor arachidonic acid. Biochemical characterization of proteins extracted from the particulate fraction of potato tubers demonstrated that a kinase belonging to the conventional isoforms of PKC is present. This was confirmed by immunoprecipitation with antibodies specific to the conventional isoforms of human PKC and in-gel kinase assays. The ability of the immunoprecipitates to phosphorylate the alpha-peptide (a PKC specific substrate) in the presence of the coactivators calcium, phosphatidylserine, and TPA strongly suggested that the immunoprecipitated kinase is similar to the kinase characterized biochemically. Finally, the similar effects of the various modulators of PKC activity on the elicitor-induced resistance against a compatible race of Phytophthora infestans implicate this kinase in the overall defense response in potato.

Selective spin-labeling of the ribosomal proteins of 70S ribosomes from Escherichia coli.

We have used a series of N-(1-oxyl-2,2,5,5-tetramethyl-3-pyrrolidinyl) maleimide spin labels of different length to label, covalently and selectively, the most reactive sulfhydryl groups of 70S ribosomal proteins of Escherichia coli. Under short periods of labeling (1--2 min), less than two spin labels per ribosome are incorporated and were shown to be distributed mainly on five ribosomal proteins in the following order: S18 greater than S21, L27 greater than S17, and S12. With a long period of labeling (3 h) up to 13 spin labels are attached to the ribosome, and protein S1 is the most labeled. The shape of the electron paramagnetic resonance (epr) signal shows two components with a predominance for the strongly immobilized orientation, and the percentage of these components in each spectra has been evaluated. When the distance between the nitroxide group and the maleimide-attaching group exceeds 6 A (1 A = 0.1 nm) the strongly immobilized orientation disappears. The effect of magnesium ions on these selectively spinlabeled ribosomes shows that the dissociation into subunits does not affect the epr signal, but more spin labels are incorporated into the subunits if labeling is performed under conditions of dissociation.

Chimeric flavonol sulfotransferases define a domain responsible for substrate and position specificities.

The pFST3 and pFST4' cDNAs encode flavonol sulfotransferases (ST) that are 69% identical in amino acid sequence yet exhibit strict substrate and position specificities. To determine the domain responsible for the properties of the flavonol STs, several chimeric flavonol STs were constructed by the reciprocal exchange of DNA fragments derived from the plasmids pFST3 and pFST4' and by the expression of the corresponding chimeric proteins in Escherichia coli. The chimeric enzymes were enzymatically active even though their activities were reduced compared to the parent enzymes. The specificity of the resulting hybrid proteins indicates that an interval of the flavonol STs spanning amino acids 92-194 of the flavonol 3-ST sequence contains the determinant of the substrate and position preferences. From the comparison of the amino acid sequences between plant and animal STs, this interval can be subdivided into a highly conserved region corresponding to positions 134-152 of the flavonol 3-ST, flanked by two regions of high divergence from 98 to 110 and 153 to 170. In view of the similarities in length and hydropathic profiles as well as the presence of four conserved regions between plant and animal STs, the results of these experiments suggest that this interval is involved in the recognition of substrates and/or catalysis in all STs.

Soybean leghemoglobin gene family: normal, pseudo, and truncated genes.

Leghemoglobin (Lb) genes in soybean represent a small family of closely related genes. Three Lb sequences isolated from a genomic library were analyzed at the nucleotide sequence level. A Lb gene present on an 11.5-kilobase (kb) EcoRI genomic fragment spans approximately 1,200 nucleotides and is interrupted at amino acid positions 32 to 33, 68 to 69, and 103 to 104. The intervening sequences, as well as the 5' and 3' flanking regions of this gene, contain the consensus sequences found in other eukaryotic genes. The length of the 5'-untranslated region is 49 bases as determined by nuclease S1 mapping. R-loop analysis of the DNA from the recombinant phage containing the 11.5-kb EcoRI genomic fragment showed that another Lb gene is located 2.5 kb away. The nucleotide sequence of the second gene showed that this gene is incomplete, containing only exons 3 and 4. The deduced amino acid sequence of this gene, although showing 76% homology with the corresponding region of the other Lb gene, is not represented in any of the known Lb proteins. Both genes are oriented in the same direction with respect to the coding strand. Analysis of the sequence present on a second genomic clone containing a 4.2-kb EcoRI fragment revealed a truncated Lb gene showing homology with the last exon and the noncoding region at the 3' end of the two other Lb genes.