scholarly journals In Silico Analysis of Genetic VapC Profiles from the Toxin-Antitoxin Type II VapBC Modules among Pathogenic, Intermediate, and Non-Pathogenic Leptospira

2019 ◽  
Vol 7 (2) ◽  
pp. 56
Author(s):  
Alexandre Lopes ◽  
Bruna Azevedo ◽  
Rebeca Emídio ◽  
Deborah Damiano ◽  
Ana Nascimento ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
In Silico Analysis ◽  
Amino Acid Sequences ◽  
Protein Alignment ◽  
Pathogenic Leptospira ◽  
Leptospira Spp ◽  
Unique Species ◽  
Silico Analysis ◽  
Leptospira Species ◽  
Complex Manner

Pathogenic Leptospira spp. is the etiological agent of leptospirosis. The high diversity among Leptospira species provides an array to look for important mediators involved in pathogenesis. Toxin-antitoxin (TA) systems represent an important survival mechanism on stress conditions. vapBC modules have been found in nearly one thousand genomes corresponding to about 40% of known TAs. In the present study, we investigated TA profiles of some strains of Leptospira using a TA database and compared them through protein alignment of VapC toxin sequences among Leptospira spp. genomes. Our analysis identified significant differences in the number of putative vapBC modules distributed in pathogenic, saprophytic, and intermediate strains: four in L. interrogans, three in L. borgpetersenii, eight in L. biflexa, and 15 in L. licerasiae. The VapC toxins show low identity among amino acid sequences within the species. Some VapC toxins appear to be exclusively conserved in unique species, others appear to be conserved among pathogenic or saprophytic strains, and some appear to be distributed randomly. The data shown here indicate that these modules evolved in a very complex manner, which highlights the strong need to identify and characterize new TAs as well as to understand their regulation networks and the possible roles of TA systems in pathogenic bacteria.

scholarly journals High Diversity of Leptospira Species Infecting Bats Captured in the Uraba Region (Antioquia-Colombia)

2021 ◽  
Author(s):  
Fernando P Monroy ◽  
Sergio Solari ◽  
Juan Alvaro Lopez ◽  
Piedad Agudelo-Florez ◽  
Ronald Guillermo Pelaez-Sanchez
Keyword(s):  
Pathogenic Bacteria ◽  
Zoonotic Disease ◽  
Feeding Strategies ◽  
Endemic Region ◽  
Glossophaga Soricina ◽  
Leptospira Spp ◽  
Leptospira Borgpetersenii ◽  
Molossus Molossus ◽  
Reservoir Hosts ◽  
Leptospira Species

Leptospirosis is a globally distributed zoonotic disease caused by pathogenic bacteria of the genus Leptospira. This zoonotic disease affects humans, domestic, or wild animals. Colombia is considered an endemic country for leptospirosis; and Antioquia is the second department in Colombia with the highest number of reported leptospirosis cases. Currently, many studies report bats as reservoirs of Leptospira spp. but its prevalence in these mammals is unknown. In the present study we aimed to better understand the role of bats as reservoir hosts of Leptospira species and to evaluate the genetic diversity of circulating Leptospira species in Antioquia-Colombia. We captured 206 bats in the municipalities of Chigorodó (43 bats), Carepa (43 bats), Apartadó (39 bats), Turbo (40 bats), and Necoclí (41 bats) in the Urabá region (Antioquia-Colombia). Twenty bats were positive for Leptospira spp. infection (20/206 - 9,70%) and the species of infected bats were Carollia perspicillata, Dermatura rava, Glossophaga soricina, Molossus molossus, Artibeus planirostris, and Uroderma convexum. These species have different feeding strategies such as frugivorous, insectivores, and nectarivores. The infecting Leptospira species identified were Leptospira borgpetersenii (3/20 – 15%), Leptospira alexanderi (2/20 – 10%), Leptospira noguchii (6/20 – 30%), Leptospira interrogans (3/2 – 15%), and Leptospira kirschneri (6/20 – 30%). The results of this research show the importance of bats in the epidemiology, ecology and evolution of Leptospira in this host-pathogen association. This is the first step in deciphering the role played by bats in the epidemiology of human leptospirosis in the endemic region of Uraba (Antioquia-Colombia).

Detection and in silico Analysis of rmpA Gene from Soilborne Pathogenic Bacteria

2019 ◽  
Vol 9 (o3) ◽  
Author(s):  
Laith AbdulHassan Mohamed-Jawad
Keyword(s):  
Klebsiella Pneumoniae ◽  
Staphylococcus Epidermidis ◽  
Pathogenic Bacteria ◽  
In Silico Analysis ◽  
Multiple Sequence ◽  
Bacterial Gene ◽  
New Approach ◽  
Geological Processes ◽  
Bacillus Spp ◽  
Silico Analysis

Soil serves as an ecosystem for diverse microbes that perform various roles and that range from useful organisms in biological and geological processes to dangerous transmitters of diseases. Most type of soilborne bacteria are harmful to humans and causing severe problems. Klebsiella pneumoniae consider a serious nosocomial pathogen that cause pneumonia, UTIs, wound and liver abscesses. One hundred fifty (150) soil samples isolated randomly during the period November 2014- February 2015. Bacterium Klebsiella pneumoniae was the commonest pathogen (36.70%) followed by Staphylococcus aureus (22.78%), Staphylococcus epidermidis (12.65%), Bacillus spp. (10.12%), Pseudomonas aeruginosa (5.06%), Enterobacter cloacae (5.06%), Streptococcus spp.(2.53%), Citrobacter spp.(1.26%) and Pantoea spp.(1.26%) respectively. All K. pneumoniae isolates detected and confirmed by conventional PCR using rmpA gene size 530bp. The positive isolates were sequenced and search for homology. The multiple sequence alignment showed that our bacterial gene have differences in NAD-dependent epimerase and NAD (p)- binding domain sequence at different sites. The differences in the nucleotides at gene sequence for the isolated strain which may give new approach for developing higher sensitive K. pneumoniae strains and for better understanding of the rmpA gene structure that should provide new tools for disease management. Keywords:

scholarly journals Potential Biological Activities of Peptides Generated during Casein Proteolysis by Curly Kale (Brassica oleracea L. var. sabellica L.) Leaf Extract: An In Silico Preliminary Study

Foods ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2877
Author(s):  
Magdalena Polak-Berecka ◽  
Magdalena Michalak-Tomczyk ◽  
Katarzyna Skrzypczak ◽  
Katarzyna Michalak ◽  
Kamila Rachwał ◽  
...  
Keyword(s):  
In Silico ◽  
Leaf Extract ◽  
Degradation Products ◽  
Biological Activities ◽  
Protein Profile ◽  
In Silico Analysis ◽  
Amino Acid Sequences ◽  
Casein Hydrolysis ◽  
Sds Page ◽  
Silico Analysis

This study is a brief report on the proteolytic activity of curly kale leaf extract against casein. Casein degradation products and an in silico analysis of the biological activity of the peptides obtained was performed. The efficiency of casein hydrolysis by curly kale extract was determined using SDS–PAGE and by peptide concentration determination. The pattern of the enzymatic activity was determined by MALDI–TOF MS analysis. The results showed that α- and β-casein were more resistant to curly kale extract hydrolysis, whereas κ-casein was absent in the protein profile after 8 h of proteolysis, and all casein fractions were completely hydrolyzed after 24 h of incubation. Based on sequence analysis, seven peptides were identified, with molecular mass in the range of 1151–3024 Da. All the peptides were products of β-casein hydrolysis. The identified amino acid sequences were analyzed in BIOPEP, MBPDB, and FeptideDB databases in order to detect the potential activities of the peptides. In silico analysis suggests that the β-casein-derived peptides possess sequences of peptides with ACE inhibitory, antioxidant, dipeptidyl peptidase IV inhibitory, antithrombotic, immunomodulatory, and antiamnesic bioactivity. Our study was first to evaluate the possibility of applying curly kale leaf extract to generate biopeptides through β-casein hydrolysis.

scholarly journals High Diversity of Leptospira Species Infecting Bats Captured in the Urabá Region (Antioquia-Colombia)

2021 ◽  
Vol 9 (9) ◽  
pp. 1897
Author(s):  
Fernando P. Monroy ◽  
Sergio Solari ◽  
Juan Álvaro Lopez ◽  
Piedad Agudelo-Flórez ◽  
Ronald Guillermo Peláez Sánchez
Keyword(s):  
Pathogenic Bacteria ◽  
Zoonotic Disease ◽  
Feeding Strategies ◽  
Endemic Region ◽  
Glossophaga Soricina ◽  
Leptospira Spp ◽  
Leptospira Borgpetersenii ◽  
Molossus Molossus ◽  
Reservoir Hosts ◽  
Leptospira Species

Leptospirosis is a globally distributed zoonotic disease caused by pathogenic bacteria of the genus Leptospira. This zoonotic disease affects humans, domestic animals and wild animals. Colombia is considered an endemic country for leptospirosis; Antioquia is the second department in Colombia, with the highest number of reported leptospirosis cases. Currently, many studies report bats as reservoirs of Leptospira spp. but the prevalence in these mammals is unknown. The goal of this study was to better understand the role of bats as reservoir hosts of Leptospira species and to evaluate the genetic diversity of circulating Leptospira species in Antioquia-Colombia. We captured 206 bats in the municipalities of Chigorodó (43 bats), Carepa (43 bats), Apartadó (39 bats), Turbo (40 bats), and Necoclí (41 bats) in the Urabá region (Antioquia-Colombia). Twenty bats tested positive for Leptospira spp. infection (20/206—9.70%) and the species of infected bats were Carollia perspicillata, Dermanura rava, Glossophaga soricina, Molossus molossus, Artibeus planirostris, and Uroderma convexum. These species have different feeding strategies such as frugivorous, insectivores, and nectarivores. The infecting Leptospira species identified were Leptospira borgpetersenii (3/20–15%), Leptospira alexanderi (2/20–10%), Leptospira noguchii (6/20–30%), Leptospira interrogans (3/20–15%), and Leptospira kirschneri (6/20–30%). Our results showed the importance of bats in the epidemiology, ecology, and evolution of Leptospira in this host-pathogen association. This is the first step in deciphering the role played by bats in the epidemiology of human leptospirosis in the endemic region of Urabá (Antioquia-Colombia).

scholarly journals The Degenerate EAL-GGDEF Domain Protein Filp Functions as a Cyclic di-GMP Receptor and Specifically Interacts with the PilZ-Domain Protein PXO_02715 to Regulate Virulence in Xanthomonas oryzae pv. oryzae

2014 ◽  
Vol 27 (6) ◽  
pp. 578-589 ◽  
Author(s):  
Fenghuan Yang ◽  
Fang Tian ◽  
Xiaotong Li ◽  
Susu Fan ◽  
Huamin Chen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pathogenic Bacteria ◽  
In Silico Analysis ◽  
Bacterial Virulence ◽  
Xanthomonas Oryzae ◽  
Glutathione S Transferase ◽  
Ggdef Domain ◽  
Domain Protein ◽  
Silico Analysis

Degenerate GGDEF and EAL domain proteins represent major types of cyclic diguanylic acid (c-di-GMP) receptors in pathogenic bacteria. Here, we characterized a FimX-like protein (Filp) which possesses both GGDEF and EAL domains in Xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight of rice. Both in silico analysis and enzyme assays indicated that the GGDEF and EAL domains of Filp were degenerate and enzymatically inactive. However, Filp bound to c-di-GMP efficiently within the EAL domain, where Q477, E653, and F654 residues were crucial for the binding. Deletion of the filp gene in X. oryzae pv. oryzae resulted in attenuated virulence in rice and reduced type III secretion system (T3SS) gene expression. Complementation analysis with different truncated proteins indicated that REC, PAS, and EAL domains but not the GGDEF domain were required for the full activity of Filp in vivo. In addition, a PilZ-domain protein (PXO_02715) was identified as a Filp interactor by yeast two-hybrid and glutathione-S-transferase pull-down assays. Deletion of the PXO_02715 gene demonstrated changes in bacterial virulence and T3SS gene expression similar to Δfilp. Moreover, both mutants were impaired in their ability to induce hypersensitive response in nonhost plants. Thus, we concluded that Filp was a novel c-di-GMP receptor of X. oryzae pv. oryzae, and its function to regulate bacterial virulence expression might be via the interaction with PXO_02715.

scholarly journals In Silico Analysis of Extended-Spectrum β-Lactamases in Bacteria

Antibiotics ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 812
Author(s):  
Patrik Mlynarcik ◽  
Hana Chudobova ◽  
Veronika Zdarska ◽  
Milan Kolar
Keyword(s):  
In Silico ◽  
Phylogenetic Trees ◽  
Bacterial Resistance ◽  
Public Health Problem ◽  
In Silico Analysis ◽  
Amino Acid Sequences ◽  
Extended Spectrum ◽  
Wide Range ◽  
Phosphoethanolamine Transferases ◽  
Silico Analysis

The growing bacterial resistance to available β-lactam antibiotics is a very serious public health problem, especially due to the production of a wide range of β-lactamases. At present, clinically important bacteria are increasingly acquiring new elements of resistance to carbapenems and polymyxins, including extended-spectrum β-lactamases (ESBLs), carbapenemases and phosphoethanolamine transferases of the MCR type. These bacterial enzymes limit therapeutic options in human and veterinary medicine. It must be emphasized that there is a real risk of losing the ability to treat serious and life-threatening infections. The present study aimed to design specific oligonucleotides for rapid PCR detection of ESBL-encoding genes and in silico analysis of selected ESBL enzymes. A total of 58 primers were designed to detect 49 types of different ESBL genes. After comparing the amino acid sequences of ESBLs (CTX-M, SHV and TEM), phylogenetic trees were created based on the presence of conserved amino acids and homologous motifs. This study indicates that the proposed primers should be able to specifically detect more than 99.8% of all described ESBL enzymes. The results suggest that the in silico tested primers could be used for PCR to detect the presence of ESBL genes in various bacteria, as well as to monitor their spread.

Xanthomonas oryzae pv. exoribonuclease R is required for complete virulence in rice, optimal motility, and growth under stress

2021 ◽  
Author(s):  
Sharmila Roy ◽  
Pragya Mittal ◽  
Lavanya Tayi ◽  
Sahitya Bondada ◽  
Malay K Ray ◽  
...  
Keyword(s):  
Bacterial Blight ◽  
Pathogenic Bacteria ◽  
Growth Curves ◽  
In Silico Analysis ◽  
Xanthomonas Oryzae ◽  
Rnase R ◽  
Amino Acid Sequence Alignment ◽  
Suboptimal Temperature ◽  
First Time ◽  
Silico Analysis

Exoribonuclease R (RNase R) is a 3’ hydrolytic exoribonuclease that can degrade structured RNA. Mutation in RNase R affects virulence of certain human pathogenic bacteria. The aim of this study was to determine whether RNase R is required for virulence of the phytopathogen that causes bacterial blight in rice, Xanthomonas oryzae pv. oryzae (Xoo). In silico analysis has indicated that RNase R is highly conserved among various Xanthomonads. Amino acid sequence alignment of Xoo RNase R with RNase R from various taxa indicated that Xoo RNase R clustered with RNase R of order Xanthomonadales. In order to study its role in virulence, a gene disruption mutant of Xoo RNase R (rnr –) was generated. The Xoo rnr – mutant is moderately virulence deficient and the complementing strain (rnr –/pHM1::rnr) rescued the virulence deficiency of the mutant. We investigated swimming and swarming motilities in both nutrient deficient minimal and nutrient optimal media. We observed that rnr – mutant has adversely affected the swimming and swarming motilities of Xoo in optimal media. However, in nutrient deficient media only swimming motility was noticeably affected. Growth curves in optimal media at suboptimal temperature (15°C, cold stress) indicate that Xoo rnr – mutant grows slower than Xoo wild type (wt) and complementing strain (rnr –/pHM1::rnr). Taken together, we report for the first time that RNase R function is necessary for complete virulence of Xoo in rice. It is also important for motility of Xoo in media and for growth of Xoo at suboptimal temperature.

scholarly journals Molecular and Serological Prevalence of Leptospira spp. in Feral Pigs (Sus scrofa) and their Habitats in Alabama, USA

Pathogens ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 857 ◽  
Author(s):  
Anil Poudel ◽  
Md Monirul Hoque ◽  
Steven Madere ◽  
Sara Bolds ◽  
Stuart Price ◽  
...  
Keyword(s):  
Environmental Samples ◽  
Domestic Animal ◽  
Serum Samples ◽  
Pathogenic Leptospira ◽  
East Central ◽  
Feral Pigs ◽  
Leptospira Spp ◽  
Potential Pathogen ◽  
Leptospira Species

Leptospirosis is a widespread zoonosis and has been recognized as a re-emerging infectious disease in humans and a variety of wild and domestic animal species. In order to understand the prevalence and diversity of Leptospira spp. in feral pig populations of Alabama, we trapped 315 feral pigs in Bullock County east-central Alabama, and collected 97 environmental samples from riparian areas in Bullock County and Macon County east-central Alabama. Two previously published PCRs followed by DNA sequencing and BLASTn were performed to identify pathogenic Leptospira species in the kidney of feral pigs (3.2%, 10/315) as well as environmental samples collected from the habitats of feral pigs (2.1%, 2/97), but not in the whole blood samples (n = 276) or spleen (n = 51). An ELISA determined that 44.2% of serum samples (122/276) were antibody-positive for Leptospira. The identification of two pathogenic Leptospira species from environmental samples and the high sero-positivity in feral pigs suggests potential pathogen shedding from feral pigs to environments, and to humans and domestic animals. In order to better understand the risk to human health associated with feral swine presence, further studies are warranted to explore the interrelationship between Leptospira spp. shedding in the urine of feral pigs and bacterial culture to explore pathogenicity. Multi-locus sequencing typing (MLST) and microscopic agglutination tests (MAT) should be performed in future studies to make a definite determination of pathogenic Leptospira in feral pigs in Alabama.

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