The involvement of trimethylamine oxide in fish meal in the production of egg taint

Endogenous trimethylamine (TMA) oxidation was inhibited by giving (±)-5-vinyl-2-oxazolidenethione to laying hens that had been bred for low TMA oxidase activity. The addition of TMA oxide to the diet (5 g kg^?1) immediately produced an enormous increase in the TMA content of their eggs and a strong crab-like taint. Hens from another flock whose eggs were tainted when they were previously fed on capelin meal as a protein supplement (100 g kg^?1) again showed this abnormality when TMA oxide was added to the diet (0.5 g kg^?1) to simulate the amounts supplied by the meal. Tests with intravenous ¹⁴C-TMA demonstrated that their ability to oxidise TMA was lower than that of unaffected hens. Dietary TMA oxide and intravenous TMA reduced the oxidation of the test dose of ¹⁴C-TMA. The oxide had no effect when given intravenously and did not inhibit TMA oxidase in vitro. It was concluded that TMA oxide is an important source of TMA in fish meal and that tainting occurs when hens with inherently low TMA oxidase activity are overloaded with TMA derived from dietary TMA oxide and choline by the action of enteric bacteria. The sporadic occurrence of the taint in the field may be due partly to wide variations in the oxide content of fish meals.     

Post-genomic applications of tissue microarrays: basic research, prognostic oncology, clinical genomics and drug discovery

Tissue microarrays (TMAs) are an ordered array of tissue cores on a glass slide. They permit immunohistochemical analysis of numerous tissue sections under identical experimental conditions. The arrays can contain samples of every organ in the human body, or a wide variety of common tumors and obscure clinical cases alongside normal controls. The arrays can also contain pellets of cultured tumor cell lines. These arrays may be used like any histological section for immunohistochemistry and in situ hybridization to detect protein and gene expression. This new technology will allow investigators to analyze numerous biomarkers over essentially identical samples, develop novel prognostic markers and validate potential drug targets. The ability to combine TMA technology with DNA microarrays and proteomics makes it a very attractive tool for analysis of gene expression in clinically stratified tumor specimens and relate expression of each particular protein with clinical outcome. Public domain software allows researchers to examine digital images of individual histological specimens from TMAs, evaluate and score them and store the quantitative data in a relational database. TMA technology may be specifically applied to the profiling of proteins of interest in other pathophysiological conditions such as congestive heart failure, renal disease, hypertension, diabetes, cystic fibrosis and neurodegenerative disorders. This review is intended to summarize the strengths and weaknesses of TMA technology which will have an increasingly important role in the laboratories of the post-genomic era.     

An immunogenetic and molecular basis for differences in outcomes of invasive group A streptococcal infections

The role of host genetic factors in conferring predisposition or protection in infectious diseases has become evident. Infection with group A streptococci causes a wide spectrum of disease ranging from pharyngitis to streptococcal toxic shock syndrome. The release of inflammatory cytokines triggered by streptococcal superantigens has a pivotal role in invasive streptococcal disease. However, individuals infected with the same strain can develop very different manifestations. We report here that the immunogenetics of the host influence the outcome of invasive streptococcal infection, and demonstrate the underlying mechanism for these genetic associations. Specific human leukocyte antigen class II haplotypes conferred strong protection from severe systemic disease, whereas others increased the risk of severe disease. Patients with the DRB1*1501/DQB1*0602 haplotype mounted significantly reduced responses and were less likely to develop severe systemic disease (P < 0.0001). We propose that human leukocyte antigen class II allelic variation contributes to differences in severity of invasive streptococcal infections through their ability to regulate cytokine responses triggered by streptococcal superantigens.     

A fluorescence assay for tetradecyltrimethylammonium mono-oxygenase activity that catalyzes the cleavage of the C-N bond with the production of trimethylamine

This article describes a simple fluorescence method for the determination of tetradecyltrimethylammonium mono-oxygenase (TTAB mono-oxygenase) activity involving N-dealkylation of tetradecyltrimethylammonium bromide with concomitant production of trimethylamine (TMA). Activity was determined by measuring the formation of TMA using the morin reagent and aluminum (Al). Morin reacts with Al to form a fluorescent complex, Al-morin. In the presence of TMA, Al is tightly associated with TMA and cannot be sequestered by morin, thus providing evidence for formation of the Al-TMA complex. The concentration of TMA is estimated by calibration graphs constructed by plotting the fluorescence intensity of the Al-morin complex versus TMA concentration. The fluorescence intensities of the Al-morin complexes quenched by TMA are linearly dependent on both the time of the TTAB mono-oxygenase reaction and the amount of protein used in the reaction. The kinetic behavior is characterized by K_0.5 = 4.26 × 10⁻⁴ M, and the apparent Hill coefficient (n_app) = 2.24. These values are both comparable to those determined by GC-MS (K_0.5 = 4.41 × 10⁻⁴ M and n_app = 2.35). The advantages of this assay include rapid and efficient implementation and potential employment for routine accurate determinations of TTAB mono-oxygenase activity over a wide range of substrate concentrations.     

Microbial trimethylamine metabolism in marine environments

Trimethylamine (TMA) is common in marine environments. Although the presence of this compound in the oceans has been known for a long time, unlike the mammalian gastrointestinal tract, where TMA metabolism by microorganisms has been studied intensely, many questions remain unanswered about the microbial metabolism of marine TMA. This minireview summarizes what is currently known about the sources and fate of TMA in marine environments and the different pathways and enzymes involved in TMA metabolism in marine bacteria. This review also raises several questions about microbial TMA metabolism in the marine environments and proposes potential directions for future studies.     

Comparison of quantum dots immunofluorescence histochemistry and conventional immunohistochemistry for the detection of caveolin-1 and PCNA in the lung cancer tissue microarray

Luminescent semiconductor quantum dots (QDs) are a new class of fluorescent label with wide ranges of applications in cell imaging. In this study, we evaluated the capability of QDs immunofluorescence histochemistry (QDs-IHC) for detecting antigens of caveolin-1 and PCNA in the lung cancer tissue microarray (TMA) in comparison with the conventional immunohistochemistry (IHC) technique. Both methods revealed consistent antigen localization and statistically non-significant detection rates of caveolin-1 and PCNA expressions in our study. However, the sensitivity of QDs-IHC was higher than IHC. The positive detection rates of caveolin-1 and PCNA by QDs-IHC were 57% (40/70) and 86% (60/70), respectively, which were higher than the detection rates of 47% (33/70) and 77% (54/70), respectively, by IHC. Moreover, QDs exhibited a much better photostability, a broader excitation spectrum and a longer fluorescence lifetime. We showed here the advantages of QDs-IHC over IHC for the detection of caveolin-1 and PCNA in lung cancer TMA.     

Feature selection using Haar wavelet power spectrum

Background  

Feature selection is an approach to overcome the 'curse of dimensionality' in complex researches like disease classification using microarrays. Statistical methods are utilized more in this domain. Most of them do not fit for a wide range of datasets. The transform oriented signal processing domains are not probed much when other fields like image and video processing utilize them well. Wavelets, one of such techniques, have the potential to be utilized in feature selection method. The aim of this paper is to assess the capability of Haar wavelet power spectrum in the problem of clustering and gene selection based on expression data in the context of disease classification and to propose a method based on Haar wavelet power spectrum.     

High-throughput proteomic analysis of formalin-fixed paraffin-embedded tissue microarrays using MALDI imaging mass spectrometry

A novel method for high-throughput proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tissue microarrays (TMA) is described using on-tissue tryptic digestion followed by MALDI imaging MS. A TMA section containing 112 needle core biopsies from lung-tumor patients was analyzed using MS and the data were correlated to a serial hematoxylin and eosin (H&E)-stained section having various histological regions marked, including cancer, non-cancer, and normal ones. By correlating each mass spectrum to a defined histological region, statistical classification models were generated that can sufficiently distinguish biopsies from adenocarcinoma from squamous cell carcinoma biopsies. These classification models were built using a training set of biopsies in the TMA and were then validated on the remaining biopsies. Peptide markers of interest were identified directly from the TMA section using MALDI MS/MS sequence analysis. The ability to detect and characterize tumor marker proteins for a large cohort of FFPE samples in a high-throughput approach will be of significant benefit not only to investigators studying tumor biology, but also to clinicians for diagnostic and prognostic purposes.     

Perspectives on epigenetic-based immune intervention for rheumatic diseases

Rheumatic disease can loosely be described as any painful condition affecting the loco-motor system, including joints, muscles, connective tissues, and soft tissues around the joints and bones. There is a wide spectrum of rheumatic diseases, many of which involve autoimmunity, including systemic lupus erythematosus and rheumatoid arthritis. A significant body of evidence now links aberrant epigenetic regulation of gene expression with rheumatic disease and points toward the use of epigenetic targeting agents as potential new treatment options, particularly for those conditions associated with an autoimmune element. In this perspective, I will briefly cover the current knowledge surrounding this area in the field of rheumatology.     

Uveitis- a rare disease often associated with systemic diseases and infections- a systematic review of 2619 patients

Gaucher disease (OMIM 230800, 230900, 231000), the most common lysosomal storage disorder, is due to a deficiency in the enzyme glucocerebrosidase. Gaucher patients display a wide spectrum of clinical presentation, with hepatosplenomegaly, haematological changes, and orthopaedic complications being the predominant symptoms. Gaucher disease is classified into three broad phenotypes based upon the presence or absence of neurological involvement: Type 1 (non-neuronopathic), Type 2 (acute neuronopathic), and Type 3 (subacute neuronopathic). Nearly 300 mutations have been identified in Gaucher patients, with the majority being missense mutations. Though studies of genotype-to-phenotype correlations have revealed significant heterogeneity, some consistent patterns have emerged to inform prognostic and therapeutic decisions. Recent research has highlighted a potential role for Gaucher disease in other comorbidities such as cancer and Parkinson's Disease. In this review, we will examine the potential relationship between Gaucher disease and the synucleinopathies, a group of neurodegenerative disorders characterized by the development of intracellular aggregates of ??-synuclein. Possible mechanisms of interaction will be discussed.     

癌症相关microRNA与靶基因的生物信息学分析

MicroRNAs(miRNAs)是一类长度约为22nt的内源性非编码RNA,通过与靶基因转录本互补结合调控基因的表达。近年来,研究发现miRNA与癌症发生密切相关,miRNA可以直接充当癌基因或者抑癌基因而影响肿瘤的发生和生长。为更进一步揭示癌症相关miRNA的特征及靶基因的功能,文章通过数据库搜索及文献检索,在人类基因组中发现了475个癌症相关miRNA,系统地比较了癌症相关miRNA与非癌症miRNA以及基因内和基因间区癌症相关miRNA在保守性、SNP位点分布、癌谱及转录调控等特性。研究发现,癌症相关miRNA比非癌症miRNA保守性要强,发生SNP概率比较低,同时发现miRNA所涉及癌症数目与保守性成正相关。基因组定位分析发现,癌症相关miRNA比非癌症miRNA更倾向于成簇存在。进一步对宿主基因、癌症相关miRNA及作用的靶基因与癌症发生进行关联分析,发现一些非癌症miRNA的宿主基因倾向于被癌症miRNA作用。本研究结果为深入理解miRNA与癌症之间的关系,以及进一步为miRNA作为癌症诊断指示物提供理论依据。     

Kallikrein-related peptidases in prostate, breast, and ovarian cancers: from pathobiology to clinical relevance

Tissue kallikrein (KLK1) and kallikrein-related peptidases (KLK2-15) comprise a family of 15 highly conserved secreted serine proteases with similar structural characteristics and a wide spectrum of functional properties. Both gene expression and protein activity of KLKs are rigorously controlled at various levels via diverse mechanisms, including extensive steroid hormone regulation, to exert their broad physiological role. Nevertheless, deregulated expression, secretion, and function of KLK family members has been observed in several pathological conditions and, particularly, in endocrine-related human malignancies, including those of the prostate, breast, and ovary. The cancer-related abnormal activity of KLKs upon substrates such as growth factors, cell adhesion molecules, cell surface receptors, and extracellular matrix proteins facilitate both tumorigenesis and disease progression to the advanced stages. The well-documented relationship between KLK status and the clinical outcome of cancer patients has led to their identification as promising diagnostic, prognostic, and treatment response monitoring biomarkers for these complex disease entities. The main objective of this review is to summarize the existing knowledge concerning the role of KLKs in prostate, breast, and ovarian cancers and to highlight their continually evolving biomarker capabilities that can provide significant benefits for the management of cancer patients.     

Fatty liver: Role of inflammation and fatty acid nutrition

Nonalcoholic fatty liver disease (NAFLD) refers to a wide spectrum of liver damage, ranging from simple steatosis to nonalcoholic steatohepatitis (NASH), advanced fibrosis, and cirrhosis. NAFLD is strongly associated with insulin resistance and is defined by accumulation of liver fat >5% per liver weight in the presence of <10 g of daily alcohol consumption. The exact prevalence of NAFLD is uncertain because of the absence of simple noninvasive diagnostic tests to facilitate an estimate of prevalence but in subgroups of people such as those with type 2 diabetes, the prevalence may be as high as 70%. NASH is an important subgroup within the spectrum of NAFLD that progresses over time with worsening fibrosis and cirrhosis, and NASH is associated with increased risk for cardiovascular disease. It is, therefore, important to understand the pathogenesis of NASH specifically, to develop strategies for interventions to treat this condition. The purpose of this review is to discuss the roles of inflammation, fatty acids and fatty acids in nutrition, in the pathogenesis and potential treatment of NAFLD.     

Trimethylamine modulates dauer formation,neurodegeneration, and lifespan through tyra‐3/daf‐11 signaling in Caenorhabditis elegans

In the nematode Caenorhabditis elegans, signals derived from bacteria in the diet, the animal''s major nutrient source, can modulate both behavior and healthspan. Here we describe a dual role for trimethylamine (TMA), a human gut flora metabolite, which acts as a nutrient signal and a neurotoxin. TMA and its associated metabolites are produced by the human gut microbiome and have been suggested to serve as risk biomarkers for diabetes and cardiovascular diseases. We demonstrate that the tyramine receptor TYRA‐3, a conserved G protein‐coupled receptor (GPCR), is required to sense TMA and mediate its responses. TMA activates guanylyl cyclase DAF‐11 signaling through TYRA‐3 in amphid neurons (ASK) and ciliated neurons (BAG) to mediate food‐sensing behavior. Bacterial mutants deficient in TMA production enhance dauer formation, extend lifespan, and are less preferred as a food source. Increased levels of TMA lead to neural damage in models of Parkinson''s disease and shorten lifespan. Our results reveal conserved signaling pathways modulated by TMA in C. elegans that are likely to be relevant for its effects in mammalian systems.     

A TMA de-arraying method for high throughput biomarker discovery in tissue research

Background

Tissue MicroArrays (TMAs) represent a potential high-throughput platform for the analysis and discovery of tissue biomarkers. As TMA slides are produced manually and subject to processing and sectioning artefacts, the layout of TMA cores on the final slide and subsequent digital scan (TMA digital slide) is often disturbed making it difficult to associate cores with their original position in the planned TMA map. Additionally, the individual cores can be greatly altered and contain numerous irregularities such as missing cores, grid rotation and stretching. These factors demand the development of a robust method for de-arraying TMAs which identifies each TMA core, and assigns them to their appropriate coordinates on the constructed TMA slide.

Methodology

This study presents a robust TMA de-arraying method consisting of three functional phases: TMA core segmentation, gridding and mapping. The segmentation of TMA cores uses a set of morphological operations to identify each TMA core. Gridding then utilises a Delaunay Triangulation based method to find the row and column indices of each TMA core. Finally, mapping correlates each TMA core from a high resolution TMA whole slide image with its name within a TMAMap.

Conclusion

This study describes a genuine robust TMA de-arraying algorithm for the rapid identification of TMA cores from digital slides. The result of this de-arraying algorithm allows the easy partition of each TMA core for further processing. Based on a test group of 19 TMA slides (3129 cores), 99.84% of cores were segmented successfully, 99.81% of cores were gridded correctly and 99.96% of cores were mapped with their correct names via TMAMaps. The gridding of TMA cores were also extensively tested using a set of 113 pseudo slide (13,536 cores) with a variety of irregular grid layouts including missing cores, rotation and stretching. 100% of the cores were gridded correctly.     

Functional characterization and signal transduction ability of nucleotide-binding site-leucine-rich repeat resistance genes in plants

Pathogen infection in plants is often limited by a multifaceted defense response triggered by resistance genes. The most prevalent class of resistance proteins includes those that contain a nucleotide-binding site-leucine-rich repeat (NBS-LRR) domain. Over the past 15 years, more than 50 novel NBS-LRR class resistance genes have been isolated and characterized; they play a significant role in activating conserved defense-signaling networks. Recent molecular research on NBS-LRR resistance proteins and their signaling networks has the potential to broaden the use of resistance genes for disease control. Various transgenic approaches have been tested to broaden the disease resistance spectrum using NBS-LRR genes. This review highlights the recent progress in understanding the structure, function, signal transduction ability of NBS-LRR resistance genes in different host-pathogen systems and suggests new strategies for engineering pathogen resistance in crop plants.     

The identification of trimethylamine excess in man: quantitative analysis and biochemical origins

The underlying biochemical causes of chronic odor problems in humans have attracted only a few investigators. This may be due, in part, to intermittent odor complaints, to the psychological problems often associated with these patients, or to the low incidence of a true metabolic disorder. One cause of intense odor is an excessive excretion of trimethylamine (TMA) in sweat, breath, and urine and was reported to be due to a defect in the liver enzyme that converts this volatile amine to its N-oxide. Other investigators have reported TMA excess as a result of liver, kidney, and/or gastrointestinal dysfunction. We report on the development of an analytical technique for urine that can be used to identify those individuals whose chronic odor is caused by a defect in their TMA pathway. A simple extension of the basic TMA analysis can be used to measure the concentration of TMA N-oxide in the affected patients. These data can, in turn, be used to demonstrate the level of activity of the N-oxide-forming enzyme in these subjects. The results obtained from using this test on more than 50 subjects indicate, in addition to a normal population, at least two types of patients with TMA excess. One group has excess TMA excretion with low activity of the N-oxide and another group shows excess TMA excretion with normal N-oxide activity.     

An up to date look at lung cancer screening

Lung cancer is the leading cause of cancer-related death worldwide. At the time of initial presentation, most patients are at an advance stage of disease and have a poor associated prognosis. Those diagnosed and treated at earlier stages have a significantly better outcome with five year survival for stage I disease approaching 75%. Ideally a screening strategy for lung cancer would detect disease at an earlier stage and allow for potential surgical cure. The purpose of this review is to examine past and current evidence as it relates to lung cancer screening.     

New tissue microarray technology for analyses of gene expression in frozen pathological samples

Tissue microarrays (TMAs) are widely used to analyze gene expression in multiple pathological samples on a single slide. Currently, most TMA slides are made by coring paraffin-embedded tissues and arraying them into a paraffin block, from which TMA sections are cut. However paraffin-based TMA technology may not be compatible with frozen clinical tissue samples, which have a higher quality of RNAs and proteins for preparing TMAs than paraffin-embedded tissue samples. In this study, we developed an alternative TMA technology that is applicable to a broader range of frozen tissue samples. Our method takes advantage of a newly developed array recipient block that can be used to array small tissue cores. After arraying tissue cores, the tissue block can be immediately sectioned on a cryostat microtome to make TMA slides. TMAs made using this method have well-defined array configurations and good tissue/cell morphology. Immunohistochemistry and in situ hybridization study also revealed well-preserved proteins and mRNAs on TMA slides. Our method significantly simplifies TMA preparation and assembly when frozen pathological tissues are used. Our technology provides an alternative tool for creating high-quality TMAs for the general research community to study gene expressions in pathological samples.