Analysis of Pseudocercospora fijiensis genes upregulated during early interaction with Musa acuminata (var. Dwarf Cavendish)

Pseudocercospora fijiensis is a filamentous, hemi[B1] biotrophic fungus whose infection process in banana comprises biotrophic and necrotrophic phases; the biotrophic phase is the longer and less damaging of the two but is nonetheless a crucial stage of fungal establishment in the host. To discover the genes essential in this stage, we conducted an interaction experiment to isolate the transcriptome of the P. fijiensis and Musa acuminata interaction during the first 9 days of infection. Of more than 7000 P. fijiensis genes identified, the fifteen most highly expressed genes (RPKM>500) were analyzed. Specific non-canonical effector candidates were identified following in silico characterization which may be fundamental to pathogenicity. This report reveals essential details of a poorly-elucidated stage of the P. fijiensis-Musa sp. pathosystem.

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THERMOCHEMICAL ENERGY STORAGE: FROM IN-SILICO CHARACTERIZATION TO FULL-SCALE EXPERIMENTATION

10.1615/ihtc16.kn.000024 ◽

2018 ◽

Author(s):

E. Iype ◽

Huaichen Zhang ◽

A.D. Pathak ◽

Shuiquan Lan ◽

C. Ferchaud ◽

...

Keyword(s):

Energy Storage ◽

In Silico ◽

Full Scale ◽

In Silico Characterization

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IN VITRO/IN SILICO CHARACTERIZATION OF ACTIVE AND PASSIVE STRESSES IN CARDIAC MUSCLE

International Journal for Multiscale Computational Engineering ◽

10.1615/intjmultcompeng.2011002352 ◽

2012 ◽

Vol 10 (2) ◽

pp. 171-188 ◽

Cited By ~ 7

Author(s):

Markus Boel ◽

Oscar J. Abilez ◽

Ahmed N Assar ◽

Christopher K. Zarins ◽

Ellen Kuhl

Keyword(s):

Cardiac Muscle ◽

In Silico ◽

In Silico Characterization

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In-Vitro and In-Silico Characterization of Xylose Reductase from Emericella nidulans

Current Chemical Biology ◽

10.2174/2212796812666180622103906 ◽

2019 ◽

Vol 13 (2) ◽

pp. 159-170 ◽

Cited By ~ 1

Author(s):

Vishal Ahuja ◽

Aashima Sharma ◽

Ranju Kumari Rathour ◽

Vaishali Sharma ◽

Nidhi Rana ◽

...

Keyword(s):

Production Process ◽

In Silico ◽

Xylose Reductase ◽

In Silico Analysis ◽

Emericella Nidulans ◽

Higher Temperature ◽

In Silico Characterization ◽

Silico Analysis

Background: Lignocellulosic residues generated by various anthropogenic activities can be a potential raw material for many commercial products such as biofuels, organic acids and nutraceuticals including xylitol. Xylitol is a low-calorie nutritive sweetener for diabetic patients. Microbial production of xylitol can be helpful in overcoming the drawbacks of traditional chemical production process and lowring cost of production. Objective: Designing efficient production process needs the characterization of required enzyme/s. Hence current work was focused on in-vitro and in-silico characterization of xylose reductase from Emericella nidulans. Methods: Xylose reductase from one of the hyper-producer isolates, Emericella nidulans Xlt-11 was used for in-vitro characterization. For in-silico characterization, XR sequence (Accession No: Q5BGA7) was used. Results: Xylose reductase from various microorganisms has been studied but the quest for better enzymes, their stability at higher temperature and pH still continues. Xylose reductase from Emericella nidulans Xlt-11 was found NADH dependent and utilizes xylose as its sole substrate for xylitol production. In comparison to whole cells, enzyme exhibited higher enzyme activity at lower cofactor concentration and could tolerate higher substrate concentration. Thermal deactivation profile showed that whole cell catalysts were more stable than enzyme at higher temperature. In-silico analysis of XR sequence from Emericella nidulans (Accession No: Q5BGA7) suggested that the structure was dominated by random coiling. Enzyme sequences have conserved active site with net negative charge and PI value in acidic pH range. Conclusion: Current investigation supported the enzyme’s specific application i.e. bioconversion of xylose to xylitol due to its higher selectivity. In-silico analysis may provide significant structural and physiological information for modifications and improved stability.

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In Silico Characterization of Toxin-Antitoxin Systems in Campylobacter Isolates Recovered from Food Sources and Sporadic Human Illness

Genes ◽

10.3390/genes12010072 ◽

2021 ◽

Vol 12 (1) ◽

pp. 72

Author(s):

Bishoy Wadie ◽

Mohamed A. Abdel-Fattah ◽

Alshymaa Yousef ◽

Shaimaa F. Mouftah ◽

Mohamed Elhadidy ◽

...

Keyword(s):

Environmental Conditions ◽

In Silico ◽

Antimicrobial Agents ◽

Food Sources ◽

Model Organisms ◽

Food Borne ◽

Food Borne Illness ◽

Human Illness ◽

Clonal Population Structure ◽

In Silico Characterization

Campylobacter spp. represents the most common cause of gastroenteritis worldwide with the potential to cause serious sequelae. The ability of Campylobacter to survive stressful environmental conditions has been directly linked with food-borne illness. Toxin-antitoxin (TA) modules play an important role as defense systems against antimicrobial agents and are considered an invaluable strategy harnessed by bacterial pathogens to survive in stressful environments. Although TA modules have been extensively studied in model organisms such as Escherichia coli K12, the TA landscape in Campylobacter remains largely unexplored. Therefore, in this study, a comprehensive in silico screen of 111 Campylobacter (90 C.jejuni and 21 C.coli) isolates recovered from different food and clinical sources was performed. We identified 10 type II TA systems belonging to four TA families predicted in Campylobacter genomes. Furthermore, there was a significant association between the clonal population structure and distribution of TA modules; more specifically, most (12/13) of the Campylobacter isolates belonging to ST-21 isolates possess HicB-HicA TA modules. Finally, we observed a high degree of shared synteny among isolates bearing certain TA systems or even coexisting pairs of TA systems. Collectively, these findings provide useful insights about the distribution of TA modules in a heterogeneous pool of Campylobacter isolates from different sources, thus developing a better understanding regarding the mechanisms by which these pathogens survive stressful environmental conditions, which will further aid in the future designing of more targeted antimicrobials.

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