Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Total RNA-sequencing Detects Transcriptome Differences in Mouse Preosteoblast Response to Bulk Nanostructured Titanium

ABSTRACT: Titanium is the most widely used alloy family in dental and orthopedic implants due to its natural ability to integrate into bone, but cytotoxic alloying elements are required in titanium for its mechanical properties to match the functionality of natural bone in high-load bearing applications. Recent advances in nanostructuring, such as Equal Channel Angular Pressing-Conform (ECAP-C), reduce the grain size and increase the strength of pure grades of titanium, thereby eliminating the need for cytotoxic elements and increasing cytocompatibilty as measured by traditional cell biology techniques. Transcriptomic profiling of cells grown on conventional coarse grain (CG) versus nanostructured ultrafine grain (UG) surfaces can simultaneously enhance our understanding of genomics and biomaterials, facilitating the development of a new generation of implantable materials. Sterile Ti discs, 13.5 mm in diameter and polished to a 2 nm average surface roughness were arrayed in a non-tissue culture treated 24-well cell culture plate using a block design, with 12 CG and 12 UG disks. Wells were re-fed after 24 hours and after 72 hours Ti discs were transferred to new plates for standard cell harvesting protocols. The cells from four wells were consolidated into one sample and were stored at -80°C in RNAlater. All subsequent steps were identical for all samples. Samples on CG were used as the control for UG-CG comparisons.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mus musculus

SUBMITTER: Terry Lowe

PROVIDER: E-MTAB-7528 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Rational: Titanium is the most widely used alloy family in dental and orthopedic implants due to its natural ability to integrate into bone, but cytotoxic alloying elements are required in titanium for its mechanical properties to match the functionality of natural bone in high-load bearing applications. Recent advances in nanostructuring, such as Continuous Equal Channel Angular Pressing (C-ECAP), reduce the grain size and increase the strength of pure grades of titanium, thereby eliminating the need for cytotoxic elements and increasing cytocompatibilty as measured by traditional cell biology techniques. Transcriptomic profiling of cells grown on conventional coarse grain (CG) versus nanostructured ultrafine grain (UG) surfaces can simultaneously enhance our understanding of genomics and biomaterials, facilitating the development of a new generation of implantable materials. Objective: We initiated this pilot project to develop a workflow for transcriptional profiling of both protein coding and non-coding RNAs (ncRNAs) in cells grown on Ti discs that are characterized for grain size, 12.1 μm for CG Ti and 0.28 μm for UG Ti. Methods: Two Ti substrates were designed for cell growth in 24-well culture dishes, CG and UG. Mouse pre-osteoblasts were cultured on Ti disc for 72 hours. Cells were harvested and total-RNA extracted. Ribosomal RNA subtraction was performed prior to Illumina sequencing library construction. Single-end 50 base pairs reads were subjected to Illumina quality control and the resulting reads were mapped to the mouse genome and annotations with Genomic Short-read Nucleotide Alignment Program (GSNAP) and HTseq-count. Read count files were normalized and statistically analyzed with empirical analysis of digital gene expression data in R (EdgeR) and filtered for low expression levels using Zipf’s Power Law. Transcripts with adequate coverage and significant expression differences were subjected to GO Biological Process term enrichment and network analyses with the Cytoscape App ClueGO. Results: Gene expression differences with an FDR≤0.05 are limited to six genes, five of which are likely ncRNAs. Of the 432 transcripts with significant differences at p≤0.05 117 form an interconnected network of genes and 12 GO biological processes (P(adj) ≤ 0.05). Biological processes that connect to predominately upregulated genes include cell division, mRNA metabolic processes, chromatin modification and protein localization to the cytoskeleton, while downregulated processes include regulation of apoptosis, of p38MAK cascade, and response to molecules of bacterial origin. Conclusions: After 72 hours, the transcriptional profile of cells on UG Ti confirms more rapid cell division than on CG. These results demonstrate that informative transcriptional profiling of cells growing on substrates that differ only in their crystallographic structure can be accomplished by a workflow that includes standard cell biology techniques, transcriptomic profiling, data mining, and network analyses.

Project description:Beef represents a major diet component and one of the major sources of protein in human. The beef industry in the United States is currently undergoing changes and is facing increased demands especially for natural grass-fed beef. The grass-fed beef obtained their nutrients directly from pastures, which contained limited assimilable energy but abundant amount of fiber. On the contrary, the grain-fed steers received a grain-based regime that served as an efficient source of high-digestible energy. Lately, ruminant animals have been accused to be a substantial contributor for the green house effect. Therefore, the concerns from environmentalism, animal welfare and public health have driven consumers to choose grass-fed beef. Rumen is one of the key workshops to digest forage constituting a critical step to supply enough nutrients for animals’ growth and production. We hypothesize that rumen may function differently in grass- and grain-fed regimes. The objective of this study was to find the differentially expressed genes in the ruminal wall of grass-fed and grain-fed steers, and then explore the potential biopathways. In this study, the RNA Sequencing (RNA-Seq) method was used to measure the gene expression level in the ruminal wall. The total number of reads per sample ranged from 24,697,373 to 36,714,704. The analysis detected 342 differentially expressed genes between ruminal wall samples of animals raised under different regimens. The Fisher’s exact test performed in the Ingenuity Pathway Analysis (IPA) software found 16 significant molecular networks. Additionally, 13 significantly enriched pathways were identified, most of which were related to cell development and biosynthesis. Our analysis demonstrated that most of the pathways enriched with the differentially expressed genes were related to cell development and biosynthesis. Our results provided valuable insights into the molecular mechanisms resulting in the phenotype difference between grass-fed and grain-fed cattle. Ruminal wall samples from two randomly chosen animals per group were obtained, totaling four samples. The animals were born, raised and maintained at the Wye Angus farm. This herd, which has been closed for almost 75 years and yielded genetically similar progenies, constitutes an excellent resource to perform transcriptomic analysis. The genetic resemblance among individuals permits us to better control the cause of variation between experimental clusters and individuals. The randomly chosen pairs of animals were part of larger sets of steers that received a particular treatment. All animals received the same diet until weaning. The grain group received conventional diet consisting of corn silage, shelled corn, soy bean and trace minerals. The grass fed steers consumed normally grazed alfalfa; during wintertime, bailage was utilized. The alfalfa has been harvested from land without any fertilizers, pesticides or other chemicals. The steers ate no animal, agricultural or industrial byproducts and never receive any type of grain. Then, the calves were randomly assigned to one diet and exclusively received that regimen until termination. Grain–fed animals reached the market weight around the age of 14 month-old, however, grass-fed steers required approximately 200 additional days to achieve the same weight. Immediately after termination at the Old Line Custom Meat Company (Baltimore, MD) a small piece of ruminal wall was excised, cleaned and preserved at -80°C for posterior processing.

Project description:The grass-fed cattle obtain nutrients directly from pastures containing limited assimilable energy but abundant amount of fiber; by contrast, grain-fed steers receive a diet that is comprised mainly of grains and serves as an efficient source of high-digestible energy. Besides energy, these two types of diet differ in a large number of nutritional components. Additionally, animals maintained on rich-energy regimen are more likely to develop metabolic disorders and infectious diseases than pasture raised individuals. Thus, we hypothesize that spleenâ??the main immune organâ??may function differently under disparate regimes. The objective of this study was to find the differentially expressed genes in the spleen of grass-fed and grain-fed steers, and furtherly explore the potential involved biopathways. Through RNA sequencing (RNA-Seq), we detected 123 differentially expressed genes. Based on these genes, we performed an Ingenuity Pathway Analysis (IPA) and identified 9 significant molecular networks and 13 enriched biological pathways. Two of the pathways, Nur77 signaling in T lymphocytes and calcium-induced T lymphocyte apoptosis which are immune related, contain a pair of genes HLA-DRA and NR4A1 with dramatically altered expression level. Collectively, our results provided valuable insights into understanding the molecular mechanism of spleen under varied feeding regimens. We collected spleen samples from two randomly chosen animals per group, totaling four samples. The animals were born and raised at the Wye Angus farm, which has produced genetically similar progenies. The genetic resemblance among individuals permitted us to better control the variation between experimental individuals, constituting an excellent resource to perform scientific research. All animals included in this study received the same diet until weaning. Next, we assigned the animals to one certain diet at random, and exclusively raised them under that regimen until termination. The diet of grain-fed group consisted of soybean, shelled corn, corn silage and trace minerals. The grass-fed steers normally received alfalfa harvested from land without any fertilizers, pesticides or other chemicals; during wintertime, bailage was supplied. Grass-fed individuals ate no animal, agricultural or industrial byproducts and never consumed any type of grain. Grain-fed animals reached the market weight around 14 month-old; however, grass-fed steers needed approximately 200 additional days to achieve the same weight. Immediately after termination at the Old Line Custom Meat Company (Baltimore, MD), a small piece of spleen was incised, washed and frozen at -80Â°C for posterior processing.

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Total RNA-sequencing Detects Transcriptome Differences in Mouse Preosteoblast Response to Bulk Nanostructured Titanium

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