In silico mapping of microbial communities and stress responses in a porcine slaughterhouse and pork products through its production chain, and the efficacy of HLE disinfectant

AbstractBiofilms are a ubiquitous mode of microbial life and display an increased tolerance to different stresses. Inside biofilms, cells may experience both externally applied stresses and internal stresses that emerge as a result of growth in spatially structured communities. In this review, we discuss the spatial scales of different stresses in the context of biofilms, and if cells in biofilms respond to these stresses as a collection of individual cells, or if there are multicellular properties associated with the response. Understanding the organizational level of stress responses in microbial communities can help to clarify multicellular functions of biofilms.

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In Silico Analyses of Rice Thionin Genes and the Antimicrobial Activity of OsTHION15 Against Phytopathogens

Phytopathology ◽

10.1094/phyto-06-17-0217-r ◽

2019 ◽

Vol 109 (1) ◽

pp. 27-35

Author(s):

Krissana Boonpa ◽

Suparuk Tantong ◽

Kamonwan Weerawanich ◽

Pawinee Panpetch ◽

Onanong Pringsulaka ◽

...

Keyword(s):

Antimicrobial Activity ◽

Stress Responses ◽

In Silico ◽

Pathogenic Bacteria ◽

Hyphal Growth ◽

In Planta ◽

Recombinant Peptide ◽

Plant Disease Control ◽

Helminthosporium Oryzae ◽

In Silico Analyses

Thionins are a family of antimicrobial peptides. We performed in silico expression analyses of the 44 rice (Oryza sativa) thionins (OsTHIONs). Modulated expression levels of OsTHIONs under different treatments suggest their involvement in many processes, including biotic, abiotic, and nutritional stress responses, and in hormone signaling. OsTHION15 (LOC_Os06g32600) was selected for further characterization based on several in silico analyses. OsTHION15 in O. sativa subsp. indica ‘KDML 105’ was expressed in all of the tissues and organs examined, including germinating seed, leaves, and roots of seedlings and mature plants, and inflorescences. To investigate the antimicrobial activity of OsTHION15, we produced a recombinant peptide in Escherichia coli Rosetta-gami (DE3). The recombinant OsTHION15 exhibited inhibitory activities toward rice-pathogenic bacteria such as Xanthomonas oryzae pv. oryzae and Pectobacterium carotovorum pv. atroseptica, with minimum inhibitory concentrations of 112.6 and 14.1 µg ml−1, respectively. A significant hyphal growth inhibition was also observed toward Fusarium oxysporum f. sp. cubense and Helminthosporium oryzae. In addition, we demonstrated the in planta antibacterial activity of this peptide in Nicotiana benthamiana against X. campestris pv. glycines. These activities suggest the possible application of OsTHION15 in plant disease control.

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Development of Capsicum EST–SSR markers for species identification and in silico mapping onto the tomato genome sequence

Molecular Breeding ◽

10.1007/s11032-012-9774-z ◽

2012 ◽

Vol 31 (1) ◽

pp. 101-110 ◽

Cited By ~ 37

Author(s):

Kenta Shirasawa ◽

Kohei Ishii ◽

Cholgwang Kim ◽

Tomohiro Ban ◽

Munenori Suzuki ◽

...

Keyword(s):

Species Identification ◽

Ssr Markers ◽

Genome Sequence ◽

In Silico ◽

Tomato Genome ◽

In Silico Mapping

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Deciphering the evolution of microbial interactions: in silico studies of two-member microbial communities

10.1101/2022.01.14.476316 ◽

2022 ◽

Author(s):

Gayathri Sambamoorthy ◽

Karthik Raman

Keyword(s):

Microbial Communities ◽

In Silico ◽

Microbial Interactions ◽

Interaction Patterns ◽

Wild Type ◽

Community Function ◽

Evolutionary Forces ◽

In Silico Studies ◽

Wide Range ◽

In The Wild

Microbes thrive in communities, embedded in a complex web of interactions. These interactions, particularly metabolic interactions, play a crucial role in maintaining the community structure and function. As the organisms thrive and evolve, a variety of evolutionary processes alter the interactions among the organisms in the community, although the community function remains intact. In this work, we simulate the evolution of two-member microbial communities in silico to study how evolutionary forces can shape the interactions between organisms. We employ genomescale metabolic models of organisms from the human gut, which exhibit a range of interaction patterns, from mutualism to parasitism. We observe that the evolution of microbial interactions varies depending upon the starting interaction and also on the metabolic capabilities of the organisms in the community. We find that evolutionary constraints play a significant role in shaping the dependencies of organisms in the community. Evolution of microbial communities yields fitness benefits in only a small fraction of the communities, and is also dependent on the interaction type of the wild-type communities. The metabolites cross-fed in the wild-type communities appear in only less than 50% of the evolved communities. A wide range of new metabolites are cross-fed as the communities evolve. Further, the dynamics of microbial interactions are not specific to the interaction of the wild-type community but vary depending on the organisms present in the community. Our approach of evolving microbial communities in silico provides an exciting glimpse of the dynamics of microbial interactions and offers several avenues for future investigations.

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Stressor interactions under differential exogenous microbial exposure in Daphnia magna

10.31219/osf.io/3vgdh ◽

2021 ◽

Author(s):

Shira Houwenhuyse ◽

Lore Bulteel ◽

Naina Goel ◽

Isabel Vanoverberghe ◽

Ellen Decaestecker

Keyword(s):

Body Size ◽

Microbial Communities ◽

Daphnia Magna ◽

Stress Responses ◽

Multiple Stressors ◽

Natural Environments ◽

Laboratory Setting ◽

Natural Conditions ◽

Aspergillus Aculeatus ◽

Diverse Microbial Community

Studies on stressor responses are often performed in controlled laboratory settings. The microbial communities in laboratory setting often differ from the natural environment, which could ultimately be reflected in different stress responses. In this study, we investigated how stressor responses differed between laboratory and natural conditions in Daphnia magna when exposed to single or multiple stressors. Daphnia individuals were exposed to the toxic cyanobacterium Microcystis aeruginosa and a fungal infection, Aspergillus aculeatus like type. Three genotypes were included to investigate genotype-specific responses. Survival, reproduction and body size were monitored for three weeks and gut microbial communities were sampled and characterized at the end of the experiment. Our study shows that natural environments have a more diverse microbial community compared with laboratory conditions, which was ultimately reflected in the gut microbiomes after inoculation. Stressor responses in Daphnia were affected by their bacterial environment for survival, but not for fecundity and body size. Fecuntiy and body size did show a main stressor effect, which could possibly be linked with stessor-specific microbiomes (for Microcystis and the combined stressor treatment). In addition, genotype-specific responses were detected for survival and fecundity, which could be linked with the selective capabilities of the Daphnia genotypes to select beneficial or neutral microbial stains from the environment.

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In Silico Mapping of Complex Disease-Related Traits in Mice

Science ◽

10.1126/science.1058889 ◽

2001 ◽

Vol 292 (5523) ◽

pp. 1915-1918 ◽

Cited By ~ 212

Author(s):

A. Grupe

Keyword(s):

In Silico ◽

Complex Disease ◽

In Silico Mapping

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Small extracellular vesicles convey the stress-induced adaptive responses of melanoma cells

Scientific Reports ◽

10.1038/s41598-019-51778-6 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 7

Author(s):

Maria Harmati ◽

Edina Gyukity-Sebestyen ◽

Gabriella Dobra ◽

Laszlo Janovak ◽

Imre Dekany ◽

...

Keyword(s):

Oxidative Stress ◽

Extracellular Vesicles ◽

Stress Responses ◽

In Silico ◽

Specific Response ◽

Response Patterns ◽

Adaptive Responses ◽

Mediated Communication ◽

Ki 67

Abstract Exosomes are small extracellular vesicles (sEVs), playing a crucial role in the intercellular communication in physiological as well as pathological processes. Here, we aimed to study whether the melanoma-derived sEV-mediated communication could adapt to microenvironmental stresses. We compared B16F1 cell-derived sEVs released under normal and stress conditions, including cytostatic, heat and oxidative stress. The miRNome and proteome showed substantial differences across the sEV groups and bioinformatics analysis of the obtained data by the Ingenuity Pathway Analysis also revealed significant functional differences. The in silico predicted functional alterations of sEVs were validated by in vitro assays. For instance, melanoma-derived sEVs elicited by oxidative stress increased Ki-67 expression of mesenchymal stem cells (MSCs); cytostatic stress-resulted sEVs facilitated melanoma cell migration; all sEV groups supported microtissue generation of MSC-B16F1 co-cultures in a 3D tumour matrix model. Based on this study, we concluded that (i) molecular patterns of tumour-derived sEVs, dictated by the microenvironmental conditions, resulted in specific response patterns in the recipient cells; (ii) in silico analyses could be useful tools to predict different stress responses; (iii) alteration of the sEV-mediated communication of tumour cells might be a therapy-induced host response, with a potential influence on treatment efficacy.

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Comprehensive In Silico Characterization and Expression Profiling of Nine Gene Families Associated with Calcium Transport in Soybean

Agronomy ◽

10.3390/agronomy10101539 ◽

2020 ◽

Vol 10 (10) ◽

pp. 1539 ◽

Cited By ~ 1

Author(s):

Houqing Zeng ◽

Bingqian Zhao ◽

Haicheng Wu ◽

Yiyong Zhu ◽

Huatao Chen

Keyword(s):

Stress Responses ◽

Expression Profiling ◽

In Silico ◽

Growth Regulation ◽

Expression Profiles ◽

Phosphorus Deficiency ◽

Critical Role ◽

Functional Characterization ◽

Gene Families ◽

Transport Proteins

Calcium (Ca2+) plays a critical role in the regulation of growth and development and environmental stress responses in plants. The membrane-associated Ca2+ transport proteins are required to mediate Ca2+ signaling and maintain Ca2+ homeostasis. Ca2+ channels, pumps (ATPases), and antiporters are three major classes of Ca2+ transporters. Although the genome-wide analysis of Ca2+ transporters in model plants Arabidopsis and rice have been well documented, the identification, classification, phylogenesis, expression profiles, and physiological functions of Ca2+ transport proteins in soybean are largely unknown. In this study, a comprehensive in silico analysis of gene families associated with Ca2+ transport was conducted, and a total of 207 putative Ca2+ transporter genes have been identified in soybean. These genes belong to nine different families, such as Ca2+-ATPase, Ca2+/cation antiporter, cyclic nucleotide-gated ion channel (CNGC), and hyperosmolality induced cytosolic Ca2+ concentration channel (OSCA). Detailed analysis of these identified genes was performed, including their classification, phylogenesis, protein domains, chromosomal distribution, and gene duplication. Expression profiling of these genes was conducted in different tissues and developmental stages, as well as under stresses using publicly available RNA-seq data. Some genes were found to be predominantly expressed in specific tissues like flowers and nodules, and some genes were found to be expressed strongly during seed development. Seventy-four genes were found to be significantly and differentially expressed under abiotic and biotic stresses, such as salt, phosphorus deficiency, and fungal pathogen inoculation. In addition, hormonal signaling- and stress response-related cis-elements and potential microRNA target sites were analyzed. This study suggests the potential roles of soybean Ca2+ transporters in stress responses and growth regulation, and provides a basis for further functional characterization of putative Ca2+ transporters in soybean.

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