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Understanding the Metabolomics of Medicinal Plants under Environmental Pollution
Published in Azamal Husen, Environmental Pollution and Medicinal Plants, 2022
Prachi Sao, Rahat Parveen, Aryan Khattri, Shubhra Sharma, Neha Tiwari, Sachidanand Singh
Quality soil yields healthy plants and products that play a vital role in vegetation. Several methods are used to combat the risk of soil erosion and ill plants (Cunningham et al., 1995). Madseniana, discovered at Cornell University, breaks down organic materials. Most species of Paraburkholderia madseniana sp. nov. are known for their ability to break down aromatic chemicals, and they can develop root nodules to store atmospheric nitrogen (Wilhelm et al., 2020). Worldwide, the detrimental effects of air pollution on the ecosystem are evident (Saxena et al., 2013; Seyyednejad et al., 2011). Smog-free towers are a competent invention to reduce air pollution. The tower sucks in pollution and expels clean air using electricity equivalent to the amount of a water boiler. The tower has faced a backlash from China after the country considered it incompetent because of not achieving desirable results (Laxmipriya et al., 2018). Another invention, the fog catcher, works in the direction of harvesting fog, working on a non-complex mechanism. The mist is caught in vertical nets trickling into a system where it is filtered and mixed with groundwater, ultimately providing clean water to households. The fog catcher has been developed by Qadir et al., but this method is not efficient on a large scale (Qadir et al., 2018).
Intestinal microflora provides biomarkers for infertile women with endometrial polyps
Published in Biomarkers, 2022
Jun Lan, Chunlin Chen, Ling Chen, Ping Liu
To illustrate the diagnostic value of the intestinal bacterial microbiota in infertile women with EPs, we constructed a model based on the differences in core genera between every two groups (InfEP– and Fertile groups, InfEP– and InfEP + groups, Fertile and InfEP + groups). The core genera that were significantly different between the groups were chosen from the top 10 genera in terms of abundance. Finally, we found that the intestinal bacterial microbiota in the Fertile and InfEP + groups best predicted EPs in infertile women, and the top 10 microbiota genera were: g__Acinetobacter, g__Aeromicrobium, g__Arthrobacter, g__Brevundimonas, g__Burkholderia-Caballeronia-Paraburkholderia, g__Massilia, g__Pseudoduganella, g__RB41, g__Ralstonia, and g__Rhodococcus. In general, the predictive model exhibited a high discriminatory potential in the discovery analysis of the Fertile and InfEP + groups, with an area under the curve of 89% (95% confidence interval: 0.79–0.96) (Figure 6). The comparison of predictive efficacies among the three groups is presented in Table 2. The models built using the other group pairs, Fertile and InfEP– (Supplementary Figure 2) and InfEP + and InfEP– (Supplementary Figure 3), were of lesser predictive ability (the closer the area under the curve is to 1, the better is the diagnostic effect).
Drug discovery through the isolation of natural products from Burkholderia
Published in Expert Opinion on Drug Discovery, 2021
Adam Foxfire, Andrew Riley Buhrow, Ravi S. Orugunty, Leif Smith
One promising source of novel antibiotics is the genus Burkholderia, a group of Gram-negative, non-sporulating bacteria which produce a broad array of antimicrobials which are the focus of this review. Its members are ubiquitous and primarily dwell in soil but can also be found within the rhizosphere of plants and in groundwater. Originally discovered in 1950 as part of the Pseudomonas genus, the RNA homology group II of Pseudomonas was reclassified into the genus Burkholderia [8]. Since this reclassification in 1992, approximately fifty species of Burkholderia were reclassified as Paraburkholderia, in 2016 [9,10]. Currently, Burkholderia contains 125 well-established members with additional species proposed [9]. Members of Burkholderia are distinct from most bacteria in that their genomes have multi-chromosomal organization, typically containing 2 to 3 chromosomes. This and their ability to utilize a wide variety of carbon sources gives rise to significant ecological diversity within the genus [11]. While this review will be focusing on the antimicrobial capabilities of the Burkholderia genus, some attention should be given to the potentially life-threatening illnesses caused by B. mallei, B. pseudomallei, and the B. cepacia complex (Bcc).
An integrated workflow for enhanced taxonomic and functional coverage of the mouse fecal metaproteome
Published in Gut Microbes, 2021
Nicolas Nalpas, Lesley Hoyles, Viktoria Anselm, Tariq Ganief, Laura Martinez-Gili, Cristina Grau, Irina Droste-Borel, Laetitia Davidovic, Xavier Altafaj, Marc-Emmanuel Dumas, Boris Macek
Thus, without a PSM count threshold, we correlated the taxonomic abundance derived from each software annotation against the known input protein from Kleiner and colleagues’ artificial samples (Figure 3c). Overall, the Unipept software provided the highest correlation (Spearman ρ = .83), as well as at most taxonomic levels (including species). Interestingly, the dynamic range of taxon detection by MS spanned two orders of magnitude, with Salmonella enterica being approximately 230 times more abundant than Nitrosomonas europaeae (Figure 3d, Table S3). Unipept was also the only software allowing identification of Nitrosomonas ureae, Paraburkholderia xenovorans and Nitrosospira multiformis. Importantly, none of the software could identify the five viral organisms present in the samples, the reason being technical since no peptide coming from those viral proteins was detected by MS. Finally, we assessed the impact of different database search strategies on taxonomic abundance derived by the Unipept software (Figure S3F). Similarly to our findings from the previous section, the F-measure metric highlighted the superiority of single-step strategy when it comes to taxonomic identification. Taken together, we show that, based on different metrics and samples of known composition, the Unipept software provides better taxonomic annotation in comparison to Kraken2 and Diamond.