Maize resistance to witchweed through changes in strigolactone biosynthesis.

Maize (Zea mays) is a major staple crop in Africa, where its yield and the livelihood of millions are compromised by the parasitic witchweed Striga. Germination of Striga is induced by strigolactones exuded from maize roots into the rhizosphere. In a maize germplasm collection, we identified two strigolactones, zealactol and zealactonoic acid, which stimulate less Striga germination than the major maize strigolactone, zealactone. We then showed that a single cytochrome P450, ZmCYP706C37, catalyzes a series of oxidative steps in the maize-strigolactone biosynthetic pathway. Reduction in activity of this enzyme and two others involved in the pathway, ZmMAX1b and ZmCLAMT1, can change strigolactone composition and reduce Striga germination and infection. These results offer prospects for breeding Striga-resistant maize.

Loss of H3K27 methylation identifies poor outcomes in adult-onset acute leukemia.

BACKGROUND: Acute leukemia is an epigenetically heterogeneous disease. The intensity of treatment is currently guided by cytogenetic and molecular genetic risk classifications; however these incompletely predict outcomes, requiring additional information for more accurate outcome predictions. We aimed to identify potential prognostic implications of epigenetic modification of histone proteins, with a focus on H3K4 and H3K27 methylation marks in relation to mutations in chromatin, splicing and transcriptional regulators in adult-onset acute lymphoblastic and myeloid leukemia. RESULTS: Histone 3 lysine 4 di- and trimethylation (H3K4me2, H3K4me3) and lysine 27 trimethylation (H3K27me3) mark expression was evaluated in 241 acute myeloid leukemia (AML), 114 B-cell acute lymphoblastic leukemia (B-ALL) and 14T-cell ALL (T-ALL) patient samples at time of diagnosis using reverse phase protein array. Expression levels of the marks were significantly lower in AML than in B and T-ALL in both bone marrow and peripheral blood, as well as compared to normal CD34+ cells. In AML, greater loss of H3K27me3 was associated with increased proliferative potential and shorter overall survival in the whole patient population, as well as in subsets with DNA methylation mutations. To study the prognostic impact of H3K27me3 in the context of cytogenetic aberrations and mutations, multivariate analysis was performed and identified lower H3K27me3 level as an independent unfavorable prognostic factor in all, as well as in TP53 mutated patients. AML with decreased H3K27me3 demonstrated an upregulated anti-apoptotic phenotype. In ALL, the relative quantity of histone methylation expression correlated with response to tyrosine kinase inhibitor in patients who carried the Philadelphia cytogenetic aberration and prior smoking behavior. CONCLUSION: This study shows that proteomic profiling of epigenetic modifications has clinical implications in acute leukemia and supports the idea that epigenetic patterns contribute to a more accurate picture of the leukemic state that complements cytogenetic and molecular genetic subgrouping. A combination of these variables may offer more accurate outcome prediction and we suggest that histone methylation mark measurement at time of diagnosis might be a suitable method to improve patient outcome prediction and subsequent treatment intensity stratification in selected subgroups.

Species-Specific Genome Sequence Databases: A Practical Review.

This chapter presents a use case illustrating the search for homologues of a known protein in species-specific genome sequence databases. The results from different species-specific resources are compared to each other and to results obtained from a more general genome sequence database (Phytozome). Various options and settings relevant when searching these databases are discussed. For example, it is shown how the choice of reference sequence set in a given database influences the results one obtains. The provided examples illustrate some problems and pitfalls related to interpreting results obtained from species-specific genome sequence databases.

Predicting sub-Golgi localization of type II membrane proteins.

MOTIVATION: Recent research underlines the importance of finegrained knowledge on protein localization. In particular, subcompartmental localization in the Golgi apparatus is important, for example, for the order of reactions performed in glycosylation pathways or the sorting functions of SNAREs, but is currently poorly understood. RESULTS: We assemble a dataset of type II transmembrane proteins with experimentally determined sub-Golgi localizations and use this information to develop a predictor based on the transmembrane domain of these proteins, making use of a dedicated proteinstructure based kernel in an SVM. Various applications demonstrate the power of our approach. In particular, comparison with a large set of glycan structures illustrates the applicability of our predictions on a 'glycomic' scale and demonstrates a significant correlation between sub-Golgi localization and the ordering of different steps in glycan biosynthesis. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control.

MOTIVATION: Transcription factor interactions are the cornerstone of combinatorial control, which is a crucial aspect of the gene regulatory system. Understanding and predicting transcription factor interactions based on their sequence alone is difficult since they are often part of families of factors sharing high sequence identity. Given the scarcity of experimental data on interactions compared to available sequence data, however, it would be most useful to have accurate methods for the prediction of such interactions. RESULTS: We present a method consisting of a Random Forest-based feature-selection procedure that selects relevant motifs out of a set found using a correlated motif search algorithm. Prediction accuracy for several transcription factor families (bZIP, MADS, homeobox and forkhead) reaches 60-90%. In addition, we identified those parts of the sequence that are important for the interaction specificity, and show that these are in agreement with available data. We also used the predictors to perform genome-wide scans for interaction partners and recovered both known and putative new interaction partners.

Data-driven docking: HADDOCK's adventures in CAPRI.

We have shown previously that given high-resolution structures of the unbound molecules, structure determination of protein complexes is possible by including biochemical and/or biophysical data as highly ambiguous distance restraints in a docking approach. We applied this method, implemented in the HADDOCK (High Ambiguity Driven DOCKing) package (Dominguez et al., J Am Chem Soc 2003;125:1731-1737), to the targets in the fourth and fifth rounds of CAPRI. Here we describe our results and analyze them in detail. Special attention is given to the role of flexibility in our docking method and the way in which this improves the docking results. We describe extensions to our approach that were developed as a direct result of our participation in CAPRI. In addition to experimental information, we also included interface residue predictions from PPISP (Protein-Protein Interaction Site Predictor; Zhou and Shan, Proteins 2001;44:336-343), a neural network method. Using HADDOCK we were able to generate acceptable structures for 6 of the 8 targets, and to submit at least 1 acceptable structure for 5 of them. Of these 5 submissions, 3 were of medium quality (Targets 10, 11, and 15) and 2 of high quality (Targets 13 and 14). In all cases, predictions were obtained containing at least 40% of the correct epitope at the interface for both ligand and receptor simultaneously.

Regional myocardial shape alterations in patients with anterior myocardial infarction.

OBJECTIVE: To assess the impact of regional left ventricular curvature in patients with an acute anterior myocardial infarction on ventricular volume. METHODS: Left ventricular curvature was calculated at 100 points from apical four chamber echocardiograms of 68 patients with an acute anterior wall infarction. Curvature at any point of the contour was defined as the reciprocal of the radius of the circle that intersects that point tangentially and was independent of volume and geometric assumptions. Curvature, volume and shape of the patient group was compared with these measurements in 20 normal volunteers. RESULTS: Diastolic curvature differed at the borderzone of the infarct and the apical area. In the basal septal area (point 9-18) mean curvature was lower in the patient group (0.1 +/- 2.7 versus 2.1 +/- 0.7; p < 0.0001) as compared to the normal individuals. In the mid-septal area (point 22 to 27), mean curvature was more concave (-0.1 +/- 2.6) in the patient group corresponding to in the normal population (-0.4 +/- 1.3) p < 0.005. In the apex point 52 and 53 diverged with a curvature of 9.9 +/- 1.9 in patients versus 9.4 +/- 2.9 p < 0.005 in normal individuals. Systolic curvature diverged at the basal septum (point 1-4) with a mean curvature of 1.4 +/- 1.1 in patients compared to 3.5 +/- 2.5 in normal individuals p < 0.01. Curvature differed also in the mid-septal region (point 9-29) with a curvature of -1.7 +/- 1.2 in patients versus 0.4 +/- 0.9 (p < 0.01) in normal individuals and in the apical septum (point 48-52) with a curvature of 16.6 +/- 5.2 in patients and 13.9 +/- 2.6 (p < 0.0001) in healthy individuals Separation of patients with the greatest curvature alteration to those with minor curvature change revealed, that baseline curvature analysis can discriminate patients at risk for left ventricular remodelling. CONCLUSION: Regional curvature analysis correctly identifies the geometric changes induced by myocardial infarction. Apical systolic curvature can distinguish those patients that are at risk for left ventricular remodelling from those who are not at risk.

Effect of coronary occlusion and reperfusion on local electrical resistivity of myocardium in dogs.

The effect of coronary occlusion and reperfusion on myocardial electrical resistivity was studied in nine anesthetized open-chest dogs. Anisotropic resistivity was measured on the anterior free wall of the left ventricle (LV) before (control) and during transient occlusion of the left anterior descending (LAD) coronary artery, and during reperfusion. To measure local resistivity longitudinal (RL) and transverse (RT) to epicardial muscle fiber direction, a sensor was developed based on the four electrode (FE) technique with an electrode distance of 1 mm. Previous calculations showed that measurements with this system were confined to a 2-mm-thick epicardial layer. Control values for RL and RT were 243 +/- 32 ohms.cm and 358 +/- 45 ohms.cm (mean +/- SD, n = 9) respectively. During a 2-min LAD occlusion, RL increased gradually by 12.4% (p < 0.05) and RT by 7.8% (p < 0.05) above the preceding control values. During a 5-min reperfusion period resistivities returned towards control values, but tended to remain elevated. RL showed a slight initial further increase during the first min of reperfusion and remained significantly above control values during 3 min of reperfusion. RT returned to values not significantly different from control after about 1 min of reperfusion.

Left ventricular segmental volume by conductance catheter and Cine-CT.

The ability of the conductance catheter method to measure left ventricular segmental and total volume was evaluated by comparison with the Cine-CT technique. In the seven dogs studied, 19 conductance catheter and simultaneous Cine-CT runs were obtained. High correlation coefficients were found for total volume and segmental volumes, except in the basal segment. However, in most cases there was a significant variability in slope and intercept between animals. Both methods are promising tools for estimating dynamic segmental left ventricular volume, each having specific advantages such as a continuous signal (conductance catheter) or anatomic detail (Cine-CT). However, the results also show the need for further improvement of both methods.

Left ventricular filling after long-term angiotensin converting enzyme inhibition in congestive heart failure.

As a rule, left ventricular relaxation is impaired in patients with coronary artery disease and congestive heart failure. In addition, the passive elastic properties in early and late diastole change when the ventricle dilates. Diastolic properties of the left ventricle were studied in 11 patients with congestive heart failure class II-IV (NYHA) before and 3 months after 10-20 mg enalapril was added to their regimen of salt restriction, a diuretic and occasionally digitalis. Haemodynamic studies were performed using radionuclide angiography and simultaneous pressure-volume measurements. Systemic vascular resistance decreased from 1479 to 1182 dynes.s.-1 cm-5 (P < 0.05) and left ventricular end-diastolic pressure from 19.2 to 15.9 mmHg (P < 0.05). Left ventricular end-diastolic volume index decreased from 130 +/- 22 to 81 +/- 22 ml (P < 0.01). Indices of early diastolic relaxation, such as peak filling rate (1.43 +/- 0.46 to 1.49 +/- 0.84 EDV/s), time to peak filling rate (460 +/- 70 to 490 +/- 70 ms), peak negative dP/dt (-903 +/- 190 to -891 +/- 190 mmHg/s) and tau, the time constant of isovolumic pressure decay (58.7 +/- 14.4 to 48.4 +/- 15.2 ms) did not change significantly. In nine patients pressure-volume loops shifted to the left in all patients but one due to reduction in end-systolic and end-diastolic volume. The steepness of the diastolic part of the pressure-volume relationship increased, indicating an increase in chamber stiffness. The stiffness constant increased about 25% towards a more normal value. The alteration in stiffness seemed to be mainly due to the change of the geometry of the ventricle and not to a major change in the visco-elastic properties of the ventricular wall. In conclusion, regression of remodelling induced by enalapril does not change diastolic function parameters in patients with chronic congestive heart failure beyond the changes caused by regression of ventricular dilation.

Systolic and diastolic pressure-volume relationships during cardiac surgery.

Seven patients undergoing elective coronary artery bypass surgery were studied to assess left ventricular (LV) performance by pressure-volume loops. LV pressure was measured by micromanometry and instantaneous LV volume by a conductance catheter. Continuous pressure-volume relationships were determined during preload reduction before and after cardiopulmonary bypass (CPB). End-systolic elastance (Ees), as the slope of the end-systolic pressure-volume relationship (ESPVR), and diastolic elastance (Ed) were calculated from these interventions. Changes in position of the Ees were assessed at V75, the value of LV end-systolic volume at 75 mm Hg of LV pressure. From pre-CPB to post-CPB, Ees increased in three patients with a decrease of V75 in two patients, and Ees decreased in four patients with a concomitant increase in V75. Ed increased significantly (P less than 0.01) following CPB, demonstrating a decrease of ventricular distensibility. It is concluded that continuous measurement of LV pressure-volume relationships using the conductance catheter is feasible and may be a useful tool to estimate LV performance during cardiac surgery.

Influence of angiotensin converting enzyme inhibition on pump function and cardiac contractility in patients with chronic congestive heart failure.

Eleven patients with coronary artery disease and chronic heart failure were studied before and three months after the angiotensin converting enzyme inhibitor enalapril was added to their frusemide medication. The following were measured: left ventricular pressure and volume with transient occlusion of the inferior vena cava, radionuclide angiography, and hormone concentrations in plasma. As in other reported studies, the clinical condition of the patients improved and their exercise tolerance increased moderately. Addition of enalapril reduced end diastolic and systolic pressure, reduced ventricular volume, and concomitantly increased the ejection fraction. The end systolic pressure-volume relation shifted to the left as it did in a similar animal study. In the animal study unloading by a vasodilator did not induce a leftward shift, so it can be inferred that in the present study unloading combined with a decrease in the angiotensin concentration was instrumental in remodelling the heart. Though unloading was expected to have a beneficial effect on the oxygen supply/demand ratio of the heart, the patients still showed the same drop in the ejection fraction during exercise as they did before treatment with enalapril, and early diastolic filling did not improve. Normally, regression of cardiac dilatation is only found if pump function improves; the present study showed that unloading in combination with angiotensin converting enzyme inhibition reshapes the ventricle without improving intrinsic pump function.

Cardiac remodelling and myocardial contractility in patients with congestive heart failure treated with furosemide and enalapril.

Eleven patients with congestive heart failure class II-IV (NYHA) caused by ischemic heart disease were studied before and three months after adding enalapril to their treatment with furosemide. After an infarction the heart dilates gradually, mainly as a result of slippage of myocardial fiber bundles. It is known that the addition of an ACE-inhibitor to the medical treatment unloads the heart and gradually, within a period of 3 months, reduces heart size. Objectives of this study were to demonstrate remodelling by recording diastolic pressure-volume relations before and after treatment. The study addresses the question of whether regression of dilation, induced by the ACE-inhibitor treatment, improves the oxygen supply-demand ratio and, as a result, the contractility of the heart muscle. Treatment resulted in a reduction of vascular resistance (1479 to 1182 dyn.s.cm-5, p less than 0.05) and of the left ventricular end-diastolic (130 to 108 ml per m2 body surface area, p less than 0.05) and end-systolic (102 to 81 ml per m2 body surface area, p less than 0.01) volume index. The slope of the end-systolic pressure-volume relation, measured using vena cava occlusion and beat-to-beat recording of pressure and volume loops, remained unchanged. Indices of oxygen-supply demand ratio such as a drop of ejection fraction during exercise and parameters of active diastolic relaxation also did not change. Addition of an ACE-inhibitor induces regression of ventricular dilation, but no indications were found that it improves the condition of the cardiac muscle.

Continuous measurement of left ventricular volume in animals and humans by conductance catheter.

An eight-electrode conductance catheter previously developed by us and used to determine stroke volume in dogs was applied in human beings and dogs to measure absolute left ventricular volume quantitatively. For calibration we developed the formula V(t) = (1/alpha)(L2/sigma b)G(t) - Vc, where V(t) is time-varying left ventricular volume, alpha is a dimensionless constant, L is the electrode separation, sigma b is the conductivity of blood obtained by a sampling cuvette, and G(t) is the measured conductance within the left ventricular cavity. Vc is a correction term caused by the parallel conductance of structures surrounding the cavity and is measured in two ways. The first method, applicable in the anesthetized animal, consists of temporary reduction of volume to zero by suction. The second method uses a transient change in sigma b by injection of a small bolus of hypertonic saline (dogs) or 10 ml of cold glucose (humans) into the pulmonary artery. The validity of the formula was previously established for the isolated postmortem canine heart. The predicted linearity, slope constant alpha, and accuracy of Vc for the left ventricle in vivo were investigated by comparing the conductance volume data with results from independent methods: electromagnetic blood flow measurement for stroke volume and indicator dilution technique for ejection fraction (dogs), thermal dilution for cardiac output (12 patients), and single-plane cineventriculography for V(t) (five patients). In all comparisons, linear regression showed high correlation (from r = .82 [n = 46] to r = .988 [n = 20]) while alpha, with one exception, ranged from 0.75 to 1.07 and the error in Vc ranged from 0.5% to 16.5% (mean 7%). After positioning of the catheter, no arrhythmias were observed. It is concluded that the conductance catheter provides a reliable and simple method to measure left ventricular volume, giving an on-line, time-varying signal that is easily calibrated. Together with left ventricular pressure obtained through the catheter lumen, the instrument may be used for instantaneous display of pressure-volume loops to facilitate assessment of left ventricular pump performance.

Continuous stroke volume and cardiac output from intra-ventricular dimensions obtained with impedance catheter.

To improve assessment of ventricular function during cardiac catheterisation there should be available a continuous registration of stroke volume and cardiac output in addition to ventricular pressure. To obtain the desired volumetric quantities a catheter has been developed which measures changes in intraventricular dimensions by electrical impedance. For this purpose, the catheter is equipped with eight electrodes spaced over a distance equal to the long axis of the left ventricle into which it is introduced. A constant current is imposed between the outermost electrodes while the inner six are used to measure resistance of volume segments of the blood contained within the ventricular cavity. The difference in resistance at the beginning and end of ejection is proportional to the contribution of each segment to stroke volume, which follows from addition to the segmental terms. Calibration is obtained by measuring electrical conductivity of a blood sample. The catheter was tested over a tenfold range of cardiac output, both in vitro, using an artificial heart model, while performance in vivo was evaluated in 12 dogs. In the animals study, stroke volume and cardiac output from the catheter were compared with flows obtained with an electromagnetic flowmeter. In both studies, linear regression analysis showed excellent correlation of cardiac output (r = 0.99, n = 10 in vitro, r = 0.95, n = 126 in vivo) while the regression equations were close to those of identity. Very good correlation (r = 0.98, n = 28) was also obtained for stroke volumes on a beat to beat basis during arrhythmia. It is concluded that the catheter, which has great potential for application in man, fulfills its primary aim of continuously recording stroke volume and cardiac output.