Screening for Primordial RNA–Peptide Interactions Using High-Density Peptide Arrays

RNA–peptide interactions are an important factor in the origin of the modern mechanism of translation and the genetic code. Despite great progress in the bioinformatics of RNA–peptide interactions due to the rapid growth in the number of known RNA–protein complexes, there is no comprehensive experimental method to take into account the influence of individual amino acids on non-covalent RNA–peptide bonds. First, we designed the combinatorial libraries of primordial peptides according to the combinatorial fusion rules based on Watson–Crick mutations. Next, we used high-density peptide arrays to investigate the interaction of primordial peptides with their cognate homo-oligonucleotides. We calculated the interaction scores of individual peptide fragments and evaluated the influence of the peptide length and its composition on the strength of RNA binding. The analysis shows that the amino acids phenylalanine, tyrosine, and proline contribute significantly to the strong binding between peptides and homo-oligonucleotides, while the sum charge of the peptide does not have a significant effect. We discuss the physicochemical implications of the combinatorial fusion cascade, a hypothesis that follows from the amino acid partition used in the work.

Substitutional landscape of a split fluorescent protein fragment using high-density peptide microarrays

Split fluorescent proteins have wide applicability as biosensors for protein-protein interactions, genetically encoded tags for protein detection and localization, as well as fusion partners in super-resolution microscopy. We have here established and validated a novel platform for functional analysis of leave-one-out split fluorescent proteins (LOO-FPs) in high throughput and with rapid turnover. We have screened more than 12,000 variants of the beta-strand split fragment using high-density peptide microarrays for binding and functional complementation in Green Fluorescent Protein. We studied the effect of peptide length and the effect of different linkers to the solid support. We further mapped the effect of all possible amino acid substitutions on each position as well as in the context of some single and double amino acid substitutions. As all peptides were tested in 12 duplicates, the analysis rests on a firm statistical basis allowing for confirmation of the robustness and precision of the method. Based on experiments in solution, we conclude that under the given conditions, the signal intensity on the peptide microarray faithfully reflects the binding affinity between the split fragments. With this, we are able to identify a peptide with 9-fold higher affinity than the starting peptide.

Combinatorial Fusion Rules to Describe Codon Assignment in the Standard Genetic Code

We propose combinatorial fusion rules that describe the codon assignment in the standard genetic code simply and uniformly for all canonical amino acids. These rules become obvious if the origin of the standard genetic code is considered as a result of a fusion of four protocodes: Two dominant AU and GC protocodes and two recessive AU and GC protocodes. The biochemical meaning of the fusion rules consists of retaining the complementarity between cognate codons of the small hydrophobic amino acids and large charged or polar amino acids within the protocodes. The proto tRNAs were assembled in form of two kissing hairpins with 9-base and 10-base loops in the case of dominant protocodes and two 9-base loops in the case of recessive protocodes. The fusion rules reveal the connection between the stop codons, the non-canonical amino acids, pyrrolysine and selenocysteine, and deviations in the translation of mitochondria. Using fusion rules, we predicted the existence of additional amino acids that are essential for the development of the standard genetic code. The validity of the proposed partition of the genetic code into dominant and recessive protocodes is considered referring to state-of-the-art hypotheses. The formation of two aminoacyl-tRNA synthetase classes is compatible with four-protocode partition.

EARLY POSTOPERATIVE COMPLICATIONS IN DENTAL IMPLANT PATIENTS

Generalized parodontitis and caries complications lead to tooth loss in individuals of different age groups. As a result of this often there is a violation of the integrity of the dentition, which leads to functional disorders of the muscular apparatus, temporomandibular joint and cosmetic defects. The effective method of restoration of the integrity of the dentition is dental implantation. With this in mind, the issue of dental implantation is of particular importance and requires further development including different age groups. Aim of the study is to improve the results of dental implantation and to avoid its complications based on identification of the causes of dental implantation complications and development of preventative measures in people of different age groups. 65 patients aged 35-60 years with secondary adentia were under observation. The main study group included 45 patients aged 35-60 years with secondary adentia caused by periodontal disease. The control group included 20 patients of the same age with secondary adentia due to caries complications. All patients of the main and control groups were subjected to a comprehensive examination of the condition of the periodontal and peri-implant area prior to the implantation in the shortest time after surgery. Microbiological study was conducted in 65 patients to study the dynamics of colonization of oral microflora. Complications after implantation were identified in 24 (53.33%) patients in the main group. The most frequent complications were: disruption of wound healing in 7 (15,56%) patients, pus in postoperative wound in 8 (17.78%), expressed pain and altered sensitivity after implantation in 4 patients (8.89%) patients, perforation of the mandible in 1 (2.22%) patient, divergence of the wound edges without exposure of the implant in 4 (8.89%) patients. A large number (53.33%) of postoperative complications in patients of the main group with secondary adentia was due to generalized periodontitis. In patients of the main group at the early stage of dental implantation were revealed qualitative and quantitative changes in the microflora of the implanted furrow with increasing aggressiveness were revealed.

Stochastic deposition of amino acids into microcavities via microparticles

All known methods for solid-phase synthesis of molecular arrays exploit positioning techniques to deposit monomers on a substrate preferably high densely. In this paper, stochastic patterning of molecule spots (250 000 spots monomers/cm²) via random allocation of the microbeads on a microstructured glass is presented. The size and shape of the microbeads and the microcavities are selected in such a way so that only one microbead can fit into the respective microcavity. Each microbead can be loaded with a certain type of molecule e.g. amino acids and is brought in the microcavities stochastically. Applying solvent vapor and heating the substrate, the molecules are released from the microbeads and coupled to the functionalized substrate. To differentiate between the microbeads carrying different molecules, quantum dot labels are preliminary introduced into the microbeads. Fluorescence imaging and subsequent data analysis enable decoding of the molecule deposition patterns. After the coupling step is completed, the microbeads are mechanically removed from the microwells. The composition of the monomer microbeads, their deposition and the conditions of the monomer extraction are studied. The stochastic monomer patterning may be used to design novel molecular arrays.

Maternal and paternal genetic variation in Estonian local horse breeds in the context of geographically adjacent and distant Eurasian breeds

The maternal and paternal genetic variation of horse breeds from the Baltic Sea region, including three local Estonian breeds, was assessed and compared with that of Altai and Yakutian horses. In the mtDNA D‐loop region, 72 haplotypes assigned to 20 haplogroups in the nine breeds were detected. In Estonian local breeds, 38 mtDNA haplotypes were found, and five of them were shared by the three breeds. More than 60% of all identified haplotypes were rare. Compared with the Estonian Native and Estonian Heavy Draught breeds, a higher haplotypic diversity was found in the Tori breed (h = 0.969). Moreover, four haplotypes shared among Finnish and Estonian local horse breeds indicated ancient ancestry, and of these, H30 (haplogroup D3) showed global sharing and genetic links between modern Baltic Sea region and Siberian horses, specifically. The studied breed set showed high variability in maternal inheritance and mixed patterns of the international and native breeds of the Siberian and Baltic regions. No variation was found in paternally inherited markers among horse breeds in the Baltic Sea region.

Renaissance Distribution for Statistically Failed Experiments

Much of the experimental data, especially in life sciences, is considered to be useless if it demonstrates a large standard deviation from the mean value. The Renaissance distribution, as presented in this study, allows one to extract true values from such statistical data with large noise. To obtain proof of the Renaissance distribution, high-throughput synthesis of deep substitutions for a target amino acid sequence was performed, and the known epitope was identified in assay with human serum antibodies. In addition, the Renaissance distribution was shown to approach the epitope affinity maturation by the deep alanine substitution. The Renaissance distribution may have an impact in the development of novel specific drugs.

Whole blood transcriptome analysis reveals footprints of cattle adaptation to sub-arctic conditions

Indigenous cattle breeds in northern Eurasia have adapted to harsh climate conditions. The local breeds are important genetic resources with cultural and historical heritages, and therefore, their preservation and genetic characterization are important. In this study, we profiled the whole‐blood transcriptome of two native breeds (Northern Finncattle and Yakutian cattle) and one commercial breed (Holstein) using high‐throughput RNA sequencing. More than 15 000 genes were identified, of which two, 89 and 162 genes were significantly upregulated exclusively in Northern Finncattle, Yakutian cattle and Holstein cattle respectively. The functional classification of these significantly differentially expressed genes identified several biological processes and pathways related to signalling mechanisms, cell differentiation and host–pathogen interactions that, in general, point towards immunity and disease resistance mechanisms. The gene expression pattern observed in Northern Finncattle was more similar to that of Yakutian cattle, despite sharing similar living conditions with the Holstein cattle included in our study. In conclusion, our study identified unique biological processes in these breeds that may have helped them to adapt and survive in northern and sub‐arctic environments.

The comparative study of influence of lactic and glycolic acids copolymers type on properties of daunorubicin loaded nanoparticles and drug release

PURPOSE

The aim of this study was to compare the physico-chemical and biological properties of polymeric nanoparticles obtained from poly(DL-lactide-co-glycolide) (PLGA) with different ratios of monomers loaded with daunorubicin (DNR).

METHODS

DNR-loaded nanoparticles (NPs) were prepared with use of modified simultaneous double-emulsion solvent evaporation/diffusion technique. NPs were characterized using dynamic light scattering, atomic force microscopy, transmission electron microscopy, scanning electron microscopy, and differential scanning calorimetry and Fourier transform infrared spectroscopy.

RESULTS

NPs with DNR were differing in size and zeta potential, depending on the type of polymer. The data obtained show that total content of DNR correlates with the values of the binding constant of DNR with polymers. The release of DNR from NPs proceeds predominantly for polymers with lower binding constants. The in vitro study of NPs on the MCF-7 cells showed similar activity of particles and substances while for the anthracycline-resistant MCF-7Adr cells the cytotoxicity of the nanoparticles was 3 to 7 times higher depending on the type of copolymer.

CONCLUSIONS

PLGA DNR-loaded nanoparticles can be used to overcome multidrug resistance (MDR) as well as for reducing the frequency of DNR reception due to the prolonged effect, which allows maintaining the concentration of the drug at the required level. The usefulness of binding constant calculations for obtaining nanoparticles with the maximum drug loading was proven. The rate of drug administration and the frequency of administration can be calculated based on the DNR release profiles and release parameters that depend on polymer type.

Maternal and paternal genealogy of Eurasian taurine cattle (Bos taurus)

Maternally inherited mitochondrial DNA (mtDNA) has been used extensively to determine origin and diversity of taurine cattle (Bos taurus) but global surveys of paternally inherited Y-chromosome diversity are lacking. Here, we provide mtDNA information on previously uncharacterised Eurasian breeds and present the most comprehensive Y-chromosomal microsatellite data on domestic cattle to date. The mitochondrial haplogroup T3 was the most frequent, whereas T4 was detected only in the Yakutian cattle from Siberia. The mtDNA data indicates that the Ukrainian and Central Asian regions are zones where hybrids between taurine and zebu (B. indicus) cattle have existed. This zebu influence appears to have subsequently spread into southern and southeastern European breeds. The most common Y-chromosomal microsatellite haplotype, termed here as H11, showed an elevated frequency in the Eurasian sample set compared with that detected in Near Eastern and Anatolian breeds. The taurine Y-chromosomal microsatellite haplotypes were found to be structured in a network according to the Y-haplogroups Y1 and Y2. These data do not support the recent hypothesis on the origin of Y1 from the local European hybridization of cattle with male aurochsen. Compared with mtDNA, the intensive culling of breeding males and male-mediated crossbreeding of locally raised native breeds has accelerated loss of Y-chromosomal variation in domestic cattle, and affected the contribution of genetic drift to diversity. In conclusion, to maintain diversity, breeds showing rare Y-haplotypes should be prioritised in the conservation of cattle genetic resources.

Analysis of population differentiation in North Eurasian cattle (Bos taurus) using single nucleotide polymorphisms in three genes associated with production traits

Single nucleotide polymorphisms (SNPs) in growth hormone 1 (GH1), insulin-like growth factor 1 (IGF1) and leptin (LEP), all candidates for production traits in cattle, were characterized in North Eurasian cattle breeds. Allele frequencies of IGF1 exhibited significant (P < 0.05) deviation from neutral expectation and therefore, might be associated with divergence in North Eurasian cattle because of genetic selection. Allele frequencies and lower heterozygosity of LEP may indicate a recent introduction of an alternative allele in this geographic region. Locus F(ST) estimates were highest for IGF1 (0.151, sigma = 0.042) and lowest for GH (0.062, sigma = 0.020). Our results suggest a slightly higher population differentiation across the candidate genes (FST = 0.108) than across microsatellites (FST = 0.095), possibly because of selection and stochastic effects.

Cerebellopontine angle meningiomas. Clinical features and surgical treatment

AIM

The aim of this study is to present the clinical picture of patients with cerebellopontine angle meningiomas and analyze the results of their operative treatment.

METHODS

A retrospective study of patients with cerebellopontine angle meningiomas operated consecutively in our department over an 11-year period has been carried out. Data regarding their clinical features, surgical treatment, morbidity, mortality and outcome have been analyzed. Forty-four patients with cerebellopontine angle meningiomas were operated during the period 1991-2001 (intervention: tumor removal via the retrosigmoid suboccipital approach).

MAIN OUTCOME MEASURES

clinical condition, MRI/ CT imaging.

RESULTS

The median duration of symptoms prior to diagnosis was 44.5 months. The most frequent initial complaints were hearing loss, tinnitus and headache. Most frequent symptoms and signs at presentation were cerebellar, followed by hearing loss and trigeminal nerve symptoms. In 98% of the cases the operative approach used was the retrosigmoidal suboccipital. Total tumor removal was achieved in 55%. After total tumor removal no recurrences have been observed. The mortality rate was 2%.

CONCLUSION

The application of different classification schemes complicates the comparison between published series. The outcome depends on their location, consistency, size and relation to the surrounding neurovascular structures. In our experience the retrosigmoid suboccipital approach is most appropriate for their surgical treatment. It offers the possibility to remove completely even large meningiomas and avoids the risk of recurrences.

Differences in dose scheduling as a factor in the etiology of anthracycline-induced cardiotoxicity in Ewing sarcoma patients

Clinical observation suggested a high prevalence of cardiac morbidity and mortality in children with Ewing sarcoma (ES) treated at B.C.'s Children's Hospital. We therefore compared 30 patients treated for Ewing sarcoma between 1978 and 1991 with 26 soft tissue sarcoma (STS) patients treated with similar chemotherapy over the same period of time. All patients were evaluated for cardiac function using echocardiography. Shortening fraction (SF) and left ventricular mass index (Massl) were compared before and after treatment. The role of chest irradiation, dose concentration (DC) of adriamycin (AD), total mean doses of AD, cyclophosphamide (CY) and actinomycin (AC) were analysed. SF for patients with ES and STS postchemotherapy was significantly lower (P < .001 and P = 0.0004, respectively) than pretreatment values. Postchemotherapy SF for ES was lower than STS (P = 0.0097). Massl for each group did not change significantly. Six of the ES patients had postchemotherapy SF of < 0.20, with three in congestive failure, two cardiac deaths and one heart transplant. One additional ES patient had sick sinus syndrome and needed a pacemaker. Among the STS patients only one had SF < .20 and none were symptomatic. There were no significant differences in the mean AD, CY and AC doses for ES versus STS. The difference in the DC of AD for ES (mean 744) compared to STS (mean = 362) was significant (P = < 0.001). Regression analysis indicated a trend for decreasing SF with increasing DC (P = 0.017). Chest irradiation did not appear to increase the likelihood of cardiotoxicity. ES patients had a higher prevalence of cardiac dysfunction compared to STS. Studies are required to evaluate the importance of the components of DC, i.e., size of the individual dose and frequency of administration of AD, and to look at other possible factors in the causation of cardiomyopathy in ES.

Early prediction of anthracycline cardiomyopathy using standard M-mode and digitized echocardiography

In this study, we attempted to identify echocardiographic findings that can be used as early predictors of left ventricular dysfunction due to anthracyclines in 26 pediatric oncology patients. Retrospective review identified six patients (group 1 mean anthracycline dose = 337 +/- 123 mg/m2) who developed clinical evidence of cardiomyopathy and 20 consecutive patients followed prospectively (group 2 mean anthracycline dose = 298 +/- 102 mg/m2) who did not. All of the patients had serial m-mode echocardiography before and at approximately every 50 mg/m2 of anthracycline treatment depending on the dosage schedule. The following measurements were recorded: left ventricular dimensions and wall thickness, indices of left ventricular function, including systolic time intervals, shortening fraction, and ejection fraction. Using digitized echocardiography, the following parameters were recorded: peak and normalized systolic and diastolic velocities of the left ventricular chamber, posterior and septal wall velocities, and percent of posterior wall thickening. Variations from established normal longitudinal bounds and actual changes from pre-anthracycline values were compared for the two groups throughout the course of therapy. At 70 mg/m2 of anthracycline, group 1 showed significant deterioration in shortening fraction (mean change = 8.8 versus 2.5, p = .03), left ventricular velocity in diastole (2.9 versus 0.21, p = .04), left ventricular normalized velocity in systole (.65 versus 0.03, p = .02), and left ventricular normalized velocity in diastole (1.15 versus 0.002, p = .04) compared to group 2. These values were mostly compensated by 125 mg/m2, but they slowly deteriorated again at higher doses of anthracycline, leading to the appearance of clinical evidence of cardiomyopathy.(ABSTRACT TRUNCATED AT 250 WORDS)

Rate-corrected mean velocity of fiber shortening-stress at peak systole as a load-independent measure of contractility

The relation of mean velocity of fiber shortening-stress at end-systole is a good load-independent index of left ventricular contractility, but involves simultaneous M-mode echocardiography, carotid tracing and blood pressure determination, which may be impractical in children. As stress at peak systole and end-systole are closely related, this study examined whether the relation of mean velocity of fiber shortening-stress at peak systole could be used as a simpler method of assessing left ventricular contractility in a normal population of children. In addition, the cross-sectional normal range for a pediatric population was obtained. In 25 normal children aged 4 to 17 years (mean age 11), rate-corrected mean velocity of fiber shortening (MVCFc), stress at peak systole (sigma PS), and end-systolic stress (sigma ES) were determined using echocardiography, carotid pulse tracing and blood pressure measurement. Six patients with cardiomyopathy (mean age 8 years) were also studied. The relation of stress at peak systole and end-systolic stress was sigma PS = 1.004 sigma ES + 12.0 (r = 0.91, SEE = 4.98; p less than 0.001) for the normal group, and sigma PS = 1.083 sigma ES + 7.7 (r = 0.99, SEE = 4.07; p less than .001) for the cardiomyopathic group. This slope of the regression line was slightly higher and the difference was statistically significant. The slope of MVCFc = 0.0066 sigma PS + 1.55 (SEE = 0.131, r = -0.52) was nearly identical to that of MVCFc = 0.0065 sigma ES + 1.46, (SEE = 0.135, r = -0.46), with no difference in the regression coefficients.(ABSTRACT TRUNCATED AT 250 WORDS)

Doppler-derived mean aortic flow velocity in children: an alternative to cardiac index

This study tested the hypothesis that mean aortic velocity is relatively constant in children. Eighty-eight normal children (aged 1 month to 15 years) were studied prospectively. Ascending aortic flow velocities were obtained by pulse Doppler and mean aortic velocities calculated. Mean aortic flow velocity was relatively constant for all ages at 28.4 +/- 4.8 cm/s. As Doppler is easy to perform, mean aortic flow velocity may be an alternative approach to the assessment of cardiac output.

Left ventricular systolic and diastolic function after total correction of tetralogy of Fallot

Left ventricular (LV) systolic and diastolic function was assessed in 12 patients after total correction of tetralogy of Fallot (age range 5 to 18 years, mean 10) and compared with 10 control patients. Only 1 patient had a shunt before total correction that was performed at a mean age of 3.5 years, (range 0.3 to 8). At cardiac catheterization the following indexed LV parameters were measured: end-diastolic and end-systolic volumes, wall mass, ejection fraction, stroke volume and end-diastolic and end-systolic pressures and stresses. The rate-corrected mean velocity of fiber shortening was calculated. LV diastolic operant chamber stiffness and myocardial stiffness were calculated from simultaneous diastolic pressures and volumes in mid- and late diastole using monoexponential formulas. The 2 groups were compared by unpaired t tests. The tetralogy group had higher mean end-diastolic (93 vs 74 ml/m2), end-systolic (29 vs 19 ml/m2) and stroke (64 vs 55 ml/m2) volumes than controls. Rate-corrected mean velocity of fiber shortening was lower in the tetralogy group (1.07 vs 1.24). Myocardial stiffness was higher in the tetralogy group (16 vs 11). Other indexes were not significantly different. Thus, LV function after total correction of tetralogy of Fallot may be abnormal with larger than normal LV size, decreased contractile function and increased myocardial stiffness.

Normal serial variability for M-mode and digitized echocardiography in a pediatric population

The normal serial variability of M-mode and digitized echocardiography was assessed in 18 healthy children aged 3-16 years. M-mode echocardiograms were done one month apart in each child and two sets of three beats were analyzed twice for each month's tracing. Ejection fraction and shortening fraction were obtained in the standard manner and the tracing digitized and analyzed for peak and normalized left ventricular velocities, and for posterior wall and septal wall velocities in systole and diastole. The component variabilities were determined by a univariate four-factor hierarchical variance components analysis and the sum of these variability limits established. Standard M-mode echocardiographic measurements of shortening fraction and ejection fraction (15% and 10% of mean) were the least variable. Peak and normalized velocities were more variable with left ventricular velocities (18%-29% of mean), posterior wall velocities (26%-45% of mean) and septal velocities (38%-68% of mean) showing increasing variabilities. Thus there is less variability in M-mode echocardiography than digitized echocardiography. The normal limits of variability are established and should be used for follow-up studies.