How does gene expression clustering work?

Clustering is often one of the first steps in gene expression analysis. How do clustering algorithms work, which ones should we use and what can we expect from them?     

α- andβ-adrenergic control of thermogenin mRNA expression in brown adipose tissue

By the use of an earlier characterised cDNA clone, CIN-1, corresponding to a sequence of the mRNA coding for the brown-fat specific uncoupling protein, thermogenin, the amount of thermogenin mRNA found in the brown adipose tissue of mice was quantitatively investigated under different physiological and pharmacological conditions.It was found that a 4 hr cold stress led to a 7-fold increase in the amount of thermogenin mRNA; injection of norepinephrine had a significant but smaller effect. Most notably, isoprenaline (-agonist) and phenylephrine (-agonist) had in themselves no effect, but when injected together were able to increase the mRNA level synergistically. In 4 hr cold-stressed mice, norepinephrine, isoprenaline and cholera toxin could all further potentiate the effect of the cold stress itself on the mRNA level. Insulin and the glucocorticoid dexamethasone both had weak stimulatory effects on the mRNA level.It is concluded that an increase in intracellular cAMP levels is a necessary and perhaps sufficient stimulus for the increase in thermogenin gene expression. However, at least underin vivo conditions, this increase requires stimulation of both - and-adrenergic pathways.     

CD36 expression and brain function: does CD36 deficiency impact learning ability?

This article first presents an overview of published literature documenting the role of the scavenger receptor CD36 in activation of brain microglia with reference to brain pathologies such as Alzheimer's and malaria. Second, the possibility that CD36 may play a role in brain FA metabolism is discussed. Long-chain polyunsaturated fatty acids (PUFAs) are important for brain function and are mostly derived from the plasma. Based on its role in facilitating FA uptake in several tissues and cell types, CD36 expressed on microvascular endothelial cells in the brain may facilitate local uptake of PUFAs. Alternatively, CD36 may influence brain FA supply indirectly via impacting utilization of dietary FA or their metabolism in tissues such as the liver. We examined the possibility that CD36 expression impacts brain function by evaluating the behavior of CD36 null mice using a battery of standard tests. Our data indicate that CD36 deficient mice have normal patterns of activity, anxiety and exploration of novel environments. However they appear to have a significant impairment in learning ability. These findings could provide a new perspective regarding the regulation of brain lipid metabolism.     

Do birds possess brown adipose tissue?

• 1.1. Fluorescence and electron microscopy were used to visualize differences between avian adipose tissue (AAT) collected from clavicular and abdominal regions of the great tit, the willow tit, the house sparrow and the Japanese quail, and interscapular brown adipose tissue (BAT) obtained from the Djungarian dwarf hamster.
• 2.2. Multilocular fat cells were found in AAT. The prerequisite for multilocularity, however, was not simply winter acclimatization [short photophase 4L:20D and low ambient temperature (< −20°C in January in Oulu)] or cold-acclimation (−25°C). Multilocular adipocytes were found during autumn and in unacclimated control birds as well. Mitochondria in the AAT were fewer and about one-sixth the length of those in BAT. This finding was associated with low cytochrome oxidase (COX) activity in the tissue homogenate and isolated mitochondrial fraction of the AAT (< 5.2% of that in BAT).
• 3.3. Catecholamine fluorescence was seen only around arteries in the AAT. Signs of sympathetic parenchymal innervation were found neither in winter- nor in cold-acclimated birds, but typically, sympathetic nerve fibers forming a basket-like network around every cell were seen in the brown fat of the hamster.
• 4.4. Our results show that AAT in the adult birds resembles white adipose tissue more than brown. Multilocularity of adipocytes may improve lipolysis to deliver fatty acids for muscle fuel of shivering or NST.

     

Protein expression of ubiquitin in interscapular brown adipose tissue during acclimation of rats to cold: the impact of ∙NO

Molecular and Cellular Biochemistry - In this study, the effects of l-arginine-nitric-oxide (∙NO)-producing pathway on protein content of ubiquitin, as an important component of...     

Photorespiration and β-carboxylation in brown macroalgae

Photorespiration has been assayed in a variety of marine macroalgae by the Warburg oxygen inhibitory effect and the percentage¹⁴C-labeling of glycine and serine. It was found that particularly the members of the brown macroalgae examined, such asFucus andLaminaria (Phaeophyceae), show a rather weak response to high O₂ partial pressure. This observation is attributed to the appreciably high potential for -carboxylation via PEP-carboxykinase, generally occurring in brown seaweeds.     

How does gene expression level contribute to thermophilic adaptation of prokaryotes? An exploration based on predictors

By analyzing the predicted gene expression levels of 33 prokaryotes with living temperature span from <10 degrees C to >100 degrees C, a universal positive correlation was found between the percentage of predicted highly expressed genes and the organisms' optimal growth temperature. A physical interpretation of the correlation revealed that highly expressed genes are statistically more thermostable than lowly expressed genes. These findings show the possibility of the significant contribution of gene expression level to the prokaryotic thermal adaptation and provide evidence for the translational selection pressure on the thermostability of natural proteins during evolution.     

Do wild brown lemurs reconcile? Not always

Post-conflict behaviour has been widely investigated in anthropoid primates but not extensively in prosimians. Here, we report the reconciliation pattern of a 14-individual group of wild brown lemurs (Eulemur fulvus) in the Berenty gallery forest (South Madagascar). We found that reconciliation occurs only in the non-feeding context and that it works in reducing the risk of renewed aggression. Thus, reconciliation would provide an immediate positive feedback that is probably independent of the quality of the relationship between opponents. Reconciliation may also be a hic-et-nunc mechanism, needed to avoid conflict spreading across group members, possibly leading to social disruption.     

Nuclear factor-κB is a common upstream signal for growth differentiation factor-5 expression in brown adipocytes exposed to pro-inflammatory cytokines and palmitate

We have previously demonstrated that genetic and acquired obesity similarly led to drastic upregulation in brown adipose tissue (BAT), rather than white adipose tissue, of expression of both mRNA and corresponding protein for the bone morphogenic protein/growth differentiation factor (GDF) member GDF5 capable of promoting brown adipogenesis. In this study, we evaluated expression profiles of GDF5 in cultured murine brown pre-adipocytes exposed to pro-inflammatory cytokines and free fatty acids (FFAs), which are all shown to play a role in the pathogenesis of obesity. Both interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α) were effective in up-regulating GDF5 expression in a concentration-dependent manner, while similar upregulation was seen in cells exposed to the saturated FFA palmitate, but not to the unsaturated FFA oleate. In silico analysis revealed existence of the putative nuclear factor-κB (NF-κB) binding site in the 5′-flanking region of mouse GDF5, whereas introduction of NF-κB subunits drastically facilitated both promoter activity and expression of GDF5 in brown pre-adipocytes. Chromatin immunoprecipitation analysis confirmed significant facilitation of the recruitment of NF-κB to the GDF5 promoter in lysed extracts of BAT from leptin-deficient ob/ob obese mice. Upregulation o GDF5 expression was invariably inhibited by an NF-κB inhibitor in cultured brown pre-adipocytes exposed to IL-1β, TNF-α and palmitate. These results suggest that obesity leads to upregulation of GDF5 expression responsible for the promotion of brown adipogenesis through a mechanism relevant to activation of the NF-κB pathway in response to particular pro-inflammatory cytokines and/or saturated FFAs in BAT.     

HSP70 expression: does it a novel fatigue signalling factor from immune system to the brain?

Integrative physiology studies have shown that immune system and central nervous system interplay very closely towards behavioural modulation. Since the 70-kDa heat shock proteins (HSP70s), whose heavy expression during exercise is well documented in the skeletal muscle and other tissues, is also extremely well conserved in nature during all evolutionary periods of species, it is conceivable that HSP70s might participate of physiologic responses such as fatigue induced by some types of physical exercise. In this way, increased circulating levels of extracellular HSP70 (eHSP70) could be envisaged as an immunomodulatory mechanism induced by exercise, besides other chemical messengers (e.g. cytokines) released during an exercise effort, that are able to binding a number of receptors in neural cells. Studies from this laboratory led us to believe that increased levels of eHSP70 in the plasma during exercise and the huge release of eHSP70 from lymphocytes during high-load exercise bouts may participate in the fatigue sensation, also acting as a danger signal from the immune system.     

Recruitment of brown fat and conversion of white into brown adipocytes: Strategies to fight the metabolic complications of obesity?

The role of white and brown adipose tissues in energy metabolism is well established. However, the existence of brown fat in adult humans was until very recently a matter of debate, and the molecular mechanisms underlying brown adipocyte development remained largely unknown. In 2009, several studies brought direct evidence for functional brown adipose tissue in adults. New factors involved in brown fat cell differentiation have been identified. Moreover, work on the origin of fat cells took an unexpected path with the recognition of different populations of brown fat cell precursors according to the anatomical location of the fat depots: a precursor common to skeletal muscle cells and brown adipocytes from brown fat depots, and a progenitor cell common to white adipocytes and brown adipocytes that appear in certain conditions in white fat depots. There is also mounting evidence that mature white adipocytes, including human fat cells, can be converted into brown fat-like adipocytes, and that the typical fatty acid storage phenotype of white adipocyte can be altered towards a fat utilization phenotype. These data open up new opportunities for the development of drugs for obesity and its metabolic and cardiovascular complications.     

Multiple Symmetrical Lipomatosis — A mitochondrial disorder of brown fat

Multiple Symmetrical Lipomatosis (MSL) is an unusual disorder characterized by the development of axial lipomas in adulthood. The pathoetiology of lipoma tissue in MSL remains unresolved. Seven patients with MSL were followed for a mean period of 12 years (8–20 years). All patients had cervical lipomas ranging from subtle lesions to disfiguring masses; six patients had peripheral neuropathy and five had proximal myopathy. Myoclonus, cerebellar ataxia and additional lipomas were variably present. All patients showed clinical progression. Muscle histopathology was consistent with mitochondrial disease. Five patients were positive for mtDNA point mutation m.8344A > G, three of whom underwent lipoma resection — all samples were positive for uncoupling protein-1 mRNA (unique to brown fat). Lipoma from one case stained positive for adipocyte fatty-acid protein-2 (unique to brown fat and immature adipocytes). This long-term study hallmarks the phenotypic heterogeneity of MSL's associated clinical features. The clinical, genetic and molecular findings substantiate the hypothesis that lipomas in MSL are due to a mitochondrial disorder of brown fat.     

Over expression of wild type or a catalytically dead mutant of Sirtuin 6 does not influence NFκB responses

SIRT6 is involved in inflammation, aging and metabolism potentially by modulating the functions of both NFκB and HIF1α. Since it is possible to make small molecule activators and inhibitors of Sirtuins we wished to establish biochemical and cellular assays both to assist in drug discovery efforts and to validate whether SIRT6 represents a valid drug target for these indications. We confirmed in cellular assays that SIRT6 can deacetylate acetylated-histone H3 lysine 9 (H3K9Ac), however this deacetylase activity is unusually low in biochemical assays. In an effort to develop alternative assay formats we observed that SIRT6 overexpression had no influence on TNFα induced nuclear translocation of NFκB, nor did it have an effect on nuclear mobility of RelA/p65. In an effort to identify a gene expression profile that could be used to identify a SIRT6 readout we conducted genome-wide expression studies. We observed that overexpression of SIRT6 had little influence on NFκB-dependent genes, but overexpression of the catalytically inactive mutant affected gene expression in developmental pathways.     

The current excitement in bioinformatics-analysis of whole-genome expression data: how does it relate to protein structure and function?

Whole-genome expression profiles provide a rich new data-trove for bioinformatics. Initial analyses of the profiles have included clustering and cross-referencing to 'external' information on protein structure and function. Expression profile clusters do relate to protein function, but the correlation is not perfect, with the discrepancies partially resulting from the difficulty in consistently defining function. Other attributes of proteins can also be related to expression-in particular, structure and localization-and sometimes show a clearer relationship than function.