scholarly journals Large-scale gene expression studies of the endometrium: what have we learnt?

Reproduction ◽  
2006 ◽  
Vol 132 (1) ◽  
pp. 1-10 ◽  
Author(s):  
Rob Sherwin ◽  
Rob Catalano ◽  
Andrew Sharkey
Keyword(s):  
Large Scale ◽  
Dna Microarrays ◽  
Disease States ◽  
Complex Interactions ◽  
Expression Studies ◽  
Proliferation And Differentiation ◽  
Potential Applications ◽  
Underlying Causes ◽  
Gene Expression Studies ◽  
The Impact

The endometrium is a dynamic tissue that undergoes coordinated changes under the influence of steroid hormones. This results in proliferation and differentiation culminating in a receptive state, followed by menstruation and endometrial repair. These functions involve complex interactions between the epithelium, stroma and leucocytes in the endometrium. Understanding the underlying causes of endometrial disorders, such as infertility, endometriosis and heavy menstrual bleeding, therefore represents a considerable challenge. Recently developed techniques, such as differential display and DNA microarrays permit the abundance of thousands of mRNA transcripts within cells or tissues to be measured simultaneously. This provides a new approach to understanding the complex interactions that underlie both healthy and disease states. Responses of the endometrium to hormones or drugs can be studied and the response of the system as an integrated whole can be assessed. Comparisons of endometrium from healthy women and those with endometrial dysfunction have advanced our understanding of key areas of endometrial physiology, including infertility, receptivity, endometriosis and cancer. Using this approach, novel genes controlling specific endometrial functions like receptivity have been identified for functional testing. This paper will review the impact of these techniques for transcript profiling on our understanding of selected areas of endometrial biology and discuss the potential applications in future.

The Potential Applications of Raman Spectroscopy in Unravelling Complex Palaeowildfire Ecosystems

2021 ◽  
Author(s):  
Thomas Theurer ◽  
David Muirhead ◽  
David Jolley ◽  
Dmitri Mauquoy
Keyword(s):  
Raman Spectroscopy ◽  
Carbonaceous Material ◽  
Complex Interactions ◽  
Intensity Changes ◽  
Potential Applications ◽  
Ecosystem Studies ◽  
History Of ◽  
The Impact ◽  
Unique Relationship

<p>Raman spectroscopy represents a novel methodology of characterising plant-fire interactions through geological history, with enormous potential. Applications of Raman spectroscopy to charcoal have shown that this is an effective method of understanding intensity changes across palaeofire regimes. Such analyses have relied on the determination of appropriate Raman parameters, given their relationship with temperature of formation and microstructural changes in reference charcoals. Quantitative assessments of charcoal microstructure have also been successfully applied to the assessment of carbonaceous maturation under alternate thermal regimes, such as pyroclastic volcanism. Palaeowildfire systems in association with volcanism may present a complex history of thermal maturation, given interactions between detrital charcoals and volcanogenic deposition. However, whilst palaeofire and volcanic maturation of carbonaceous material are well understood individually, their interaction has yet to be characterised. Here we present the first analysis of palaeofire charcoals derived from volcanic ignition utilising Raman spectroscopy. Our results indicate that complex interactions between volcanism and palaeofire systems may be better understood by the characterisation of charcoal microstructure, alongside palaeobotanical and ecosystem studies. Understanding the unique relationship between wildfires and volcanism, and the impact that this has on the fossil record, may better assist our understanding of wildfire systems in deep history. Further still, this highlights the potential for better understanding the socioecological impacts of modern and future wildfire systems closely associated with volcanic centres. </p>

Changes in mechanisms and intensity of Western U.S. floods, 1960-2013

2021 ◽  
Author(s):  
Jessica Fayne ◽  
Huilin Huang ◽  
Mike Fischella ◽  
Yufei Liu ◽  
Zhaoxin Ban ◽  
...  
Keyword(s):  
Extreme Precipitation ◽  
Large Scale ◽  
Critical Factor ◽  
Flood Frequency ◽  
Atmospheric Rivers ◽  
Convective Storms ◽  
Noticeable Increase ◽  
Complex Interactions ◽  
Different Types ◽  
The Impact

<p>Extreme precipitation, a critical factor in flooding, has selectively increased with warmer temperatures in the Western U.S. Despite this, the streamflow measurements have captured no noticeable increase in large-scale flood frequency or intensity. As flood studies have mostly focused on specific flood events in particular areas, analyses of large-scale floods and their changes have been scarce. For floods during 1960-2013, we identify six flood generating mechanisms (FGMs) that are prominent across the Western U.S., including atmospheric rivers and non-atmospheric rivers, monsoons, convective storms, radiation-driven snowmelt, and rain-on-snow, in order to identify to what extent different types of floods are changing based on the dominant FGM. The inconsistency between extreme precipitation and lack of flood increase suggests that the impact of climate change on flood risk has been modulated by hydro-meteorological and physiographic processes such as sharp increases in temperature that drive increased evapotranspiration and decreased soil moisture. Our results emphasize the importance of FGMs in understanding the complex interactions of flooding and climatic changes and explain the broad spatiotemporal changes that have occurred across the vast Western U.S. for the past 50 years.</p>

scholarly journals Trisomy 21 and Down syndrome: a short review

2008 ◽  
Vol 68 (2) ◽  
pp. 447-452 ◽  
Author(s):  
CA. Sommer ◽  
F. Henrique-Silva
Keyword(s):  
Gene Expression ◽  
Down Syndrome ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Global Gene Expression ◽  
Short Review ◽  
Complex Disorder ◽  
Expression Studies ◽  
Gene Expression Studies ◽  
Chromosome Segments

Even though the molecular mechanisms underlying the Down syndrome (DS) phenotypes remain obscure, the characterization of the genes and conserved non-genic sequences of HSA21 together with large-scale gene expression studies in DS tissues are enhancing our understanding of this complex disorder. Also, mouse models of DS provide invaluable tools to correlate genes or chromosome segments to specific phenotypes. Here we discuss the possible contribution of HSA21 genes to DS and data from global gene expression studies of trisomic samples.

scholarly journals Isolation and long-term expansion of murine epidermal stem-like cells

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0254731
Author(s):  
Jingjing Wang ◽  
Maureen Mongan ◽  
Xiang Zhang ◽  
Ying Xia
Keyword(s):  
Epithelial Cell ◽  
Intercellular Junctions ◽  
Global Gene Expression ◽  
Cell Types ◽  
Proliferation Markers ◽  
Expression Studies ◽  
Sustainable Culture ◽  
Proliferation And Differentiation ◽  
Epidermal Homeostasis ◽  
Gene Expression Studies

Epidermis is the most outer layer of the skin and a physical barrier protecting the internal tissues from mechanical and environmental insults. The basal keratinocytes, which, through proliferation and differentiation, supply diverse cell types for epidermal homeostasis and injury repair. Sustainable culture of murine keratinocyte, however, is a major obstacle. Here we developed murine keratinocyte lines using low-Ca2+ (0.06 mM) keratinocyte serum-free medium (KSFM-Ca2+) without feeder cells. Cells derived in this condition could be subcultured for >70 passages. They displayed basal epithelial cell morphology and expressed keratin (Krt) 14, but lacked the epithelial-characteristic intercellular junctions. Moreover, these cells could be adapted to grow in the Defined-KSFM (DKSFM) media containing 0.15 mM Ca2+, and the adapted cells established tight- and adherens-junctions and exhibited increased Krt1/10 expression while retained subculture capacity. Global gene expression studies showed cells derived in KSFM-Ca2+ media had enriched stem/proliferation markers and cells adapted in DKSFM media had epithelial progenitor signatures. Correspondingly, KSFM-Ca2+-derived cells exhibited a remarkable capacity of clonal expansion, whereas DKSFM-adapted cells could differentiate to suprabasal epithelial cell types in 3-dimentional (3D) organoids. The generation of stem-like murine keratinocyte lines and the conversion of these cells to epithelial progenitors capable of terminal differentiation provide the critically needed resources for skin research.

scholarly journals Interpreting Intervention Induced Neuroplasticity with fMRI: The Case for Multimodal Imaging Strategies

2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
Lee B. Reid ◽  
Roslyn N. Boyd ◽  
Ross Cunnington ◽  
Stephen E. Rose
Keyword(s):  
Brain Function ◽  
Multimodal Imaging ◽  
Brain Injuries ◽  
Imaging Modality ◽  
Motor Rehabilitation ◽  
Activation Patterns ◽  
Disease States ◽  
Underlying Causes ◽  
The Impact ◽  
Processing Steps

Direct measurement of recovery from brain injury is an important goal in neurorehabilitation, and requires reliable, objective, and interpretable measures of changes in brain function, referred to generally as “neuroplasticity.” One popular imaging modality for measuring neuroplasticity is task-based functional magnetic resonance imaging (t-fMRI). In the field of neurorehabilitation, however, assessing neuroplasticity using t-fMRI presents a significant challenge. This commentary reviews t-fMRI changes commonly reported in patients with cerebral palsy or acquired brain injuries, with a focus on studies of motor rehabilitation, and discusses complexities surrounding their interpretations. Specifically, we discuss the difficulties in interpreting t-fMRI changes in terms of their underlying causes, that is, differentiating whether they reflect genuine reorganisation, neurological restoration, compensation, use of preexisting redundancies, changes in strategy, or maladaptive processes. Furthermore, we discuss the impact of heterogeneous disease states and essential t-fMRI processing steps on the interpretability of activation patterns. To better understand therapy-induced neuroplastic changes, we suggest that researchers utilising t-fMRI consider concurrently acquiring information from an additional modality, to quantify, for example, haemodynamic differences or microstructural changes. We outline a variety of such supplementary measures for investigating brain reorganisation and discuss situations in which they may prove beneficial to the interpretation of t-fMRI data.

scholarly journals GREP: genome for REPositioning drugs

2019 ◽  
Vol 35 (19) ◽  
pp. 3821-3823 ◽  
Author(s):  
Saori Sakaue ◽  
Yukinori Okada
Keyword(s):  
Large Scale ◽  
Human Genetics ◽  
Association Studies ◽  
Enrichment Analysis ◽  
Supplementary Information ◽  
Clinical Indication ◽  
Genome Wide Association Studies ◽  
Expression Studies ◽  
Gene Expression Studies ◽  
Approved Drugs

AbstractSummaryMaking use of accumulated genetic knowledge for clinical practice is our next goal in human genetics. Here we introduce GREP (Genome for REPositioning drugs), a standalone python software to quantify an enrichment of the user-defined set of genes in the target of clinical indication categories and to capture potentially repositionable drugs targeting the gene set. We show that genes identified by the large-scale genome-wide association studies were robustly enriched in the approved drugs to treat the trait of interest. This enrichment analysis was also highly applicable to other sets of biological genes such as those identified by gene expression studies and genes somatically mutated in cancers. This software should accelerate investigators to reposition drugs to other indications with the guidance of known genomics.Availability and implementationGREP is available at https://github.com/saorisakaue/GREP as a python source code.Supplementary informationSupplementary data are available at Bioinformatics online.

scholarly journals SMART-RDA: A Galaxy Workflow for RNA-Seq Data Analysis

2017 ◽  
Vol 3 (4) ◽  
pp. 186
Author(s):  
Redi Aditama ◽  
Zulfikar Achmad Tanjung ◽  
Widyartini Made Sudania ◽  
Toni Liwang
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Analysis Tool ◽  
Rna Seq ◽  
Expression Studies ◽  
Galaxy Server ◽  
Local Facility ◽  
Computational Workflow ◽  
Gene Expression Studies ◽  
Next Generation Sequencing Ngs

<p class="Els-Abstract-text">RNA-seq using the Next Generation Sequencing (NGS) approach is a common technology to analyze large-scale RNA transcript data for gene expression studies. However, an appropriate bioinformatics tool is needed to analyze a large amount of transcriptomes data from RNA-seq experiment. The aim of this study was to construct a system that can be easily applied to analyze RNA-seq data. RNA-seq analysis tool as SMART-RDA was constructed in this study. It is a computational workflow based on Galaxy framework to be used for analyzing RNA-seq raw data into gene expression information. This workflow was adapted from a well-known Tuxedo Protocol for RNA-seq analysis with some modifications. Expression value from each transcriptome was quantitatively stated as Fragments Per Kilobase of exon per Million fragments (FPKM). RNA-seq data of sterile and fertile oil palm (Pisifera) pollens derived from Sequence Read Archive (SRA) NCBI were used to test this workflow in local facility Galaxy server. The results showed that differentially gene expression in pollens might be responsible for sterile and fertile characteristics in palm oil Pisifera.</p><p><strong>Keywords:</strong> FPKM; Galaxy workflow; Gene expression; RNA sequencing.</p>

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