scholarly journals The danger of epigenetics misconceptions (epigenetics and stuff…)

2015 ◽  
Vol 93 (6) ◽  
pp. 626-629 ◽  
Author(s):  
Philippe T. Georgel
Keyword(s):  
Gene Expression ◽  
Structure And Function ◽  
Epigenetic Mechanisms ◽  
Research Groups ◽  
Post Translational Modifications ◽  
The Past ◽  
Associated Proteins ◽  
New Research ◽  
The Right ◽  
And Function

Within the past two decades, the fields of chromatin structure and function and transcription regulation research started to fuse and overlap, as evidence mounted to support a very strong regulatory role in gene expression that was associated with histone post-translational modifications, DNA methylation, as well as various chromatin-associated proteins (the pillars of the “Epigenetics” building). The fusion and convergence of these complementary fields is now often simply referred to as “Epigenetics”. During these same 20 years, numerous new research groups have started to recognize the importance of chromatin composition, conformation, and its plasticity. However, as the field started to grow exponentially, its growth came with the spreading of several important misconceptions, which have unfortunately led to improper or hasty conclusions. The goal of this short “opinion” piece is to attempt to minimize future misinterpretations of experimental results and ensure that the right sets of experiment are used to reach the proper conclusion, at least as far as epigenetic mechanisms are concerned.

Osseointegration interface of calcified bone and endosseous implants

1992 ◽  
Vol 50 (2) ◽  
pp. 1096-1097
Author(s):  
K.E. Krizan ◽  
J.E. Laffoon ◽  
M.J. Buckley
Keyword(s):  
Structure And Function ◽  
Titanium Implants ◽  
En Bloc ◽  
Endosseous Implants ◽  
Ultrastructural Studies ◽  
The Past ◽  
Cacodylate Buffer ◽  
One Year ◽  
And Function

With increase use of tissue-integrated prostheses in recent years it is a goal to understand what is happening at the interface between haversion bone and bulk metal. This study uses electron microscopy (EM) techniques to establish parameters for osseointegration (structure and function between bone and nonload-carrying implants) in an animal model. In the past the interface has been evaluated extensively with light microscopy methods. Today researchers are using the EM for ultrastructural studies of the bone tissue and implant responses to an in vivo environment. Under general anesthesia nine adult mongrel dogs received three Brånemark (Nobelpharma) 3.75 × 7 mm titanium implants surgical placed in their left zygomatic arch. After a one year healing period the animals were injected with a routine bone marker (oxytetracycline), euthanized and perfused via aortic cannulation with 3% glutaraldehyde in 0.1M cacodylate buffer pH 7.2. Implants were retrieved en bloc, harvest radiographs made (Fig. 1), and routinely embedded in plastic. Tissue and implants were cut into 300 micron thick wafers, longitudinally to the implant with an Isomet saw and diamond wafering blade [Beuhler] until the center of the implant was reached.

Structure and function of seed lipid body-associated proteins

2008 ◽  
Vol 331 (10) ◽  
pp. 746-754 ◽  
Author(s):  
Zita Purkrtova ◽  
Pascale Jolivet ◽  
Martine Miquel ◽  
Thierry Chardot
Keyword(s):  
Lipid Body ◽  
Structure And Function ◽  
Seed Lipid ◽  
Associated Proteins ◽  
And Function

scholarly journals Molecular biology approaches in bioadhesion research

2014 ◽  
Vol 5 ◽  
pp. 983-993 ◽  
Author(s):  
Marcelo Rodrigues ◽  
Birgit Lengerer ◽  
Thomas Ostermann ◽  
Peter Ladurner
Keyword(s):  
Molecular Biology ◽  
Biological Function ◽  
Molecular Approach ◽  
Research Groups ◽  
Blast Search ◽  
Search Facility ◽  
New Research ◽  
And Function ◽  
Functional Analyses

The use of molecular biology tools in the field of bioadhesion is still in its infancy. For new research groups who are considering taking a molecular approach, the techniques presented here are essential to unravelling the sequence of a gene, its expression and its biological function. Here we provide an outline for addressing adhesion-related genes in diverse organisms. We show how to gradually narrow down the number of candidate transcripts that are involved in adhesion by (1) generating a transcriptome and a differentially expressed cDNA list enriched for adhesion-related transcripts, (2) setting up a BLAST search facility, (3) perform an in situ hybridization screen, and (4) functional analyses of selected genes by using RNA interference knock-down. Furthermore, latest developments in genome-editing are presented as new tools to study gene function. By using this iterative multi-technologies approach, the identification, isolation, expression and function of adhesion-related genes can be studied in most organisms. These tools will improve our understanding of the diversity of molecules used for adhesion in different organisms and these findings will help to develop innovative bio-inspired adhesives.

Reflections on team culture, structure and function of an intensive support service centred on positive behavioural support

2016 ◽  
Vol 21 (4) ◽  
pp. 203-211 ◽  
Author(s):  
Lawrence A. Patterson ◽  
Samuel Berry
Keyword(s):  
Social Services ◽  
Support Service ◽  
Structure And Function ◽  
Content Type ◽  
Case Examples ◽  
Behavioural Support ◽  
Team Culture ◽  
Shared Identity ◽  
The Right ◽  
And Function

Purpose The purpose of this paper is to explore experiences of team culture, structure and function of an intensive support service (ISS) within the context of the recent service guidance “Building the Right Support” (NHS England, Local Government Association and Association of Directors of Adult Social Services, 2015). Reflections on the Hampshire and Southampton ISS set up in 2010 are discussed with a view to informing a debate about frameworks for ISS services nationally. Design/methodology/approach A reflective piece, drawing on experience and case examples. Findings This paper describes that a key function of an ISS is making individuals safe and this is significantly assisted by using shared team formulation, which can enable information and perspectives to be shared between and within teams as rapidly as possible. Further, a case is made for recognising the importance of inter-disciplinary practice, as the Southampton and Hampshire ISS has removed the “old fashioned” demarcations that led to individuals seeing a “procession” of different professionals from different disciplines. This relates to team structure, but importantly is about a culture of holding a shared identity based on positive behavioural support values, rather than a traditional uni-disciplinary perspective. Practical implications ISS models are being proposed by NHS England and this paper suggests some important practical aspects. Originality/value Limited literature exists examining the team culture within ISSs, which contributes to desired outcomes for service users. This paper opens a debate about structural and functional aspects of service delivery in this service model.

Neural system-enriched gene expression: relationship to biological pathways and neurological diseases

2004 ◽  
Vol 18 (2) ◽  
pp. 167-183 ◽  
Author(s):  
Jianhua Zhang ◽  
Amy Moseley ◽  
Anil G. Jegga ◽  
Ashima Gupta ◽  
David P. Witte ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nervous System ◽  
Intracellular Signaling ◽  
Large Scale ◽  
Expression Profiles ◽  
Gene List ◽  
Structure And Function ◽  
System Structure ◽  
Psychiatric Disease ◽  
And Function

To understand the commitment of the genome to nervous system differentiation and function, we sought to compare nervous system gene expression to that of a wide variety of other tissues by gene expression database construction and mining. Gene expression profiles of 10 different adult nervous tissues were compared with that of 72 other tissues. Using ANOVA, we identified 1,361 genes whose expression was higher in the nervous system than other organs and, separately, 600 genes whose expression was at least threefold higher in one or more regions of the nervous system compared with their median expression across all organs. Of the 600 genes, 381 overlapped with the 1,361-gene list. Limited in situ gene expression analysis confirmed that identified genes did represent nervous system-enriched gene expression, and we therefore sought to evaluate the validity and significance of these top-ranked nervous system genes using known gene literature and gene ontology categorization criteria. Diverse functional categories were present in the 381 genes, including genes involved in intracellular signaling, cytoskeleton structure and function, enzymes, RNA metabolism and transcription, membrane proteins, as well as cell differentiation, death, proliferation, and division. We searched existing public sites and identified 110 known genes related to mental retardation, neurological disease, and neurodegeneration. Twenty-one of the 381 genes were within the 110-gene list, compared with a random expectation of 5. This suggests that the 381 genes provide a candidate set for further analyses in neurological and psychiatric disease studies and that as a field, we are as yet, far from a large-scale understanding of the genes that are critical for nervous system structure and function. Together, our data indicate the power of profiling an individual biologic system in a multisystem context to gain insight into the genomic basis of its structure and function.

scholarly journals The essential activities of the bacterial sigma factor

2017 ◽  
Vol 63 (2) ◽  
pp. 89-99 ◽  
Author(s):  
Maria C. Davis ◽  
Christopher A. Kesthely ◽  
Emily A. Franklin ◽  
Shawn R. MacLellan
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Rna Synthesis ◽  
Gene Expression Regulation ◽  
Structure And Function ◽  
Structural Studies ◽  
General Transcription Factors ◽  
Transcription Process ◽  
Promoter Dna ◽  
And Function

Transcription is the first and most heavily regulated step in gene expression. Sigma (σ) factors are general transcription factors that reversibly bind RNA polymerase (RNAP) and mediate transcription of all genes in bacteria. σ Factors play 3 major roles in the RNA synthesis initiation process: they (i) target RNAP holoenzyme to specific promoters, (ii) melt a region of double-stranded promoter DNA and stabilize it as a single-stranded open complex, and (iii) interact with other DNA-binding transcription factors to contribute complexity to gene expression regulation schemes. Recent structural studies have demonstrated that when σ factors bind promoter DNA, they capture 1 or more nucleotides that are flipped out of the helical DNA stack and this stabilizes the promoter open-complex intermediate that is required for the initiation of RNA synthesis. This review describes the structure and function of the σ70 family of σ proteins and the essential roles they play in the transcription process.

scholarly journals Renal ischemia alters expression of mitochondria-related genes and impairs mitochondrial structure and function in swine scattered tubular-like cells

2020 ◽  
Vol 319 (1) ◽  
pp. F19-F28 ◽  
Author(s):  
Rahele A. Farahani ◽  
Xiang-Yang Zhu ◽  
Hui Tang ◽  
Kyra L. Jordan ◽  
Lilach O. Lerman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Structural Damage ◽  
Nuclear Dna ◽  
Mitochondrial Genes ◽  
Structure And Function ◽  
Mitochondrial Damage ◽  
Renal Ischemia ◽  
Gene Gain ◽  
Mitochondrial Structure ◽  
And Function

Scattered tubular-like cells (STCs) are dedifferentiated surviving tubular epithelial cells that repair neighboring injured cells. Experimental renal artery stenosis (RAS) impairs STC reparative potency by inducing mitochondrial injury, but the exact mechanisms of mitochondrial damage remain unknown. We hypothesized that RAS alters expression of mitochondria-related genes, contributing to mitochondrial structural damage and dysfunction in swine STCs. CD24+/CD133+ STCs were isolated from pig kidneys after 10 wk of RAS or sham ( n = 3 each). mRNA sequencing was performed, and nuclear DNA (nDNA)-encoded mitochondrial genes and mitochondrial DNA (mtDNA)-encoded genes were identified. Mitochondrial structure, ATP generation, biogenesis, and expression of mitochondria-associated microRNAs were also assessed. There were 96 nDNA-encoded mitochondrial genes upregulated and 12 mtDNA-encoded genes downregulated in RAS-STCs versus normal STCs. Functional analysis revealed that nDNA-encoded and mtDNA-encoded differentially expressed genes were primarily implicated in mitochondrial respiration and ATP synthesis. Mitochondria from RAS STCs were swollen and showed cristae remodeling and loss and decreased ATP production. Immunoreactivity of the mitochondrial biogenesis marker peroxisome proliferator-activated receptor-γ coactivator (PGC)-1α and expression of the mitochondria-associated microRNAs miR-15a, miR-181a, miR-196a, and miR-296-3p, which target several mtDNA genes, were higher in RAS-STCs compared with normal STCs, suggesting a potential modulation of mitochondria-related gene expression. These results demonstrate that RAS induces an imbalance in mtDNA- and nDNA-mitochondrial gene expression, impairing mitochondrial structure and function in swine STCs. These observations support development of gene gain- and loss-of-function strategies to ameliorate mitochondrial damage and preserve the reparative potency of STCs in patients with renal ischemia.

Human impacts on hydrology in the Pantanal wetland of South America

2002 ◽  
Vol 45 (11) ◽  
pp. 35-44 ◽  
Author(s):  
S.K. Hamilton
Keyword(s):  
South America ◽  
Human Activities ◽  
Human Impacts ◽  
Structure And Function ◽  
Natural State ◽  
Ecological Structure ◽  
The Past ◽  
Influences Of Human Activities ◽  
And Function ◽  
Pantanal Wetland

Inundation patterns in the Pantanal remain in a relatively natural state, yet a number of significant human influences have occurred in the past, and there is potential for more severe human impacts as development of the region continues in the future. The objectives of this paper are 1) to briefly review the linkages between hydrology and ecological structure and function in the Pantanal; 2) to review some documented cases of historical influences of human activities on hydrology in the region; and 3) to consider potential future impacts, particularly in regard to the recently proposed navigation project known as the Paraguay-Paraná Waterway (or Hidrovía).

scholarly journals Applications of Infrared and Raman Microspectroscopy of Cells and Tissue in Medical Diagnostics: Present Status and Future Promises

2012 ◽  
Vol 27 ◽  
pp. 463-496 ◽  
Author(s):  
Max Diem ◽  
Miloš Miljković ◽  
Benjamin Bird ◽  
Tatyana Chernenko ◽  
Jen Schubert ◽  
...  
Keyword(s):  
Data Analysis ◽  
Vibrational Spectra ◽  
Medical Diagnostics ◽  
Cellular Biology ◽  
Steady Increase ◽  
Research Groups ◽  
The Past ◽  
New Research ◽  
Raman And Ir Spectroscopy

This paper summarizes the progress achieved over the past fifteen years in applying vibrational (Raman and IR) spectroscopy to problems of medical diagnostics and cellular biology. During this time, a number of research groups have verified the enormous information content of vibrational spectra; in fact, genomic, proteomic, and metabolomic information can be deduced by decoding the observed vibrational spectra. This decoding process is aided enormously by the availability of high-power computer workstations and advanced algorithms for data analysis. Furthermore, commercial instrumentation for the fast collection of both Raman and infrared microspectral data has rendered practical the collection of images based solely on spectral data. The progress in the field has been manifested by a steady increase in the number and quality of publications submitted by established and new research groups in vibrational biological and biomedical arenas.

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