scholarly journals Structure Prediction, Characterization, and Functional Annotation of Uncharacterized Protein BCRIVMBC126_02492 of Bacillus cereus: An In Silico Approach

2020 ◽  
pp. 104-111
Keyword(s):  
Bacillus Cereus ◽  
Structure Prediction ◽  
Functional Annotation ◽  
Protein A ◽  
Food Poisoning ◽  
Structural Quality ◽  
Functional Protein ◽  
Model Quality ◽  
Uncharacterized Protein ◽  
Comparison Of The Results

Bacillus cereus is enteropathogenic and widely distributed pathogen in the environment, which is mainly associated with food poisoning. In the intestine, B. cereus produces enterotoxins resulting in diarrhoea, abdominal distress and vomiting, and a range of infections in humans. BCRIVMBC126_02492 is a functional protein of B. cereus, which is related to oxidation glutathione persulfide in the mitochondria, cyanide fixation, and also has a variety of biological functions. Nevertheless, protein BCRIVMBC126_02492 is not explored. Therefore, the structure prediction, functional annotation, and characterization of the protein are proposed in this study. Modeller, Swiss-model, and Phyre2 are used for generating tertiary structures. The structural quality assessment of the protein determined by Ramachandran Plot analysis, Swiss-Model Interactive Workplace, and Verify 3D tools. Furthermore, Z-scores applied to detect the overall tertiary model quality of the protein. A comparison of the results showed that the models generated by Modeller were more suitable than Phyre2 and Swiss Models. This investigation decoded the role of this unexplored protein of B. cereus. Therefore, it can bolster the way for enriching our knowledge for pathogenesis and drug and vaccine targeting opportunities against B. cereus infection.

scholarly journals Characterization and Functional Annotation of Uncharacterized ABC Transporter ATP-Binding Protein Rv0986 of Mycobacterium tuberculosis (Strain ATCC 25618 / H37Rv)

2020 ◽  
Author(s):  
Abu Saim Mohammad Saikat
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Functional Annotation ◽  
Mycobacterial Infection ◽  
Structural Quality ◽  
Atp Binding ◽  
Model Quality ◽  
Uncharacterized Protein ◽  
Z Scores ◽  
Atp Binding Protein ◽  
Human Death

AbstractThe most significant ancient infectious disease tuberculosis is causes by a human pathogen, Mycobacterium tuberculosis (MTB). Amazingly, tuberculosis (TB) has become one of the major causes of human death worldwide. The protein Rv0986 is associated with the ATP-binding cassette domain of the transporters involved in the export of lipoprotein and macrolide, and cell division protein, therefore, related to mycobacterial infection. But the protein Rv0986 is not yet explored. As a result, identification, characterization, and functional annotation of uncharacterized protein Rv0986 were predicted where the structure modeling was generated by using Modeller, Phyre2, and Swiss Model with the structural quality assessment by Ramachandran Plot (PROCHECK), Verify 3d, and Swiss-Model Interactive Workplace as well. Z-scores obtained from Prosa-web were also applied for overall 3D model quality. This in-silico method will uncover the significance of undiscovered uncharacterized protein Rv0986 present in MTB, and indeed it can accelerate the way to enrich our knowledge in the pathogenesis and drug-targeting opportunity against infection by MTB.

State-of-the-art web services for de novo protein structure prediction

2020 ◽  
Author(s):  
Luciano A Abriata ◽  
Matteo Dal Peraro
Keyword(s):  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
De Novo ◽  
State Of The Art ◽  
Data Bank ◽  
End Users ◽  
Model Quality ◽  
Uncharacterized Protein

Abstract Residue coevolution estimations coupled to machine learning methods are revolutionizing the ability of protein structure prediction approaches to model proteins that lack clear homologous templates in the Protein Data Bank (PDB). This has been patent in the last round of the Critical Assessment of Structure Prediction (CASP), which presented several very good models for the hardest targets. Unfortunately, literature reporting on these advances often lacks digests tailored to lay end users; moreover, some of the top-ranking predictors do not provide webservers that can be used by nonexperts. How can then end users benefit from these advances and correctly interpret the predicted models? Here we review the web resources that biologists can use today to take advantage of these state-of-the-art methods in their research, including not only the best de novo modeling servers but also datasets of models precomputed by experts for structurally uncharacterized protein families. We highlight their features, advantages and pitfalls for predicting structures of proteins without clear templates. We present a broad number of applications that span from driving forward biochemical investigations that lack experimental structures to actually assisting experimental structure determination in X-ray diffraction, cryo-EM and other forms of integrative modeling. We also discuss issues that must be considered by users yet still require further developments, such as global and residue-wise model quality estimates and sources of residue coevolution other than monomeric tertiary structure.

KEJADIAN LUAR BIASA KERACUNAN “CUMI-CUMIAN” DI SEKOLAH DASAR NEGERI 1 TRASAN BANDONGAN KABUPATEN MAGELANG

2018 ◽  
Vol 7 (2) ◽  
pp. 131-136
Author(s):  
Nasir Ahmad
Keyword(s):  
Abdominal Pain ◽  
Bacillus Cereus ◽  
Rhodamine B ◽  
Attack Rate ◽  
Food Poisoning ◽  
Health Department ◽  
Analysis Data ◽  
Food Samples ◽  
Bivariate Analysis ◽  
School Committee

Background: On May 4th, 2016, at 12:30 district surveillance officer of Magelang Health Department received reports from Public Health Center of Bandongan about 21 students of SDN 1 Trasan who suffered from the same food-poisoning symptoms. Objective: Investigation was carried out to identify the source, how it spread and how to control it. Methods: This study used descriptive analytic and mapping the cases distribution location. The case was people experiencing symptoms of dizziness or abdominal pain or nausea or vomiting. Data analysis was done by using bivariate analysis. Data collection were done through interviews, observations and laboratory tests on the food samples. Results: The case was 50 students (from 1-6 grade students). The perceived symptoms were dizziness (77%), nausea (42%), abdominal pain (40%) and vomiting (8%). Attack rate found ranged from 14.3% to 60% with the highest Attack rate found on class three (60%). The incubation period of 15-240 minutes (mean 72.3 minutes). Calamari like positive Bacillus cereus and Rhodamine-B 10 mg/kg. Conclusion: The outbreak of food poisoning because calamari like contaminated Bacillus cereus. We suggested the school committee to provide the socialization of harmful food for the students. The teachers should restrict the permission for the food vendor to sell at school.   Keywords: Bacillus cereus, , Food Poisoning, Outbreak, Rhodamine B, School Food

scholarly journals Incidence and characterisation of Bacillus cereus bacteriophages from Thua Nao, a Thai fermented soybean product

2021 ◽  
Vol 12 (1) ◽  
pp. 85-93
Author(s):  
Wallapat Phongtang ◽  
Ekachai Chukeatirote
Keyword(s):  
Bacillus Cereus ◽  
Food Industry ◽  
Pathogenic Bacteria ◽  
Morphological Analysis ◽  
Food Poisoning ◽  
Fermented Soybean ◽  
Foodborne Pathogenic Bacteria ◽  
Ph Range ◽  
Potential Use

Abstract Bacillus cereus is considered to be an important food poisoning agent causing diarrhea and vomiting. In this study, the occurrence of B. cereus bacteriophages in Thai fermented soybean products (Thua Nao) was studied using five B. cereus sensu lato indicator strains (four B. cereus strains and one B. thuringiensis strain). In a total of 26 Thua Nao samples, there were only two bacteriophages namely BaceFT01 and BaceCM02 exhibiting lytic activity against B. cereus. Morphological analysis revealed that these two bacteriophages belonged to the Myoviridae. Both phages were specific to B. cereus and not able to lyse other tested bacteria including B. licheniformis and B. subtilis. The two phages were able to survive in a pH range between 5 and 12. However, both phages were inactive either by treatment of 50°C for 2 h or exposure of UV for 2 h. It should be noted that both phages were chloroform-insensitive, however. This is the first report describing the presence of bacteriophages in Thua Nao products. The characterization of these two phages is expected to be useful in the food industry for an alternative strategy including the potential use of the phages as a biocontrol candidate against foodborne pathogenic bacteria.

scholarly journals Production of the Vacuolation Factor of Bacillus cereus Isolated from Vomiting-Type Food Poisoning.

1992 ◽  
Vol 54 (3) ◽  
pp. 443-446 ◽  
Author(s):  
Kunihiro SHINAGAWA ◽  
Shoji OTAKE ◽  
Naonori MATSUSAKA ◽  
Shunji SUGII
Keyword(s):  
Bacillus Cereus ◽  
Food Poisoning

scholarly journals The CasKR Two-Component System Is Required for the Growth of Mesophilic and Psychrotolerant Bacillus cereus Strains at Low Temperatures

2014 ◽  
Vol 80 (8) ◽  
pp. 2493-2503 ◽  
Author(s):  
Sara Esther Diomandé ◽  
Stéphanie Chamot ◽  
Vera Antolinos ◽  
Florian Vasai ◽  
Marie-Hélène Guinebretière ◽  
...  
Keyword(s):  
Bacillus Cereus ◽  
Food Poisoning ◽  
Two Component System ◽  
Diverse Range ◽  
Component System ◽  
Content Type ◽  
Two Component ◽  
Temperature Ranges ◽  
Different Strains

ABSTRACTThe different strains ofBacillus cereuscan grow at temperatures covering a very diverse range. SomeB. cereusstrains can grow in chilled food and consequently cause food poisoning. We have identified a new sensor/regulator mechanism involved in low-temperatureB. cereusgrowth. Construction of a mutant of this two-component system enabled us to show that this system, called CasKR, is required for growth at the minimal temperature (Tmin). CasKR was also involved in optimal cold growth aboveTminand in cell survival belowTmin. Microscopic observation showed that CasKR plays a key role in cell shape during cold growth. Introducing thecasKRgenes in a ΔcasKRmutant restored its ability to grow atTmin. Although it was first identified in the ATCC 14579 model strain, this mechanism has been conserved in most strains of theB. cereusgroup. We show that the role of CasKR in cold growth is similar in otherB. cereus sensu latostrains with different growth temperature ranges, including psychrotolerant strains.

Bacillus cereus Food Poisoning

2017 ◽  
pp. 395-405 ◽  
Author(s):  
M.W. Griffiths ◽  
H. Schraft
Keyword(s):  
Bacillus Cereus ◽  
Food Poisoning
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