Construction and Analyses of Human Large-Scale Tissue Specific Networks

Construction and analyses of tissue specific networks is crucial to unveil the function and organizational structure of biological systems. As a direct method to detect protein dynamics, human proteome-wide expression data provide an valuable resource to investigate the tissue specificity of proteins and interactions. By integrating protein expression data with large-scale interaction network, we constructed 30 tissue/cell specific networks in human and analyzed their properties and functions. Rather than the tissue specificity of proteins, we mainly focused on the tissue specificity of interactions to distill tissue specific networks. Through comparing our tissue specific networks with those inferred from gene expression data, we found our networks have larger scales and higher reliability. Furthermore, we investigated the similar extent of multiple tissue specific networks, which proved that tissues with similar functions tend to contain more common interactions. Finally, we found that the tissue specific networks differed from the static network in multiple topological properties. The proteins in tissue specific networks are interacting looser and the hubs play more important roles than those in the static network.     

Probable Identity of Tissue Specific Historie with Encephalitogenic Protein

SOME years ago Tomasi and Kornguth isolated a basic protein from the brains of adult pigs¹. Fluorescent immunohisto-chemical studies indicated that it was localized in the nuclei of neurones and spermatogonia and the suggestion was made that it was a tissue-specific histone². The amino-acid composition of this brain protein is very similar to that of a basic encephalitogenic protein isolated from myelin of a variety of animal species^3–12.     

Search for Tissue Specific Plant Lectins A Preliminary Report

Extract of the seeds ofAnona reticulata, Camellia sinensis, Bauhinia acuminata, Cassia tomentosa, Malus sylvestris, Trigonella foenumgraecum, Cephalandra indica, Lawsonia inermis, Anacardium occidentale, Mangifera indica, Nephelium litchi, Citrus lemoni, Aegle marmelos, Quassia amara, Mimusops elengi, Achras sapota, Datura stramonium, Thevetia nerifolia, Persea americana andCycas circinalis, were screened for lectin activity by haemagglutination and haemagglutination inhibition assays. Lectin-like activity was detected only in the seeds ofMangifera indica and Perseaamericana. The conventional methods for the isolation of lectins could not separate the haemagglutinins from the extracts. The properties of these agglutinins suggest that they are not lectins.     

miTALOS v2: Analyzing Tissue Specific microRNA Function

MicroRNAs are involved in almost all biological processes and have emerged as regulators of signaling pathways. We show that miRNA target genes and pathway genes are not uniformly expressed across human tissues. To capture tissue specific effects, we developed a novel methodology for tissue specific pathway analysis of miRNAs. We incorporated the most recent and highest quality miRNA targeting data (TargetScan and StarBase), RNA-seq based gene expression data (EBI Expression Atlas) and multiple new pathway data sources to increase the biological relevance of the predicted miRNA-pathway associations. We identified new potential roles of miR-199a-3p, miR-199b-3p and the miR-200 family in hepatocellular carcinoma, involving the regulation of metastasis through MAPK and Wnt signaling. Also, an association of miR-571 and Notch signaling in liver fibrosis was proposed. To facilitate data update and future extensions of our tool, we developed a flexible database backend using the graph database neo4j. The new backend as well as the novel methodology were included in the updated miTALOS v2, a tool that provides insights into tissue specific miRNA regulation of biological pathways. miTALOS v2 is available at http://mips.helmholtz-muenchen.de/mitalos.     

Sensing of Barrier Tissue Disruption with an Organic Electrochemical Transistor

The gastrointestinal tract is an example of barrier tissue that provides a physical barrier against entry of pathogens and toxins, while allowing the passage of necessary ions and molecules. A breach in this barrier can be caused by a reduction in the extracellular calcium concentration. This reduction in calcium concentration causes a conformational change in proteins involved in the sealing of the barrier, leading to an increase of the paracellular flux. To mimic this effect the calcium chelator ethylene glycol-bis(beta-aminoethyl ether)-N,N,N'',N''-tetra acetic acid (EGTA) was used on a monolayer of cells known to be representative of the gastrointestinal tract. Different methods to detect the disruption of the barrier tissue already exist, such as immunofluorescence and permeability assays. However, these methods are time-consuming and costly and not suited to dynamic or high-throughput measurements. Electronic methods for measuring barrier tissue integrity also exist for measurement of the transepithelial resistance (TER), however these are often costly and complex. The development of rapid, cheap, and sensitive methods is urgently needed as the integrity of barrier tissue is a key parameter in drug discovery and pathogen/toxin diagnostics. The organic electrochemical transistor (OECT) integrated with barrier tissue forming cells has been shown as a new device capable of dynamically monitoring barrier tissue integrity. The device is able to measure minute variations in ionic flux with unprecedented temporal resolution and sensitivity, in real time, as an indicator of barrier tissue integrity. This new method is based on a simple device that can be compatible with high throughput screening applications and fabricated at low cost.     

Specific Visualization of Glioma Cells in Living Low-Grade Tumor Tissue

Background

The current therapy of malignant gliomas is based on surgical resection, radio-chemotherapy and chemotherapy. Recent retrospective case-series have highlighted the significance of the extent of resection as a prognostic factor predicting the course of the disease. Complete resection in low-grade gliomas that show no MRI-enhanced images are especially difficult. The aim in this study was to develop a robust, specific, new fluorescent probe for glioma cells that is easy to apply to live tumor biopsies and could identify tumor cells from normal brain cells at all levels of magnification.

Methodology/Principal Findings

In this investigation we employed brightly fluorescent, photostable quantum dots (QDs) to specifically target epidermal growth factor receptor (EGFR) that is upregulated in many gliomas. Living glioma and normal cells or tissue biopsies were incubated with QDs coupled to EGF and/or monoclonal antibodies against EGFR for 30 minutes, washed and imaged. The data include results from cell-culture, animal model and ex vivo human tumor biopsies of both low-grade and high-grade gliomas and show high probe specificity. Tumor cells could be visualized from the macroscopic to single cell level with contrast ratios as high as 1000: 1 compared to normal brain tissue.

Conclusions/Significance

The ability of the targeted probes to clearly distinguish tumor cells in low-grade tumor biopsies, where no enhanced MRI image was obtained, demonstrates the great potential of the method. We propose that future application of specifically targeted fluorescent particles during surgery could allow intraoperative guidance for the removal of residual tumor cells from the resection cavity and thus increase patient survival.     

欧洲白榆UlGLK基因克隆及组织表达特异性研究

GLK转录因子是GARP转录因子超家族成员,具有参与调控植物叶绿体发育、生物胁迫和非生物胁迫、植物衰老和激素信号转导等功能,该基因在叶色改良方面已成功应用于白桦（Betula platyphylla）及银中杨（Populus alba×P.berolinensis）等林木。为了探讨欧洲白榆（Ulmus laevis）UlGLK基因的功能,为后续白榆的分子设计育种提供参考,以欧洲白榆为研究材料,开展UlGLK基因克隆及序列分析,筛选qRT-PCR分析用的内参基因,分析UlGLK基因的组织表达特性。研究结果显示,UlGLK基因的cDNA长度为1 353 bp,编码450个氨基酸,与大麻（Cannabis sativa）、川桑（Morus notabilis）的同源性高。以白榆根、茎和叶组织cDNA为模板,根据Ubiquitin、Actin、Tubulin基因在上述3种组织中的表达水平,确定ubiquitin基因可作为后续qRT-PCR分析内参基因。UlGLK基因的组织表达特性分析显示,该基因在叶片组织中表达量最高,在根和茎组织中表达量较低。研究结果为欧洲白榆后续分子设计育种提供参考。     

Specific Features of Cultivation of Iris ensata Thunb. Callus Tissue

A continuous callus culture was obtained from zygotic embryos of Japanese iris (Iris ensata Thunb.) on Murashige–Skoog medium supplemented with 2 mg/l -naphthylacetic acid and 0.5 mg/l 6-benzylaminopurine (BAP). It was found that successful callusogenesis required isolated embryos at the wax stage of endosperm development. The optimal combination of phytohormones for the growth of callus tissue was 1 mg/l 2,4-dichlorophenoxyacetic acid and 0.5 mg/l BAP. The pigment composition of I. ensata callus tissue was studied. It was demonstrated that subcultivated callus tissue contained red pigments of flavonoid nature. Under stress cultivation conditions, yellow pigments were formed and the content of red pigments increased.     

Ethnic‐Specific Differences in Abdominal Subcutaneous Adipose Tissue Compartments

South Asians have a higher prevalence of cardiovascular disease (CVD) than Europeans. Studies have identified distinct subcompartments of subcutaneous adipose tissue (SAT) that provide insight into the relationship between abdominal obesity and metabolic risk factors in different ethnic groups. Our objective was to determine the relationship between SAT compartments and fat‐free mass (FFM) between South Asian and European cohorts, and between men and women. Healthy Europeans and South Asians (n = 408) were assessed for FFM via dual energy X‐ray absorptiometry, and SAT areas by computed tomography (CT). SAT was subdivided into superficial subcutaneous abdominal adipose tissue (SSAT) and deep subcutaneous abdominal adipose tissue (DSAT). Linear regression analyses were performed using DSAT and SSAT as separate dependent variables and FFM and ethnicity as primary independent variables adjusting for age, gender, income, education, and smoking status. Results showed that South Asian men had significantly higher amounts of DSAT (median 187.65 cm² vs. 145.15 cm², P < 0.001), SSAT (median 92.0 cm² vs. 76.1 cm², P = 0.046), and body fat mass (BFM) (25.1 kg vs. 22.6 kg, P = 0.049) than European men. In a fully adjusted model, South Asians showed significantly greater DSAT at any FFM than Europeans. Women had more SSAT at any given FFM than men and less DSAT at any given FFM than men, irrespective of ethnic background. In conclusion, South Asians had more DSAT than Europeans and men had relatively more DSAT than women. These data suggest that specific fat depots are influenced by ethnicity and gender; therefore, could provide insight into the relationship between ethnicity, gender and subsequent risk for CVD.     

Acetylcholine and Choline in Neuronal Tissue Measured by HPLC with Electrochemical Detection

Abstract: A simple, rapid method is presented for the determination of acetylcholine (ACh) and choline (Ch) in neuronal tissue using HPLC with electrochemical detection. The method is based on the separation of ACh and Ch by reverse-phase HPLC and mixing the effluent as it emerges from the column with acetylcholinesterase and Ch oxidase, which converts endogenous Ch and Ch produced by the hydrolysis of ACh to betaine and hydrogen peroxide. Production of hydrogen peroxide is continuously monitored electrochemically. The sensitivity of the procedure is 1 pmol for Ch and 2 pmol for ACh. Specificity of the method is based on HPLC, two specific enzymatic reactions, and the detection of hydrogen peroxide.     

Effects of Fixation and Tissue Processing on Immunohistochemical Demonstration of Specific Antigens

Identification of biomarkers in archival tissues using immunochemistry is becoming increasingly important for determining the diagnosis and prognosis of tumors, for characterizing preinvasive neoplastic changes in glandular tissues such as prostate, for evaluating the response of tumors and preinvasive neoplastic changes to certain therapies (i.e., as a surrogate intermediate end point), for selecting patients who are candidates for specific therapies (e.g., immunotherapy) and for retrospective studies. For detecting specific biomarkers it is important to understand the limitations imposed by the fixation methods and processing of the tissues. This study was designed to determine the effects of fixation on the detection in archival paraffin blocks of selected antigens postulated to be important in tumor biology. We evaluated the antigens TGFα, p185^erbB-2, broad spectrum keratins, p53, and TAG-72 (B72.3). Fixatives evaluated included standard preparations of neutral buffered formalin, acid formalin, zinc formalin, alcoholic formalin, ethanol, methanol, and Bouin's fixative. We found that in general neutral buffered formalin is the poorest fixative for maintaining antigen recognition by immunohistochemistry and that no single fixative was best for all antigens. The dehydrating (coagulant) fixatives (e.g., ethanol and methanol) preserved immunorecognition of p53 and broad spectrum keratins best while the slow cross-linking fixatives (e.g., unbuffered zinc formalin) were best for demonstrating TGFα and p185^erbB-2. Fixatives other than neutral buffered formalin produced equivalent recognition of the epitope of TAG-72 by B72.3. In formalin fixed archival tissues, only a portion of the antigen signal can be detected by routine immunohistologic methods.     

Enhancing the Prioritization of Disease-Causing Genes through Tissue Specific Protein Interaction Networks

The prioritization of candidate disease-causing genes is a fundamental challenge in the post-genomic era. Current state of the art methods exploit a protein-protein interaction (PPI) network for this task. They are based on the observation that genes causing phenotypically-similar diseases tend to lie close to one another in a PPI network. However, to date, these methods have used a static picture of human PPIs, while diseases impact specific tissues in which the PPI networks may be dramatically different. Here, for the first time, we perform a large-scale assessment of the contribution of tissue-specific information to gene prioritization. By integrating tissue-specific gene expression data with PPI information, we construct tissue-specific PPI networks for 60 tissues and investigate their prioritization power. We find that tissue-specific PPI networks considerably improve the prioritization results compared to those obtained using a generic PPI network. Furthermore, they allow predicting novel disease-tissue associations, pointing to sub-clinical tissue effects that may escape early detection.     

Selection for Electron Microscopy of Specific Areas in Large Epoxy Tissue Sections

Tissue blocks 2 × 2 × 0.4 cm were fixed 6-24 hr in phosphate-buffered 6% glutaraldehyde then sliced to 2 × 2 × 0.1 cm and rinsed in phosphate buffer for at least 12 hr. Fixation was continued for 2 hr in phosphate-buffered 1-2% OsO₄. The slices were dehydrated, infiltrated with Araldite, and embedded in flat-bottomed plastic molds. Sectioning at 4-8 μ with a sliding microtome was facilitated by addition of 10% dibutylphalate to the standard epoxy mixture. The sections were spread on water and attached to coverslips by drying, then heating to 80 C for 1 min. Staining 2 min with 1-3% KMnO₄ and temporary mounting in glycerol on a slide allowed the desired area for electron microscopy to be selected and marked. This area was then cemented to the facet of a conventional epoxy casting with a drop of epoxy resin (without added dibutylphthalate). After polymerization, the coverslip was removed by quick cooling leaving a flat re-embedded portion of the original section. This portion was viewed by transillumination in a dissecting microscope and trimmed of surplus tissue. Ultrathin sections for electron microscopy were obtained in the usual manner.     

Tissue Specific Roles for the Ribosome Biogenesis Factor Wdr43 in Zebrafish Development

During vertebrate craniofacial development, neural crest cells (NCCs) contribute to most of the craniofacial pharyngeal skeleton. Defects in NCC specification, migration and differentiation resulting in malformations in the craniofacial complex are associated with human craniofacial disorders including Treacher-Collins Syndrome, caused by mutations in TCOF1. It has been hypothesized that perturbed ribosome biogenesis and resulting p53 mediated neuroepithelial apoptosis results in NCC hypoplasia in mouse Tcof1 mutants. However, the underlying mechanisms linking ribosome biogenesis and NCC development remain poorly understood. Here we report a new zebrafish mutant, fantome (fan), which harbors a point mutation and predicted premature stop codon in zebrafish wdr43, the ortholog to yeast UTP5. Although wdr43 mRNA is widely expressed during early zebrafish development, and its deficiency triggers early neural, eye, heart and pharyngeal arch defects, later defects appear fairly restricted to NCC derived craniofacial cartilages. Here we show that the C-terminus of Wdr43, which is absent in fan mutant protein, is both necessary and sufficient to mediate its nucleolar localization and protein interactions in metazoans. We demonstrate that Wdr43 functions in ribosome biogenesis, and that defects observed in fan mutants are mediated by a p53 dependent pathway. Finally, we show that proper localization of a variety of nucleolar proteins, including TCOF1, is dependent on that of WDR43. Together, our findings provide new insight into roles for Wdr43 in development, ribosome biogenesis, and also ribosomopathy-induced craniofacial phenotypes including Treacher-Collins Syndrome.     

Regulation of Epithelial Na+ Permeability by Protein Kinase C is Tissue Specific

Protein kinase C (PKC) is a major regulator of a broad range of cellular functions. Activation of PKC has been reported to stimulate Na⁺ transport across frog skin epithelium by increasing the apical Na⁺ permeability. This positive natriferic response has not been observed with other epithelial preparations, and could reflect the specific experimental conditions of different laboratories, or species or organ specificity of the response to PKC. In the present study, measurements were conducted with skins and urinary bladders from the same animals of two different species. The PKC activator TPA uniformly increased the transepithelial Na⁺ transport (measured as amiloride-sensitive short-circuit current, I _SC, across skins from Rana temporaria and Bufo marinus, and inhibited I _SC across bladders from the same animals. Inhibitors of PKC (staurosporine, H-7 and chelerythrine) partially blocked the TPA-induced stimulation of I _SC across frog skin. The specificity of the PKC response by amphibian skin could have reflected an induction of moulting, similar to that observed with aldosterone. However, light micrographs of paired areas of frog skin revealed no evidence of the putative moulting. Separation of stratum corneum from the underlying stratum granulosum could be detected following application of aldosterone. We conclude that the effect of PKC on epithelial Na⁺ channels is organ, and not species specific. The stimulation of Na⁺ permeability in amphibian skin does not arise from sloughing of the stratum corneum. These observations are consistent with the hypothesis that the natriferic action arises from the calcium-independent isozyme of PKC previously detected in frog skin. Received: 19 January 1996/Revised: 10 April 1996