scholarly journals Gcorn fungi: A Web Tool for Detecting Biases between Gene Evolution and Speciation in Fungi

2021 ◽  
Vol 7 (11) ◽  
pp. 959
Author(s):  
Taiga Kawachi ◽  
Yuta Inuki ◽  
Yoshiyuki Ogata
Keyword(s):  
Amino Acid ◽  
Open Access ◽  
Horizontal Gene Transfer ◽  
Gene Evolution ◽  
Gene Mutations ◽  
Amino Acid Sequences ◽  
Web Tool ◽  
Homologous Genes ◽  
Open Access Database ◽  
Fungal Genes

(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.

scholarly journals Clonal hematopoiesis in adult pure red cell aplasia

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Naohito Fujishima ◽  
Junki Kohmaru ◽  
Souichi Koyota ◽  
Keiji Kuba ◽  
Tomoo Saga ◽  
...  
Keyword(s):  
Amino Acid ◽  
Gene Mutations ◽  
Pure Red Cell Aplasia ◽  
Amino Acid Sequences ◽  
Driver Mutations ◽  
Red Cell ◽  
Clonal Hematopoiesis ◽  
Red Cell Aplasia ◽  
Myeloid Neoplasm ◽  
Immune Mediated

AbstractIdiopathic pure red cell aplasia (PRCA) and secondary PRCA associated with thymoma and large granular lymphocyte leukemia are generally considered to be immune-mediated. The PRCA2004/2006 study showed that poor responses to immunosuppression and anemia relapse were associated with death. PRCA may represent the prodrome to MDS. Thus, clonal hematopoiesis may be responsible for treatment failure. We investigated gene mutations in myeloid neoplasm-associated genes in acquired PRCA. We identified 21 mutations affecting amino acid sequences in 11 of the 38 adult PRCA patients (28.9%) using stringent filtering of the error-prone sequences and SNPs. Four PRCA patients showed 7 driver mutations in TET2, DNMT3A and KDM6A, and 2 PRCA patients carried multiple mutations in TET2. Five PRCA patients had mutations with high VAFs exceeding 0.3. These results suggest that clonal hematopoiesis by stem/progenitor cells might be related to the pathophysiology of chronic PRCA in certain adult patients.

Three-dimensional structure and ligand-binding site of carp fishelectin (FEL)

2015 ◽  
Vol 71 (5) ◽  
pp. 1123-1135 ◽  
Author(s):  
Stefano Capaldi ◽  
Beniamino Faggion ◽  
Maria E. Carrizo ◽  
Laura Destefanis ◽  
Maria C. Gonzalez ◽  
...  
Keyword(s):  
Amino Acid ◽  
Ligand Binding ◽  
Three Dimensional ◽  
Biochemical Properties ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
X Ray Crystallography ◽  
Homologous Genes ◽  
Density Maps ◽  
Conserved Water Molecules

Carp FEL (fishelectin or fish-egg lectin) is a 238-amino-acid lectin that can be purified from fish eggs by exploiting its selective binding to Sepharose followed by elution withN-acetylglucosamine. Its amino-acid sequence and other biochemical properties have previously been reported. The glycoprotein has four disulfide bridges and the structure of the oligosaccharides linked to Asn27 has been described. Here, the three-dimensional structures of apo carp FEL (cFEL) and of its complex withN-acetylglucosamine determined by X-ray crystallography at resolutions of 1.35 and 1.70 Å, respectively, are reported. The molecule folds as a six-bladed β-propeller and internal short consensus amino-acid sequences have been identified in all of the blades. A calcium atom binds at the bottom of the funnel-shaped tunnel located in the centre of the propeller. Two ligand-binding sites, α and β, are present in each of the two protomers in the dimer. The first site, α, is closer to the N-terminus of the chain and is located in the crevice between the second and the third blades, while the second site, β, is located between the fourth and the fifth blades. The amino acids that participate in the contacts have been identified, as well as the conserved water molecules in all of the sites. Both sites can bind the two anomers, α and β, ofN-acetylglucosamine, as is clearly recognizable in the electron-density maps. The lectin presents sequence homology to members of the tachylectin family, which are known to have a function in the innate immune system of arthropods, and homologous genes are present in the genomes of other fish and amphibians. This structure is the first of a protein of this group and, given the degree of homology with other members of the family, it is expected that it will be useful to experimentally determine other crystal structures using the coordinates of cFEL as a search probe in molecular replacement.

scholarly journals Effects of hypoxia on the mRNA expressions of TRAILmediated cell death related genes in hypoxia-tolerant rodent (Nannospalax nehringi) and some characteristics of these proteins

2020 ◽  
pp. 53-53
Author(s):  
Barış Yıldız ◽  
Nadide Kamiloğlu ◽  
Cem Öziç ◽  
Yüksel Coşkun
Keyword(s):  
Cell Death ◽  
Amino Acid ◽  
Mrna Expression ◽  
Expression Profiles ◽  
Gene Mutations ◽  
Amino Acid Sequences ◽  
Gas Mixture ◽  
Similar Species ◽  
Hypoxia Group ◽  
The Brain

The aim of the present study was to determine the mRNA expression profiles of TRAILmediated cell death related genes of the hypoxia-tolerant rodent Nannospalax nehringi under hypoxia. The nucleotide and amino acid sequences of these genes were identified. Captured Nannospalax nehringi were randomly divided into normoxia and hypoxia groups. The hypoxia group was exposed to a 7% O2 + 93% N2 gas mixture for 52 h, while animals in the normoxia group were housed under normoxic conditions. Total RNAs were isolated from brain and lung tissues. The cIAP-1, cIAP-2, XIAP, DcR1, DcR2, FLIP and OPG genes were PCR amplified, and the cIAP-1, cIAP-2, XIAP, OPG, TRAIL and FLIP genes were sequenced. Sequenced genes were translated into amino acid sequences and compared with reliable sequences of closely similar species. The genes in the brain were regulated for protection against hypoxia; however, the genes in the lung were regulated differently. Many mutations and insertions were observed on the conserved regions of the cIAP-1, cIAP-2, XIAP, OPG and TRAIL genes in N. nehringi. We propose that these gene mutations and insertions contribute to the anti-hypoxic properties of N. nehringi.

scholarly journals A Tiling Algorithm-Based String Similarity Measure

2021 ◽  
Vol 9 ◽  
pp. 109-112
Author(s):  
Peter Z. Revesz
Keyword(s):  
Amino Acid ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Similarity Measure ◽  
Amino Acid Sequences ◽  
String Similarity

This paper describes a similarity measure for strings based on a tiling algorithm. The algorithm is applied to a pair of proteins that are described by their respective amino acid sequences. The paper also describes how the algorithm can be used to find highly conserved amino acid sequences and examples of horizontal gene transfer between different species

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

1993 ◽  
Vol 69 (04) ◽  
pp. 351-360 ◽  
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.

Bovine Factors X1And X2: Activation Peptide Based Chromatographic Differences

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).

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)

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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