Areas covered: Researchers worldwide have contributed innovative experimental and computational approaches that have driven the rapidly evolving field of ‘functional proteomics’. These include mass spectrometry-based methods to characterize macromolecular complexes on a global-scale and sophisticated data analysis tools – most notably machine learning – that allow for the generation of high-quality protein association maps.
Expert commentary: Here, we recount some key lessons learned, with an emphasis on successful workflows, and challenges, arising from our own and other groups’ ongoing efforts to generate, interpret and report proteome-scale interaction networks in increasingly diverse biological contexts. 相似文献
Areas covered: This article reviews the existing Boolean network modeling approaches, which provide in comparison with alternative modeling techniques several advantages for the processing of proteomics data. Application of methods for inference, reduction and validation of protein co-expression networks that are derived from quantitative high-throughput proteomics measurements is presented. It’s also shown how Boolean models can be used to derive system-theoretic characteristics that describe both the dynamical behavior of such networks as a whole and the properties of different cell states (e.g. healthy or diseased cell states). Furthermore, application of methods derived from control theory is proposed in order to simulate the effects of therapeutic interventions on such networks, which is a promising approach for the computer-assisted discovery of biomarkers and drug targets. Finally, the clinical application of Boolean modeling analyses is discussed.
Expert commentary: Boolean modeling of proteomics data is still in its infancy. Progress in this field strongly depends on provision of a repository with public access to relevant reference models. Also required are community supported standards that facilitate input of both proteomics and patient related data (e.g. age, gender, laboratory results, etc.). 相似文献
Areas covered: This review highlights recent developments in proteomic tools that facilitate the discovery of AMPs, RiPPs and NRPs as well as the elucidation of action mechanisms of AMPs and resistance mechanisms of pathogens to them.
Expert commentary: Proteomic approaches have emerged as useful tools for the study of bioactive peptides, especially mass spectrometry-based peptidomics profiling, a promising strategy for AMP discovery. Furthermore, the rapidly expanding fields of genome mining and genome sequencing techniques, as well as mass spectrometry, have revolutionized the discovery of novel RiPPs and NRPs from complex biological samples. 相似文献
Aims: To apply new quantitative methods to assess the sensitivity of such terrain to physical stress.
Methods: We investigated two components of the mechanical properties of the terrain on 10 plateaux underlain by several different lithologies: the tensile strength of the vegetation mat and underlying root zone, and the shear and compressional strengths of the substrate.
Results: Significant differences in tensile strength occur amongst plant communities, but there is also large within-site and between-site variation for particular communities. A significant component of such variability is attributable to the proportional representation of co-dominant species within communities, and inter-site variability is partly explained by substrate granulometry: particular communities exhibit lower strength characteristics when rooted in sandy substrates derived from coarse-grained lithologies than the same communities on silt-rich soils derived from fine-grained lithologies.
Conclusions: Terrain sensitivity to physical stress is conditioned by the interaction of vegetation and substrate characteristics. Generally, grass-dominated (particularly Nardus-dominated) communities tend to be most robust, and communities dominated by bryophytes and prostrate Calluna vulgaris are typically most sensitive. We identify a continuum of substrate strength: peat is the most sensitive substrate type, followed by other organic-rich soils, sandy matrix-supported substrates and silt-rich matrix-supported substrates. Clast-supported substrates and openwork blockfields are the most robust substrate types. Because the near-surface layers of mineral substrates are weakest, erosion is likely to remove these to expose the underlying robust but sterile clast-supported layers, altering soil status and inhibiting plant recolonisation on eroded substrates. 相似文献
Results: Oleaginous yeasts such as Rhodosporidium toruloides, Yarrowia lipolytica, Rhodotorula mucilaginosa, and Aureobasidium melanogenum, which can accumulate over 50% lipid of their cell dry weight, have many advantages over other oleaginous microorganisms. The fatty acids from the oleaginous yeasts have many potential applications. Many oleaginous yeasts have now been genetically modified to over-produce fatty acids and their derivatives. The most important features of the oleaginous yeasts are that they have special enzymatic systems for enhanced biosynthesis and regulation of fatty acids in their lipid particles. Recently, some oleaginous yeasts such as R. toruloides have been found to have a unique fatty acids synthetase and other oleaginous yeasts such as A. melanogenum have a unique highly reducing polyketide synthase (HR-PKS) involved in the biosynthesis of hydroxyl fatty acids.
Conclusions: It is necessary to further enhance lipid biosynthesis using metabolic engineering and explore new applications of fatty acids in biotechnology. 相似文献
Methods: Quinolinic acid, a metabolite of the kynurenine pathway of tryptophan catabolism, plays a role in the oxidative stress associated with many neurological disorders and is used to simulate disorders such as Parkinson’s disease.
Results: In these models, phytochemicals have been shown to reduce striatal lesion size, reduce inflammation and prevent lipid peroxidation caused by quinolinic acid.
Conclusion: These results suggest that phenolic compounds, a class of phytochemicals, including flavonoids and diarylheptanoids, should be further studied to develop new treatments for oxidative stress related neurological disorders. 相似文献
Objective: To identify potential epigenomic biomarkers of health in women aged 18–40 participating in a six-month lifestyle intervention, next level health.
Materials and methods: Methylation data were obtained by reduced representation bisulphite sequencing of 21 female intervention participants as well as three non-participants. The Differential Methylation Analysis Package (DMAP) was used to investigate inter- and intra-individual variability and to identify potential targets of transient epigenetic control in the population studied.
Results: Eleven genes were identified as significantly differentially methylated post- intervention in all 21 participants. 1884 genomic locations were found to be differentially methylated amongst the total female population studied representing potential epigenomic biomarkers.
Conclusions: The ability to demonstrate epigenetic changes arising from a lifestyle intervention can provide key information on the relationship between gene regulation, human behaviour and health. 相似文献
Areas covered: To understand the molecular mechanisms of lung cancer and its subtypes, chronic obstructive pulmonary disease (COPD), asthma and others, great efforts have been taken to identify numerous relevant proteins by MS-based clinical proteomic approaches. Since lung cancer is a multifactorial disease that is biologically associated with asthma and COPD among various lung diseases, this study focused on proteomic studies on biomarker discovery using various clinical specimens for lung cancer, COPD, and asthma.
Expert commentary: MS-based exploratory proteomics utilizing clinical specimens, which can incorporate both experimental and bioinformatic analysis of protein-protein interaction and also can adopt proteogenomic approaches, makes it possible to reveal molecular networks that are relevant to a disease subgroup and that could differentiate between drug responders and non-responders, good and poor prognoses, drug resistance, and so on. 相似文献
Objective: In this review, we describe the main discoveries leading to the idea of using circulating microparticles as a promising and complementary tool in the evaluation of cardiovascular risk.
Methods: A Medline search for the terms cardiovascular diseases, microparticles, miRNAs, diagnosis, prognosis, biomarkers and microvesicles was performed.
Results: We found (i) nine articles, which were relevant to forming the idea of using microparticles as biomarkers in CVDs, and (ii) 15 and 12 experimental clinical studies which describe their potential in primary and secondary CVD prevention, respectively.
Conclusions: The levels of circulating microparticles have been associated with cardiovascular damage in asymptomatic patients as well as in patients who suffered a cardiovascular event, becoming promising diagnostics or prediction biomarkers in recent years. 相似文献