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Orvosi Hetilap
Authors: Mihály Dió, Tibor Deutsch, and Judit Mészáros

References 1 Dimitrov, D. V.: Systems patientomics: the virtual in-silico patient. EPMA J., 2014, 5 (Suppl. 1), A53. 2 Díaz

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for the drugs based on the stress degradation behavior, and, (5) finally, predict in-silico carcinogenicity, mutagenicity, and hepatotoxicity of drugs and DPs by using in-silico toxicity software's. Experimental

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Rajendrakumar, P., Biswal, A. K., Balachandran, S. M., Sundaram, R. M. (2008) In silico analysis of microsatellites in organellar genomes of major cereals for understanding their phylogenetic relationships. In Silico Biol. 8 , 87

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Acta Agronomica Hungarica
Authors: D. Polgári, B. Kalapos, V. Tisza, L. Kovács, B. Kerti, L. Heszky, and E. Kiss

The aim of this study was to characterize a gene associated with ripening in strawberry, a non-climacteric fruit. Differently expressed transcripts of candidate genes functioning in fruit development and ripening were identified from strawberry ( Fragaria × ananassa Duch.) in four ripening stages using the cDNA-AFLP method. The cDNA fragment designated C11M32M003 was selected from the putative ripening-related genes for further analysis. This transcript accumulated in the green receptacle, and the achene, but gene expression decreased in both tissues in parallel with the progress of ripening (Balogh, 2006). In silico analysis revealed that both the cDNA-AFLP fragment (C11M32M003) and the full-length cDNA AY695666 showed over 60% homology at the nucleotide level with two gene groups found in various plant species, including Arabidopsis thaliana . One of the candidate groups consisted of NITRILASE sequences thought to be related to auxin biosynthesis. As an alternative, a lesser known gene group named SPIRAL was suggested. The results of the detailed bioinformatic comparisons presented in this paper prove that the strawberry sequence analysed belongs to the SPIRAL gene family.

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Total mineral uptake capacity of zucchini (Cucurbita pepo L. cv. giromontiina) grown in an experimental field at Gödöllő was studied. The mineral content of the soil (brown acidic sandy forest soil) showed unexpectedly high content (mg kg−1 DW) of Ba (95.5), Cr (32.9), Ni (27.8), Pb (15.4) and Zn (53.3). Boron (B) concentration of the soil was relatively low (7.1 mg kg−1 DW), but its bioaccumulation content in root, (2.5) shoot, (33.1) and leaf (50.1) tissues of the plant (mg kg−1 DW). Zinc (Zn) was also bioaccumulated in the plant with contents (mg kg−1 DW) of 47.1 (roots), 23.0 (shoots) and 56.1 (leaves) as compared with 53.3 (in the soil). Toxic element exclusion was observed in zucchini (mg kg−1 DW) concerning Ba (29.0), Co (0.2), Cr (5.3), Ni (5.8) and Pb (3.4) measured in the roots when compared with their concentrations in the soil: Ba (95.5), Co (10.2), Cr (32.9), Ni (27.8) and Pb (15.4). In silico sequence analyses of nucleotide and amino acid sequences of aquaporins (NIP, TIP, SIP and Si-TRP), boron-exporters (BOR), and rbcL of cpDNA revealed plant species with high sequence similarities to the sequences of Cucurbits, which predicted additional plants with intensive mineral (B and Zn) uptake capacity, similar to Cucurbits with phytoextraction potential.

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Biologia Futura
Authors: Mughal Qayum, Muhammad Nisar, Abdur Rauf, Imran Khan, Waqar Ahmad Kaleem, Muslim Raza, Nasiara Karim, Munawar Ahmad Saleem, Saud Bawazeer, Sengul Uysal, Gokhan Zengin, Saqib Jahan, and Mohamed Fawzy Ramadan

taxawallin isolated from T. wallichiana as well as investigating their in silico activities on EGFR tyrosine kinase enzyme. Materials and Methods Plant material and extraction The bark of the plant ( T

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Leaf senescence is a notably important trait that limits the yield and biomass accumulation of agronomic crops. Therefore, determining the chromosomal position of the expression sequence tags (ESTs) that are associated with leaf senescence is notably interesting in the manipulation of leaf senescence for crop improvement. A total of 32 ESTs that were previously identified during the delaying leaf senescence stage in the stay-green wheat cultivar CN17 were mapped to 42 chromosomes, a chloroplast, a mitochondrion, and a ribosome using in silico mapping. Then, we developed 19 pairs of primers based on these sequences and used them to determine the polymorphisms between the stay-green cultivars (CN12, CN17, and CN18) and the control cultivar MY11. Among the 19 pairs of primers, 5 pairs produced polymorphisms between the stay-green cultivar and the non-stay-green control. Further studies of Chinese Spring nullisomic-tetrasomics show that JK738991 is mapped to 3B, JK738983 is mapped to 5D, and JK738989 is mapped to 2A, 4A, and 3D. The other two ESTs, JK738994 and JK739003, were not assigned to a chromosome using the Chinese Spring nullisomic-tetrasomics, which indicates that these ESTs may be derived from rye DNA in the wide cross. In particular, the ESTs that produce polymorphisms are notably useful in identifying the stay-green cultivar using molecular marker-assisted selection. The results also suggest that the in silico mapping data, even from a comparison genomic analysis based on the homogeneous comparison, are useful at some points, but the data were not always reliable, which requires further investigation using experimental methods.

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A database of potentially biologically active peptide sequences, named BIOPEP (http://www.uwm.edu.pl/biochemia), has been developed and applied for classification of numerous food proteins as potential sources of peptides with antihypertensive activity. More than one hundred proteins included in the BIOPEP database were analyzed and classified according to the frequency of the occurrence of antihypertensive fragments. As the example of detailed profile of potential biological activity, the bovine beta-globulin A is presented. It was found that apart from the dominant antihypertensive activity, other effects (opioid, dipeptidyl peptidase IV inhibitory, immunomodulative, antioxidative) may be present. It can be concluded that this method may be a useful tool in this field. The antihypertensive activity was the most dominant because fragments with such activity were present in all of the examined proteins. It encouraged us to classify proteins into families, which may be better or the worse source of antihypertensive fragments. We found statistically significant differences between the values of parameter A (P<0.001) among the all five families we obtained. We found that in silico analysis can be useful in the analysis of the large quantities of data in the field of proteins as the source of biologically active peptides.

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Magyar Sebészet
Authors: János Imre Barabás, Miklós Pólos, László Daróczi, Tivadar Hüttl, Kálmán Benke, Ferenc Horkay, Zoltán Szabolcs, and István Hartyánszky

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Bevezetés: A sebészi diszciplínákban a műtétetek megtervezése statikus modelleken alapulnak. Azonban a számítástechnikai fejlődése lehetőséget nyitott a dinamikus modellek preoperatív megtervezésére és intraoperatív alkalmazásukra. Célunk volt, olyan döntéstámogató rendszer megalkotása a szívsebészeti gyakorlatban, melynek segítségével az áramlástani, kamramorfológiai, térfogat és posztoperatív kamrafunkció predikcióját végezhetjük kamrarekonstrukciós műtéteknél. Módszerek: Saját fejlesztésű szoftver használatával DICOM fájlok importálását követően a dilatált bal kamrát három dimenzióban modellezzük. Ezt követő áramlástani modellezések segítségével az idővel és a kamratérfogat változásával dinamikusan változó paramétereket: az áramlástani profilt, turbulenciát és a bal kamrában fellépő nyíróerők hatását a myocardium funkciójára kiszámítjuk. In silico modellben – a prediktált adatokat felhasználva – megtervezzük a balkamra-rekonstrukciós műtét egyes lépéseit. A tervezés alapján a kiszámított rezekciós vonalak hosszát alkalmazva történtek a műtétek. Eredmények: Összesen 50 esetben történt 3D tervezés. A bal kamra geometriáját jellemző konicitási és sphericitási indexek szignifikánsan javultak a műtétet követően (0,42 vs. 0,67 és 0,36 vs. 0,72, p < 0,05). A bal kamra izomzatára ható nyíróerő szignifikánsan 83%-kal csökkent, illetve a kamra turbulens áramlásprofilja szignifikánsan javult (2712 vs. 1823, p < 0,05). Következésképpen a szív pumpafunkciója javult a műtétet követően. Konklúzió: Technikánk alkalmazásával a balkamra-rekonstrukciós műtétek egyes lépéseinek standardizálásával és e lépések intraoperatív alkalmazásának kidolgozásával sikerült egy új sebészi döntéstámogató rendszert létrehoznunk. Az így megtervezett és személyre szabott műtétekkel növelhettük ezen magas kockázatú betegcsoport posztoperatív életminőségét és túlélését.

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Complete genome sequences of bovine viral diarrhoea virus types 1 and 2 (BVDV-1 and 2) deposited in the GenBank were submitted to bioinformatic analysis using a recombination-detecting software. The results indicate that recombination events are not rare in the case of BVDV, which frequently causes immunotolerance and, consequently, persistent infection in calves. The lack of specific immunity provides an ideal possibility for multiple infections by antigenically related but genetically different BVDV strains, and hence recombinations may occur. Among the 62 BVDV-1 genomes five recombinants and their possible parent strains, while among the 50 BVDV-2 genomes one simple recombinant and its parent strains were identified, which were supported by extremely strong probability values (P values varying between 1.26 × 10–4 and 1.58 × 10–310). Besides the newly identified recombinants, recombination events described previously were confirmed, but in some of these cases former information was completed with new data, or different parent(s) were suggested by the programme (RDP 4.46 BETA) used in this study.

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