scholarly journals The impact of rotator cuff deficiency on structure, mechanical properties, and gene expression profiles of the long head of the biceps tendon (LHBT): Implications for management of the LHBT during primary shoulder arthroplasty

2015 ◽  
Vol 33 (8) ◽  
pp. 1158-1164 ◽  
Author(s):  
Michael D. Kurdziel ◽  
James E. Moravek ◽  
Brett P. Wiater ◽  
Abigail Davidson ◽  
Joseph Seta ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mechanical Properties ◽  
Rotator Cuff ◽  
Shoulder Arthroplasty ◽  
Expression Profiles ◽  
Biceps Tendon ◽  
Gene Expression Profiles ◽  
Long Head ◽  
Rotator Cuff Deficiency ◽  
The Impact

scholarly journals Transcriptomic Modification in the Cerebral Cortex following Noninvasive Brain Stimulation: RNA-Sequencing Approach

2016 ◽  
Vol 2016 ◽  
pp. 1-15 ◽  
Author(s):  
Ben Holmes ◽  
Seung Ho Jung ◽  
Jing Lu ◽  
Jessica A. Wagner ◽  
Liudmilla Rubbi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cerebral Cortex ◽  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Current Intensity ◽  
Beneficial Effects ◽  
Group A ◽  
The Impact

Transcranial direct current stimulation (tDCS) has been shown to modulate neuroplasticity. Beneficial effects are observed in patients with psychiatric disorders and enhancement of brain performance in healthy individuals has been observed following tDCS. However, few studies have attempted to elucidate the underlying molecular mechanisms of tDCS in the brain. This study was conducted to assess the impact of tDCS on gene expression within the rat cerebral cortex. Anodal tDCS was applied at 3 different intensities followed by RNA-sequencing and analysis. In each current intensity, approximately 1,000 genes demonstrated statistically significant differences compared to the sham group. A variety of functional pathways, biological processes, and molecular categories were found to be modified by tDCS. The impact of tDCS on gene expression was dependent on current intensity. Results show that inflammatory pathways, antidepressant-related pathways (GTP signaling, calcium ion binding, and transmembrane/signal peptide pathways), and receptor signaling pathways (serotonergic, adrenergic, GABAergic, dopaminergic, and glutamate) were most affected. Of the gene expression profiles induced by tDCS, some changes were observed across multiple current intensities while other changes were unique to a single stimulation intensity. This study demonstrates that tDCS can modify the expression profile of various genes in the cerebral cortex and that these tDCS-induced alterations are dependent on the current intensity applied.

Rotator Cuff Tear Size Regulates Fibroadipogenic Progenitor Number and Gene Expression Profile in the Supraspinatus Independent of Patient Age

2021 ◽  
pp. 036354652110545
Author(s):  
Michael R. Davies ◽  
Hannah Chi ◽  
Gurbani Kaur ◽  
Mengyao Liu ◽  
C. Benjamin Ma ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rotator Cuff ◽  
Rotator Cuff Tear ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Patient Age ◽  
Cuff Tear ◽  
Patient Âgé ◽  
Beige Adipocytes ◽  
Tear Size

Background: Fatty infiltration of rotator cuff muscle is a limiting factor in the success of repairs. Fibroadipogenic progenitors (FAPs) are a population of stem cells within the rotator cuff that can differentiate into white adipocytes, fibroblasts, and beige adipocytes. The effects of patient age and rotator cuff tendon tear size on the number, differentiation patterns, and gene expression profiles of FAPs have not yet been analyzed. Purpose: To determine if patient age and rotator cuff tear size independently regulate FAP number, differentiation patterns, and gene expression profiles. Study Design: Controlled laboratory study. Methods: Supraspinatus muscle samples were collected from 26 patients between the ages of 42 and 76 years with partial- or full-thickness rotator cuff tears. FAPs were quantified using fluorescence-activated cell sorting. Gene expression analysis was performed across a custom 96-gene panel using NanoString. In vitro differentiation assays of FAPs were conducted using adipogenic, fibrogenic, and beige-inducing (amibegron-treated) media, and quantitative polymerase chain reaction was used to assess gene expression differences between adipogenic and amibegron media conditions. Multivariable linear regressions were performed using Stata to independently analyze the effects of age and rotator cuff tear size on FAP number, differentiation, and gene expression. Results: Increasing age and tear size were independently correlated with increased FAP number (βage = 0.21, P = .03; βtear size = 3.86, P = .05). There was no clear association between age and gene expression of freshly sorted FAPs. Under adipogenic and fibrogenic media conditions, increasing age and tear size were independently associated with increased adipogenic and fibrogenic differentiation of FAPs. Under amibegron treatment conditions, age positively correlated with increased beige differentiation (β = 1.03; P < .0001), while increasing tear size showed a trend toward decreased beige differentiation (β = −4.87; P = .1). When gene expression patterns between adipogenic and amibegron media conditions were compared, larger tear size strongly inhibited beige gene expression, while advanced age did not. Conclusion: Patient age and rotator cuff tear size independently regulated FAP number, differentiation, and gene expression. Age and tear size were positively correlated with increased FAP number and fibrogenic/adipogenic differentiation. Advancing patient age did not limit FAP beige differentiation and gene expression, while increasing rotator cuff tear size strongly inhibited these processes.

scholarly journals RNAseq Studies Reveal Distinct Transcriptional Response to Vitamin a (VA) Deficiency in Small Intestine (SI) versus Colon, Discovering Novel VA-regulated Genes (P15-002-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Zhi Chai ◽  
Yafei Lyu ◽  
Qiuyan Chen ◽  
Cheng-Hsin Wei ◽  
Lindsay Snyder ◽  
...  
Keyword(s):  
Gene Expression ◽  
Small Intestine ◽  
Vitamin A ◽  
Target Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Differentially Expressed Gene ◽  
Gene Expression Profiles ◽  
Illumina Hiseq ◽  
The Impact

Abstract Objectives To characterize and compare the impact of vitamin A (VA) deficiency on gene expression patterns in the small intestine (SI) and the colon, and to discover novel target genes in VA-related biological pathways. Methods vitamin A deficient (VAD) mice were generated by feeding VAD diet to pregnant C57/BL6 dams and their post-weaning offspring. Total mRNA extracted from SI and colon were sequenced using Illumina HiSeq 2500 platform. Differentially Expressed Gene (DEG), Gene Ontology (GO) enrichment, and Weighted Gene Co-expression Network Analysis (WGCNA) were performed to characterize expression patterns and co-expression patterns. Results The comparison between vitamin A sufficient (VAS) and VAD groups detected 49 and 94 DEGs in SI and colon, respectively. According to GO information, DEGs in the SI demonstrated significant enrichment in categories relevant to retinoid metabolic process, molecule binding, and immune function. Immunity related pathways, such as “humoral immune response” and “complement activation,” were positively associated with VA in SI. On the contrary, in colon, “cell division” was the only enriched category and was negatively associated with VA. WGCNA identified modules significantly correlated with VA status in SI and in colon. One of those modules contained five known retinoic acid targets. Therefore we have prioritized the other module members (e.g., Mbl2, Mmp9, Mmp13, Cxcl14 and Pkd1l2) to be investigated as candidate genes regulated by VA. Comparison of co-expression modules between SI and colon indicated distinct VA effects on these two organs. Conclusions The results show that VA deficiency alters the gene expression profiles in SI and colon quite differently. Some immune-related genes (Mbl2, Mmp9, Mmp13, Cxcl14 and Pkd1l2) may be novel targets under the control of VA in SI. Funding Sources NIH training grant and NIH research grant. Supporting Tables, Images and/or Graphs

Gene Expression Profiles of Early Implant Adherent Cells in Smokers and Nonsmokers

2015 ◽  
Vol 41 (6) ◽  
pp. 640-645 ◽  
Author(s):  
Ghadeer Thalji ◽  
Lyndon F. Cooper ◽  
Salvador Nares
Keyword(s):  
Gene Expression ◽  
Early Stage ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Whole Genome ◽  
Adherent Cells ◽  
Mini Implants ◽  
Molecular Events ◽  
The Impact

The objective of this study was to evaluate the impact of smoking on the early molecular events involved in peri-implant healing at either a micro-roughened or a micro-roughened with superimposed nanofeatures surface implant in humans. Twenty-one subjects, 10 smokers and 11 nonsmokers received 4 mini-implants (2.2 × 5.0 mm; 2 of each surface). After 3 and 7 days, paired mini-implants were retrieved by reverse threading and RNA isolated from implant adherent cells. Whole genome microarrays were used interrogate the gene expression profiles. The study failed to identify differences in the gene expression profiles of implant adherent cells at this early stage of osseointegration (up to day 7) comparing smoker and nonsmoker individuals.

Interaction of Stem Cells and Their Niche: Behavior and Gene Expression Profiles of CD34+/CD38− Cells upon Co-Cultivation with AFT024.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 1281-1281
Author(s):  
Wolfgang Wagner ◽  
Rainer Saffrich ◽  
Ute Wirkner ◽  
Volker Eckstein ◽  
Jonathon Blake ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Bone Marrow ◽  
Differential Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Nuclear Antigen ◽  
Cd34 Cells ◽  
Differential Gene ◽  
The Impact

Abstract Cell-cell contact between stem cells and cellular determinants of the microenvironment plays an essential role in the regulation of self-renewal and differentiation. The stromal cell line derived from murine fetal liver (AFT024) has been shown to support maintenance of primitive human hematopoietic progenitor cells (HPC) in vitro. We have studied the interaction between HPC (defined as CD34+/CD38− umbilical cord blood cells) and AFT024 and the impact of co-cultivation on the behavior and gene expression of HPC. By time lapse microscopy the mobility and behavior of CD34+/CD38− cells were monitored. Approximately 30% of the CD34+/CD38− cells adhered to the cellular niche through an uropod. CD44 and CD34 were co-localized at the site of contact. Gene expression profiles of CD34+/CD38− cells were then compared upon co-cultivation either with or without AFT024. After cultivation for 16h, 20h, 48h or 72h the HPC were separated form the feeder layer cells by a second FAC-Sort. Differential gene expression was analyzed using our Human Genome cDNA Microarray of over 51,145 ESTs. Among the genes with the highest up-regulation in contact with AFT024 were several genes involved in cell adhesion, proliferation and DNA-modification including tubulin genes, ezrin, complement component 1 q subcomponent 1 (C1QR1), proto-oncogene proteins c-fos and v-fos, proliferating cell nuclear antigen (PCNA), HLA-DR, gamma-glutamyl hydrolase (GGH), minichromosome maintenance deficient 6 (MCM6), uracil-DNA glycolase (UNG) and DNA-methyltransferase 1 (DNMT1). In contrast, genes that were down-regulated after contact with AFT024 included collagenase type iv (MMP2), elastin (ELN) and hemoglobin genes. Differential expression of six genes was confirmed by RT-PCR. Other authors have reported on the differential gene expression profiles of CD34+ cells derived from the bone marrow versus those from G-CSF mobilized blood. As CD34+ cells from the bone marrow might represent cells exposed to the natural HPC niche we have then compared our findings with these experiments. In these comparisons we identified several overlapping genes that are involved in regulation of cell cycle and DNA repair including PCNA, DNMT1, MCM6, MCM2, CDC28 protein kinase regulatory subunit 1B (CKS1B), Topoisomerase II (TOP2a), DNA Ligase 1 (LIG1) and DNA mismatch repair protein MLH1. All these genes were up-regulated among CD34+/CD38− cells upon co-culture with AFT024, as well as among CD34+ cells derived from the bone marrow versus those from peripheral blood. Our studies support the hypothesis that intimate contact and adhesive interaction of HPC with their niche profoundly influenced their proliferative potential and their differentiation program.

scholarly journals Hippocampal transcriptomic responses to cellular dissociation

2017 ◽  
Author(s):  
Rayna M. Harris ◽  
Hsin-Yi Kao ◽  
Juan Marcos Alarcón ◽  
Hans A. Hofmann ◽  
André A. Fenton
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Research Effort ◽  
Expression Profiles ◽  
Research Question ◽  
Gene Expression Profiles ◽  
Long Term Potentiation ◽  
System Structure ◽  
Neural Function ◽  
The Impact

AbstractSingle-neuron gene expression studies may be especially important for understanding nervous system structure and function because of the neuron-specific functionality and plasticity that defines functional neural circuits. Cellular dissociation is a prerequisite technical manipulation for single-cell and single cell-population studies, but the extent to which the cellular dissociation process affects neural gene expression has not been determined. This information is necessary for interpreting the results of experimental manipulations that affect neural function such as learning and memory. The goal of this research was to determine the impact of chemical cell dissociation on brain transcriptomes. We compared gene expression of microdissected samples from the dentate gyrus (DG), CA3, and CA1 subfields of the mouse hippocampus either prepared by a standard tissue homogenization protocol or subjected to a chemical cellular dissociation procedure. We report that compared to homogenization, chemical cellular dissociation alters about 350 genes or 2% of the hippocampal transcriptome. While only a few genes canonically implicated in long-term potentiation (LTP) and fear memory change expression levels in response to the dissociation procedure, these data indicate that sample preparation can affect gene expression profiles, which might confound interpretation of results depending on the research question. This study is important for the investigation of any complex tissues as research effort moves from subfield level analysis to single cell analysis of gene expression.

The Impact of Gene Expression Microarrays in the Evaluation of Lung Carcinoma Subtypes and DNA Copy Number

2008 ◽  
Vol 132 (10) ◽  
pp. 1562-1565
Author(s):  
Montserrat Sanchez-Cespedes
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Gene Amplification ◽  
Genetic Background ◽  
Expression Profiles ◽  
Global Analysis ◽  
Tumor Development ◽  
Gene Expression Profiles ◽  
Molecular Alterations ◽  
The Impact

Abstract Context.—The development of targeted therapies creates a need to accurately classify tumors. Among the more pressing needs are the identification of the complete catalog of genes that are altered in cancer and the accurate discrimination of tumors based on their genetic background. Objectives.—To discuss the use of gene expression profiles to recapitulate the pathology and to distinguish the genetic background of non–small cell lung cancer. Also, to comment on using global analysis of gene expression to identify chromosomal regions carrying clusters of highly expressed genes, likely due to gene amplification. Gene amplification at these regions may target the activation of an oncogene critical to tumor development and potentially important in therapy. Data Sources.—Review of relevant, recent literature on molecular alterations and expression analysis in lung cancer. Conclusions.—The complexity of genetic and epigenetic alterations and the cell type of origin confer marked patterns of gene expression to lung tumors, which differentiate different tumor entities.

Interspecies bacterial interactions stabilize transcriptional responses of ancestral wild types and biofilm-optimised variants

2020 ◽  
Author(s):  
Mette Burmølle ◽  
Nanna Mee Coops Olsen ◽  
Samuel Jacquiod ◽  
Henriette Lyng Røder
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Niche Partitioning ◽  
Gene Expression Profiles ◽  
Biotic Interactions ◽  
Culture Conditions ◽  
Differentially Expressed ◽  
Natural Environments ◽  
Transcriptional Responses ◽  
The Impact

&lt;p&gt;Most bacteria in natural environments live in multispecies biofilms, featuring high diversity and chemical heterogeneity. The cell-to-cell proximity found in these biofilms results in biotic interactions and niche-partitioning, facilitating co-existence of species that may otherwise out-compete each other. Additionally, due to the fast generation time of microbes and ceaseless biotic interactions, biofilms accelerate adaptation through the emergence of more fit genetic variants, most probably in response to niche-partitioning and local constraints. We have previously isolated and characterized biofilm-optimised (wrinkled) variants of &lt;em&gt;Xanthomonas retroflexus&lt;/em&gt;. These variants emerged in biofilm co-cultures with &lt;em&gt;Paenibacillus amylolyticus&lt;/em&gt; and reinforced the original interspecific mutualistic interaction, due to altered c-di-GMP regulation and spatial organisation.&lt;/p&gt; &lt;p&gt;The aim of the present study was to examine the impact on gene expression profiles of either co-cultivation of the wild type (WT) or the wrinkled variant &lt;em&gt;X. retroflexus&lt;/em&gt; with &lt;em&gt;P. amylolyticus&lt;/em&gt; or its supernatant. We hypothesised that the gene expression of the two &lt;em&gt;X. retroflexus&lt;/em&gt; strains would differ significantly and that these differences would be even more pronounced when co-cultured with &lt;em&gt;P. amylolyticus&lt;/em&gt; or its supernatant.&lt;/p&gt; &lt;p&gt;Mono- and dual species biofilms were grown in 24-well plates for 24 h. The liquid culture was removed, and the remaining biofilm from the sides of the wells and the air-liquid interface was sampled and processed for mRNA sequencing. After sequencing, &lt;em&gt;X. retroflexus&amp;#160;&lt;/em&gt;reads were mapped against its concatenated genome and genes of which expression differed by fold changes of log2 &lt;-1 and &gt;1 were considered differentially expressed.&lt;/p&gt; &lt;p&gt;Unexpectedly, most marked differences in gene expression were observed when comparing mono-cultures of the WT and the wrinkled &lt;em&gt;X. retroflexus&lt;/em&gt;, as approximately 500 genes were differentially expressed in these biofilms. Of these, 30 genes were predicted to encode biofilm-associated functions. When exposed to either live &lt;em&gt;P. amylolyticus&lt;/em&gt; or its supernatant, expression profiles of the WT and the wrinkled variant were more similar, with the living partner &lt;em&gt;P. amylolyticus&lt;/em&gt; being the key factor of this stabilization. Specifically, the stabilisation was caused by opposite regulation of specific genes in the wrinkled &lt;em&gt;X. retroflexus&amp;#160;&lt;/em&gt;variant compared to the WT in mono- vs. co-culture conditions.&lt;/p&gt; &lt;p&gt;In conclusion, our data indicates that differences in gene expression of &lt;em&gt;X. retroflexus&lt;/em&gt; WT and the biofilm-optimised variant were neutralised by co-cultivation with &lt;em&gt;P. amylolyticus&lt;/em&gt;. To our knowledge, such comparative analyses of ancestral and biofilm-optimised variants have not previously been presented, despite being instrumental in elucidating evolutionary trajectories of such variants in complex environments.&lt;/p&gt;

scholarly journals Gene expression stasis and plasticity following migration into a foreign environment

2017 ◽  
Author(s):  
Brian K. Lohman ◽  
William E. Stutz ◽  
Daniel I. Bolnick
Keyword(s):  
Gene Expression ◽  
Phenotypic Plasticity ◽  
Expression Profile ◽  
Gasterosteus Aculeatus ◽  
Expression Profiles ◽  
Survival Rates ◽  
Gene Expression Profiles ◽  
Genes Expression ◽  
The Impact ◽  
Fish Performance

AbstractSelection against migrants is key to maintaining genetic differences between populations linked by dispersal. Yet, migrants are not just passively weeded out by selection. Migrants may mitigate fitness costs by proactively choosing among available habitats, or by phenotypic plasticity. We previously reported that a reciprocal transplant of lake and stream stickleback (Gasterosteus aculeatus) found little support for divergent selection. We revisit that experiment to test whether phenotypic plasticity in gene expression may have helped migrants adjust to unfamiliar habitats. We measured gene expression profiles in stickleback via TagSeq and tested whether migrants between lake and stream habitats exhibited a plastic response to their new environment that allowed them to converge on the expression profile of adapted natives. We report extensive gene expression differences between genetically divergent lake and stream stickleback, despite gene flow. But for many genes, expression was highly plastic. Fish transplanted into the adjoining habitat partially converged on the expression profile typical of their new habitat. This suggests that expression plasticity may soften the impact of migration. Nonetheless, lake and stream fish differed in survival rates and parasite infection rates in our study, implying that expression plasticity is not fast or extensive enough to fully homogenize fish performance.

Sign in / Sign up

Export Citation Format

Share Document