scholarly journals Pro-biomics: Omics Technologies To Unravel the Role of Probiotics in Health and Disease

2021 ◽  
Author(s):  
Despoina Eugenia Kiousi ◽  
Marina Rathosi ◽  
Margaritis Tsifintaris ◽  
Pelagia Chondrou ◽  
Alex Galanis
Keyword(s):  
Probiotic Supplementation ◽  
Future Directions ◽  
Current Trends ◽  
Metabolomic Data ◽  
Analysis Of Results ◽  
Health And Disease ◽  
Multiple Levels ◽  
Comprehensive Characterization

ABSTRACT The comprehensive characterization of probiotic action has flourished during the past few decades, alongside the evolution of high-throughput, multiomics platforms. The integration of these platforms into probiotic animal and human studies has provided valuable insights into the holistic effects of probiotic supplementation on intestinal and extraintestinal diseases. Indeed, these methodologies have informed about global molecular changes induced in the host and residing commensals at multiple levels, providing a bulk of metagenomic, transcriptomic, proteomic, and metabolomic data. The meaningful interpretation of generated data remains a challenge; however, the maturation of the field of systems biology and artificial intelligence has supported analysis of results. In this review article, we present current literature on the use of multiomics approaches in probiotic studies, we discuss current trends in probiotic research, and examine the possibility of tailor-made probiotic supplementation. Lastly, we delve deeper into newer technologies that have been developed in the last few years, such as single-cell multiomics analyses, and provide future directions for the maximization of probiotic efficacy.

scholarly journals Phosphorylation of key podocyte proteins and the association with proteinuric kidney disease

2020 ◽  
Vol 319 (2) ◽  
pp. F284-F291 ◽  
Author(s):  
Di Feng
Keyword(s):  
Chronic Kidney Disease ◽  
Kidney Disease ◽  
Human Kidney ◽  
Future Directions ◽  
Genetic Studies ◽  
New Therapies ◽  
Podocyte Proteins

Podocyte dysfunction contributes to proteinuric chronic kidney disease. A number of key proteins are essential for podocyte function, including nephrin, podocin, CD2-associated protein (CD2AP), synaptopodin, and α-actinin-4 (ACTN4). Although most of these proteins were first identified through genetic studies associated with human kidney disease, subsequent studies have identified phosphorylation of these proteins as an important posttranslational event that regulates their function. In this review, a brief overview of the function of these key podocyte proteins is provided. Second, the role of phosphorylation in regulating the function of these proteins is described. Third, the association between these phosphorylation pathways and kidney disease is reviewed. Finally, challenges and future directions in studying phosphorylation are discussed. Better characterization of these phosphorylation pathways and others yet to be discovered holds promise for translating this knowledge into new therapies for patients with proteinuric chronic kidney disease.

scholarly journals Conceptualizing consumption in the imagination

2017 ◽  
Vol 18 (3) ◽  
pp. 327-347 ◽  
Author(s):  
Rebecca Jenkins ◽  
Mike Molesworth
Keyword(s):  
Consumer Research ◽  
Macro Level ◽  
Market Structures ◽  
Level Of Abstraction ◽  
Temporal Location ◽  
Individual Consumption ◽  
Presence And Absence ◽  
Comprehensive Characterization

In this article we extend theory relating to the imagination and markets by reviewing explicit and implicit work in marketing, consumer research and sociology, drawing on a broader literature that provides a more comprehensive characterization of imagining. We map consumption in the imagination in order to better define the concept and to differentiate forms of imagining according to a number of characteristics that are identified in the literature. These are as follows: (1) temporal location, (2) range of emotions, (3) degree of elaboration, (4) level of abstraction (5) purpose, and (6) prompts. We also consider the role of consumption in terms of its level of presence and absence in the imagination. We then present a trajectory of consumption in the imagination that seeks to account for the relationships and movements between forms of imagining and the marketplace, noting the importance of the imagination in terms of implications for macro-level market structures and individual consumption practice.

scholarly journals Towards Mass Spectrometry-Based Chemical Exposome: Current Approaches, Challenges, and Future Directions

Toxics ◽  
2019 ◽  
Vol 7 (3) ◽  
pp. 41 ◽  
Author(s):  
Jingchuan Xue ◽  
Yunjia Lai ◽  
Chih-Wei Liu ◽  
Hongyu Ru
Keyword(s):  
Mass Spectrometry ◽  
Data Analysis ◽  
Measurement Techniques ◽  
Future Directions ◽  
Computational Tools ◽  
High Throughput Data ◽  
Chemical Pollutants ◽  
Health And Disease ◽  
High Throughput Data Analysis

The proposal of the “exposome” concept represents a shift of the research paradigm in studying exposure-disease relationships from an isolated and partial way to a systematic and agnostic approach. Nevertheless, exposome implementation is facing a variety of challenges including measurement techniques and data analysis. Here we focus on the chemical exposome, which refers to the mixtures of chemical pollutants people are exposed to from embryo onwards. We review the current chemical exposome measurement approaches with a focus on those based on the mass spectrometry. We further explore the strategies in implementing the concept of chemical exposome and discuss the available chemical exposome studies. Early progresses in the chemical exposome research are outlined, and major challenges are highlighted. In conclusion, efforts towards chemical exposome have only uncovered the tip of the iceberg, and further advancement in measurement techniques, computational tools, high-throughput data analysis, and standardization may allow more exciting discoveries concerning the role of exposome in human health and disease.

scholarly journals Systematic multi-level analysis of an organelle proteome reveals new peroxisomal functions

2021 ◽  
Author(s):  
Eden Yifrach ◽  
Duncan Holbrook-Smith ◽  
Jérôme Bürgi ◽  
Alaa Othman ◽  
Miriam Eisenstein ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Targeting ◽  
Cellular Metabolism ◽  
Metabolomic Analysis ◽  
Health And Disease ◽  
Multi Level ◽  
Crucial Part ◽  
Level Analysis

AbstractSeventy years following the discovery of peroxisomes, their proteome remains undefined. Uncovering the complete peroxisomal proteome, the peroxi-ome, is crucial for understanding peroxisomal activities and cellular metabolism. We used high- content microscopy to uncover the peroxi-ome of the model eukaryote – Saccharomyces cerevisiae. This strategy enabled us to expand the known organellar proteome by ∼40% and paved the way for performing systematic, whole-organellar proteome assays. Coupled with targeted experiments this allowed us to discover new peroxisomal functions. By characterizing the sub-organellar localization and protein targeting dependencies into the organelle, we unveiled non-canonical targeting routes. Metabolomic analysis of the peroxi-ome revealed the role of several newly-identified resident enzymes. Importantly, we found a regulatory role of peroxisomes during gluconeogenesis, which is fundamental for understanding cellular metabolism. With the current recognition that peroxisomes play a crucial part in organismal physiology, our approach lays the foundation for deep characterization of peroxisome function in health and disease.

The Role of Machine Learning in Game Development Domain - A Review of Current Trends and Future Directions

2021 ◽  
Author(s):  
Gemma Edwards ◽  
Nicholas Subianto ◽  
David Englund ◽  
Jun Wei Goh ◽  
Nathan Coughran ◽  
...  
Keyword(s):  
Machine Learning ◽  
Game Development ◽  
Future Directions ◽  
Current Trends

scholarly journals The common marmoset monkey: avenues for exploring the prenatal, placental, and postnatal mechanisms in developmental programming of pediatric obesity

2018 ◽  
Vol 314 (5) ◽  
pp. R684-R692 ◽  
Author(s):  
Laren Riesche ◽  
Suzette D. Tardif ◽  
Corinna N. Ross ◽  
Victoria A. deMartelly ◽  
Toni Ziegler ◽  
...  
Keyword(s):  
Early Life ◽  
World Monkey ◽  
Common Marmoset ◽  
Developmental Programming ◽  
Intrauterine Environment ◽  
Future Directions ◽  
Marmoset Monkey ◽  
Health And Disease ◽  
The Common

Animal models have been critical in building evidence that the prenatal experience and intrauterine environment are capable of exerting profound and permanent effects on metabolic health through developmental programming of obesity. However, despite physiological and evolutionary similarities, nonhuman primate models are relatively rare. The common marmoset monkey ( Callithrix jacchus) is a New World monkey that has been used as a biomedical model for well more than 50 years and has recently been framed as an appropriate model for exploring early-life impacts on later health and disease. The spontaneous, multifactorial, and early-life development of obesity in the common marmoset make it a valuable research model for advancing our knowledge about the role of the prenatal and placental mechanisms involved in developmental programming of obesity. This paper provides a brief overview of obesity in the common marmoset, followed by a discussion of marmoset reproduction and placental characteristics. We then discuss the occurrence and utility of variable intrauterine environments in developmental programming in marmosets. Evidence of developmental programming of obesity will be given, and finally, we put forward future directions and innovations for including the placenta in developmental programming of obesity in the common marmoset.

scholarly journals Preliminary Characterization of Phage-like Particles from the Male-Killing Mollicute Spiroplasma poulsonii (an Endosymbiont of Drosophila)

2021 ◽  
Author(s):  
Paulino Ramirez ◽  
Justin C. Leavitt ◽  
Jason J. Gill ◽  
Mariana Mateos
Keyword(s):  
Insertion Element ◽  
Future Directions ◽  
Bacterial Populations ◽  
Endosymbiotic Bacteria ◽  
Male Killing ◽  
New Hosts ◽  
Genome Assemblies ◽  
And Control

Viruses are vastly abundant and influential in all ecosystems, and are generally regarded as pathogens. Viruses of prokaryotes (themselves highly diverse and abundant) are known as bacteriophages or phages. Phages engage in diverse associations with their hosts, and contribute to regulation of biogeochemical processes, horizontal movement of genes, and control of bacterial populations. Recent studies have revealed the influential role of phage in the association of arthropods and their heritable endosymbiotic bacteria (e.g. the Proteobacteria genera Wolbachia and Hamiltonella). Despite prior studies (~30 years ago) documenting presence of phage in the mollicute Spiroplasma infecting Drosophila, genomic sequences of such phage are lacking, and their effects on the Spiroplasma-Drosophila interaction have not been comprehensively characterized. The present work isolated phage-like particles from the male-killing Spiroplasma poulsonii (strains NSRO and MSRO-Br) harbored by Drosophila melanogaster. Isolated particles were subjected to DNA sequencing, assembly, and annotation. Our results recovered three ~19 kb phage-like contigs (two in NSRO and one in MSRO-Br), and two smaller non-phage-like contigs encoding a known Spiroplasma toxin and an insertion element. Whole or parts of the particle-derived contigs were found in the genome assemblies of members of the Spiroplasma poulsonii clade. Although our results do not allow us to distinguish whether the contigs obtained represent infective phage-like particles capable of transmitting their DNA to new hosts, their encoding of several typical phage genes suggests that they are at least remnants of functional phage. We discuss potential implications of our findings and suggest future directions.

scholarly journals Comprehensive analysis of clustered mutations in cancer reveals recurrent APOBEC3 mutagenesis of ecDNA

2021 ◽  
Author(s):  
Erik N Bergstrom ◽  
Jens-Christian Luebeck ◽  
Mia Petljak ◽  
Vineet Bafna ◽  
Paul S. Mischel ◽  
...  
Keyword(s):  
Somatic Mutations ◽  
Human Cancer ◽  
Cancer Genes ◽  
Base Substitutions ◽  
Cancer Genomes ◽  
Cancer Types ◽  
Mutational Processes ◽  
Comprehensive Characterization

Clustered somatic mutations are common in cancer genomes with prior analyses revealing several types of clustered single-base substitutions, including doublet- and multi-base substitutions, diffuse hypermutation termed omikli, and longer strand-coordinated events termed kataegis. Here, we provide a comprehensive characterization of clustered substitutions and clustered small insertions and deletions (indels) across 2,583 whole-genome sequenced cancers from 30 cancer types. While only 3.7% of substitutions and 0.9% of indels were found to be clustered, they contributed 8.4% and 6.9% of substitution and indel drivers, respectively. Multiple distinct mutational processes gave rise to clustered indels including signatures enriched in tobacco smokers and homologous-recombination deficient cancers. Doublet-base substitutions were caused by at least 12 mutational processes, while the majority of multi-base substitutions were generated by either tobacco smoking or exposure to ultraviolet light. Omikli events, previously attributed to the activity of APOBEC3 deaminases, accounted for a large proportion of clustered substitutions. However, only 16.2% of omikli matched APOBEC3 patterns with experimental validation confirming additional mutational processes giving rise to omikli. Kataegis was generated by multiple mutational processes with 76.1% of all kataegic events exhibiting AID/APOBEC3-associated mutational patterns. Co-occurrence of APOBEC3 kataegis and extrachromosomal-DNA (ecDNA) was observed in 31% of samples with ecDNA. Multiple distinct APOBEC3 kataegic events were observed on most mutated ecDNA. ecDNA containing known cancer genes exhibited both positive selection and kataegic hypermutation. Our results reveal the diversity of clustered mutational processes in human cancer and the role of APOBEC3 in recurrently mutating and fueling the evolution of ecDNA.

Abstract 3147: Comprehensive characterization of the role of T-type calcium channels in glioblastoma

2017 ◽  
Author(s):  
Ying Zhang ◽  
Nichola Cruickshanks ◽  
Fang Yuan ◽  
Baomin Wang ◽  
Mary Pahuski ◽  
...  
Keyword(s):  
Calcium Channels ◽  
Comprehensive Characterization

The role of 4-nitrobenzoic acid polymorphs in the crystallization process of organic acid–base multicomponent systems

CrystEngComm ◽  
2019 ◽  
Vol 21 (40) ◽  
pp. 6038-6047 ◽  
Author(s):  
Lilia Croitor ◽  
Mihaela F. Petric ◽  
Elisabeta I. Szerb ◽  
Gabriela Vlase ◽  
Paulina N. Bourosh ◽  
...  
Keyword(s):  
Solid State ◽  
Organic Acid ◽  
Crystallization Process ◽  
Time Dependent ◽  
Multicomponent Systems ◽  
Acid Base ◽  
Nitrobenzoic Acid ◽  
Comprehensive Characterization

An investigation of the role of 4-nitrobenzoic acid polymorphs in the crystallization process of dimethylethanolammonium 4-nitrobenzoate from solution and comprehensive characterization of time-dependent changes associated with solid-state transformations are presented.

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