Open Access DNA, Rna and Amino Acid Sequences: The Consequences and Solutions for the International Regulation of Access and Benefit Sharing

(1) Background: Fungi contain several millions of species, and the diversification of fungal genes has been achieved by speciation, gene duplication, and horizontal gene transfer. Although several databases provide information on orthologous and paralogous events, these databases show no information on biases between gene mutation and speciation. Here, we designed the Gcorn fungi database to better understand such biases. (2) Methods: Amino acid sequences of fungal genes in 249 species, which contain 2,345,743 sequences, were used for this database. Homologous genes were grouped at various thresholds of the homology index, which was based on the percentages of gene mutations. By grouping genes that showed highly similar homology indices to each other, we showed functional and evolutionary traits in the phylogenetic tree depicted for the gene of interest. (3) Results: Gcorn fungi provides well-summarized information on the evolution of a gene lineage and on the biases between gene evolution and speciation, which are quantitatively identified by the Robinson–Foulds metric. The database helps users visualize these traits using various depictions. (4) Conclusions: Gcorn fungi is an open access database that provides a variety of information with which to understand gene function and evolution.

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Compatible or incompatible? DSI, open access, and benefit-sharing

10.31235/osf.io/nw8g9 ◽

2021 ◽

Author(s):

Rodrigo Sara ◽

Andrew Lee Hufton ◽

Amber Hartman Scholz

Keyword(s):

Open Access ◽

Scientific Community ◽

Biological Diversity ◽

Benefit Sharing ◽

Convention On Biological Diversity ◽

Sequence Information ◽

Policy Options ◽

Access And Benefit Sharing ◽

Key Points ◽

Differences Of Opinion

The scientific community has a strong tradition of sharing digital sequence information (DSI) in an unrestricted manner through public databases. While this tradition of “open access” sharing has many benefits, it has created tension in the context of the Convention on Biological Diversity (CBD). Differences of opinion on open access to DSI underlie key points of divergence in ongoing negotiations. The CBD has provided a set of policy options for DSI, but they are not granular enough to assess whether they are compatible with open access principles. Here, we explain what open access to DSI means in practice, assess the CBD DSI policy options through a more granular, technical lens, and discuss which policy options best enable open access. We show that de-coupled benefit-sharing mechanisms for DSI are the most compatible with open access practices and multilateral mechanisms, in general, are the most suited for benefit-sharing if fully de-coupled mechanisms become politically unrealistic.

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Subcellular immuno-localization, amino acid composition and partial amino acid sequences of alpha-1,4-glucan phosphorylase of Gracilarria spp (Rhodophyta)

Physiologia Plantarum ◽

10.1034/j.1399-3054.1993.890103.x ◽

1993 ◽

Vol 89 (1) ◽

pp. 11-20

Author(s):

S. Yu ◽

J.-L. Gomez-Pinchetti ◽

B. Ek ◽

G. Garcia-Reina ◽

M. Pedersen

Keyword(s):

Amino Acid ◽

Amino Acid Composition ◽

Acid Composition ◽

Amino Acid Sequences ◽

Glucan Phosphorylase

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Diversity of Primary Structures of the Carboxy-terminal Regions of Mammalian Fibrinogen Aα-Chains

Thrombosis and Haemostasis ◽

10.1055/s-0038-1651611 ◽

1993 ◽

Vol 69 (04) ◽

pp. 351-360 ◽

Cited By ~ 26

Author(s):

Masahiro Murakawa ◽

Takashi Okamura ◽

Takumi Kamura ◽

Tsunefumi Shibuya ◽

Mine Harada ◽

...

Keyword(s):

Amino Acid ◽

Rhesus Monkey ◽

Syrian Hamster ◽

Tandem Repeats ◽

Mammalian Species ◽

Amino Acid Sequences ◽

Point Of View ◽

Cross Linking ◽

Amino Terminal ◽

Rgd Sequence

SummaryThe partial amino acid sequences of fibrinogen Aα-chains from five mammalian species have been inferred by means of the polymerase chain reaction (PCR). From the genomic DNA of the rhesus monkey, pig, dog, mouse and Syrian hamster, the DNA fragments coding for α-C domains in the Aα-chains were amplified and sequenced. In all species examined, four cysteine residues were always conserved at the homologous positions. The carboxy- and amino-terminal portions of the α-C domains showed a considerable homology among the species. However, the sizes of the middle portions, which corresponded to the internal repeat structures, showed an apparent variability because of several insertions and/or deletions. In the rhesus monkey, pig, mouse and Syrian hamster, 13 amino acid tandem repeats fundamentally similar to those in humans and the rat were identified. In the dog, however, tandem repeats were found to consist of 18 amino acids, suggesting an independent multiplication of the canine repeats. The sites of the α-chain cross-linking acceptor and α2-plasmin inhibitor cross-linking donor were not always evolutionally conserved. The arginyl-glycyl-aspartic acid (RGD) sequence was not found in the amplified region of either the rhesus monkey or the pig. In the canine α-C domain, two RGD sequences were identified at the homologous positions to both rat and human RGD S. In the Syrian hamster, a single RGD sequence was found at the same position to that of the rat. Triplication of the RGD sequences was seen in the murine fibrinogen α-C domain around the homologous site to the rat RGDS sequence. These findings are of some interest from the point of view of structure-function and evolutionary relationships in the mammalian fibrinogen Aα-chains.

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Bovine Factors X1And X2: Activation Peptide Based Chromatographic Differences

10.1055/s-0038-1665665 ◽

1979 ◽

Author(s):

Takashi Morita ◽

Craig Jackson

Keyword(s):

Amino Acid ◽

Anion Exchange ◽

Gel Filtration ◽

Heart Association ◽

Personal Communication ◽

Exchange Chromatography ◽

Amino Acid Sequences ◽

Factor X ◽

Activation Peptide ◽

Activation Peptides

Bovine Factor X is eluted in two forms (X1and X2) from anion exchange chromatographic columns. These two forms have indistinguishable amino acid compositions, molecular weights and specific activities. The amino acid sequences containing the γ-carboxyglutamic acid residues have been shown to be identical in X1 and X2(H. Morris, personal communication). An activation peptide is released from the N-terminal region of the heavy chain of Factor X by an activator from Russell’s viper venom. This peptide can be isolated after activation by gel filtration on Sephadex G-100 under nondenaturing conditions. The activation peptides from a mixture of Factors X1 and X2 were separated into two forms by anion-exchange chromatography. The activation peptide (AP1) which eluted first was shown to be derived from Factor X1. while the activation peptiae (AP2) which eluted second was shown to be derived from X2 on the basis of chromatographic separations carried out on Factors X1 and X2 separately. Factor Xa was eluted as a symmetrical single peak. On the basis of these and other data characterizing these products, we conclude that the difference between X1 and X2 are properties of the structures of the activation peptides. (Supported by a grant HL 12820 from the National Heart, Lung and Blood Institute. C.M.J. is an Established Investigator of the American Heart Association).

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Application of the Innovative and Non-Invasive Technique, Molecular Music Therapy (MMT), Bio-Frequency Therapy, for the Treatment of a Wide Range of Disorders and Pathologies, with Consequent Verification of Molecular Parameters by Using Bi-Digital O-Ring Test (BDORT)

Acupuncture & Electro-Therapeutics Research ◽

10.3727/036012920x15779969212928 ◽

2020 ◽

Vol 44 (3) ◽

pp. 177-189

Author(s):

Momir Dunjic ◽

Stefano Turini ◽

Dejan Krstic ◽

Katarina Dunjic ◽

Marija Dunjic ◽

...

Keyword(s):

Amino Acid ◽

Music Therapy ◽

Amino Acid Sequences ◽

Sirtuin 1 ◽

Ring Test ◽

Invasive Technique ◽

Specific Gene ◽

Radiofrequency Therapy ◽

Wide Range ◽

Clinical Pictures

Radiofrequency therapy is an unconventional method, already applied for some time, with numerous results in numerous clinical pictures. Our group has developed a software, later called SONGENPROT-SOLARIS, capable of directly converting nucleotide sequences (DNA and/or RNA) and amino acid sequences (polypeptides and proteins) into musical sequences, based on mathematic matrices, designed by the French physicist and musician Joel Sternheimer, which allows to associate a musical note with a nucleotide or an amino acid. Innovation in our software is that, in the algorithm that defines it, a variant is directly implemented that allows the reproduction of sounds, phase-shifted by 30 Hz, between one ear and another reproducing the phenomenon of Binaural Tones, capable of induce a specific brain activity and also the release of particles called solitons. Thanks to this software we have developed a technique called MMT (Molecular Music Therapy) and currently, we are in the phase of applying the technique on a cohort of 91 patients, with a high spectrum of clinical pictures, examining the same, using the technique Bi-Digital-ORing-Test (BDORT), before and after treatment with MMT. Aim of project is to stimulate the expression of a specific gene (the same genetic sequence that the patient listens to, translated into music), only through the use of sound sequences. We have concentrated our attention on three main molecules: Sirtuin-1, Telomers and TP-53. The results obtained with BDORT, after treatment with MMT, showed a significant increase in the values of the three molecules, on all the examined patients, demonstrating the operative efficacy of the technique and the its applicability to numerous diseases. In order to confirm the data obtained by BDORT, we propose, with the help of an accredited laboratory, to perform epigenetic tests on the three parameters listed above, paving the way to understanding how frequencies can influence gene expression.

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