Impact of genomics on the field of probiotic research: historical perspectives to modern paradigms.
Ontology highlight
ABSTRACT:
SUBMITTER: Johnson BR
PROVIDER: S-EPMC4064118 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The flaviviruses are small single-stranded RNA viruses that are typically transmitted by mosquito or tick vectors. These "arboviruses" are found around the world and account for a significant number of cases of human disease. The flaviviruses cause diseases ranging from mild or sub-clinical infections to lethal hemorrhagic fever or encephalitis. In many cases, survivors of neurologic flavivirus infections suffer long-term debilitating sequelae. Much like the emergence of West Nile virus in the United States in 1999, the recent emergence of Zika virus in the Americas has significantly increased the awareness of mosquito-borne viruses. The diseases caused by several flaviviruses have been recognized for decades, if not centuries. However, there is still a lot that is unknown about the flaviviruses as the recent experience with Zika virus has taught us. The objective of this review is to provide a general overview and some historical perspective on several flaviviruses that cause significant human disease. In addition, available medical countermeasures and significant gaps in our understanding of flavivirus biology are also discussed.
| S-EPMC5454410 | biostudies-literature
Project description:Chordoma is a low-grade notochordal tumor of the skull base, mobile spine and sacrum which behaves malignantly and confers a poor prognosis despite indolent growth patterns. These tumors often present late in the disease course, tend to encapsulate adjacent neurovascular anatomy, seed resection cavities, recur locally and respond poorly to radiotherapy and conventional chemotherapy, all of which make chordomas challenging to treat. Extent of surgical resection and adequacy of surgical margins are the most important prognostic factors and thus patients with chordoma should be cared for by a highly experienced, multi-disciplinary surgical team in a quaternary center. Ongoing research into the molecular pathophysiology of chordoma has led to the discovery of several pathways that may serve as potential targets for molecular therapy, including a multitude of receptor tyrosine kinases (e.g., platelet-derived growth factor receptor [PDGFR], epidermal growth factor receptor [EGFR]), downstream cascades (e.g., phosphoinositide 3-kinase [PI3K]/protein kinase B [Akt]/mechanistic target of rapamycin [mTOR]), brachyury-a transcription factor expressed ubiquitously in chordoma but not in other tissues-and the fibroblast growth factor [FGF]/mitogen-activated protein kinase kinase [MEK]/extracellular signal-regulated kinase [ERK] pathway. In this review article, the pathophysiology, diagnosis and modern treatment paradigms of chordoma will be discussed with an emphasis on the ongoing research and advances in the field that may lead to improved outcomes for patients with this challenging disease.
| S-EPMC7961966 | biostudies-literature
Project description:Distinct photophysical behavior of nucleobase adenine and its constitutional isomer, 2-aminopurine, has been studied by using quantum chemical methods, in particular an accurate ab initio multiconfigurational second-order perturbation theory. After light irradiation, the efficient, ultrafast energy dissipation observed for nonfluorescent 9H-adenine is explained here by the nonradiative internal conversion process taking place along a barrierless reaction path from the initially populated 1(pipi* La) excited state toward a low-lying conical intersection (CI) connected with the ground state. In contrast, the strong fluorescence recorded for 2-aminopurine at 4.0 eV with large decay lifetime is interpreted by the presence of a minimum in the 1(pipi* La) hypersurface lying below the lowest CI and the subsequent potential energy barrier required to reach the funnel to the ground state. Secondary deactivation channels were found in the two systems related to additional CIs involving the 1(pipi* Lb) and 1(npi*) states. Although in 9H-adenine a population switch between both states is proposed, in 7H-adenine this may be perturbed by a relatively larger barrier to access the 1(npi*) state, and, therefore, the 1(pipi* Lb) state becomes responsible for the weak fluorescence measured in aqueous adenine at approximately 4.5 eV. In contrast to previous models that explained fluorescence quenching in adenine, unlike in 2-aminopurine, on the basis of the vibronic coupling of the nearby 1(pipi*) and 1(npi*) states, the present results indicate that the 1(npi*) state does not contribute to the leading photophysical event and establish the prevalence of a model based on the CI concept in modern photochemistry.
| S-EPMC1482641 | biostudies-literature
Project description:In this review, we discuss some of the most recent developments in genomics research and their relevance to the field of pediatrics. In particular, we examine 3 major approaches that are being used to identify genetic correlates of disease: genome-wide association studies, copy number variation studies, and next-generation sequencing. In the past few years, these approaches have yielded major insights into the causes and pathophysiology of a wide range of diseases but are also constrained by certain limitations. This review provides an overview of the genomic landscape in complex pediatric disorders and sets the stage for translating new discoveries into clinical practice, the future of genomic medicine.
| S-EPMC3362911 | biostudies-literature
Project description:Recently we have highlighted the importance of hypergolic reactions in carbon materials synthesis. In an effort to expand this topic with additional new paradigms, herein we present novel preparations of carbon nanomaterials, such-like carbon nanosheets and fullerols (hydroxylated fullerenes), through spontaneous ignition of coffee-sodium peroxide (Na2O2) and C60-Na2O2 hypergolic mixtures, respectively. In these cases, coffee and fullerenes played the role of the combustible fuel, whereas sodium peroxide the role of the strong oxidizer (e.g., source of highly concentrated H2O2). The involved reactions are both thermodynamically and kinetically favoured, thus allowing rapid product formation at ambient conditions. In addition, we provide tips on how to exploit the released energy of such highly exothermic reactions in the generation of useful work.
| S-EPMC7249011 | biostudies-literature
Project description:Adipose tissue is an important regulator of whole-body metabolism and energy homeostasis. The unprecedented growth of obesity and metabolic disease worldwide has required paralleled advancements in research on this dynamic endocrine organ system. Single-cell RNA sequencing (scRNA-seq), a highly meticulous methodology used to dissect tissue heterogeneity through the transcriptional characterization of individual cells, is responsible for facilitating critical advancements in this area. The unique investigative capabilities achieved by the combination of nanotechnology, molecular biology, and informatics are expanding our understanding of adipose tissue's composition and compartmentalized functional specialization, which underlie physiologic and pathogenic states, including adaptive thermogenesis, adipose tissue aging, and obesity. In this review, we will summarize the use of scRNA-seq and single-nuclei RNA-seq (snRNA-seq) in adipocyte biology and their applications to obesity and diabetes research in the hopes of increasing awareness of the capabilities of this technology and acting as a catalyst for its expanded use in further investigation.
| S-EPMC7369959 | biostudies-literature
Project description:Since the advent of modern plant breeding in the 1930s, North American maize has undergone a dramatic adaptation to high-input agriculture. Despite the importance of genetic contributions to historical yield increases, little is known about the underlying genomic changes. Here we use high-density SNP genotyping to characterize a set of North American maize lines spanning the history of modern breeding. We provide a unique analysis of genome-wide developments in genetic diversity, ancestry, and selection. The genomic history of maize is marked by a steady increase in genetic differentiation and linkage disequilibrium, whereas allele frequencies in the total population have remained relatively constant. These changes are associated with increasing genetic separation of breeding pools and decreased diversity in the ancestry of individual lines. We confirm that modern heterotic groups are the product of ongoing divergence from a relatively homogeneous landrace population, but show that differential landrace ancestry remains evident. Using a recent association approach, we characterize signals of directional selection throughout the genome, identifying a number of candidate genes of potential agronomic relevance. However, overall we find that selection has had limited impact on genome-wide patterns of diversity and ancestry, with little evidence for individual lines contributing disproportionately to the accumulation of favorable alleles in today's elite germplasm. Our data suggest breeding progress has mainly involved selection and recombination of relatively common alleles, contributed by a representative but limited set of ancestral lines.
| S-EPMC3412004 | biostudies-literature
Project description:BackgroundThe return of genetics and genomics research results has been a subject of ongoing global debate. Such feedback is ethically desirable to update participants on research findings particularly those deemed clinically significant. Although there is limited literature, debate continues in African on what constitutes appropriate practice regarding the return of results for genetics and genomics research. This study explored perspectives and ethical considerations of Ugandan genomics researchers regarding the return of genetics and genomics research results.MethodsThis was a qualitative study that employed in-depth interviews. Thirty participants were purposively selected based on their expertise as genomics researchers in Uganda. Data were analysed through content analysis along the main themes of the study using a comprehensive thematic matrix, to identify common patterns arising from the narratives. NVivo software 12 was used to support data analysis.ResultsThe return of genetics and genomics research results was generally acceptable to researchers, and some indicated that they had previously returned individual or aggregate results to participants and communities. The main reasons cited for sharing research results with participants included their clinical utility, actionability and overall benefit to society. Ethical considerations for appropriate return of results included a need for effective community engagement, genetic counselling prior to disclosure of the results, adequate informed consent, and proper assessment of the implications of, or consequences of returning of results. However, the approaches to return of results were perceived as unstandardized due to the lack of appropriate regulatory frameworks.ConclusionsThe return of genetic and genomic research results is generally acceptable to researchers despite the lack of appropriate regulatory frameworks. Ethical considerations for return of genetics and genomics research results are highly divergent, hence the need for national ethical guidelines to appropriately regulate the practice.
| S-EPMC8603565 | biostudies-literature
Project description:Centuries of zoological studies have amassed billions of specimens in collections worldwide. Genomics of these specimens promises to reinvigorate biodiversity research. However, because DNA degrades with age in historical specimens, it is a challenge to obtain genomic data for them and analyze degraded genomes. We developed experimental and computational protocols to overcome these challenges and applied our methods to resolve a series of long-standing controversies involving a group of butterflies. We deduced the geographical origins of several historical specimens of uncertain provenance that are at the heart of these debates. Here, genomics tackles one of the greatest problems in zoology: countless old specimens that serve as irreplaceable embodiments of species concepts cannot be confidently assigned to extant species or population due to the lack of diagnostic morphological features and clear documentation of the collection locality. The ability to determine where they were collected will resolve many on-going disputes. More broadly, we show the utility of applying genomics to historical museum specimens to delineate the boundaries of species and populations, and to hypothesize about genotypic determinants of phenotypic traits.
| S-EPMC8097301 | biostudies-literature
Project description:Modern controlled environment facilities (CEFs) enable the simulation of dynamic microclimates in controlled ecological experiments through their technical ability to precisely control multiple environmental parameters. However, few CEF studies exploit the technical possibilities of their facilities, as climate change treatments are frequently applied by static manipulation of an inadequate number of climate change drivers, ignoring intra-annual variability and covariation of multiple meteorological variables. We present a method for generating regionalized climate series in high temporal resolution that was developed to force the TUMmesa Model EcoSystem Analyzer with dynamic climate simulations. The climate series represent annual cycles for a reference period (1987-2016) and the climate change scenarios RCP2.6 and RCP8.5 (2071-2100) regionalized for a climate station situated in a forested region of the German Spessart mountains. Based on the EURO-CORDEX and ReKliEs-DE model ensembles, typical annual courses of daily resolved climatologies for the reference period and the RCP scenarios were calculated from multimodel means of temperature (ta), relative humidity (rh), global radiation (Rg), air pressure (P), and ground-level ozone and complemented by CO2. To account for intra-annual variation and the covariability of multiple climate variables, daily values were substituted by hourly resolved data resampled from the historical record. The resulting present climate Test Reference Year (TRY) well represented a possible annual cycle within the reference period, and expected shifts in future mean values (e.g., higher ta) were reproduced within the RCP TRYs. The TRYs were executed in eight climate chambers of the TUMmesa facility and-accounting for the technical boundaries of the facility-reproduced with high precision. Especially, as an alternative to CEF simulations that reproduce mere day/night cycles and static manipulations of climate change drivers, the method presented here proved well suited for simulating regionalized and highly dynamic annual cycles for ecological CEF studies.
| S-EPMC8668799 | biostudies-literature