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Objective: Medical questionnaires, which enable collection, comparison and analysis of appropriate data as a means of written communication between a patient and a doctor, must be easily readable, and understandable. Here, we measure the readability and understandability of questionnaires used in andrology and examine the relationship between the educational status of the patients and the understandability of the forms., Material and Methods: Seven questionnaires (SHIM, AIPE, IIEF, MSHQ-EjD, PEDT, NIH-CPSI and IPSS) used to diagnose andological diseases were selected from the European Association of Urology guidelines. The number of syllables per word, the number of words in a sentence, and the average word and sentence lengths were calculated for each Turkish validated form. Readability scores were calculated, and closet tests were used to measure the understandability of the texts., Results: Three hundred and twenty-seven male volunteers participated in the study. Two hundred and sixteen of the participants (66%) had a high school or college education. The readability level of the seven forms was determined to be "Difficult" or "Very Difficult," and at least a high school education level was required to understand the forms. As education level and monthly income increased, the understandability of the forms increased; as the readability of the forms became more difficult, their understandability decreased (p<0.001)., Conclusion: The readability levels of questionnaires used in andrology are well above the reading level of Turkey. Health providers can help patients to fill out forms to increase doctor-patient communication.

Purpose: To assess the relationship between De Ritis (aspartate aminotransaminase [AST]/Alanine aminotransaminase [ALT]) ratio and pathological variables and whether it is an independent prognostic factor., Materials and Methods: We analyzed 298 consecutive patients who underwent radical or partial nephrectomy for non-metastatic renal cell carcinoma (RCC) between 2006 and 2015. The association between De Ritis ratio and pathological variables including tumor size, presence of renal vein invasion, vena cava invasion, renal capsule infiltration, Gerota fascia invasion, renal sinus involvement, renal pelvic invasion, angiolymphatic invasion, adrenal gland involvement, lymph node involvement, tumor necrosis, and Fuhrman's grade was tested. Multivariable Cox analysis was performed to evaluate the impact of this ratio on overall survival and cancer-specific survival., Results: An increased preoperative De Ritis ratio was significantly associated with renal vein invasion, renal capsule infiltration and renal pelvis involvement (p<0.05) in non-metastatic RCC. On multivariate analysis we found that tumor size, Fuhrman grade and lymph node involvement were independent prognostic factors for cancerspecific survival. AST/ALT ratio had no influence on the risk of overall and cancerspecific survival., Conclusion: An increased preoperative AST/ALT ratio had a significant association with renal vein invasion, renal capsule infiltration and renal pelvis involvement in patients with non-metastatic RCC. However, it does not appear to be an independent prognostic marker in non-metastatic RCC., Competing Interests: Conflict of interest: None declared., (Copyright® by the International Brazilian Journal of Urology.)

In vitro reconstitution systems of ribosomal subunits from free ribosomal RNA and ribosomal proteins are helpful tool for studies on the structure, function and assembly of ribosome. Using this system mutant or modified ribosomal proteins or ribosomal RNA can be incorporated into ribosomal subunits for studying ribosome structure and function. Developing the protocol for reconstitution of 30S subunits from an extreme thermophilic bacterium Thermus thermophilus can be beneficial especially for structural studies, as proteins and nucleic acids from this organism are very stable and crystallize easier than those from mesophilic organisms.

The crystal structure of a 70-kilodalton ribonucleoprotein complex from the central domain of the Thermus thermophilus 30S ribosomal subunit was solved at 2.6 angstrom resolution. The complex consists of a 104-nucleotide RNA fragment composed of two three-helix junctions that lie at the end of a central helix, and the ribosomal proteins S15, S6, and S18. S15 binds the ribosomal RNA early in the assembly of the 30S ribosomal subunit, stabilizing a conformational reorganization of the two three-helix junctions that creates the RNA fold necessary for subsequent binding of S6 and S18. The structure of the complex demonstrates the central role of S15-induced reorganization of central domain RNA for the subsequent steps of ribosome assembly.

Beginning with the framework that has been developed for the assembly of the 30 S ribosomal subunit, we have identified a series of RNAs that are minimal binding sites for proteins S15, S6, S18, and S11 in the central domain from Thermus thermophilus. The minimal binding RNA for proteins S15, S6, and S18 consists of helix 22 and three-way junctions at both ends composed of portions of helices 20, 21, and 23. Addition of the remaining portion of helix 23 to this construct results in the minimal site for S11. Surprisingly, almost half of the central domain (helices 24, 25, and 26) is dispensable for binding the central domain proteins. Thus, at least two classes of RNA elements can be identified in ribosomal RNA. A protein-binding core element (such as helices 20, 21, 22, and 23) is required for the association of ribosomal proteins, whereas secondary binding elements (such as helices 24, 25, and 26) associate only with the preformed core RNP complex. Apparently, there may be a hierarchy of ribosomal RNA elements similar to the hierarchy of primary, secondary, and tertiary binding ribosomal proteins.

Fragments of the 16S rRNA of Thermus thermophilus representing the 3' domain (nucleotides 890-1515) and the 5' domain (nucleotides 1-539) have been prepared by transcription in vitro. Incubation of these fragments with total 30S ribosomal proteins of T. thermophilus resulted in formation of specific RNPs. The particle assembled on the 3' RNA domain contained seven proteins corresponding to Escherichia coli ribosomal proteins S3, S7, S9, S10, S13, S14, and S19. All of them have previously been shown to interact with the 3' domain of the 16S RNA and to be localized in the head of the 30S ribosomal subunit. The particle formed on the 5' RNA domain contained five ribosomal proteins corresponding to E. coli proteins S4, S12, S17, S16, and S20. These proteins are known to be localized in the main part of the body of the 30S subunit. Both types of particle were compact and had sedimentation coefficients of 15.5 S and 13 S, respectively. Together with our recent demonstration of the reconstitution of the RNA particle representing the platform of the T. thermophilus 30S ribosomal subunit [Agalarov, S.C., Zheleznyakova, E.N., Selivanova, O.M., Zheleznaya, L.A., Matvienko, N.I., Vasiliev, V.D. & Spirin, A.S. (1998) Proc. Natl Acad. Sci. USA 95, 999-1003], these experiments establish that all three main structural lobes of the small ribosomal subunit can be reconstituted independently of each other and prepared in the individual state.

Oligodesoxyribonucleotide-directed cleavage of protein-deficient Thermus thermophilus derivatives of the 30S ribosomal subunits with RNase H is described. A homogeneous RNP fragment has been isolated as a result of the cleavage and subsequent purification in the sucrose gradient. It corresponds to the central and 5' domains of the 30S ribosomal subunit. The high compactness of the fragment in solution suggests that it can be considered as a 'beheaded' derivative of the 30S ribosomal subunit. The absence of a reconstitution stage in isolation of the 22S RNP fragment provides for its preparation in large amounts.

A procedure for isolation in preparative amounts of 15 individual proteins from ribosomal 30S subparticles of Thermus thermophilus under non-denaturing conditions, has been developed. The amino acid composition and molecular masses of the proteins have been determined and the UV absorption spectra and extinction coefficients measured. A homology of 13 proteins to corresponding ribosomal proteins of E. coli has been established.

In parallel with crystallographic studies of ribosomes from Thermus thermophilus, a long-term program on the crystallization and structural investigations of ribosomal proteins from the same microorganism has been started at the Institute of Protein Research (Pushchino, Russia). At present, more than half of the individual ribosomal proteins from T thermophilus have been purified without denaturating agents on a preparative scale and some of them have been obtained in the crystalline form. X-ray structural analysis of two ribosomal proteins, L1 and S6, is being carried out jointly with the Institute of Molecular Biology (Moscow, Russia) and laboratory of professor A Liljas (Lund University, Sweden). L1 is the large protein of the large ribosomal subunit. It can bind not only to a specific site on the 23S rRNA, but also to the mRNA that codes for L1 and L11, thereby acting as a translational repressor for the synthesis of these proteins. The crystals of L1 are orthorhombic and diffract to about 2 A resolution. Native data and data for several heavy atom derivatives have been collected. S6 is a small acidic protein from the small ribosomal subunit. The crystals of S6 are orthorhombic and diffract to 2 A resolution. Native data and derivatives' data have been collected.

Crystals of protein S6 from the small ribosomal subunit of an extreme thermophile, Thermus thermophilus, have been obtained by the hanging-drop/vapor diffusion technique using methane pentanediol as a precipitant in the presence of potassium fluoride. The crystals belong to the space group C222 with cell parameters a = 106.7, b = 52.8, c = 41.0 A. They diffract to 2.0 A resolution.

Crystals have been obtained of protein L1 from the large ribosomal subunit of an extreme thermophile. Thermus thermophilus, using a mixed solution of ammonium sulphate/methane pentanediol. The crystals belong to the space group P2(1)2(1)2, with cell parameters a = 82.7 A, b = 63.4 A, c = 44.7 A. They diffract X-rays to 2.3 A resolution.

X-ray and neutron scattering, as well as velocity sedimentation, were used to study the shape and dimensions (compactness) of isolated ribosomal (16S and 23S) RNA's and their complexes with ribosomal proteins. The neutron scattering of ribosomal particles in 42% 2H2O where the protein component is contrast-matched, were taken as a standard of comparison characterizing the dimensions and shape of the 16S and 23S RNA in situ. This comparison allowed the following conclusions: (1) The shape of the isolated 16S RNA at a sufficient Mg2+ concentration (e. g., in the reconstruction buffer) is similar to that of the 16S RNA in situ, but its compactness is somewhat less. (2) The 16S RNA in the complex with protein S4 has a shape and compactness similar to those of the isolated 16S RNA. (3) The 16S RNA in the complex with four core proteins, namely S4, S7, S8 and S15, has a shape and compactness similar to those of the isolated 16S RNA. (4). The six ribosomal proteins, S4, S7, S8, S15, S16, and S17, are necessary and sufficient for the 16S RNA to acquire a compactness similar to that in situ.

X-ray scattering, neutron scattering and velocity sedimentation techniques were used for studies of ribosomal 16 S RNA in the isolated state and in different complexes with ribosomal proteins. The neutron scattering curve of the ribosomal 30 S subparticle in 42% 2H2O where the protein component is contrast-matched, was taken as a standard of comparison characterizing the dimensions and shape of the 16 S RNA in situ. The following deductions result from the comparisons. The shape of the isolated 16 S RNA at a sufficient Mg2+ concentration (e.g., in the reconstruction buffer) is similar to that of the 16 S RNA in situ, i.e. in the 30 S particle, but it is somewhat less compact. The 16 S RNA in the complex with protein S4 has a shape and compactness similar to those of the isolated 16 S RNA. The 16 S RNA in the complex with four core proteins, namely S4, S7, S8 and S15, has a shape and compactness similar to those of the isolated 16 S RNA. The six ribosomal proteins S4, S7, S8, S15, S16 and S17 are necessary and sufficient for the 16 S RNA to acquire a compactness similar to that within the 30 S particle. The general conclusion is that the overall specific folding of the 16 S RNA is governed and maintained by its own intramolecular interactions, but the additional folding-up (about one-fourth of the linear size of the whole molecule) or the stabilization of the final compactness requires some ribosomal proteins.

A detailed comparative analysis of tryptophan fluorescence spectra of 'sodium' and 'potassium' forms of (Na+, K+)-activated ATPase was carried out. The 'potassium' form spectrum is shifted relative to that of the 'sodium' form by approximately 0.5-1 nm towards shorter wavelengths. The maximal amplitude of the difference spectrum for these forms makes up about 2% of maximal fluorescence intensity of any of the forms. The shape of the difference spectrum does not depend on the solution temperature or ionic strength. The spectral differences between the forms are reversible upon addition of a functionally opposite cation (K+ for 'sodium' form and vice versa) into the medium. The results suggest that if the differences in fluorescence spectra of the 'sodium' and 'potassium' forms of (Na+, K+)-ATPase resulted from the differences in the protein structure, they may be caused by an alteration in local environment of no more than one or two tryptophan residues.