Determination of an Epitope of the Diffuse Scleroderma Marker Antigen Topoisomerase I. Sequence Similarity with Retroviral p30gag Protein Suggests a Possible Cause for Autoimmunity in Scleroderma

Author(s):  
G. G. Maul ◽  
S. A. Juminez ◽  
D. Ziemnicka-Kotula
Toxins ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 359 ◽  
Author(s):  
Maria Romero-Gutiérrez ◽  
Carlos Santibáñez-López ◽  
Juana Jiménez-Vargas ◽  
Cesar Batista ◽  
Ernesto Ortiz ◽  
...  

To understand the diversity of scorpion venom, RNA from venomous glands from a sawfinger scorpion, Serradigitus gertschi, of the family Vaejovidae, was extracted and used for transcriptomic analysis. A total of 84,835 transcripts were assembled after Illumina sequencing. From those, 119 transcripts were annotated and found to putatively code for peptides or proteins that share sequence similarities with the previously reported venom components of other species. In accordance with sequence similarity, the transcripts were classified as potentially coding for 37 ion channel toxins; 17 host defense peptides; 28 enzymes, including phospholipases, hyaluronidases, metalloproteases, and serine proteases; nine protease inhibitor-like peptides; 10 peptides of the cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 protein superfamily; seven La1-like peptides; and 11 sequences classified as “other venom components”. A mass fingerprint performed by mass spectrometry identified 204 components with molecular masses varying from 444.26 Da to 12,432.80 Da, plus several higher molecular weight proteins whose precise masses were not determined. The LC-MS/MS analysis of a tryptic digestion of the soluble venom resulted in the de novo determination of 16,840 peptide sequences, 24 of which matched sequences predicted from the translated transcriptome. The database presented here increases our general knowledge of the biodiversity of venom components from neglected non-buthid scorpions.


1999 ◽  
Vol 89 (4) ◽  
pp. 938-945 ◽  
Author(s):  
Gene A. Ichinose ◽  
Kenneth D. Smith ◽  
John G. Anderson

Abstract An accident at the Sierra Chemical Company Kean Canyon plant, 16 km east of Reno, Nevada, resulted in two explosions 3.52 sec apart that devastated the facility. An investigation into a possible cause for the accident required the determination of the chronological order of the explosions. We resolved the high-precision relative locations and chronology of the explosions using a cross-correlation method applied to both seismic and air waves. The difference in relative arrival times of air waves between the explosions indicated that the first explosion occurred at the northern site. We then determined two station centroid separations between explosions, which average about 73 m with uncertainties ranging from ± 17 to 41 m depending on the alignment of station pairs. We estimated a centroid separation of 80 m using P waves with a larger uncertainty of ± 340 m. We performed a grid search for an optimal separation and the azimuth by combining air-wave arrivals from three station pairs. The best solution for the relative location of the second explosion is 73.2 m S35°E from the first explosion. This estimate is well within the uncertainties of the survey by the U.S. Chemical Safety and Hazard Investigation Board (CSB). The CSB reported a separation of approximately 76.2 m S33°E. The spectral amplitudes of P waves are 3 to 4 times higher for the second explosion relative to the first explosion, but the air waves have similar spectral amplitudes. We suggest that this difference is due to the partitioning of energy between the ground and air caused by downward directivity at the southern explosion, and upward directivity at the northern explosion. This is consistent with the absence of a crater for the first explosion and a 1.8-m-deep crater for the second explosion.


2021 ◽  
Author(s):  
Nieng Yan ◽  
Chuangye Yan ◽  
Renhong Yan ◽  
Pingping Cao ◽  
Wenqi Song ◽  
...  

The sterol regulatory element-binding protein (SREBP) pathway senses the cellular cholesterol level through sterol regulated association between Scap and Insig. Despite the recent structural determination of the transmembrane domains of human Scap and Insig-2 bound to 25-hydroxycholesterol (25HC), the structure and regulatory mechanism of the luminal domains of Scap by cholesterol remains elusive. Here, combining cryo-EM analysis and artificial intelligence-facilitated structural prediction, we report the structure of the human Scap/Insig-2 complex in the presence of digitonin instead of 25HC. Despite the lack of sequence similarity, the structure of the luminal domain Loop 1 and a co-folded segment in Loop 7 of Scap resembles that of the luminal/extracellular domain in NPC1 and related proteins. Comparison of the sterol-loaded structures of these proteins provides clues of the regulation of Loop 1/7 interaction by cholesterol. We also show that the structure of Scap(D428A), which suppresses SREBP activation under sterol depletion, is identical to WT when complexed with Insig-2, although the gain of function may also involve a later step in protein trafficking.


2011 ◽  
Vol 61 (5) ◽  
pp. 1114-1117 ◽  
Author(s):  
Ya Wen ◽  
Xing Huang ◽  
Yu Zhou ◽  
Qing Hong ◽  
Shunpeng Li

A novel Gram-negative, aerobic, coccoid-shaped strain designated S 113T was isolated from a polluted-soil sample collected in Jiangsu Province, China. A polyphasic taxonomic study including phylogenetic analysis based on the 16S rRNA gene sequence and determination of phenotypic characteristics was performed on the new isolate. The highest 16S rRNA gene sequence similarity was 96.8 %, with Hansschlegelia plantiphila S1 T. The predominant respiratory quinone was ubiquinone 10 (Q-10). The major fatty acids were C18 : 1ω7c and C16 : 0. The G+C content of the DNA was about 65.7 mol%. DNA–DNA hybridization experiments showed 44.9 % relatedness for strain S 113T with its closest relative, H. plantiphila NCIMB 14035T. The dominant phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and phosphatidylcholine. The results of our polyphasic taxonomic analysis indicate that strain S 113T represents a novel species within the genus Hansschlegelia, for which the name Hansschlegelia zhihuaiae sp. nov. is proposed. The type strain is S 113T ( = DSM 18984T  = CCTCC AB 206143T  = KCTC 12880T).


Genetics ◽  
2002 ◽  
Vol 160 (2) ◽  
pp. 457-461 ◽  
Author(s):  
Michael E Hood

Abstract Fungi often mate as haploids, and sex chromosomes (i.e., mating-type chromosomes) that are dimorphic for their size or overall DNA content have never been reported in this kingdom. Using electrophoretic techniques for karyotype analysis, a highly dimorphic chromosome pair that determines mating compatibility is shown to occur in populations of the fungus Microbotryum violaceum. This substantiates the evolution of such dimorphism as a general feature associated with haploid determination of mating compatibility, which previously had been known only in haplodioecious plants (mosses and liverworts). Size-dimorphic sex chromosomes are present in a lineage of M. violaceum native to Europe, as well as a lineage native to North America. However, they are very different in size between these lineages, indicating either independent evolution of the dimorphism or a large degree of divergence since their isolation. Several DNA sequences that show sequence similarity to transposons were isolated from these sex chromosomes.


Author(s):  
V. F. Bezhenar ◽  
L. A. Ivanova ◽  
N. V. Belitchenko

Antenatal death is the cessation of fetal heart contractions during pregnancy for more than 22 weeks prior to the onset of labor. Objective: to evaluate the capabilities of the method of ultrasound in antenatal fetal death. Tasks of ultrasound in the presence of a dead fetus: a statement of his death; determining the position, presentation, size, estimated fetal weight and gestational age; detection of congenital malformations (CM) and possible causes of death; clarification of the statute of limitations of death. We have analyzed 126 standard ultrasound protocols of pregnant women with antenatal fetal death. Ascertaining the cessation of heart contractions and determining the location of the fetus present no difficulties for the ultrasound doctor. The assessment of the conformity of the size of the fetus to the gestational period during antenatal death is better determined by measuring the diaphysis of the long bones. Head sizes are used only when it is possible to clearly assess the typical structures of a biparietal slice. The determination of the estimated mass of the fetus is difficult due to autolytic changes and, usually, lack of water. The diagnosis of CM, first established after ascertaining antenatal fetal death, should cause the doctor to doubt that it is in front of us — a developmental defect, as a possible cause of intrauterine death or post-mortem changes that depend on previous intravital changes, cause and duration of death. The article describes the dynamics of the appearance of post-mortem changes. Conclusions: with antenatal fetal death, it is impractical to determine the expected mass of the fetus, it is preferable to estimate the period of probable cessation of development from the measurement of long tubular bones; during an ultrasound of the deceased fetus, it is often impossible to reliably determine the presence/absence of CM and the exact time of death; change in the amount of amniotic fluid is not a reliable diagnostic criterion for the duration of death.


2021 ◽  
Author(s):  
ASIT KUMAR CHAKRABORTY

We previously predicted Nsp2 Corona virus protein as RNA topoisomerase through amino acid homology among Vibrio haemolytica DNA topoisomerase IA/IV as well as DNA primase, DNA gyrase and bi-subunit Trypanosoma brucei DNA topoisomerase IB. Many DNA topoisomerase I/III have RNA topoisomerase activity and such ubiquitous enzymes are conserved and involved in the regulation of replication and transcription. We have checked here mutational profile of Nsp2 RNA topoisomerase analyzing >10000 orf1a 4405 amino acid length Corona virus polyprotein. Mutant proteins were selected by BLAST search having 99.84% sequence similarity and 181-818aa portion Nsp2 protein (protein id. QIU82057) was analyzed using CLUSTAL Omega software. We found 26 different mutations where most changes were selected at Isoleucine and Alanine into Valine or Leucine into Phenylanaline pinpointing conserved nature of the Corona virus RNA topoisomerase. Major nonsense very abundant mutations were found at I120F (Isoleucine to Phenylalanine). Other important mutations were R27C, I198V, T85I, L410F, I559V and P583S. The I120F mutation was abundant in Australian isolates and its spread was seen in the Bangladesh and other countries like USA. We suggest that abundant I120F mutation of Nsp2 Topoisomerase may increase transmission of Corona virus by stabilizing RNA structure for efficient virus pakaging. Interestingly, such mutations were found in association of D614G mutation of Spike protein, known to >70% increase infectivity. On the contrary, all P583S Nsp2 mutants analyzed had no concurrence D614G spike protein mutation. Many silent mutations (5-7) were detected by genome wide analysis but no N501Y Spike protein mutation. This is first report that predicts a link of greater Corona virus transmission with Nsp2 protein I120F and spike protein D614G mutations.


1999 ◽  
Vol 380 (5) ◽  
pp. 561-568 ◽  
Author(s):  
V. Choumet ◽  
P. Lafaye ◽  
C. Demangel ◽  
C. Bon ◽  
J.-C. Mazié

Abstract Crotoxin is a heterodimeric phospholipase A2 neurotoxin formed by the non-covalent association of an acidic and non-toxic subunit, CA, and a basic and weakly toxic phospholipase A2, CB. The two subunits behave in a synergistic manner. CA enhances the lethal potency of CB by increasing its selectivity of action. The mAb A-56.36, directed against the non-toxic subunit CA, was previously shown to neutralize crotoxin toxicity by dissociating the crotoxin complex. In the present report, a polypeptide sequence similarity was observed between some CDRs of mAb A-56.36 and two regions of CB (pos. 60–80 and 95–110). Phage displayed peptides corresponding to VH2 and VH3 of mAb A-56.36 and to their homologous sequences in CB bind CA to different extents. This observation shows that mAb A-56.36 interacts with a region of CA involved in its interaction with CB, therefore mimicking the binding of CB to CA. A similar approach was used to determine the regions of ammodytoxin A and of agkistrodotoxin, two phospholipase A2 neurotoxins similar to CB, which are involved in the formation of heterocomplexes with CA. The analysis of these data contributes to the determination of stretches of amino acids which could constitute the paratope of mAb A-56.36, as well as the region of association of CB with CA in crotoxin.


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