Cryptic species of Paracoccidioides brasiliensis: impact on paracoccidioidomycosis immunodiagnosis

We aimed to evaluate whether the occurrence of cryptic species of Paracoccidioides brasiliensis, S1, PS2, PS3 and Paracoccidioides lutzii, has implications in the immunodiagnosis of paracoccidioidomycosis (PCM). Small quantities of the antigen gp43 were found in culture filtrates of P. lutzii strains and this molecule appeared to be more variable within P. lutzii because the synonymous-nonsynonymous mutation rate was lower, indicating an evolutionary process different from that of the remaining genotypes. The production of gp43 also varied between isolates belonging to the same species, indicating that speciation events are important, but not sufficient to fully explain the diversity in the production of this antigen. The culture filtrate antigen AgEpm83, which was obtained from a PS3 isolate, showed large quantities of gp43 and reactivity by immunodiffusion assays, similar to the standard antigen (AgB-339) from an S1 isolate. Furthermore, AgEpm83 was capable of serologically differentiating five serum samples from patients from the Botucatu and Jundiaí regions. These patients had confirmed PCM but, were non-reactive to the standard antigen, thus demonstrating an alternative for serological diagnosis in regions in which S1 and PS2 occur. We also emphasise that it is not advisable to use a single antigen preparation to diagnose PCM, a disease that is caused by highly diverse pathogens.

Evaluation of canine and feline leishmaniasis by the association of blood culture, immunofluorescent antibody test and polymerase chain reaction

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Hypobromous acid, a powerful endogenous electrophile: Experimental and theoretical studies

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Determination of flagellar types by PCR-RFLP analysis of enteropathogenic Escherichia coli (EPEC) and Shiga toxin-producing E. coli (STEC) strains isolated from animals in Sao Paulo, Brazil

This study evaluated the polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) analysis of fliC for typing flagella antigen (H) of Shiga toxin-producing Escherichia coil (STEC) and enteropathogenic E. coli (EPEC) strains isolated from different animals. The molecular typing of the H type was efficient in the determination of 93 (85%) strains. Two nonmotile (H-) E. coil strains showed a PCR-RFLP electrophoretic profile that did not match known H type patterns. The fliC nucleotide sequence of strains B2N and 4a revealed a nucleotide substitution at the restriction site and a nucleotide insertion that generated a stop codon, respectively. The results of this study showed that PCR-RFLP analysis of fliC is faster, less laborious and as efficient for the determination of H type E. coli isolated from animals, compared to serotyping and that it is useful in determining H type in nonmotile strains and strains expressing non-reactive H antigens. Moreover, the fliC sequence of strain B2N suggests that we could have found a new flagellin antigen type. (C) 2010 Elsevier Ltd. All rights reserved.

ERYTHROGRAM PROFILE DURING POSTPARTUM PERIOD IN HOLSTEIN COWS

With the intention to evaluate the erythrogram profile during postpartum period in Holstein cows, 142 blood samples were collected from cows during the first 90 days after parturition. Blood samples were collected from clinically healthy cows that were non-reactive to the antigen of bovine leukosis virus (GP 51). These animals were divided into nine experimental groups based on the time of the postpartum sample collection. The blood samples were collected with EDTA and submitted to the following tests: erythrocyte counts, packed cell volume, hemoglobin concentration and calculated blood indices (MCV, MCH, MCHC). There was influence of the postpartum period on the erythrogram. These alterations were observed during the first 24 h after parturition. The hemoconcentration observed during the parturition disappeared during the first 24h of postpartum. Variation of the values were observed: red blood, 5.08 +/- 0.60 and 6.11 +/- 0.72 cells /mu L; hemoglobin concentration, 9.85 +/- 1.6 and 11.46 +/- 1,40 g/dL; packed cell volume, 27.9 +/- 3.3 and 31.9 +/- 3.6 %; MVC, 50.10 +/- 5.90 and 55.27 +/- 6.88 fL; MHC, 18.19 +/- 1.63 and 19.50 +/- 2.76 pg; MCHC, 34.83 +/- 2.07 and 36.88 +/- 1.67 %. The values of the hematological components obtained in this study did not exceed the limits of the reference values, obtained from cows raised within the state of Sao Paulo.

Performance of six diagnostic tests to screen for Chagas disease in blood banks and prevalence of Trypanosoma cruzi infection among donors with inconclusive serology screening based on the analysis of epidemiological variables

OBJECTIVE: The frequent occurrence of inconclusive serology in blood banks and the absence of a gold standard test for Chagas'disease led us to examine the efficacy of the blood culture test and five commercial tests (ELISA, IIF, HAI, c-ELISA, rec-ELISA) used in screening blood donors for Chagas disease, as well as to investigate the prevalence of Trypanosoma cruzi infection among donors with inconclusive serology screening in respect to some epidemiological variables. METHODS: To obtain estimates of interest we considered a Bayesian latent class model with inclusion of covariates from the logit link. RESULTS: A better performance was observed with some categories of epidemiological variables. In addition, all pairs of tests (excluding the blood culture test) presented as good alternatives for both screening (sensitivity > 99.96% in parallel testing) and for confirmation (specificity > 99.93% in serial testing) of Chagas disease. The prevalence of 13.30% observed in the stratum of donors with inconclusive serology, means that probably most of these are non-reactive serology. In addition, depending on the level of specific epidemiological variables, the absence of infection can be predicted with a probability of 100% in this group from the pairs of tests using parallel testing. CONCLUSION: The epidemiological variables can lead to improved test results and thus assist in the clarification of inconclusive serology screening results. Moreover, all combinations of pairs using the five commercial tests are good alternatives to confirm results.

Mass transport in polymers

The study of mass transport in polymeric membranes has grown in importance due to its potential application in many processes such as separation of gases and vapors, packaging, controlled drug release. The diffusion of a low molecular weight species in a polymer is often accompanied by other phenomena like swelling, reactions, stresses, that have not been investigated in all their aspects yet. Furthermore, novel materials have been developed that include inorganic fillers, reactive functional groups or ions, that make the scenery even more complicated. The present work focused on the experimental study of systems where the diffusion is accompanied by other processes; suitable models were also developed to describe the particular circumstances in order to understand the underlying concepts and be able to design the performances of the material. The effect of solvent-induced deformation in polymeric films during sorption processes was studied since the dilation, especially in constrained membranes, can cause the development of stresses and therefore early failures of the material. The bending beam technique was used to test the effects of the dilation and the stress induced in the polymer by penetrant diffusion. A model based on the laminate theory was developed that accounts for the swelling and is able to predict the stress that raise in the material. The addition of inorganic fillers affects the transport properties of polymeric films. Mixed matrix membranes based on fluorinated, high free volume matrices show attractive performances for separation purposes but there is a need for deeper investigation of the selectivity properties towards gases and vapors. A new procedure based on the NELF model was tested on the experimental data; it allows to predict solubility of every penetrant on the basis of data for one vapor. The method has proved to be useful also for the determination of the diffusion coefficient and for an estimation of the permeability in the composite materials. Oxygen scavenging systems can overcome lack of barrier properties in common polymers that forbids their application in sensitive applications as food packaging. The final goal of obtaining a membrane almost impermeable to oxygen leads to experimental times out of reach. Hence, a simple model was developed in order to describe the transport of oxygen in a membrane with also reactive groups and analyze the experimental data collected on SBS copolymers that show attractive scavenging capacity. Furthermore, a model for predicting the oxygen barrier behavior of a film formed as a blend of OSP in a common packaging material was built, considering particles capable of reactions with oxygen embedded in a non-reactive matrix. Perfluorosulphonic acid ionomers (PFSI) are capturing attention due to a high thermal and chemical resistance coupled with very peculiar transport properties, that make them appropriate to be used in fuel cells. The possible effect of different formation procedure was studied together with the swelling due to water sorption since both water uptake and dilation can dramatically affect the fuel cells performances. The water diffusion and sorption was studied with a FTIR-ATR spectrometer that can give deeper information on the bonds between water molecules and the sulphonic hydrophilic groups and, therefore, on the microstructure of the hydrated ionomer.

Phasenverhalten von Polyethylen in Mischsystemen

Die vorliegende Arbeit beschäftigt sich mit dem Phasenverhalten von Polyethylen (PE) in nicht-reaktiven und in reaktiven Systemen. Von drei eng verteilten Polyethylenen (Mw = 6,4, 82 bzw. 380 kg/mol) in n-Hexan sowie für das System 2,2-Dimethylbutan / PE 82 wurde die Entmischung in Abhängigkeit von der Zusammensetzung, dem Druck und der Temperatur experimentell bestimmt. Die Modellierung der Trübungskurven erfolgte nach der Theorie von Sanchez und Lacombe. Dieser Ansatz beschreibt die Ergebnisse qualitativ und kann in einem engen Temperatur- und Druckbereich für gegebenes Molekulargewicht die kritische Temperatur und den kritischen Druck quantitativ vorhersagen. Durch Extrapolation der kritischen Temperatur der verschiedenen Lösungen von PE in n-Hexan auf unendliches Molekulargewicht nach Shultz-Flory wurde im Druckbereich von 20 bis 100 bar und im Temperaturbereich von 130 bis 200 °C eine Grenzlinie bestimmt. Diese Linie trennt unabhängig vom Molekulargewicht des Polymers und der Zusammensetzung der Mischung das Zweiphasengebiet vom homogenen Bereich. Im Fall des Mischlösungsmittels n-Hexan / 2,2-Dimethylbutan wurde für eine annähernd kritische Polymerkonzentration die Abhängigkeit der Entmischungsbedingungen von der Zusammensetzung untersucht. Durch einfache Erweiterung der Sanchez-Lacombe-Theorie und Einführen eines Fitparameters konnte das ternäre System beschrieben werden. An einer breit verteilten PE-Probe wurden Experimente zur Fraktionierung von PE in n-Hexan durchgeführt. Die Analyse der in den koexistenten Phasen enthaltenen Polymere lieferte Informationen über die Konzentration und die Molekulargewichtsverteilung des PE in diesen Phasen sowie die kritische Zusammensetzung der Mischung. Von verschiedenen PE-Lösungen (Mw = 0,5 kg/mol) wurde die polymerisationsinduzierte Phasenseparation in Isobornylmethacrylat mit und ohne Vernetzer untersucht. Mit 15 Gew.-% PE und in Abwesenheit von Vernetzer findet die Entmischung erst bei hohen Umsätzen statt. Die Charakterisierung der resultierenden Proben zeigte, dass sich etwas mehr als 5 Gew.-% PE im Polyisobornylmethacrylat lösen. Die Glasübergangstemperaturen der Polymermischungen steigen mit steigender Vernetzer- und sinkender Polyethylenkonzentration. Bei Proben mit 15 Gew.-% PE zeigte sich folgendes: 5 Gew.-% Vernetzer führen zu großen PE-Bereichen (150 - 200 nm) in der Matrix und der Kristallinitätsgrad ist gering. Bei der Polymermischung mit 10 Gew.-% Vernetzer bilden sich sehr kleine Polyethylenkristalle (< 80 nm) und der Kristallinitätsgrad ist hoch. Ohne Vernetzer hängt der Kristallinitätsgrad - wie bei reinem PE - von der Abkühlrate ab, mit Vernetzer ist er von ihr unabhängig.

Regulation der Stress-aktivierten Proteinkinasen durch den gentoxischen Benzo[a]pyren-Metaboliten BPDE

Polyzyklische aromatische Kohlenwasserstoffe (PAK) sind ubiquitäre Verschmutzungen der Umwelt und entstehen während der unvollständigen Verbrennung organischen Materials wie Holz, Kohle und Erdöl. Werden diese chemisch nicht reaktiven PAK in den Körper aufgenommen, durchlaufen sie eine Reihe von enzymatischen Umsetzungen, die unter der Bezeichnung Fremdstoffmetabolismus zusammengefasst werden. Die chemische Umsetzung des PAK und Prokarzinogens Benzo[a]pyren (B[a]P) führt u.a. zur Bildung des reaktiven Metaboliten B[a]P-7,8-dihydrodiol-9,10-epoxid (BPDE). BPDE ist stark elektrophil und kann auf Grund dieser Eigenschaft an nukleophile Makromoleküle wie Proteine und DNA binden. Die Bildung von BPDE-DNA-Addukten resultiert in der Entstehung von Mutationen und kann zur Tumorbildung führen. Im Rahmen der vorliegenden Arbeit sollte die Wirkung von BPDE als Modellsubstanz für gentoxische Agenzien auf intrazelluläre Signalkaskaden und die Konsequenzen der BPDE-Exposition bezüglich der Zellaktivität untersucht werden. Es konnte gezeigt werden, dass BPDE-Behandlung von Mausfibroblasten eine intrazelluläre Signalkaskade induziert, welche zur Aktivierung der Stressaktivierten Proteinkinasen (SAPK) JNK und p38 führt. An dieser Signalkaskade sind Src-ähnliche Kinasen beteiligt. BPDE-Behandlung führt in den untersuchten Mausfibroblasten zur Induktion von DNA-Einzelstrangbrüchen, deren Auftreten zeitlich mit der SAPK-Aktivierung korreliert. Die BPDEinduzierten DNA-Strangbrüche sind die Folge der Entfernung dieser Läsionen aus dem Genom durch die Nukleotidexzisionsreparatur (NER). Erkannt werden BPDE-DNA-Addukte durch die NERProteine XPA und XPC (Xeroderma Pigmentosum Komplementationsgruppe A und C). Nach der Erkennung von BPDE-DNA-Addukten kommt es zur Rekrutierung von Nukleasen, welche die vorliegende Läsion und umliegende Nukleotide aus dem Genom entfernen. In XPA- und XPCdefizienten Mausfibroblasten induziert BPDE daher keine DNA-Strangbrüche. Jedoch ist nur in XPCdefizienten Zellen, aber nicht in XPA-defizienten Zellen, die SAPK-Aktivierung drastisch reduziert. Behandlung von Mausfibroblasten mit Benzo[c]phenanthren-3,4-Diol-1,2-Epoxid, einem PAK, dessen DNA-Addukte schlecht durch NER-Faktoren erkannt und repariert werden, führt zu keiner SAPKAktivierung. Die Aktivierung von p38 und JNK scheint demnach abhängig zu sein von der Erkennung des primären DNA-Schadens. Die XPC-abhängige SAPK-Aktivierung schützt die Zellen vor BPDEabhängiger Toxizität, da sowohl XPC- als auch p38-defiziente Mausfibroblasten eine höhere Sensitivität gegenüber BPDE zeigen als korrespondierende Wildtypzellen. Zusamenfassend konnte in dieser Arbeit ein neuer Signalweg beschrieben werden, in dem DNASchäden, verursacht durch BPDE, über die XPC-abhängige DNA-Schadenserkennung, die Aktivierung der SAPK induziert. Diese Aktivierung der SAPK schützt vor BPDE-induzierter Toxizität.

Computer simulations of microstructures related to the olivine spinel transition

Tiefherd-Beben, die im oberen Erdmantel in einer Tiefe von ca. 400 km auftreten, werden gewöhnlich mit dem in gleicher Tiefe auftretenden druckabhängigen, polymorphen Phasenübergang von Olivine (α-Phase) zu Spinel (β-Phase) in Verbindung gebracht. Es ist jedoch nach wie vor unklar, wie der Phasenübergang mit dem mechanischen Versagen des Mantelmaterials zusammenhängt. Zur Zeit werden im Wesentlichen zwei Modelle diskutiert, die entweder Mikrostrukturen, die durch den Phasenübergang entstehen, oder aber die rheologischen Veränderungen des Mantelgesteins durch den Phasenübergang dafür verantwortlich machen. Dabei sind Untersuchungen der Olivin→Spinel Umwandlung durch die Unzugänglichkeit des natürlichen Materials vollständig auf theoretische Überlegungen sowie Hochdruck-Experimente und Numerische Simulationen beschränkt. Das zentrale Thema dieser Dissertation war es, ein funktionierendes Computermodell zur Simulation der Mikrostrukturen zu entwickeln, die durch den Phasenübergang entstehen. Des Weiteren wurde das Computer Modell angewandt um die mikrostrukturelle Entwicklung von Spinelkörnern und die Kontrollparameter zu untersuchen. Die Arbeit ist daher in zwei Teile unterteilt: Der erste Teil (Kap. 2 und 3) behandelt die physikalischen Gesetzmäßigkeiten und die prinzipielle Funktionsweise des Computer Modells, das auf der Kombination von Gleichungen zur Errechnung der kinetischen Reaktionsgeschwindigkeit mit Gesetzen der Nichtgleichgewichtsthermodynamik unter nicht-hydostatischen Bedingungen beruht. Das Computermodell erweitert ein Federnetzwerk der Software latte aus dem Programmpaket elle. Der wichtigste Parameter ist dabei die Normalspannung auf der Kornoberfläche von Spinel. Darüber hinaus berücksichtigt das Programm die Latenzwärme der Reaktion, die Oberflächenenergie und die geringe Viskosität von Mantelmaterial als weitere wesentliche Parameter in der Berechnung der Reaktionskinetic. Das Wachstumsverhalten und die fraktale Dimension von errechneten Spinelkörnern ist dabei in guter Übereinstimmung mit Spinelstrukturen aus Hochdruckexperimenten. Im zweiten Teil der Arbeit wird das Computermodell angewandt, um die Entwicklung der Oberflächenstruktur von Spinelkörnern unter verschiedenen Bedigungen zu eruieren. Die sogenannte ’anticrack theory of faulting’, die den katastrophalen Verlauf der Olivine→Spinel Umwandlung in olivinhaltigem Material unter differentieller Spannung durch Spannungskonzentrationen erklärt, wurde anhand des Computermodells untersucht. Der entsprechende Mechanismus konnte dabei nicht bestätigt werden. Stattdessen können Oberflächenstrukturen, die Ähnlichkeiten zu Anticracks aufweisen, durch Unreinheiten des Materials erklärt werden (Kap. 4). Eine Reihe von Simulationen wurde der Herleitung der wichtigsten Kontrollparameter der Reaktion in monomineralischem Olivin gewidmet (Kap. 5 and Kap. 6). Als wichtigste Einflüsse auf die Kornform von Spinel stellten sich dabei die Hauptnormalspannungen auf dem System sowie Heterogenitäten im Wirtsminerals und die Viskosität heraus. Im weiteren Verlauf wurden die Nukleierung und das Wachstum von Spinel in polymineralischen Mineralparagenesen untersucht (Kap. 7). Die Reaktionsgeschwindigkeit der Olivine→Spinel Umwandlung und die Entwicklung von Spinelnetzwerken und Clustern wird durch die Gegenwart nicht-reaktiver Minerale wie Granat oder Pyroxen erheblich beschleunigt. Die Bildung von Spinelnetzwerken hat das Potential, die mechanischen Eigenschaften von Mantelgestein erheblich zu beeinflussen, sei es durch die Bildung potentieller Scherzonen oder durch Gerüstbildung. Dieser Lokalisierungprozess des Spinelwachstums in Mantelgesteinen kann daher ein neues Erklärungsmuster für Tiefbeben darstellen.

Collagen response and glycoprotein VI function decline progressively as canine platelets age in vivo

Clinical and experimental observations suggest that platelet function deteriorates quickly with cell age. However, efforts to define age-dependent alterations have detected only modest biochemical changes occurring late in the cell life span. In this report, we demonstrate two significant alterations of the collagen response occurring during in vivo aging of canine platelets: a progressive increase in the EC50 for collagen types I, III and V and the emergence of a population of aged platelets which are refractory to collagen. Experiments with convulxin, a specific agonist for the collagen receptor glycoprotein VI (GPVI), also demonstrate an age-dependent decline in activation and the appearance of a non-reactive, aged population as observed with native collagens. Our studies indicate that canine platelets have two distinct binding levels for FITC-labeled convulxin and that the higher binding level disappears upon cell aging. During these studies one dog (#428) was identified whose platelets not only failed to demonstrate an age-dependent decrease in convulxin reactivity but also maintained a high convulxin-binding ability throughout their otherwise normal life span. Transfusion of biotinylated platelets from control dogs into dog #428 showed that the expected changes in collagen response and GPVI function did not occur in the transfused platelets. These observations demonstrate that the canine platelet response towards collagen is strongly dependent upon cell-age and suggest that this functional decline is at least partly due to an extrinsic-mediated alteration, possibly proteolytic, of GPVI.

DEVELOPMENT OF A CONCEPTUAL MODEL AND PARAMETERIZATION OF A MATHEMATICAL MODEL FOR SEDIMENT PHOSPHORUS DIAGENESIS, SORPTION AND RELEASE FROM ONONDAGA LAKE SYRACUSE, NEW YORK

Eutrophication is a persistent problem in many fresh water lakes. Delay in lake recovery following reductions in external loading of phosphorus, the limiting nutrient in fresh water ecosystems, is often observed. Models have been created to assist with lake remediation efforts, however, the application of management tools to sediment diagenesis is often neglected due to conceptual and mathematical complexity. SED2K (Chapra et al. 2012) is proposed as a "middle way", offering engineering rigor while being accessible to users. An objective of this research is to further support the development and application SED2K for sediment phosphorus diagenesis and release to the water column of Onondaga Lake. Application of SED2K has been made to eutrophic Lake Alice in Minnesota. The more homogenous sediment characteristics of Lake Alice, compared with the industrially polluted sediment layers of Onondaga Lake, allowed for an invariant rate coefficient to be applied to describe first order decay kinetics of phosphorus. When a similar approach was attempted on Onondaga Lake an invariant rate coefficient failed to simulate the sediment phosphorus profile. Therefore, labile P was accounted for by progressive preservation after burial and a rate coefficient which gradual decreased with depth was applied. In this study, profile sediment samples were chemically extracted into five operationally-defined fractions: CaCO3-P, Fe/Al-P, Biogenic-P, Ca Mineral-P and Residual-P. Chemical fractionation data, from this study, showed that preservation is not the only mechanism by which phosphorus may be maintained in a non-reactive state in the profile. Sorption has been shown to contribute substantially to P burial within the profile. A new kinetic approach involving partitioning of P into process based fractions is applied here. Results from this approach indicate that labile P (Ca Mineral and Organic P) is contributing to internal P loading to Onondaga Lake, through diagenesis and diffusion to the water column, while the sorbed P fraction (Fe/Al-P and CaCO3-P) is remaining consistent. Sediment profile concentrations of labile and total phosphorus at time of deposition were also modeled and compared with current labile and total phosphorus, to quantify the extent to which remaining phosphorus which will continue to contribute to internal P loading and influence the trophic status of Onondaga Lake. Results presented here also allowed for estimation of the depth of the active sediment layer and the attendant response time as well as the sediment burden of labile P and associated efflux.

Bilateral posterior ischaemic optic neuropathy after severe diabetic ketoacidosis, cardiopulmonary resuscitation and respiratory failure

A 44-year-old male European with type I diabetes mellitus fell into diabetic ketoacidosis. In the emergency room, he developed an episode of asystole and respiratory failure requiring one cycle of cardiopulmonary resuscitation and extracorporeal membrane oxygenation (ECMO). Waking up 7 days later, he presented a bilateral complete loss of vision. Ophthalmological examination including funduscopy on days 1 and 10, after extubation, showed bilateral large round pupils non-reactive to light and a normal fundus. Neuroimaging studies, including MRI and MRA of the brain, were all within normal limits. A lumbar puncture and comprehensive serological testing excluded an infectious or rheumatic cause. An empirical high-dose intravenous steroid treatment administered for 5 days had no effect on his vision. His eye examination at 1.5 months follow-up showed a normal fundus except for progressive bilateral optic nerve disc pallor, which pointed towards the diagnosis of a posterior ischaemic optic neuropathy.

Tracer profiles across argillaceous formations: A tool to constrain transport processes.

The spatial distributions of non-reactive natural tracers (anions, stable water isotopes, noble gases) in pore water of clay-rich formations were studied at nine sites. Regular curved profiles were identified in most cases. Transport modeling considering diffusion, advection and available constraints on the paleo-hydrogeological evolution indicates generally that diffusion alone can explain the observations, whereas a marked advective component would distort the profiles and so is not consistent with the data.

From stellar nebula to planets: The refractory components

Context. To date, calculations of planet formation have mainly focused on dynamics, and only a few have considered the chemical composition of refractory elements and compounds in the planetary bodies. While many studies have been concentrating on the chemical composition of volatile compounds (such as H2O, CO, CO2) incorporated in planets, only a few have considered the refractory materials as well, although they are of great importance for the formation of rocky planets. Aims. We computed the abundance of refractory elements in planetary bodies formed in stellar systems with a solar chemical composition by combining models of chemical composition and planet formation. We also considered the formation of refractory organic compounds, which have been ignored in previous studies on this topic. Methods. We used the commercial software package HSC Chemistry to compute the condensation sequence and chemical composition of refractory minerals incorporated into planets. The problem of refractory organic material is approached with two distinct model calculations: the first considers that the fraction of atoms used in the formation of organic compounds is removed from the system (i.e., organic compounds are formed in the gas phase and are non-reactive); and the second assumes that organic compounds are formed by the reaction between different compounds that had previously condensed from the gas phase. Results. Results show that refractory material represents more than 50 wt % of the mass of solids accreted by the simulated planets with up to 30 wt % of the total mass composed of refractory organic compounds. Carbide and silicate abundances are consistent with C/O and Mg/Si elemental ratios of 0.5 and 1.02 for the Sun. Less than 1 wt % of carbides are present in the planets, and pyroxene and olivine are formed in similar quantities. The model predicts planets that are similar in composition to those of the solar system. Starting from a common initial nebula composition, it also shows that a wide variety of chemically different planets can form, which means that the differences in planetary compositions are due to differences in the planetary formation process. Conclusions. We show that a model in which refractory organic material is absent from the system is more compatible with observations. The use of a planet formation model is essential to form a wide diversity of planets in a consistent way.