Purification and structural analysis of interferon

1982 ◽  
Vol 299 (1094) ◽  
pp. 39-50 ◽  
Keyword(s):  
Biochemical Characterization ◽  
Structural Information ◽  
Scale Up ◽  
Structural Data ◽  
Highly Sensitive ◽  
Complete Sequences ◽  
Degree Of Confidence ◽  
Copy Dna ◽  
High Degree ◽  
Cdna Fragments

Studies with crude or partly purified interferon have provided a significant amount of structural information. However, complete biochemical characterization required purification to homogeneity. Earlier work on fractionation has met with many difficulties because interferon was available only in minute quantities. A scale-up of production, adaptation of multi-step purification schemes, use of high-resolution separation techniques and highly sensitive analytical methods have yielded pure interferons and hence many structural data. Specific activities, amino-acid compositions, partial sequences and structural homologies of many interferons were determined. Finally, cloned copy DNA (cDNA) fragments derived from specific interferon mRNA, as well as isolated interferon genes, have been sequenced and the data were used to elucidate complete sequences of many interferons with a high degree of confidence.

scholarly journals Integrating genome sequence and structural data for statistical learning to predict transcription factor binding sites

2020 ◽  
Vol 48 (22) ◽  
pp. 12604-12617
Author(s):  
Pengpeng Long ◽  
Lu Zhang ◽  
Bin Huang ◽  
Quan Chen ◽  
Haiyan Liu
Keyword(s):  
Genome Sequence ◽  
Energy Function ◽  
Structural Information ◽  
Structural Data ◽  
P Values ◽  
A Genome ◽  
Z Scores ◽  
Transcription Regulators ◽  
Dna Specificity ◽  
Tetracycline Repressor

Abstract We report an approach to predict DNA specificity of the tetracycline repressor (TetR) family transcription regulators (TFRs). First, a genome sequence-based method was streamlined with quantitative P-values defined to filter out reliable predictions. Then, a framework was introduced to incorporate structural data and to train a statistical energy function to score the pairing between TFR and TFR binding site (TFBS) based on sequences. The predictions benchmarked against experiments, TFBSs for 29 out of 30 TFRs were correctly predicted by either the genome sequence-based or the statistical energy-based method. Using P-values or Z-scores as indicators, we estimate that 59.6% of TFRs are covered with relatively reliable predictions by at least one of the two methods, while only 28.7% are covered by the genome sequence-based method alone. Our approach predicts a large number of new TFBs which cannot be correctly retrieved from public databases such as FootprintDB. High-throughput experimental assays suggest that the statistical energy can model the TFBSs of a significant number of TFRs reliably. Thus the energy function may be applied to explore for new TFBSs in respective genomes. It is possible to extend our approach to other transcriptional factor families with sufficient structural information.

scholarly journals PGPR Characteristics of Rhizospheric Bacteria to Understand the Mechanisms of Faba Bean Growth

Proceedings ◽  
2021 ◽  
Vol 66 (1) ◽  
pp. 27
Author(s):  
Rim Tinhinen Maougal ◽  
Maya Kechid ◽  
Chaima Ladjabi ◽  
Abdelhamid Djekoun
Keyword(s):  
Plant Growth ◽  
Faba Bean ◽  
Biochemical Characterization ◽  
Plant Growth Promoting Rhizobacteria ◽  
Bacterial Strains ◽  
Rhizospheric Bacteria ◽  
Plant Growth Promoting ◽  
Pgpr Traits ◽  
Taxonomic Groups ◽  
High Degree

Rhizobacteria play an important role in maintaining soil balance. Among these bacteria, there are those taht have shown their ability to promote the growth of plants, known as Plant Growth Promoting Rhizobacteria (PGPR). In our work, we are interested in characterizing 110 bacterial strains isolated in the field in the region of Ben Badis (Constantine Algeria) from 5 varieties of faba bean. Phenotypic and biochemical characterization showed that most of the isolates are cream-colored, slightly raised, flat and opaque, Gram−, catalase+ and oxidase−, and Bacillus form. PCA analysis allowed us to select 40 isolates with a high degree of variability to continue our work. The results obtained have directed us towards different taxonomic groups (rhizobium, Pseudomonas, Bacillus etc.). The evaluation of the PGPR potential of bacteria (phytostimulation, biofertilization and biocontrol), showed that 100% of bacteria are able to produce auxin at different concentrations, with the highest concentration (177.77 µg/mL) for the isolate 6, and that more than 50% of isolates are capable of producing nitrogen, ammonia and phytate mineralization. These PGPR traits have a direct effect on plant growth of five varieties of the faba bean and can be used to select the best performing bacteria for inoculation tests.

scholarly journals Alpha Amylase from Bacillus pacificus Associated with Brown Algae Turbinaria ornata: Cultural Conditions, Purification, and Biochemical Characterization

Processes ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 16
Author(s):  
Mona Alonazi ◽  
Aida Karray ◽  
Ahmed Yacine Badjah-Hadj-Ahmed ◽  
Abir Ben Bacha
Keyword(s):  
Biochemical Characterization ◽  
Alpha Amylase ◽  
Bacterial Symbionts ◽  
Terminal Sequence ◽  
Turbinaria Ornata ◽  
Substrate Analogs ◽  
Cultural Conditions ◽  
Initial Ph ◽  
Application Data ◽  
High Degree

We aimed in the current study, the identification of a marine bacterial amylase produced by Bacillus pacificus, which was associated with Turbinaria ornata. Cultural conditions were optimized for the highest amylase production on Tryptic soy broth media supplemented with starch 1% at initial pH 9, 55 °C for 24 h. The newly purified amylase was characterized for a possible biotechnological application. Data indicated that the obtained amylase with a molecular weight of 40 kD and the N-terminal sequence of the first 30 amino acids of amBp showed a high degree of homology with known alpha amylase, and was stable at 60 °C of pH 11. Among the tested substrate analogs, amBp was almost fully active on Alylose and Alylopectine (97%), but moderately hydrolyzed glycogen < sucrose < maltose < lactose. Therefore, the current amylase mainly generated maltohexaose from starch. Mg2+ and Zn2+ improved amylase activity up to 170%. While ethylenediamine tetraacetic acid (EDTA) similarly induced the greatest activity with purified amylase, PCMB had the least effect. Regarding all these characteristics, amylase from marine bacterial symbionts amBp has a new promising feature for probable therapeutic, industrial, and nutritional applications.

scholarly journals Mechanisms Applied by Protein Inhibitors to Inhibit Cysteine Proteases

2021 ◽  
Vol 22 (3) ◽  
pp. 997
Author(s):  
Livija Tušar ◽  
Aleksandra Usenik ◽  
Boris Turk ◽  
Dušan Turk
Keyword(s):  
Binding Site ◽  
Structural Information ◽  
General Rule ◽  
Structural Data ◽  
Cysteine Proteases ◽  
Protein Inhibitors ◽  
Active Site Cleft ◽  
Living Organisms ◽  
And Control ◽  
Binding Mechanisms

Protein inhibitors of proteases are an important tool of nature to regulate and control proteolysis in living organisms under physiological and pathological conditions. In this review, we analyzed the mechanisms of inhibition of cysteine proteases on the basis of structural information and compiled kinetic data. The gathered structural data indicate that the protein fold is not a major obstacle for the evolution of a protease inhibitor. It appears that nature can convert almost any starting fold into an inhibitor of a protease. In addition, there appears to be no general rule governing the inhibitory mechanism. The structural data make it clear that the “lock and key” mechanism is a historical concept with limited validity. However, the analysis suggests that the shape of the active site cleft of proteases imposes some restraints. When the S1 binding site is shaped as a pocket buried in the structure of protease, inhibitors can apply substrate-like binding mechanisms. In contrast, when the S1 binding site is in part exposed to solvent, the substrate-like inhibition cannot be employed. It appears that all proteases, with the exception of papain-like proteases, belong to the first group of proteases. Finally, we show a number of examples and provide hints on how to engineer protein inhibitors.

Myeloid Sarcoma of the Head and Neck Region

2013 ◽  
Vol 137 (11) ◽  
pp. 1560-1568 ◽  
Author(s):  
Jane Zhou ◽  
Diana Bell ◽  
L. Jeffrey Medeiros
Keyword(s):  
Head And Neck ◽  
Low Frequency ◽  
Neck Region ◽  
Immunohistochemical Analysis ◽  
Myeloid Sarcoma ◽  
Head And Neck Region ◽  
Bone Marrow Disease ◽  
Highly Sensitive ◽  
History Of ◽  
High Degree

Context.—Myeloid sarcoma of the head and neck region can pose diagnostic challenges because of the low frequency of myeloid sarcoma and the potential for tumors of almost any lineage to occur in the head and neck. Objective.—To study the clinicopathologic and immunohistochemical characteristics of myeloid sarcoma in the head and neck region and to review the differential diagnosis. Design.—We searched for cases of myeloid sarcoma involving the head and neck region for a 24-year period at our institution. The medical records and pathology slides were reviewed. Additional immunohistochemical stains were performed. Results.—We identified 17 patients, age 17 to 85 years. Most tumors involved the oral cavity. Myeloid sarcoma was the initial diagnosis in 9 patients (53%); the remaining 8 patients (47%) had a history of bone marrow disease. Immunohistochemical analysis using antibodies specific for lysozyme, CD43, and CD68 were highly sensitive for diagnosis but were not specific. By contrast, assessment for myeloperoxidase in this study was less sensitive but more specific. We also used antibodies specific for CD11c and CD33 in a subset of cases, and these reagents seem helpful as well. Conclusions.—The clinical presentation of myeloid sarcoma involving the head and neck, particularly the mouth, is often nonspecific, and a high degree of suspicion for the possibility of myeloid sarcoma is needed. Immunohistochemistry is very helpful for establishing the diagnosis.

scholarly journals Marine Prasinovirus Genomes Show Low Evolutionary Divergence and Acquisition of Protein Metabolism Genes by Horizontal Gene Transfer

2010 ◽  
Vol 84 (24) ◽  
pp. 12555-12563 ◽  
Author(s):  
Hervé Moreau ◽  
Gwenael Piganeau ◽  
Yves Desdevises ◽  
Richard Cooke ◽  
Evelyne Derelle ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Viral Evolution ◽  
Genome Comparison ◽  
Evolutionary Divergence ◽  
Gene Repertoire ◽  
Whole Genomes ◽  
Complete Sequences ◽  
Virus Genomes ◽  
High Degree ◽  
Ostreococcus Lucimarinus

ABSTRACT Although marine picophytoplankton are at the base of the global food chain, accounting for half of the planetary primary production, they are outnumbered 10 to 1 and are largely controlled by hugely diverse populations of viruses. Eukaryotic microalgae form a ubiquitous and particularly dynamic fraction of such plankton, with environmental clone libraries from coastal regions sometimes being dominated by one or more of the three genera Bathycoccus, Micromonas, and Ostreococcus (class Prasinophyceae). The complete sequences of two double-stranded (dsDNA) Bathycoccus, one dsDNA Micromonas, and one new dsDNA Ostreococcus virus genomes are described. Genome comparison of these giant viruses revealed a high degree of conservation, both for orthologous genes and for synteny, except for one 36-kb inversion in the Ostreococcus lucimarinus virus and two very large predicted proteins in Bathycoccus prasinos viruses. These viruses encode a gene repertoire of certain amino acid biosynthesis pathways never previously observed in viruses that are likely to have been acquired from lateral gene transfer from their host or from bacteria. Pairwise comparisons of whole genomes using all coding sequences with homologous counterparts, either between viruses or between their corresponding hosts, revealed that the evolutionary divergences between viruses are lower than those between their hosts, suggesting either multiple recent host transfers or lower viral evolution rates.

Determination of Sample Size in Service Inspection

1997 ◽  
Vol 119 (1) ◽  
pp. 57-60
Author(s):  
S. Qin ◽  
G. E. O. Widera
Keyword(s):  
Sample Size ◽  
Large Volume ◽  
Analysis Method ◽  
Degree Of Confidence ◽  
Impossible Task ◽  
The Mean ◽  
High Degree ◽  
Service Inspection ◽  
False Rejection

When performing inservice inspection on a large volume of identical components, it becomes an almost impossible task to inspect all those in which defects may exist, even if their failure probabilities are known. As a result, an appropriate sample size needs to be determined when setting up an inspection program. In this paper, a probabilistic analysis method is employed to solve this problem. It is assumed that the characteristic data of components has a certain distribution which can be taken as known when the mean and standard deviations of serviceable and defective sets of components are estimated. The sample size can then be determined within an acceptable assigned error range. In this way, both false rejection and acceptance can be avoided with a high degree of confidence.

scholarly journals Water–DNA interactions as studied by X–ray and neutron fibre diffraction

2004 ◽  
Vol 359 (1448) ◽  
pp. 1237-1248 ◽  
Author(s):  
Watson Fuller ◽  
Trevor Forsyth ◽  
Arumugam Mahendrasingam
Keyword(s):  
Structural Information ◽  
Double Helix ◽  
Water Environment ◽  
Structural Features ◽  
Molecular Conformations ◽  
X Ray ◽  
Biochemical Processes ◽  
Fibre Diffraction ◽  
Dna Double Helix ◽  
High Degree

X–ray fibre–diffraction studies indicate a high degree of stereochemical specificity in interactions between water and the DNA double helix. Evidence for this comes from data that show that the molecular conformations assumed by DNA in fibres are highly reproducible and that the hydration–driven transitions between these conformations are fully reversible. These conformational transitions are induced by varying the relative humidity of the fibre environment and hence its water content. Further evidence for stereochemical specificity comes from the observed dependence of the conformation assumed on the ionic content of the fibre and the nucleotide sequence of the DNA. For some transitions, information on stereochemical pathways has come from real–time X–ray fibre diffraction using synchrotron radiation; information on the location of water with respect to the double helix for a number of DNA conformations has come from neutron fibre diffraction. This structural information from fibre–diffraction studies of DNA is complemented by information from X–ray single–crystal studies of oligonucleotides. If the biochemical processes involving DNA have evolved to exploit the structural features observed in DNA fibres and oligonucleotide single crystals, the challenges in developing alternatives to a water environment can be expected to be very severe.

A current assessment of photosystem II structure

1996 ◽  
Vol 16 (2) ◽  
pp. 159-187 ◽  
Author(s):  
William V. Nicholson ◽  
Robert C. Ford ◽  
Andreas Holzenburg
Keyword(s):  
Photosystem Ii ◽  
Structural Information ◽  
Three Dimensional ◽  
Structural Data ◽  
X Ray Diffraction ◽  
Membrane Protein Complex ◽  
Fast Absorption ◽  
Current Assessment ◽  
Electron Microscopical ◽  
A Current

This review covers the recent progress in the elucidation of the structure of photosystem II (PSII). Because much of the structural information for this membrane protein complex has been revealed by electron microscopy (EM), the review will also consider the specific technical and interpretation problems that arise with EM where they are of particular relevance to the structural data. Most recent reviews of photosystem II structure have concentrated on molecular studies of the PSII genes and on the likely roles of the subunits that they encode or they were mainly concerned with the biophysical data and fast absorption spectroscopy largely relating to electron transfer in various purified PSII preparations. In this review, we will focus on the approaches to the three-dimensional architecture of the complex and the lipid bilayer in which it is located (the thylakoid membrane) with special emphasis placed upon electron microscopical studies of PSII-containing thylakoid membranes. There are a few reports of 3D crystals of PSII and of associated X-ray diffraction measurements and although little structural information has so far been obtained from such studies (because of the lack of 3D crystals of sufficient quality), the prospects for such studies are also assessed.

scholarly journals A crystallographic study of crystalline casts and pseudomorphs from the 3.5 Ga Dresser Formation, Pilbara Craton (Australia)

2018 ◽  
Vol 51 (4) ◽  
pp. 1050-1058 ◽  
Author(s):  
Fermin Otálora ◽  
A. Mazurier ◽  
J. M. Garcia-Ruiz ◽  
M. J. Van Kranendonk ◽  
E. Kotopoulou ◽  
...  
Keyword(s):  
High Temperature ◽  
Geological History ◽  
X Ray Diffraction ◽  
Mineral Phase ◽  
X Ray ◽  
Crystallographic Study ◽  
History Of ◽  
Degree Of Confidence ◽  
High Degree ◽  
Pilbara Craton

Crystallography has a long history of providing knowledge and methods for applications in other disciplines. The identification of minerals using X-ray diffraction is one of the most important contributions of crystallography to earth sciences. However, when the crystal itself has been dissolved, replaced or deeply modified during the geological history of the rocks, diffraction information is not available. Instead, the morphology of the crystal cast provides the only crystallographic information on the original mineral phase and the environment of crystal growth. This article reports an investigation of crystal pseudomorphs and crystal casts found in a carbonate-chert facies from the 3.48 Ga-old Dresser Formation (Pilbara Craton, Australia), considered to host some of the oldest remnants of life. A combination of X-ray microtomography, energy-dispersive X-ray spectroscopy and crystallographic methods has been used to reveal the original phases of these Archean pseudomorphs. It is found with a high degree of confidence that the original crystals forming in Archean times were hollow aragonite, the high-temperature polymorphs of calcium carbonate, rather than other possible alternatives such as gypsum (CaSO4·2H20) and nahcolite (NaHCO3). The methodology used is described in detail.

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