scholarly journals Structural analysis of leucine, lysine and tryptophan mitochondrial tRNA of nesting turtles Caretta caretta (Testudines: Chelonioidea) in the Colombian Caribbean

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9204
Author(s):  
Harvey Infante-Rojas ◽  
Leonardo Marino-Ramirez ◽  
Javier Hernández-Fernández
Keyword(s):  
Functional Properties ◽  
Structural Changes ◽  
Protein Biosynthesis ◽  
Variable Region ◽  
Caretta Caretta ◽  
Nucleotide Position ◽  
Mitochondrial Trna ◽  
3D Structures ◽  
Mitochondrial Transfer ◽  
2D And 3D

The understanding of the functional properties of mitochondrial transfer RNA (mt tRNAs) depend on the knowledge of its structure. tRNA acts as an interface between polynucleotides and polypeptides thus, they are key molecules in protein biosynthesis. The tRNA molecule has a functional design and, given its importance in the translation of mitochondrial genes, it is plausible that modifications of the structure can affect the synthesis of proteins and the functional properties of the mitochondria. In a previous work, the mitochondrial genome of an individual of the nesting Caretta caretta of the Colombian Caribbean was obtained, where specific mutations were identified in the only tRNALeu (CUN), tRNATrp and tRNALys genes. In order to analyze the effect of these mutations on these three mt tRNAs, the prediction of 2D and 3D structures was performed. Genes were sequenced in 11 nesting loggerhead turtles from the Colombian Caribbean. Two-dimensional structures were inferred using the ARWEN program, and three-dimensional structures were obtained with the RNA Composer 3D program. Two polymorphisms were identified in tRNATrp and another one was located in tRNALys, both specific to C. caretta. The thymine substitution in nucleotide position 14 of tRNATrp could constitute an endemic polymorphism of the nesting colony of the Colombian Caribbean. Two 2D and three 3D patterns were obtained for tRNATrp. In the case of tRNALys and tRNALeu 2D and 3D structures were obtained respectively, which showed compliance to canonical structures, with 4 bp in the D-arm, 4–5 bp in the T-arm, and 5 bp in the anticodon arm. Moderate deviations were found, such as a change in the number of nucleotides, elongation in loops or stems and non-Watson–Crick base pairing: adenine–adenine in stem D of tRNATrp, uracil–uracil and adenine–cytosine in the acceptor arm of the tRNALys and cytosine–cytosine in the anticodon stem of the tRNALeu. In addition, distortions or lack of typical interactions in 3D structures gave them unique characteristics. According to the size of the variable region (4–5 nt), the three analyzed tRNAs belong to class I. The interactions in the three studied tRNAs occur mainly between D loop—variable region, and between spacer bases—variable region, which classifies them as tRNA of typology II. The polymorphisms and structural changes described can, apparently, be post-transcriptionally stabilized. It will be crucial to perform studies at the population and functional levels to elucidate the synthetic pathways affected by these genes. This article analyses for the first time the 1D, 2D and 3D structures of the mitochondrial tRNALys, tRNATrp and tRNALeu in the loggerhead turtle.

scholarly journals Analysis of menstrual and reproductive function in women with infertility and varicose gonadic veins

2018 ◽  
Vol 22 (4) ◽  
pp. 660-665
Author(s):  
O.V. Astakhova ◽  
O.B. Malinina ◽  
A.M. Grigorenko
Keyword(s):  
Menstrual Cycle ◽  
Functional Properties ◽  
Structural Changes ◽  
Varicose Veins ◽  
Venous Blood ◽  
Reproductive Function ◽  
Uterine Bleeding ◽  
Endocrine Function ◽  
Venous Blood Flow ◽  
Significant Percentage

The problem of reproductive health in Ukraine over the last decade has become very important. The greatest clinical interest is infertility, which is accompanied by a violation of the ovulatory function of the ovaries due to hypothalamic-pituitary-ovarian failure. Sustained anovulation for a long time, as well as the lack of adequate correction of menstrual disorders, lead to the development of endocrine-dependent gynecological diseases, the manifestation of which is primary or secondary infertility. Increased flow of venous blood through the ovarian veins is accompanied by phlebostasis and phlebohypertension in the venous sector of the internal genital organs. Increasing the viscosity and rheological properties of blood that occurs at the same time leads to a deterioration of transcapillary metabolism and transport of oxygen to tissues. In the ischemic ovary, degenerative changes in the follicular apparatus, yellow bodies, followed by spreading to all the ovarian structural elements, which leads to its atrophy and reduced functional properties. Considering the importance of venous blood flow in the development of hormonal imbalance as a result of a violation of the endocrine function of the ovaries, the purpose of our study was to assess the menstrual and reproductive function of infertile women against the background of varicose veins. The reproductive function of women with infertility and varicose changes in ovarian veins is represented by a significant percentage of unauthorized miscarriages (41.9%) in the period of pregnancy after 6 weeks (30.6%). In patients with varicose veins in the ovaries, there was a tendency to increase the duration of infertility compared with patients without varicose dilatation of ovarian veins, which may indirectly indicate more significant functional and structural changes in the reproductive organs. In women, both the primary and the comparator groups are predominantly the late and early menarche, but the rates in groups differ slightly in their direction in women with infertility and varicose veins in the ovaries, although they do not reach statistically significant values. The menstrual function of women in the main group is characterized by a regular menstrual cycle (77.5%), regular duration (43.6%) with excessive blood loss during menstruation (54.8%) and a duration of more than 6 days (50.1%) with acyclic uterine bleeding (37.1%), dysmenorrhea (56.4%) and premenstrual disorders (51.6%), which significantly impairs the quality of life of women. At the same time, the violation of the menstrual cycle in the form of its shortening of 16,1% and acyclic uterine bleeding — 6,5%, was gradually increasing with age and was statistically significant against women from the comparison group. Conclusion in the analysis of clinical characteristics, the more significant percentage of changes in the menstrual cycle, reproductive function in women with functional infertility and varicose veins of the ovary compared with patients with infertility without structural changes in ovarian veins indicates the significant importance of venous hemodynamics in the functional properties of the ovary.

Ecotoxicity prediction by adaptive fuzzy partitioning: comparing descriptors computed on 2D and 3D structures

2006 ◽  
Vol 17 (2) ◽  
pp. 225-251 ◽  
Author(s):  
N. Piclin ◽  
M. Pintore ◽  
C. Wechman ◽  
A. Roncaglioni ◽  
E. Benfenati ◽  
...  
Keyword(s):  
3D Structures ◽  
Adaptive Fuzzy ◽  
Fuzzy Partitioning ◽  
2D And 3D

scholarly journals Understanding the impact of moderate-intensity pulsed electric fields (MIPEF) on structural and functional characteristics of pea, rice and gluten concentrates

2020 ◽  
Vol 13 (12) ◽  
pp. 2145-2155
Author(s):  
Sofia Melchior ◽  
Sonia Calligaris ◽  
Giulia Bisson ◽  
Lara Manzocco
Keyword(s):  
Electric Fields ◽  
Functional Properties ◽  
Structural Changes ◽  
Pulsed Electric Fields ◽  
Moderate Intensity ◽  
Intramolecular Rearrangement ◽  
Structural Modifications ◽  
Protein Concentrates ◽  
Protein Nature ◽  
The Impact

Abstract Aim The effect of moderate-intensity pulsed electric fields (MIPEF) was evaluated on vegetable protein concentrates from pea, rice, and gluten. Methods Five percent (w/w) suspensions of protein concentrates (pH 5 and 6) were exposed to up to 60,000 MIPEF pulses at 1.65 kV/cm. Both structural modifications (absorbance at 280 nm, free sulfhydryl groups, FT-IR-spectra) and functional properties (solubility, water and oil holding capacity, foamability) were analyzed. Results MIPEF was able to modify protein structure by inducing unfolding, intramolecular rearrangement, and formation of aggregates. However, these effects were strongly dependent on protein nature and pH. In the case of rice and pea samples, structural changes were associated with negligible modifications in functional properties. By contrast, noticeable changes in these properties were observed for gluten samples, especially after exposure to 20,000 pulses. In particular, at pH 6, an increase in water and oil holding capacity of gluten was detected, while at pH 5, its solubility almost doubled. Conclusion These results suggest the potential of MIPEF to steer structure of proteins and enhance their technological functionality.

scholarly journals Pre-Clinical Drug Testing in 2D and 3D Human In Vitro Models of Glioblastoma Incorporating Non-Neoplastic Astrocytes: Tunneling Nano Tubules and Mitochondrial Transfer Modulates Cell Behavior and Therapeutic Response

2019 ◽  
Vol 20 (23) ◽  
pp. 6017 ◽  
Author(s):  
Prospero Civita ◽  
Diana M. Leite ◽  
Geoffrey Pilkington
Keyword(s):  
Drug Resistance ◽  
Hyaluronic Acid ◽  
Drug Testing ◽  
Tunneling Nanotubes ◽  
Mitochondrial Transfer ◽  
Culture Models ◽  
And Migration ◽  
2D And 3D

The role of astrocytes in the glioblastoma (GBM) microenvironment is poorly understood; particularly with regard to cell invasion and drug resistance. To assess this role of astrocytes in GBMs we established an all human 2D co-culture model and a 3D hyaluronic acid-gelatin based hydrogel model (HyStem™-HP) with different ratios of GBM cells to astrocytes. A contact co-culture of fluorescently labelled GBM cells and astrocytes showed that the latter promotes tumour growth and migration of GBM cells. Notably, the presence of non-neoplastic astrocytes in direct contact, even in low amounts in co-culture, elicited drug resistance in GBM. Recent studies showed that non-neoplastic cells can transfer mitochondria along tunneling nanotubes (TNT) and rescue damaged target cancer cells. In these studies, we explored TNT formation and mitochondrial transfer using 2D and 3D in vitro co-culture models of GBM and astrocytes. TNT formation occurs in glial fibrillary acidic protein (GFAP) positive “reactive” astrocytes after 48 h co-culture and the increase of TNT formations was greater in 3D hyaluronic acid-gelatin based hydrogel models. This study shows that human astrocytes in the tumour microenvironment, both in 2D and 3D in vitro co-culture models, could form TNT connections with GBM cells. We postulate that the association on TNT delivery non-neoplastic mitochondria via a TNT connection may be related to GBM drug response as well as proliferation and migration.

scholarly journals On the structural stability and optical properties of germanium-based schwarzites: a density functional theory investigation

2020 ◽  
Vol 22 (28) ◽  
pp. 16286-16293
Author(s):  
Raphael M. Tromer ◽  
Levi C. Felix ◽  
Cristiano F. Woellner ◽  
Douglas S. Galvao
Keyword(s):  
Density Functional Theory ◽  
Optical Properties ◽  
Structural Stability ◽  
Density Functional ◽  
Functional Theory ◽  
3D Structures ◽  
Carbon Allotropes ◽  
2D And 3D

Since graphene was synthesized the interest in building new 2D and 3D structures based on carbon allotropes has been growing every day.

RiboVision suite for visualization and analysis of ribosomes

2014 ◽  
Vol 169 ◽  
pp. 195-207 ◽  
Author(s):  
Chad R. Bernier ◽  
Anton S. Petrov ◽  
Chris C. Waterbury ◽  
James Jett ◽  
Fengbo Li ◽  
...  
Keyword(s):  
Molecular Interactions ◽  
Ribosomal Proteins ◽  
Secondary Structures ◽  
Macromolecular Complex ◽  
Analysis Tool ◽  
Complex Data ◽  
Helical Structures ◽  
Haloarcula Marismortui ◽  
3D Structures ◽  
2D And 3D

RiboVision is a visualization and analysis tool for the simultaneous display of multiple layers of diverse information on primary (1D), secondary (2D), and three-dimensional (3D) structures of ribosomes. The ribosome is a macromolecular complex containing ribosomal RNA and ribosomal proteins and is a key component of life responsible for the synthesis of proteins in all living organisms. RiboVision is intended for rapid retrieval, analysis, filtering, and display of a variety of ribosomal data. Preloaded information includes 1D, 2D, and 3D structures augmented by base-pairing, base-stacking, and other molecular interactions. RiboVision is preloaded with rRNA secondary structures, rRNA domains and helical structures, phylogeny, crystallographic thermal factors,etc.RiboVision contains structures of ribosomal proteins and a database of their molecular interactions with rRNA. RiboVision contains preloaded structures and data for two bacterial ribosomes (Thermus thermophilusandEscherichia coli), one archaeal ribosome (Haloarcula marismortui), and three eukaryotic ribosomes (Saccharomyces cerevisiae,Drosophila melanogaster, andHomo sapiens). RiboVision revealed several major discrepancies between the 2D and 3D structures of the rRNAs of the small and large subunits (SSU and LSU). Revised structures mapped with a variety of data are available in RiboVision as well as in a public gallery (http://apollo.chemistry.gatech.edu/RibosomeGallery). RiboVision is designed to allow users to distill complex data quickly and to easily generate publication-quality images of data mapped onto secondary structures. Users can readily import and analyze their own data in the context of other work. This package allows users to import and map data from CSV files directly onto 1D, 2D, and 3D levels of structure. RiboVision has features in rough analogy with web-based map services capable of seamlessly switching the type of data displayed and the resolution or magnification of the display. RiboVision is available at http://apollo.chemistry.gatech.edu/RiboVision.

A new family of 1D, 2D and 3D frameworks aggregated from Ni5, Ni4 and Ni7 building units: synthesis, structure, and magnetism

2016 ◽  
Vol 45 (22) ◽  
pp. 9267-9278 ◽  
Author(s):  
Ya-Hui Liu ◽  
Li-Ping Lu ◽  
Miao-Li Zhu ◽  
Si-Si Feng ◽  
Feng Su
Keyword(s):  
Tricarboxylic Acid ◽  
Ferromagnetic Coupling ◽  
Magnetic Studies ◽  
3D Structures ◽  
New Family ◽  
Magnetic Chain ◽  
2D And 3D

Three polynuclear nickel(ii) complexes with 1D, 2D and 3D structures are controlled by carboxylate bridges of biphenyl-3,4′,5-tricarboxylic acid. Magnetic studies reveal that the polymers have ferromagnetic coupling features for 1 and 2 and an alternating magnetic chain behavior for 3.

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