Analysis of the Compartmentalized Metabolome – A Validation of the Non-Aqueous Fractionation Technique

With the development of high-throughput metabolic technologies, a plethora of primary and secondary compounds have been detected in the plant cell. However, there are still major gaps in our understanding of the plant metabolome. This is especially true with regards to the compartmental localization of these identified metabolites. Non-aqueous fractionation (NAF) is a powerful technique for the determination of subcellular metabolite distributions in eukaryotic cells, and it has become the method of choice to analyze the distribution of a large number of metabolites concurrently. However, the NAF technique produces a continuous gradient of metabolite distributions, not discrete assignments. Resolution of these distributions requires computational analyses based on marker molecules to resolve compartmental localizations. In this article we focus on expanding the computational analysis of data derived from NAF. Along with an experimental workflow, we describe the critical steps in NAF experiments and how computational approaches can aid in assessing the quality and robustness of the derived data. For this, we have developed and provide a new version (v1.2) of the BestFit command line tool for calculation and evaluation of subcellular metabolite distributions. Furthermore, using both simulated and experimental data we show the influence on estimated subcellular distributions by modulating important parameters, such as the number of fractions taken or which marker molecule is selected. Finally, we discuss caveats and benefits of NAF analysis in the context of the compartmentalized metabolome

Targeted in vivo expression of the cyclin-dependent kinase inhibitor p21 halts hepatocyte cell-cycle progression, postnatal liver development and regeneration.

The CDK inhibitor p21 (WAF-1/CIP-1/SDI-1) has been implicated in DNA damage-induced p53-mediated G1 arrest, as well as in physiological processes, such as cell differentiation and senescence, that do not involve p53 function. To determine the impact of p21 on normal development and cell-cycle regulation in vivo, we have generated transgenic mice that abundantly express p21 specifically in hepatocytes. During postnatal liver development, when transgenic p-21 protein becomes detectable, hepatocyte proliferation is inhibited dramatically. This disturbance causes a reduction in the overall number of adult hepatocytes, resulting in aberrant tissue organization, runted liver and body growth, and increased mortality. The transgenic p21 protein is associated with most, if not all, of the cyclin D1-CDK4 in liver but not significantly with other cyclin/CDK proteins, indicating the importance of cyclin D1-CDK4 function in normal liver development. The appearance of large polyploid nuclei in some hepatocytes indicates that p21 may also cause arrest during the G2 phase of the cell cycle. Significantly, partial hepatectomy failed to stimulate hepatocytes to proliferate in p21 transgenic animals. These results provide the first in vivo evidence that appropriate p21 levels are critical in normal development and further implicate p21 in the control of multiple cell-cycle phases

Bone mineral density in young adult survivors of acute lymphoblastic leukemia

BACKGROUND. The purpose of the current study was to determine the prevalence of low bone mineral density (BMD) (ie, osteopenia) and identify factors associated with low BMD in young adult survivors of childhood acute lymphoblastic leukemia (ALL). METHODS. Dual energy x-ray absorptiometry was used to evaluate BMD in 74 randomly selected, long-term childhood ALL survivors initially treated in Minneapolis/St. Paul, Minnesota. Growth hormone (GH)-releasing hormone–arginine stimulation testing was conducted to evaluate peak GH level, and insulin-like growth factor I (IGF-I) and other markers of endocrine functioning were also evaluated in relation to BMD. RESULTS. The mean age at the time of interview was 30 years, and the mean time since diagnosis was 24 years. Low BMD (Z-score, ≤−1) was present in 24% of subjects, including 1 with osteoporosis. Low BMD was substantially more prevalent in men than in women and was strongly associated with short height. The mean height Z-score for those with low BMD was −1.44, compared with a height Z-score of −0.39 ( P < .01) for those with normal BMD. GH insufficiency, low IGF-I Z-score, and current smoking were also suggestive risk factors for low BMD. CONCLUSIONS. In this long-term follow-up study of childhood ALL survivors, low BMD was found to be more prevalent than expected based on population normative data, specifically in men. The health consequences of early-onset BMD problems in childhood ALL survivors need to be carefully monitored. Cancer 2008. © 2008 American Cancer Society.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/61319/1/23912_ftp.pd

PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments

BACKGROUND: Microarray technology has become a widely accepted and standardized tool in biology. The first microarray data analysis programs were developed to support pair-wise comparison. However, as microarray experiments have become more routine, large scale experiments have become more common, which investigate multiple time points or sets of mutants or transgenics. To extract biological information from such high-throughput expression data, it is necessary to develop efficient analytical platforms, which combine manually curated gene ontologies with efficient visualization and navigation tools. Currently, most tools focus on a few limited biological aspects, rather than offering a holistic, integrated analysis. RESULTS: Here we introduce PageMan, a multiplatform, user-friendly, and stand-alone software tool that annotates, investigates, and condenses high-throughput microarray data in the context of functional ontologies. It includes a GUI tool to transform different ontologies into a suitable format, enabling the user to compare and choose between different ontologies. It is equipped with several statistical modules for data analysis, including over-representation analysis and Wilcoxon statistical testing. Results are exported in a graphical format for direct use, or for further editing in graphics programs. PageMan provides a fast overview of single treatments, allows genome-level responses to be compared across several microarray experiments covering, for example, stress responses at multiple time points. This aids in searching for trait-specific changes in pathways using mutants or transgenics, analyzing development time-courses, and comparison between species. In a case study, we analyze the results of publicly available microarrays of multiple cold stress experiments using PageMan, and compare the results to a previously published meta-analysis. PageMan offers a complete user's guide, a web-based over-representation analysis as well as a tutorial, and is freely available at . CONCLUSION: PageMan allows multiple microarray experiments to be efficiently condensed into a single page graphical display. The flexible interface allows data to be quickly and easily visualized, facilitating comparisons within experiments and to published experiments, thus enabling researchers to gain a rapid overview of the biological responses in the experiments

A knowledge-based taxonomy of critical factors for adopting electronic health record systems by physicians: a systematic literature review

<p>Abstract</p> <p>Background</p> <p>The health care sector is an area of social and economic interest in several countries; therefore, there have been lots of efforts in the use of electronic health records. Nevertheless, there is evidence suggesting that these systems have not been adopted as it was expected, and although there are some proposals to support their adoption, the proposed support is not by means of information and communication technology which can provide automatic tools of support. The aim of this study is to identify the critical adoption factors for electronic health records by physicians and to use them as a guide to support their adoption process automatically.</p> <p>Methods</p> <p>This paper presents, based on the PRISMA statement, a systematic literature review in electronic databases with adoption studies of electronic health records published in English. Software applications that manage and process the data in the electronic health record have been considered, i.e.: computerized physician prescription, electronic medical records, and electronic capture of clinical data. Our review was conducted with the purpose of obtaining a taxonomy of the physicians main barriers for adopting electronic health records, that can be addressed by means of information and communication technology; in particular with the information technology roles of the knowledge management processes. Which take us to the question that we want to address in this work: "What are the critical adoption factors of electronic health records that can be supported by information and communication technology?". Reports from eight databases covering electronic health records adoption studies in the medical domain, in particular those focused on physicians, were analyzed.</p> <p>Results</p> <p>The review identifies two main issues: 1) a knowledge-based classification of critical factors for adopting electronic health records by physicians; and 2) the definition of a base for the design of a conceptual framework for supporting the design of knowledge-based systems, to assist the adoption process of electronic health records in an automatic fashion. From our review, six critical adoption factors have been identified: user attitude towards information systems, workflow impact, interoperability, technical support, communication among users, and expert support. The main limitation of the taxonomy is the different impact of the adoption factors of electronic health records reported by some studies depending on the type of practice, setting, or attention level; however, these features are a determinant aspect with regard to the adoption rate for the latter rather than the presence of a specific critical adoption factor.</p> <p>Conclusions</p> <p>The critical adoption factors established here provide a sound theoretical basis for research to understand, support, and facilitate the adoption of electronic health records to physicians in benefit of patients.</p

The histidine kinase-related domain participates in phytochrome B function but is dispensable

Phytochromes are photoreceptors that control many plant light responses. Phytochromes have two carboxyl-terminal structural domains called the PAS repeat domain and the histidine kinase-related domain. These domains are each related to bacterial histidine kinase domains, and biochemical studies suggest that phytochromes are light-regulated kinases. The PAS repeat domain is important for proper phytochrome function and can interact with putative signaling partners. We have characterized several new phytochrome B mutants in Arabidopsis that express phyB protein, three of which affect the histidine kinase-related domain. Point mutations in the histidine kinase-related domain cause phenotypes similar to those of null mutants, indicating that this domain is important for phyB signaling. However, a truncation that removes most of the histidine kinase-related domain results in a phyB molecule with partial activity, suggesting that this domain is dispensable. These results suggest that phytochromes evolved in modular fashion. We discuss possible functions of the histidine kinase-related domain in phytochrome signaling

ScRNA-seq and ST-seq in liver research

Abstract Spatial transcriptomics, which combine gene expression data with spatial information, has quickly expanded in recent years. With application of this method in liver research, our knowledge about liver development, regeneration, and diseases have been greatly improved. While this field is moving forward, a variety of problems still need to be addressed, including sensitivity, limited capacity to obtain exact single-cell information, data processing methods, as well as others. Methods like single-cell RNA sequencing (scRNA-seq) are usually used together with spatial transcriptome sequencing (ST-seq) to clarify cell-specific gene expression. In this review, we explore how advances of scRNA-seq and ST-seq, especially ST-seq, will pave the way to new opportunities to investigate fundamental questions in liver research. Finally, we will discuss the strengths, limitations, and future perspectives of ST-seq in liver research