An integrated computational and experimental study to investigate Staphylococcus aureus metabolism

Islam, Mohammad Mazharul; Thomas, Vinai Chittezham; Beek, Matthew Van; Ahn, Jongsam; Alqarzaee, Abdulelah A.; Zhou, Chunyi; Fey, Paul D.; Bayles, Kenneth W.; Saha, Rajib

doi:10.1038/s41540-019-0122-3

Cited by 13 publications

(1 citation statement)

References 93 publications

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“…This classification is available (in tabular form) at shorturl.at/D1234. [24], [15] [18], [17], [20], [22], [25], Techniques [27], [28], [43], [64], [30], [32], [34], [38], [40], [45], [46], [47], [49], [54], [55], [56], [57], [59], [60], [61], [66], [68], [69], [70], [73], [74], [75], [77], [26], [42], [44], [11], [13], [36]. [12], [14], [16], [19], [21], [23], [29], [31], [35], [39], [41], …”

Section: Data Extraction and Classificationmentioning

confidence: 99%

Data Curation and Optimization Techniques: A Systematic Mapping Study

Azevedo

Musicante

Costa

2022

Preprint

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We develop a Systematic Mapping Study to observe trends and research opportunities around the concepts and techniques used in Data Curation for Big Data. Our work investigates scientific publications with the aim of identifying how data curation has been used recently, to organize and publish big data corpora. We are interested in browsing, identifying the mathematical and computational tools used in data curation. We focus on identifying how data curation has been modeled in different scenarios and which computational/mathematical techniques have contributed to improve data curation, with the aim of answering the following questions: (i) What mathematical fields have most contributed in the context of Data Curation? (ii) Which classes of optimization algorithms are used in the context of Data Curation? (iii) What application domains have benefited the most from Data Curation? While our main focus is on the definition of new methods and algorithms, we identified a large number of papers that concentrates just on applying known techniques to specific domains. Our study may be useful to identify challenges and opportunities for further theoretical studies, as well as to show the use of some formal techniques in real-life applications.

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Section: Data Extraction and Classificationmentioning

confidence: 99%

Data Curation and Optimization Techniques: A Systematic Mapping Study

Azevedo

Musicante

Costa

2022

Preprint

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Metabolic potential of microbial community and distribution mechanism of Staphylococcus species during broad bean paste fermentation

Jia

Niu

et al. 2021

Food Research International

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Staphylococcal ClpXP protease targets the cellular antioxidant system to eliminate fitness-compromised cells in stationary phase

Alqarzaee

Chaudhari

Islam

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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The transition from growth to stationary phase is a natural response of bacteria to starvation and stress. When stress is alleviated and more favorable growth conditions return, bacteria resume proliferation without a significant loss in fitness. Although specific adaptations that enhance the persistence and survival of bacteria in stationary phase have been identified, mechanisms that help maintain the competitive fitness potential of nondividing bacterial populations have remained obscure. Here, we demonstrate that staphylococci that enter stationary phase following growth in media supplemented with excess glucose, undergo regulated cell death to maintain the competitive fitness potential of the population. Upon a decrease in extracellular pH, the acetate generated as a byproduct of glucose metabolism induces cytoplasmic acidification and extensive protein damage in nondividing cells. Although cell death ensues, it does not occur as a passive consequence of protein damage. Instead, we demonstrate that the expression and activity of the ClpXP protease is induced, resulting in the degeneration of cellular antioxidant capacity and, ultimately, cell death. Under these conditions, inactivation of either clpX or clpP resulted in the extended survival of unfit cells in stationary phase, but at the cost of maintaining population fitness. Finally, we show that cell death from antibiotics that interfere with bacterial protein synthesis can also be partly ascribed to the corresponding increase in clpP expression and activity. The functional conservation of ClpP in eukaryotes and bacteria suggests that ClpP-dependent cell death and fitness maintenance may be a widespread phenomenon in these domains of life.

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An integrated computational and experimental study to investigate Staphylococcus aureus metabolism

Cited by 13 publications

References 93 publications

Data Curation and Optimization Techniques: A Systematic Mapping Study

Data Curation and Optimization Techniques: A Systematic Mapping Study

Metabolic potential of microbial community and distribution mechanism of Staphylococcus species during broad bean paste fermentation

Staphylococcal ClpXP protease targets the cellular antioxidant system to eliminate fitness-compromised cells in stationary phase

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