bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of growth at low temperature on the alternative pathway respiration in Acanthamoeba castellanii mitochondria.
Authors: Jarmuszkiewicz W , Fraczyk O , Hryniewiecka L
Published: December 2019

Mitochondria of amoeba Acanthamoeba castellanii in addition to the conventional cytochrome pathway possess, like plant mitochondria, a cyanide-resistant alternative quinol oxidase. In mitochondria isolated from amoeba batch culture grown temporarily at low temperature (6 degrees C), higher respiration was accompanied by lower coupling parameters as compared to control culture (grown at 28 degrees C). In the presence of benzohydroxamate, respiratory rates and coupling parameters were similar in both types of mitochondria indicating that growth in cold conditions did not disturb the cytochrome pathway. Increased contribution of alternative oxidase in total mitochondrial respiration in low-temperature-grown amoeba cells was confirmed by calculation of its contribution using ADP/O measurements. Furthermore, in mitochondria from low-temperature- grown cells the content of the alternative oxidase was increased and correlated with the increase in the unstimulated and GMP-stimulated cyanide-resistant respiratory activity. A possible physiological role of higher activity of alternative oxidase as response to growth at a low temperature in unicellular organisms, such as amoeba, is discussed.
Expression level of adenosine kinase in rat tissues. Lack of phosphate effect on the enzyme activity.
Authors: Sakowicz M , Grdeń M , Pawełczyk T
Published: December 2019

In this report we describe cloning and expression of rat adenosine kinase (AK) in Esccherichaia coli cells as a fusion protein with 6xHis. The recombinant protein was purified and polyclonal antibodies to AK were generated in rabbits. Immunoblot analysis of extracts obtained from various rat tissues revealed two protein bands reactive with anti-AK IgG. The apparent molecular mass of these bands was 48 and 38 kDa in rat kidney, liver, spleen, brain, and lung. In heart and muscle the proteins that react with AK antibodies have the molecular masses of 48 and 40.5 kDa. In order to assess the relative AK mRNA level in rat tissues we used the multiplex PCR technique with beta-actin mRNA as a reference. We found the highest level of AK mRNA in the liver, which decreased in the order kidney > spleen > lung > heart > brain > muscle. Measurement of AK activity in cytosolic fractions of rat tissues showed the highest activity in the liver (0.58 U/g), which decreased in the order kidney > spleen > lung > brain > heart > skeletal muscle. Kinetic studies on recombinant AK as well as on AK in the cytosolic fraction of various rat tissues showed that this enzyme is not affected by phosphate ions. The data presented indicate that in the rat tissues investigated at least two isoforms of adenosine kinase are expressed, and that the expression of the AK gene appears to have some degree of tissue specificity.
Cytochrome P4502C9 genotype in Southeast Anatolia and possible relation with some serum tumour markers and cytokines.
Authors: Yilmaz N , Erbağci A B , Aynacioğlu A S
Published: December 2019

Substrates for CYP2C9 include fluoxetine, phenytoin, warfarin, losartam and numerous nonsteroidal anti-inflammatory drugs. Polymorphisms in the coding region of the CYP2C9 gene produce variants at amino-acid residues 144 Arg/Cys and 359 Ile/Leu of the CYP2C9 protein. Individuals homozygous for Leu359 have markedly diminished metabolic capacities for most CYP2C9 substrates, the frequency of this allele is, however, rather low. Consistently with the modulation of enzyme activity by genetic and other factors, wide interindividual variability occurs in the elimination and/or dosage requirements of prototypic CYP2C9 substrates. The polymorphic enzyme CYP2C9 takes part in the metabolism of alkylating agents and polycyclic aromatic hydrocarbons like benzo(a)pyrene, a carcinogen present in tobacco smoke. Although the impact of impaired enzyme activity in metabolism of carcinogens and procarcinogens has not been fully defined, an association of CYP2C9 variant alleles to DNA adduct levels in lung tissues as well as to lung cancer risk have been reported. In this study 64 healthy subjects (44M/22F) were analysed for CYP2C9 genotype with PCR-RFLP and for serum carcinoembryonic antigen (CEA), alpha-fetoprotein (AFP), CA 19-9, CA 15-3, ferritin, IL-6, IL-8 concentrations by chemiluminescence or electrochemiluminescence methods. CYP2C9*1 was found to be the most prevalent allele and CYP2C9*1/CYP2C9*1 was the most frequent genotype represented in 64% of the population in southeastern Anatolia (Gaziantep). Although slight differences in serum tumour marker and cytokine concentrations were observed for CYP2C9 genotypes the differences were statistically insignificant (P > 0.05). This could be due to the complexity of the role of CYP2C9 in benzo(a)pyrene metabolism as well as from other contributing factors like interindividual variability of diverse enzymes participating in the same metabolic pathway, unequal expression of the variant alleles and differences in exposure to carcinogens. However, determination of CYP2C9 phenotypes in a larger group of subjects might clarify these slight differences.
Comparative studies of nuclear DNA content in benign and malignant thyroid lesions.
Authors: Konarska L , Skierski J , Ellert A , Steinbrich J , Woźniak A , Kalczak M
Published: December 2019

Currently available data suggest that DNA aneuploidy is associated with aggressive behavior of and unfavorable prognosis in several malignant human tumors as compared with diploid malignancies. However, the diagnostic and prognostic importance of flow cytometric DNA measurements in the case of thyroid neoplasms remains controversial. Therefore, the aim of our study was to evaluate utility of DNA index (DI) and proliferative index (PI) in distinguishing benign from malignant thyroid lesions taking into account the possible influence of intra-tumor heterogeneity and tissue preparation mode on DNA flow-cytometry measurements. A retrospective study was performed on 71 paraffin-embedded specimens from 57 patients with benign and malignant thyroid pathologies: 13 colloid goitres, 12 parenchymatous goitres, 19 adenomas and 13 carcinomas. In 14 of 57 cases two separate specimens taken from different areas of the same lesion were analysed and DNA parameters were compared. Additionally, flow cytometry DNA analysis was parallelly performed on 3 adjacent but differently processed tissue sections (fresh, formalin-fixed and paraffin-embedded) taken from each of 26 surgically excised thyroid lesions. DNA content was also analysed in both fresh and formalin-fixed twin specimens of normal pig thyroid glands (N = 6). We demonstrated that all tumors diagnosed as thyroid carcinomas were associated with abnormal nuclear DNA content although aneuploidy was not found specific to malignant thyroid tumors. Aneuploid samples of benign thyroid lesions exhibited higher proliferative activity, expressed as mean PI values, than diploid ones. In carcinomas the mean PI values were significantly higher than in benign lesions, independently whether they concerned aneuploid or diploid tissues. Considering intra-tumor heterogeneity, the flow cytometric DNA parameters can be assumed as reproducible despite differences in the mode of tissue fixation and preparation for analysis.
Direct in vivo transfer of plasmid DNA into murine tumors: effects of endotoxin presence and transgene localization.
Authors: Budryk M , Cichoń T , Szala S
Published: December 2019

The purpose of this study was to investigate the effect of endotoxin presence in plasmid DNA preparations on the efficiency of transfection achieved in vivo with B16(F10) and Renca tumors and to determine transgene localization. Our data show that endotoxin markedly decreases the efficiency of transfection. Furthermore, the transgene transferred in vivo can be found in both neoplastic and normal (most likely myofibroblast) cells lying in proximity of the administration site.
Genomics and the evolution of aminoacyl-tRNA synthesis.
Authors: Ruan B , Ahel I , Ambrogelly A , Becker H D , Bunjun S , Feng L , Tumbula-Hansen D , Ibba M , Korencic D , Kobayashi H , Jacquin-Becker C , Mejlhede N , Min B , Raczniak G , Rinehart J , Stathopoulos C , Li T , Söll D
Published: December 2019

Translation is the process by which ribosomes direct protein synthesis using the genetic information contained in messenger RNA (mRNA). Transfer RNAs (tRNAs) are charged with an amino acid and brought to the ribosome, where they are paired with the corresponding trinucleotide codon in mRNA. The amino acid is attached to the nascent polypeptide and the ribosome moves on to the next codon. Thus, the sequential pairing of codons in mRNA with tRNA anticodons determines the order of amino acids in a protein. It is therefore imperative for accurate translation that tRNAs are only coupled to amino acids corresponding to the RNA anticodon. This is mostly, but not exclusively, achieved by the direct attachment of the appropriate amino acid to the 3'-end of the corresponding tRNA by the aminoacyl-tRNA synthetases. To ensure the accurate translation of genetic information, the aminoacyl-tRNA synthetases must display an extremely high level of substrate specificity. Despite this highly conserved function, recent studies arising from the analysis of whole genomes have shown a significant degree of evolutionary diversity in aminoacyl-tRNA synthesis. For example, non-canonical routes have been identified for the synthesis of Asn-tRNA, Cys-tRNA, Gln-tRNA and Lys-tRNA. Characterization of non-canonical aminoacyl-tRNA synthesis has revealed an unexpected level of evolutionary divergence and has also provided new insights into the possible precursors of contemporary aminoacyl-tRNA synthetases.
Methionyl-tRNA synthetase.
Authors: Deniziak M A , Barciszewski J
Published: December 2019

Methionyl-tRNA synthetase (MetRS) belongs to the family of 20 enzymes essential for protein biosynthesis. It links covalently methionine with its cognate tRNA. Crystal structures solved for bacterial MetRSs have given a number of interesting insights into enzyme architecture and methionylation catalysis. A comparison of sequences of MetRSs belonging to all kingdoms of life, as well as numerous biochemical and genetic studies have revealed the presence of various additional domains appended to the catalytic core of synthetase. They are responsible for interactions with tRNA and proteins. Tertiary structure of C-terminal tRNA-binding appendices can be deduced from those determined for their homologues: tRNA binding protein 111 and endothelial monocyte-activating polypeptide II. Contacts between MetRS and other proteins could be mediated not only by noncatalytic peptides but also by structural elements present in the catalytic core, e.g. Arg-Gly-Asp (RGD) motifs. Additional activities involve MetRS in the maintenance of translational fidelity and in coordination of ribosome biogenesis with protein synthesis.
MADS-box genes are involved in floral development and evolution.
Authors: Saedler H , Becker A , Winter K U , Kirchner C , Theissen G
Published: December 2019

MADS-box genes encode transcription factors in all eukaryotic organisms thus far studied. Plant MADS-box proteins contain a DNA-binding (M), an intervening (I), a Keratin-like (K) and a C-terminal C-domain, thus plant MADS-box proteins are of the MIKC type. In higher plants most of the well-characterized genes are involved in floral development. They control the transition from vegetative to generative growth and determine inflorescence meristem identity. They specify floral organ identity as outlined in the ABC model of floral development. Moreover, in Antirrhinum majus the MADS-box gene products DEF/GLO and PLE control cell proliferation in the developing flower bud. In this species the DEF/GLO and the SQUA proteins form a ternary complex which determines the overall "Bauplan" of the flower. Phylogenetic reconstructions of MADS-box sequences obtained from ferns, gymnosperms and higher eudicots reveal that, although ferns possess already MIKC type genes, these are not orthologous to the well characterized MADS-box genes from gymnosperms or angiosperms. Putative orthologs of floral homeotic B- and C-function genes have been identified in different gymnosperms suggesting that these genes evolved some 300-400 million years ago. Both gymnosperms and angiosperms also contain a hitherto unknown sister clade of the B-genes, which we termed Bsister. A novel hypothesis will be described suggesting that B and Bsister might be involved in sex determination of male and female reproductive organs, respectively.
Nod genes and Nod signals and the evolution of the Rhizobium legume symbiosis.
Authors: Debellé F , Moulin L , Mangin B , Dénarié J , Boivin C
Published: December 2019

The establishment of the nitrogen-fixing symbiosis between rhizobia and legumes requires an exchange of signals between the two partners. In response to flavonoids excreted by the host plant, rhizobia synthesize Nod factors (NFs) which elicit, at very low concentrations and in a specific manner, various symbiotic responses on the roots of the legume hosts. NFs from several rhizobial species have been characterized. They all are lipo-chitooligosaccharides, consisting of a backbone of generally four or five glucosamine residues N-acylated at the non-reducing end, and carrying various O-substituents. The N-acyl chain and the other substituents are important determinants of the rhizobial host specificity. A number of nodulation genes which specify the synthesis of NFs have been identified. All rhizobia, in spite of their diversity, possess conserved nodABC genes responsible for the synthesis of the N-acylated oligosaccharide core of NFs, which suggests that these genes are of a monophyletic origin. Other genes, the host specific nod genes, specify the substitutions of NFs. The central role of NFs and nod genes in the Rhizobium-legume symbiosis suggests that these factors could be used as molecular markers to study the evolution of this symbiosis. We have studied a number of NFs which are N-acylated by alpha,beta-unsaturated fatty acids. We found that the ability to synthesize such NFs does not correlate with taxonomic position of the rhizobia. However, all rhizobia that produce NFs such nodulate plants belonging to related tribes of legumes, the Trifolieae, Vicieae, and Galegeae, all of them being members of the so-called galegoid group. This suggests that the ability to recognize the NFs with alpha-beta-unsaturated fatty acids is limited to this group of legumes, and thus might have appeared only once in the course of legume evolution, in the galegoid phylum.
Reduction of bacterial genome size and expansion resulting from obligate intracellular lifestyle and adaptation to soil habitat.
Authors: Stepkowski T , Legocki A B
Published: December 2019

Prokaryotic organisms are exposed in the course of evolution to various impacts, resulting often in drastic changes of their genome size. Depending on circumstances, the same lineage may diverge into species having substantially reduced genomes, or such whose genomes have undergone considerable enlargement. Genome reduction is a consequence of obligate intracellular lifestyle rendering numerous genes expendable. Another consequence of intracellular lifestyle is reduction of effective population size and limited possibility of gene acquirement via lateral transfer. This causes a state of relaxed selection resulting in accumulation of mildly deleterious mutations that can not be corrected by recombination with the wild type copy. Thus, gene loss is usually irreversible. Additionally, constant environment of the eukaryotic cell renders that some bacterial genes involved in DNA repair are expandable. The loss of these genes is a probable cause of mutational bias resulting in a high A+T content. While causes of genome reduction are rather indisputable, those resulting in genome expansion seem to be less obvious. Presumably, the genome enlargement is an indirect consequence of adaptation to changing environmental conditions and requires the acquisition and integration of numerous genes. It seems that the need for a great number of capabilities is common among soil bacteria irrespective of their phylogenetic relationship. However, this would not be possible if soil bacteria lacked indigenous abilities to exchange and accumulate genetic information. The latter are considerably facilitated when housekeeping genes are physically separated from adaptive loci which are useful only in certain circumstances.
Ribozymes of the hepatitis delta virus: recent findings on their structure, mechanism of catalysis and possible applications.
Authors: Ciesiolka J , Wrzesinski J , Legiewicz M , Smólska B , Dutkiewicz M
Published: December 2019

Although the delta ribozymes have been studied for more than ten years the most important information concerning their structure and mechanism of catalysis were only obtained very recently. The crystal structure of the genomic delta ribozyme turns out to be an excellent example of the extraordinary properties of RNA molecules to fold into uniquely compact structures. Details of the X-ray structure have greatly stimulated further studies on the folding of the ribozymes into functionally active molecules as well as on the mechanism of RNA catalysis. The ability of the delta ribozymes to carry out general acid-base catalysis by nucleotide side chains has been assumed in two proposed mechanisms of self-cleavage. Recently, considerable progress has been also made in characterizing the catalytic properties of trans-acting ribozyme variants that are potentially attractive tools in the strategy of directed RNA degradation.
Structure-function relationship of serine protease-protein inhibitor interaction.
Authors: Otlewski J , Jaskólski M , Buczek O , Cierpicki T , Czapińska H , Krowarsch D , Smalas A O , Stachowiak D , Szpineta A , Dadlez M
Published: December 2019

We report our progress in understanding the structure-function relationship of the interaction between protein inhibitors and several serine proteases. Recently, we have determined high resolution solution structures of two inhibitors Apis mellifera chymotrypsin inhibitor-1 (AMCI-I) and Linum usitatissimum trypsin inhibitor (LUTI) in the free state and an ultra high resolution X-ray structure of BPTI. All three inhibitors, despite totally different scaffolds, contain a solvent exposed loop of similar conformation which is highly complementary to the enzyme active site. Isothermal calo- rimetry data show that the interaction between wild type BPTI and chymotrypsin is entropy driven and that the enthalpy component opposes complex formation. Our research is focused on extensive mutagenesis of the four positions from the protease binding loop of BPTI: P1, P1', P3, and P4. We mutated these residues to different amino acids and the variants were characterized by determination of the association constants, stability parameters and crystal structures of protease-inhibitor complexes. Accommodation of the P1 residue in the S1 pocket of four proteases: chymotrypsin, trypsin, neutrophil elastase and cathepsin G was probed with 18 P1 variants. High resolution X-ray structures of ten complexes between bovine trypsin and P1 variants of BPTI have been determined and compared with the cognate P1 Lys side chain. Mutations of the wild type Ala16 (P1') to larger side chains always caused a drop of the association constant. According to the crystal structure of the Leu16 BPTI-trypsin complex, introduction of the larger residue at the P1' position leads to steric conflicts in the vicinity of the mutation. Finally, mutations at the P4 site allowed an improvement of the association with several serine proteases involved in blood clotting. Conversely, introduction of Ser, Val, and Phe in place of Gly12 (P4) had invariably a destabilizing effect on the complex with these proteases.
Organismal view of a plant and a plant cell.
Authors: Wojtaszek P
Published: December 2019

Cell walls are at the basis of a structural, four-dimensional framework of plant form and growth time. Recent rapid progress of cell wall research has led to the situation where the old, long-lasting juxtaposition: "living" protoplast--"dead" cell wall, had to be dropped. Various attempts of re-interpretation cast, however, some doubts over the very nature of plant cell and the status of the walls within such a cell. Following a comparison of exocellular matrices of plants and animals, their position in relation to cells and organisms is analysed. A multitude of perspectives of the biological organisation of living beings is presented with particular attention paid to the cellular and organismal theories. Basic tenets and resulting corollaries of both theories are compared, and evolutionary and developmental implications are considered. Based on these data, "The Plant Body"--an organismal concept of plants and plant cells is described.
The cell-free protein biosynthesis--applications and analysis of the system.
Authors: Lamla T , Mammeri K , Erdmann V A
Published: December 2019

The in vitro protein biosynthesis has the potentials to become a powerful technology for biochemical research. Beside the determination of structure and function the in vitro evolution of proteins is also of great interest. The system described was used to produce bovine heart fatty acid binding protein (FABP) and bacterial chloramphenicol acetyltransferase (CAT) with and without fusion of the Strep-tag II affinity peptide. The proteins were purified after and during protein biosynthesis by using a StrepTactin Sepharose matrix. No significant influence of the Strep-tag and the conditions during the affinity chromatography on maturation or activity of the protein was observed. The in vitro evolution of proteins is feasible by means of ribosome display. The selection of a specific mRNA coding for a shortened FABP with a N-terminal His-tag via the accompanying protein property was shown. Goal of the selection was to bind the FABP via the His-tag on Ni(II)-IDA-agarose. After nine cycles of transcription, translation, affinity selection and RT-PCR the protein with the His-tag could be enriched 10(8)-fold. In order to correlate a possible relationship between changes in protein population and biological function studies were initiated in which 2-dimensional protein patterns of the total in vitro system were compared after 0 and 2 h reaction time. The very interesting findings are that a number of proteins disappear, while others are newly formed during protein synthesis.
Genetic variability of potato spindle tuber viroid RNA replicon.
Authors: Góra-Sochacka A , Candresse T , Zagórski W
Published: December 2019

The genetic continuity of the potato spindle tuber viroid (PSTVd) genome was analysed after infection of tomato plants with cloned cDNAs of parental strains. During the six weeks of the experiment, several new sequence variants appeared. The sequence variants detected in the progeny population induced sequence-specific disease symptoms. The PSTVd genome therefore follows the pattern expected for typical pseudo-strains propagating in plants as a population of similar sequences. Assessing further the replicon continuity, a PSTVd cDNA mutant with a deletion in the central conserved region was constructed and proven to be non-infectious. Surprisingly, in a sub-population of potato transformants expressing the same deleted PSTVd RNA an infectious viroid was detected. This suggests specific transcript conversion followed by recovery of the full-length pathogen genome.
Sequence determination and analysis of S-adenosyl-L-homocysteine hydrolase from yellow lupine (Lupinus luteus).
Authors: Brzeziński K , Janowski R , Podkowiński J , Jaskólski M
Published: December 2019

The coding sequences of two S-adenosyl-L-homocysteine hydrolases (SAHases) were identified in yellow lupine by screenig of a cDNA library. One of them, corresponding to the complete protein, was sequenced and compared with 52 other SAHase sequences. Phylogenetic analysis of these proteins identified three groups of the enzymes. Group A comprises only bacterial sequences. Group B is subdivided into two subgroups, one of which (B1) is formed by animal sequences. Subgroup B2 consist of two distinct clusters, B2a and B2b. Cluster B2b comprises all known plant sequences, including the yellow lupine enzyme, which are distinguished by a 50-residue insert. Group C is heterogeneous and contains SAHases from Archaea as well as a new class of animal enzymes, distinctly different from those in group B1.
Mg2+ ions do not induce expansion of the melted DNA region in the open complex formed by Escherichia coli RNA polymerase at a cognate synthetic Pa promoter. A quantitative KMnO4 footprinting study.
Authors: Loziiński T , Wierzchowski K L
Published: December 2019

Footprinting studies of prokaryotic open transcription complexes (RPO), based on oxidation of pyrimidine residues by KMnO4 and/or OsO4 at a single oxidant dose, have suggested that the extent of DNA melting in the transcription bubble region increases in the presence of Mg . In this work, quantitative KMnO4 footprinting in function of the oxidant dose of RPO, using Escherichia coli RNA polymerase (E(sigma)70) at a fully functional synthetic promoter Pa having -35 and -10 consensus hexamers, has been used to determine individual rate constants of oxidation of T residues in this region at 37degrees C in the absence of Mg2+ and in the presence of 10 mM MgCl2, and to evaluate therefrom the effect of Mg2+ on the extent of DNA melting. Population distributions of end-labeled DNA fragments corresponding to oxidized Ts were quantified and analyzed according to the single-hit kinetic model. Pseudo-first order reactivity rate constants, ki, thus obtained demonstrated that Mg2+ ions bound to RPO merely enhanced the reactivity of all 11 oxidizable thymines between the +3 and -11 promoter sites by a position-dependent factor: 3-4 for those located close to the transcription start point +1 in either DNA strand, and about 1.6 for those located more distantly therefrom. On the basis of these observations, we conclude that Mg2+ ions bound to RPO at Pa do not influence the length of the melted DNA region and propose that the higher reactivity of thymines results mainly from lower local repulsive electrostatic barriers to MnO4 diffusion around carboxylate binding sites in the catalytic center of RPO and promoter DNA phosphates.
Repair of gamma-ray-induced base damage in L5178Y sublines is damage type-dependent and unrelated to radiation sensitivity.
Authors: Kruszewski M , Zastawny T H , Szumiel I
Published: December 2019

The L5178Y (LY) murine lymphoma sublines LY-R and LY-S are differentially sensitive to ionizing radiation. The high radiation sensitivity of LY-S cells is related to impaired rejoining of DNA double strand breaks. We found previously that the gamma-ray-induced base damage is higher in the more radiosensitive LY-S subline. Here, we examine the role of the repair of ionizing radiation induced base damage in relation to the radiosensitivity difference of these sublines. We used the GS/MS technique to estimate the repair rates of six types of base damage in gamma-irradiated LY cells. All modified DNA bases identified in the course of this study were typical for irradiated chromatin. The total amount of initial base damage was higher in the radiation sensitive LY-S subline than in the radiation resistant LY-R subline. The repair rates of 5-OHMeUra, 5-OHCyt, 8-OHAde were similar in both cell lines, the repair rates of FapyAde and 8-OHGua were higher in the radiosensitive LY-S cell line, whereas the repair of 5-OHUra was faster in its radioresistant counter, the LY-R. Altogether, the repair rates of the y-ray-induced DNA base damage in LY sublines are related neither to the initial amounts of the damaged bases nor to the differential lethal or mutagenic effects of ionizing radiation in these sublines.
Background level of 8-oxo-2'-deoxyguanosine in lymphocyte DNA does not correlate with the concentration of antioxidant vitamins in blood plasma.
Authors: Gackowski D , Ciecierski M , Jawień A , Oliński R
Published: December 2019

Antioxidant vitamins, being effective free radical scavengers, can protect cellular DNA from oxidative damage. Therefore, in the present study we report on the relationship between basal level of 8-oxo-2'-deoxyguanosine in human lymphocyte DNA and the concentration of antioxidant vitamins (A, C and E). The average level of 8-oxo-2'-deoxyguanosine in lymphocytes of the studied group (15 males and 20 females) was 9.57 per 10(6) dG molecules. The endogenous level of ascorbic acid (vitamin C) in the plasma was, on average, 56.78 microM, while the mean concentrations of retinol (vitamin A) and alpha-tocopherol (vitamin E) were 1.24 uM and 25.74,uM, respectively. No correlations were found between individual 8-oxo-2 micro-deoxyguanosine levels in lymphocyte DNA and endogenous concentration of the vitamins.
Effects of wheat germ agglutinin and concanavalin A on the accumulation of glycosaminoglycans in pericellular matrix of human dermal fibroblasts. A comparison with insulin.
Authors: Yevdokimova N Y , Yefimov A S
Published: December 2019

The effect of insulin, wheat germ agglutinin (WGA), peanut agglutinin (PNA) and concanavalin A (ConA) on [3H]glucosamine incorporation into pericellular glycosaminoglycans (GAGs) was investigated in two lines of cultured human dermal fibroblasts. Insulin and WGA stimulated [3H]glucosamine incorporation into hyaluronic acid (HA) and heparan sulphate (HS) without any alteration of chondroitin sulphate (CS) and dermatan sulphate (DS) contents. ConA increased [3H]glucosamine incorporation into HS, CS and DS, but had no effect on [3Hglucosamine incorporation into HA. PNA affected neither the content, nor the composition of GAGs. In contrast to PNA, ConA and WGA stimulated glycolysis and demonstrated an evident antiproliferative effect on dermal fibroblasts. Thus, both the insulin-like action of WGA and ConA on cultured dermal fibroblasts and the differences between the effects of lectins on modulation of GAGs synthesis appear to be determined by their chemical structure.
Kinetics of inactivation of glutamate decarboxylase by cysteine-specific reagents.
Authors: McCormick S J , Tunnicliff G
Published: December 2019

Mercuric chloride, p-chloromercuribenzoate and 5,5'-dithiobis(2-nitrobenzoic acid) irreversibly inhibited the activity of Escherichia coli glutamate decarboxylase. Their second order rate constants for inactivation are 0.463 microM(-1) min(-1), 0.034 microM(-1) min(-1), 0.018 microM(-1) min(-1), respectively. The characteristics of the inhibition by the three thiol-group reagents supports the idea that cysteinyl residues at the binding sites for the cofactor and/or the substrate are important for enzyme activity in E. coli.
Search for polyprenols in leaves of evergreen and deciduous Ericaceae plants.
Authors: Ranjan R , Marczewski A , Chojnacki T , Hertel J , Swiezewska E
Published: December 2019

Various species and cultivars of Ericaceae family were checked for the presence of long-chain polyprenols in their leaves. In the genus Rhododendron no polyprenols were found in the ever-green species, while they were present in the deciduous type. The polyprenols were of chain-length of 14-20 isoprene residues and they occurred in the form of acetic acid esters. The polyprenol accumulation is discussed with respect to senescence of leaves.
Cladonia uncialis as a valuable raw material of biosynthetic compounds against clinical strains of bacteria and fungi
Authors: Studzińska-Sroka Elżbieta , Hanna Tomczak  , Natalia Malińska  , Marta Wrońska  , Robert Kleszcz  , Agnieszka Galanty  , Judyta Cielecka-Piontek  , Dorota Latek  , Jarosław Paluszczak
Published: December 2019

Cladonia uncialis is a lichen species with confirmed antibacterial activity and whose genome has been recently sequenced, enabling first attempts in its functional characterization. In this work, we investigated activity of the C. uncialis acetone extract (CUE) and usnic acid (UA) enantiomers against ten clinical microbial strains causing skin infections. The results showed that CUE, containing (–)-UA and squamatic acid, assayed at the same concentrations as UA, was noticeably more active than (–)-UA alone, in its pure form. The studied CUE displayed an activity that was comparable to that of (+)-UA observed for Staphylococcus epidermidis and Enterococcus faecium (18-24 mm zone of growth inhibition), but did not display any activity against fungal strains. The CUE demonstrated low cytotoxicity against HaCaT cells, in comparison to UA enantiomers, which is important for its therapeutic use. Results of the antioxidant assay (DPPH) indicated low antioxidant activity (IC50>200 µg/mL) of CUE, while the total phenolic content was 70.36 mg Gallic Acid Equivalent/g of the dry extract.
A morphological study of vertebral centra in extant species of pike, Esox (Teleostei: Esociformes)
Authors: Sinha Sinjini , Brinkman Don B , Murray Alison M.
Published: December 2019

Isolated centra of members of the Esocidae occur frequently in vertebrate microfossil localities of Late Cretaceous and early Paleocene age and are an important source of data on the early history of the family. However, morphological variation along the vertebral column can lead to incorrect interpretations of diversity if they are not recognized. To facilitate the use of centra for interpreting the diversity and distribution of esocids in Cretaceous vertebrate microfossil localities, the variation along the column in five extant species of esocids is described. Comparison with Cretaceous centra referred to the Esocidae allows identification of a series of features in which species of Esox differ from basal members of the family. These include the presence of a mid-ventral groove bordered by a pair of low budges on centra in the anterior end of the column, and antero-lateral processes on the posterior abdominal and anterior caudal centra. These differences provide a basis for recognizing early occurrences of the genus Esox in the fossil record and thus will allow centra to be used to document the timing of origin of the genus.
An Analysis of the Relationship between Teachers’ Subjective Wellbeing and Their Occupational Resilience
Authors: ÇETİN Abdullah
Published: December 2019

This research aims to determine teachers’ perception levels regarding subjective well-being and their occupational resilience, and reveal the relationship between these two variables. Having a relational survey design, the research was carried out with teachers working at schools located within the province of Şanlıurfa in Turkey. The sample held a total of 346 teachers who work at different school types during the 2017-2018 academic year. Among the participants, 163 were women and 183 were men. This research deployed “Personal Information Form”, “Teacher Subjective Wellbeing Questionnaire (TSWQ)” and “Occupational Resilience Beliefs Scale for Teacher Candidates” as data collection tools. The research data were analyzed through the use of SPSS 21 statistical package program. Frequency, arithmetic mean and standard deviation values were calculated in order to determine the teachers’ perception levels regarding the subjective well-being and their occupational resilience. Pearson-Moment Product Correlation method was used to identify whether there was a significant relationship between the teachers' subjective well-being and their occupational resilience perception levels. Besides, multiple regression analysis was performed to determine as to whether the teachers’ subjective well-being predicted their occupational resilience. Research findings revealed that the teachers’ perception levels regarding subjective well-being and occupational resilience beliefs were quite high. A medium, positive and significant relationship was noted between the teachers’ subjective well-being and their occupational resilience. The subjective well-being of the teachers was found to significantly predict the occupational resilience and explains 71% of the total variance.
Critical thinking, metacognitive skills, and cognitive learning outcomes: a correlation study in genetic studies
Authors: Miharja Fuad Jaya , Hindun Iin , Fauzi Ahmad
Published: December 2019

Understanding the concept of genetics needs to be balanced with high-level thinking skills and excellent metacognitive skills. However, efforts to measure the correlation between these two factors are still carried out partially. This study aims to determine the correlation between critical thinking, metacognitive skills, and cognitive learning outcomes in genetic studies. This study is correlational that measures the relationship between variables students’ critical thinking skills (X1), metacognitive skills (X2), and students’ cognitive learning outcomes (Y). As much as 118 students who took the genetic course were involved as the population as well as research subjects. Data collection instruments in this study consisted of tests of critical thinking skills and metacognitive skills tests as well as students' cognitive assessment sheets. The results showed that the achievement of student cognitive learning outcomes was influenced by 94% of the dependent variables examined in this study, while other variables influenced the remaining 6%. The conclusion of this study recommends that the regression models and coefficients used in this regression can be used to predict cognitive learning outcomes.
Note-taking roundhouse diagram strategy: improving student retention on body defense system concepts
Authors: Trilipi Desi , Subali Bambang , Anwar Yenny , Santoso Lucia Maria
Published: December 2019

Note-taking Roundhouse diagrams strategy is a students' conceptual framework for interesting notes. This study aims to improve student retention on body defense system material through note-taking roundhouse diagram strategy. The method used was the one-group pretest-posttest design. The sample in this study was taken by simple random sampling technique. The number of samples in this study was 30 students. The instrument used in the study was a test instrument used multiple choice. This research was conducted during six meetings. Three meetings using roundhouse diagram with pretest and posttest. After four weeks, three more meetings were held to collect the second posttest (retest). The data were analyzed by t-test statistical analysis. Based on the results of the t-test statistical analysis at a significant level α = 0.05, it can be seen that t count > t table for short-term retention and long-term retention. The retention category also showed very satisfying results. Average results of N-gain score for short and long-term retention too very good. It can be included, the note-taking roundhouse diagram strategy on the body's defense system concept can improve student retention.
Misconceptions identification on biodiversity and protist using multiple choice open reason (mcor)
Authors: Yunanda Intan , Susilo Herawati , Ghofur Abdul
Published: December 2019

This research aims to identify misconceptions of Biodiversity and Protist material. This type of research is a quantitative descriptive study. The sampling technique is purposive sampling with the provisions that misconceptions have not been identified, and students have received Biodiversity and protists. The object of the research is the students of class XI SMA Islam Malang, SMAN 1 Trenggalek, MAN 2 Lamongan, and SMAN 1 Pare, each in one class with a total of 127 students. Retrieval of data using a diagnostic instrument in the form of multiple-choice open reason (MCOR) with a total of 15 questions about Biodiversity and 15 questions about Protist. The results showed the average of misconceptions of 22,08% experienced by students on Biodiversity and the mean of misconceptions of 13,25% experienced by students on Protist. The highest misconception occurred in the threat indicator of biodiversity damage that is equal to 35,91%. Whereas for Protist, the highest misconception occurred in the sub-indicator identification of the general characteristics of Protist like an animal that is 26,28%. The conclusion is the misconception on the material of Biodiversity and Protist, including misconception type 2 or Mi-2, that is, students answer incorrectly to the core questions and are accompanied by the right reasons. A suggestion from the research that has been done is that it is necessary to develop a level three diagnostic instrument used by experts to find out students' misconceptions so that the results are more detailed. Besides, it is necessary to identify the causes of misconceptions and identify misconceptions in student handbooks on Biodiversity and Protist.
Motoric mechanism with problem based learning: impact on students’ higher order thinking skill
Authors: Nabilah Siti , Anwar Yenny , Riyanto R
Published: December 2019

This study aims to determine the effect of Problem Based Learning (PBL) model on higher-order thinking skills (HOTS) of Eleventh-grade students on motion system material in SMA Negeri 1 Indralaya Utara. The research method used was Quasi-Experimental with the research design of Non-equivalent Control Group Design. The sampling method used was Saturated Sampling Techniques. The instruments of data collection are HOTS test questions in the form of multiple choices with five answer choices in twenty-five questions. Observation instrument of learning implementation used Checklist with twelve observation items. The response instruments of students use questionnaires with a Likert scale. HOTS data were tested using the Mann-Whitney test, and then the learning implementation data and students’ response data were analyzed descriptively. This data processing uses SPSS twenty-three. Based on the results of the hypothesis test, the sig value is 0.00 (sig <0.05), which shows an effect studied was significant. The implementation of learning has Good Category, while the response of students has very good and good categories of the two types of the response of students measured. Based on the hypothesis test results can be concluded that the PBL’s model can significantly influence higher-order thinking skills of Eleventh-grade students on motion system material in SMA Negeri 1 Indralaya Utara.
Evoking the four dimensions of student knowledge in ecosystem: effectiveness of real object, web, and blended learning
Authors: Musyaddad Anwar , Suyanto Slamet
Published: December 2019

This research aims to: identify whether there is a significant difference in influence between learning media based on real object, web, and blended learning on student knowledge dimension, which covers factual, conceptual, procedural, and metacognitive knowledge on ecosystem material. It was a quasi-experiment with a pretest-posttest comparison group design. The population in this study was all students of class X MIA in SMA N 1 Bantul and SMA N 2 Bantul in semester 2 of the 2018/2019 academic year. The sample in this study used three experimental classes that were randomly selected using cluster random sampling techniques. The data were collected using tests of factual, conceptual, procedural, and metacognitive knowledge and student's metacognitive questionnaire. These data were then analyzed using the Multivariate Analysis of Variants test. The results demonstrate that: (1) learning media based on real object, web and blended learning affect the student’s factual, conceptual, procedural and metacognitive knowledge, (2) there is a significant difference in effectiveness between learning media based on real object, web and blended learning on students' factual, conceptual and metacognitive knowledge, (3) there is no significant difference in effectiveness between learning media based on real object, web and blended learning on students' procedural knowledge. Based on this, it can be recommended that biology learning media based on real object and blended learning can be applied by the teacher to improve students' factual, conceptual, and metacognitive knowledge.
Exploring respiratory system to improve biological learning motivation: resysmart media application
Authors: Ningsih Luthfi Rahayu , Rusdi R , Miarsyah Mieke
Published: December 2019

Resysmart is an interactive media on the Respiratory system material, which stands for Smart Respiratory System. This media uses the Adobe Flash CC application. This study aims to measure the effectiveness of Resysmart interactive media in increasing learning motivation. This study used a quasi-experimental method with a non-equivalent control group design. The learning model used was Problem Based Learning. Samples in this study were students of the eleventh grade of social class at SMAN 3 Cibinong, Indonesia, as many as 60 people. The results showed that there was an increase in learning motivation in the experimental class with a pre-test value of 69.20 and a post-test value of 82.00, with a Gain Score of 12.80. N-Gain Score in the experimental class was 0.42, which was classified as moderate, while the control class is 0.08, which was classified as low. After an independent t-test, a significance value of 0.00 <0.05 was obtained, which means there was a significant difference in learning motivation between Resysmart interactive media classes with classes that didn't use Resysmart interactive media. This study concluded that Resysmart interactive learning media effectively increases students' learning motivation. Based on these results, it was expected that this interactive media could be developed in other materials so that students' learning motivation can be maintained and improved.
Optimizing the potential of children learning in science (clis) with brain gym: review on human circulatory concepts
Authors: Sele Yunawati
Published: December 2019

Learning innovation is an effort to improve the quality of learning. One form of innovation is the integration of brain gym learning techniques and various learning models, including the Children Learning in Science (CLIS) model.  However, so far, there has never been a study of learning innovations through the integration of brain gym techniques with the CLIS model. This study aims at finding out the optimizing of the Children Learning in Science (CLIS) models with brain gym to empower students' human circulatory conception. This study is quasi-experimental research of pretest-posttest Nonequivalent control group design. The population of this study was the students of class XI MIA SMA Negeri 7 Kupang, which consisted of 173 students. The sample of this study were students of class XI MIA1 and XI MIA 2, which consisted of 61 students. The instrument used was a test of human circulatory conception developed by Andriani (2017). The results showed that the increase in students' human circulatory conception in CLIS learning combined with a gym is 40.61% higher than the increase in students' human circulatory conception in CLIS learning. It can be concluded that the application of brain gym can optimize Children Learning In Science (CLIS) potential in empowering students' human circulatory conception.