scholarly journals Interaction of Antimicrobial Peptide Ponericin W1, Thanatin, and Mastatopara-S with Geotrichum citri-aurantii Genomic DNA

Foods ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1919
Author(s):  
Hongyan Zhang ◽  
Sha Liu ◽  
Xindan Li ◽  
Wenjun Wang ◽  
Lili Deng ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Double Helix ◽  
Membrane Integrity ◽  
Citrus Fruit ◽  
Base Pairs ◽  
Spectra Analysis ◽  
Dna And Rna ◽  
Visible Spectra ◽  
Double Helix Structure

Antimicrobial peptides of mastatopara-S (M-S), thanatin, and ponericin W1(P W1) were able to disrupt the membrane integrity and alter the morphology of the hyphae of Geotrichum citri-aurantii and then reduced the sour rot of citrus fruit. In order to understand the mechanisms of thanatin, P W1 and M-S other than membrane disruption, the interaction betwixt the peptides and G. citri-aurantii DNA were investigated in this research. The laser confocal microscopy found that P W1, thanatin, and M-S could penetrate the cell membrane. Gel retardation assay demonstrated that P W1, thanatin, and M-S could bind to the G. citri-aurantii genomic DNA in vitro. UV-visible spectra and fluorescence spectra analysis further confirmed that the peptides can bind to the DNA, and then insert into the base pairs in the DNA helix, followed by wrecking the double-helix structure. In addition, M-S, thanatin, and P W1 can suppress the synthesis of DNA and RNA of G. citri-aurantii.

scholarly journals James Watson’s genius (dedicated to the 90th birth anniversary)

2018 ◽  
Vol 22 ◽  
pp. 363-367
Author(s):  
H. B. Humeniuk ◽  
M. Z. Mosula ◽  
I. B. Chen ◽  
N. M. Drobyk
Keyword(s):  
Molecular Biology ◽  
Nobel Prize ◽  
Cell Biology ◽  
Recombinant Dna ◽  
Double Helix ◽  
X Rays ◽  
Recombinant Dna Technology ◽  
Molecular Oncology ◽  
Double Helix Structure

The scientific and organizational activities of the worldwide known scientist in the field of molecular biology James Dewey Watson were described in this article. 55 years ago James Watson and Francis Crick made one of the key discoveries of the twentieth century. They have found that DNA has a double helix structure. This discovery was based on the X-rays patterns obtained by Maurice Wilkson and Rosalind Franklin. Subsequently, this DNA model had been proved, and J. Watson and F. Crick were awarded with the Nobel Prize in Physiology or Medicine in 1962. Since, our knowledge of the main molecule of life has been greatly expanded. A significant flowering of molecular genetics has began: synthesis of RNA and DNA in vitro, decoding of genetic code, recombinant DNA technology, genetic engineering, sequencing of genomes and post genomic technologies. James Watson is one of the authors of the cell biology classic textbook “Molecular Biology of the Cell”. In addition, he has developed the current areas of molecular biology such as  molecular oncology and molecular neurobiology. Today genomes of different animals and humans have been decoded and the functions of many genes have been determined. But at present still unknown how the DNA starts and how it affects the work of the organs and the organism as a system. Keywords: James Watson, DNA structure, Nobel Prize in physiology or medicine, Molecular Biology of the Cell.

scholarly journals The Bacterial Amyloid-Like Hfq Promotes In Vitro DNA Alignment

2019 ◽  
Vol 7 (12) ◽  
pp. 639 ◽  
Author(s):  
Frank Wien ◽  
Denis Martinez ◽  
Etienne Le Brun ◽  
Nykola C. Jones ◽  
Søren Vrønning Hoffmann ◽  
...  
Keyword(s):  
Double Helix ◽  
Local Alignment ◽  
Gram Negative Bacteria ◽  
Direct Role ◽  
Dna Compaction ◽  
Functional Consequences ◽  
Double Helix Structure ◽  
Dna Alignment ◽  
Precise Role

The Hfq protein is reported to be involved in environmental adaptation and virulence of several bacteria. In Gram-negative bacteria, Hfq mediates the interaction between regulatory noncoding RNAs and their target mRNAs. Besides these RNA-related functions, Hfq is also associated with DNA and is a part of the bacterial chromatin. Its precise role in DNA structuration is, however, unclear and whether Hfq plays a direct role in DNA-related processes such as replication or recombination is controversial. In previous works, we showed that Escherichia coli Hfq, or more precisely its amyloid-like C-terminal region (CTR), induces DNA compaction into a condensed form. In this paper, we evidence a new property for Hfq; precisely we show that its CTR influences double helix structure and base tilting, resulting in a strong local alignment of nucleoprotein Hfq:DNA fibers. The significance of this alignment is discussed in terms of chromatin structuration and possible functional consequences on evolutionary processes and adaptation to environment.

Procreative Liberty in the Era of Genomics

2003 ◽  
Vol 29 (4) ◽  
pp. 439-487
Author(s):  
John A. Robertson
Keyword(s):  
Human Genome ◽  
Evolutionary Biology ◽  
Prime Minister ◽  
Double Helix ◽  
Genetic Mutations ◽  
Base Pairs ◽  
Procreative Liberty ◽  
Helix Structure ◽  
Actual Sequence ◽  
Double Helix Structure

Twentieth century biology began with the rediscovery of Gregor Mendel's work on peas and ended with the sequencing of the human genome. In between came Thomas Morgan's studies of fruit flies, the grand synthesis between genetics and evolutionary biology in the 1930s, and Watson and Crick's publication in 1953 of the double helix structure of deoxyribose nucleic acid (“DNA”), the substance in the nucleus of cells, which carries the genetic code of all eukaryotic life.The genetics of the second half of the century focused on learning how DNA coded for proteins, how to splice, clone, and recombine pieces of DNA, and how genetic mutations caused disease. In the late 1980s, a project to identify the actual sequence of all 3.2 billion base pairs of the human genome began. In June 1999, President Clinton and Prime Minister Blair announced that a working draft of the human genome was complete, with the final completed draft to 99.9% accuracy expected in May 2003, fifty years after the publication of Watson and Crick's landmark paper.

Moving one DNA double helix through another by a type II DNA topoisomerase: the story of a simple molecular machine

1998 ◽  
Vol 31 (2) ◽  
pp. 107-144 ◽  
Author(s):  
JAMES C. WANG
Keyword(s):  
Double Helix ◽  
Viscous Drag ◽  
Helical Axis ◽  
Replication Rate ◽  
Mechanical Problem ◽  
Base Pairs ◽  
Dna Topoisomerase ◽  
Helical Geometry ◽  
Double Helix Structure ◽  
Dna Double Helix

The discovery of the double helix structure of DNA led immediately to questions on the mechanics of unravelling its intertwined strands during replication. If a parental DNA is to be duplicated into two progeny molecules by separating its two strands and copying each, then the strands must untwine rapidly during replication (Watson & Crick, 1953).That DNA indeed replicates in such a semiconservative fashion was soon demonstrated by the Meselson–Stahl experiment (1958). At first, it appeared that the unravelling of the intertwined strands should not pose an insurmountable mechanical problem. The two strands at one end of a linear DNA, for example, can be pulled apart with concomitant rotation of the double-stranded portion of the molecule around its helical axis. If the strands of a DNA double helix are to separate at an estimated replication rate of 100000 base pairs (bp) per minute, then the speed of this rotation would be 10000 revolutions per minute from the 10 bp per turn helical geometry of the double helix. This speed, though impressive, seemed reasonable: owing to the slender rod-like shape of the double helix, the estimated viscous drag for this rotational motion is actually rather modest (Meselson, 1972).

DNA Inspirited Rational Construction of Nonconventional Luminophores with Efficient and Color-Tunable Afterglow

2020 ◽  
Author(s):  
Yunzhong Wang ◽  
Saixing Tang ◽  
Yating Wen ◽  
Shuyuan Zheng ◽  
Bing Yang ◽  
...  
Keyword(s):  
Rational Design ◽  
Room Temperature ◽  
Double Helix ◽  
Mechanical Grinding ◽  
Room Temperature Phosphorescence ◽  
Color Tunable ◽  
Potential Applications ◽  
Rational Construction ◽  
Double Helix Structure ◽  
Made In

<div>Persistent room-temperature phosphorescence (p-RTP) from pure organics is attractive </div><div>due to its fundamental importance and potential applications in molecular imaging, </div><div>sensing, encryption, anticounterfeiting, etc.1-4 Recently, efforts have been also made in </div><div>obtaining color-tunable p-RTP in aromatic phosphors5 and nonconjugated polymers6,7. </div><div>The origin of color-tunable p-RTP and the rational design of such luminogens, </div><div>particularly those with explicit structure and molecular packing, remain challenging. </div><div>Noteworthily, nonconventional luminophores without significant conjugations generally </div><div>possess excitation-dependent photoluminescence (PL) because of the coexistence of </div><div>diverse clustered chromophores6,8, which strongly implicates the possibility to achieve </div><div>color-tunable p-RTP from their molecular crystals assisted by effective intermolecular </div><div>interactions. Here, inspirited by the highly stable double-helix structure and multiple </div><div>hydrogen bonds in DNA, we reported a series of nonconventional luminophores based on </div><div>hydantoin (HA), which demonstrate excitation-dependent PL and color-tunable p-RTP </div><div>from sky-blue to yellowish-green, accompanying unprecedentedly high PL and p-RTP </div><div>efficiencies of up to 87.5% and 21.8%, respectively. Meanwhile, the p-RTP emissions are </div><div>resistant to vigorous mechanical grinding, with lifetimes of up to 1.74 s. Such robust, </div><div>color-tunable and highly efficient p-RTP render the luminophores promising for varying </div><div>applications. These findings provide mechanism insights into the origin of color-tunable </div><div>p-RTP, and surely advance the exploitation of efficient nonconventional luminophores.</div>

IMPACT OF SORBITOL- INDUCED OSMOTIC STRESS ON SOME BIOCHEMICAL TRAITS OF POTATO IN VITRO

2020 ◽  
Vol 51 (4) ◽  
pp. 1038-1047
Author(s):  
Mawia & et al.
Keyword(s):  
Ascorbic Acid ◽  
Osmotic Stress ◽  
Cytoplasmic Membrane ◽  
Genotypic Variation ◽  
Membrane Damage ◽  
Membrane Integrity ◽  
Culture Collection ◽  
Nutritive Medium ◽  
Starting Point

This study had as principal objective identification of osmotic-tolerant potato genotypes by using "in vitro" tissue culture and sorbitol as a stimulating agent, to induce water stress, which was added to the  culture nutritive medium in different concentration (0,50, 110, 220, 330 and 440 mM).  The starting point was represented by plantlets culture collection, belonging to eleven potato genotypes: Barcelona, Nectar, Alison, Jelly, Malice, Nazca, Toronto, Farida, Fabulla, Colomba and Spunta. Plantlets were multiplied between two internodes to obtain microcuttings (in sterile condition), which were inoculated on medium. Sorbitol-induced osmotic stress caused a significant reduction in the ascorbic acid, while the concentration of proline, H2O2 and solutes leakage increased compared with the control. Increased the proline content prevented lipid peroxidation, which played a pivotal role in the maintenance of membrane integrity under osmotic stress conditions. The extent of the cytoplasmic membrane damage depends on osmotic stress severity and the genotypic variation in the maintenance of membranes stability was highly associated with the ability of producing more amounts of osmoprotectants (proline) and the non-enzymic antioxidant ascorbic acid in response to osmotic stress level. The results showed that the genotypes Jelly, Nectar, Allison, Toronto, and Colomba are classified as highly osmotic stress tolerant genotypes, while the genotypes Nazca and Farida are classified as osmotic stress susceptible ones.

scholarly journals A high-throughput screening method for evolving a demethylase enzyme with improved and new functionalities

2020 ◽  
Author(s):  
Yuru Wang ◽  
Christopher D Katanski ◽  
Christopher Watkins ◽  
Jessica N Pan ◽  
Qing Dai ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Screening Method ◽  
Targeted Mutagenesis ◽  
Rna Repair ◽  
Dna And Rna ◽  
Modified Dna ◽  
Dna Substrates ◽  
Trna Sequencing

Abstract AlkB is a DNA/RNA repair enzyme that removes base alkylations such as N1-methyladenosine (m1A) or N3-methylcytosine (m3C) from DNA and RNA. The AlkB enzyme has been used as a critical tool to facilitate tRNA sequencing and identification of mRNA modifications. As a tool, AlkB mutants with better reactivity and new functionalities are highly desired; however, previous identification of such AlkB mutants was based on the classical approach of targeted mutagenesis. Here, we introduce a high-throughput screening method to evaluate libraries of AlkB variants for demethylation activity on RNA and DNA substrates. This method is based on a fluorogenic RNA aptamer with an internal modified RNA/DNA residue which can block reverse transcription or introduce mutations leading to loss of fluorescence inherent in the cDNA product. Demethylation by an AlkB variant eliminates the blockage or mutation thereby restores the fluorescence signals. We applied our screening method to sites D135 and R210 in the Escherichia coli AlkB protein and identified a variant with improved activity beyond a previously known hyperactive mutant toward N1-methylguanosine (m1G) in RNA. We also applied our method to O6-methylguanosine (O6mG) modified DNA substrates and identified candidate AlkB variants with demethylating activity. Our study provides a high-throughput screening method for in vitro evolution of any demethylase enzyme.

scholarly journals Biological Effects of XyloCore, a Glucose Sparing PD Solution, on Mesothelial Cells: Focus on Mesothelial-Mesenchymal Transition, Inflammation and Angiogenesis

Nutrients ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 2282
Author(s):  
Valentina Masola ◽  
Mario Bonomini ◽  
Maurizio Onisto ◽  
Pietro Manuel Ferraro ◽  
Arduino Arduini ◽  
...  
Keyword(s):  
Endothelial Cell ◽  
Cell Viability ◽  
Biological Effects ◽  
Membrane Integrity ◽  
Glucose Content ◽  
Mesenchymal Transition ◽  
Low Glucose ◽  
Endothelial To Mesenchymal Transition ◽  
Osmotic Agents

Glucose-based solutions remain the most used osmotic agents in peritoneal dialysis (PD), but unavoidably they contribute to the loss of peritoneal filtration capacity. Here, we evaluated at a molecular level the effects of XyloCore, a new PD solution with a low glucose content, in mesothelial and endothelial cells. Cell viability, integrity of mesothelial and endothelial cell membrane, activation of mesothelial and endothelial to mesenchymal transition programs, inflammation, and angiogenesis were evaluated by several techniques. Results showed that XyloCore preserves mesothelial and endothelial cell viability and membrane integrity. Moreover XyloCore, unlike glucose-based solutions, does not exert pro-fibrotic, -inflammatory, and -angiogenic effects. Overall, the in vitro evidence suggests that XyloCore could represent a potential biocompatible solution promising better outcomes in clinical practice.

An In Vitro Cytotoxicity Assay Using Rat Hepatocytes and MTT and Coomassie Blue Dye as Indicators

1991 ◽  
Vol 19 (3) ◽  
pp. 352-360
Author(s):  
Kazuhiko Otoguro ◽  
Kanki Komiyama ◽  
Satoshi Ωmura ◽  
Charles A. Tyson
Keyword(s):  
Mtt Assay ◽  
Membrane Integrity ◽  
Cell Number ◽  
Cellular Protein ◽  
Blue Dye ◽  
Tetrazolium Salt ◽  
Sprague Dawley ◽  
Lactate Dehydrogenase Activity ◽  
Coomassie Blue

Isolated hepatocytes from male Sprague-Dawley rats suspended in culture medium supplemented with either 0.2 or 2% bovine serum albumin (BSA) were allowed to attach to collagen coated 96-well dishes. Ten test chemicals from the MEIC list and salicylic acid were added individually to the dishes, and at the end of 24 and 48 hours, cytotoxicity was determined by measuring MTT (tetrazolium salt) reduction (mitochondrial integrity) and total cellular protein using Coomassie blue dye (reflecting cell number). Total cellular lactate dehydrogenase activity was also determined in some experiments, as an indicator of plasma membrane integrity. The relative toxicities of the test chemicals were quantified by the estimation of EC10, EC20 and EC50 values for each parameter. Except for one chemical, digoxin, in the MTT assay, cytotoxic potency increased with incubation time. The hepatocytes tended to be more sensitive to the chemicals in medium containing 0.2% BSA than in medium containing 2% BSA. Simple linear regression analyses of the log transformed data from the MTT assay versus log oral LD50 in rats for the test chemicals gave the best results using EC10 at 24 hours (r2 = 0.86). With protein as the cytotoxic indicator, the best results were obtained with EC values in the medium containing 2% BSA, again at 24 hours (r2 = 0.83). These results suggest that the MTT and Coomassie blue dye assays could be useful indicators for testing the cytotoxic potential of chemicals in rat hepatocyte cultures.

scholarly journals Seminal Plasma: Relevant for Fertility?

2021 ◽  
Vol 22 (9) ◽  
pp. 4368
Author(s):  
Heriberto Rodriguez-Martinez ◽  
Emilio A. Martinez ◽  
Juan J. Calvete ◽  
Fernando J. Peña Vega ◽  
Jordi Roca
Keyword(s):  
Seminal Plasma ◽  
Current Knowledge ◽  
Inorganic Ions ◽  
Vitro Fertilization ◽  
Dna And Rna ◽  
Model Animal ◽  
Sexual Glands ◽  
Species Specific

Seminal plasma (SP), the non-cellular component of semen, is a heterogeneous composite fluid built by secretions of the testis, the epididymis and the accessory sexual glands. Its composition, despite species-specific anatomical peculiarities, consistently contains inorganic ions, specific hormones, proteins and peptides, including cytokines and enzymes, cholesterol, DNA and RNA—the latter often protected within epididymis- or prostate-derived extracellular vesicles. It is beyond question that the SP participates in diverse aspects of sperm function pre-fertilization events. The SP also interacts with the various compartments of the tubular genital tract, triggering changes in gene function that prepares for an eventual successful pregnancy; thus, it ultimately modulates fertility. Despite these concepts, it is imperative to remember that SP-free spermatozoa (epididymal or washed ejaculated) are still fertile, so this review shall focus on the differences between the in vivo roles of the SP following semen deposition in the female and those regarding additions of SP on spermatozoa handled for artificial reproduction, including cryopreservation, from artificial insemination to in vitro fertilization. This review attempts, including our own results on model animal species, to critically summarize the current knowledge of the reproductive roles played by SP components, particularly in our own species, which is increasingly affected by infertility. The ultimate goal is to reconcile the delicate balance between the SP molecular concentration and their concerted effects after temporal exposure in vivo. We aim to appraise the functions of the SP components, their relevance as diagnostic biomarkers and their value as eventual additives to refine reproductive strategies, including biotechnologies, in livestock models and humans.

Sign in / Sign up

Export Citation Format

Share Document