Linking microarray reporters with protein functions

Background  

The analysis of microarray experiments requires accurate and up-to-date functional annotation of the microarray reporters to optimize the interpretation of the biological processes involved. Pathway visualization tools are used to connect gene expression data with existing biological pathways by using specific database identifiers that link reporters with elements in the pathways.     

Impacts of bottom and suspended cultures of mussels <Emphasis Type="Italic">Mytilus</Emphasis> spp. on the surrounding sedimentary environment and macrobenthic biodiversity

The aim of this study was to quantify the effect of bottom and suspended mussel cultures, cultured in different physical environments, on the sedimentary environmental conditions and thereby the biodiversity structure of the associated macrofaunal community. We compared two bottom cultures (Limfjorden: microtidal, wind-driven; Oosterschelde: macrotidal) and one suspended culture (Ria de Vigo in an upwelling coastal region). The sedimentary environmental conditions (mud fraction, POC, PON, phosphorus content, chl a breakdown products) were significantly elevated underneath and surrounding bottom and suspended cultures compared to culture-free sediments that were nearby and hydrodynamically similar. The relative change in environmental conditions was more pronounced in the Oosterschelde compared to Limfjorden, most likely due to differences in hydrodynamic forcing and characteristics of the mussel bed. The effect of the suspended cultures in Ria de Vigo on the surrounding sediments was influenced by local topographic and hydrodynamic conditions. The impact of mussels on the benthic community due to biodeposition was clearly seen in the community structure. The species composition changed from species which are typically present in sandy environments to more small opportunistic species, which are typically present in organically enriched sediments. The impact of bottom cultures on the benthic community due to changes in the habitat under the presence of mussels was positive, especially in the Oosterschelde where an increase in the number of epibenthic species was seen. The influence of bottom cultures on the sedimentary environment and on the macrobenthic community seems to be very local. Within the mussel site in Limfjorden, differences were detected between sites where none or almost no mussels were present with sites where mussels were very abundant.     

Staphylococcal enterotoxin A: a candidate for the amplification of physiological immunoregulatory responses in the gut

Staphylococcal enterotoxin A (SEA) is one of the bacterial products tested for modulation of unwanted immune responses. Of all the staphylococcal enterotoxins, SEA is the most potent stimulator of T cells. When administered orally, SEA acts as a superantigen (SA), producing unspecific stimulation of intra-epithelial lymphocytes (IELs) in the intestinal mucosa. This stimulation results in amplification of the normal local immunologic responses, which are mainly regulatory. This amplification is based on increased local production of IFN-γ by IELs, which acts on the nearby enterocytes. As a result, the enterocytes produce large amounts of tolerosomes, cellular corpuscles which detach themselves from the basal poles of the enterocytes and contain antigenic peptides that are conditioned to be interpreted as tolerogenic by the gut immune system. Tolerosomes are physiologically produced as a response to dietary peptides; it is already known that enterocytes posses the molecular mechanisms for processing peptides in a similar manner to lymphocytes. The fate of tolerosomes is not precisely known, but it seems that they merge with intestinal dendritic cells, conveying to them the information that orally administered peptides must be interpreted as tolerogens. SEA can stimulate this mechanism, thus favoring the development of tolerance to peptides/proteins administered subsequently via the oral route. This characteristic of SEA might be useful in therapy for regulating immune responses. The present paper reviews the current status of research regarding the impact of SEA on the enteric immune system and its potential use in the treatment of allergic and autoimmune diseases.     

Proinflammatory cytokines: an insight into pancreatic oncogenesis

Pancreatic cancer is a highly lethal disease, being one of the five leading death causes among oncologic patients. It is usually diagnosed late due to the paucity of clinical signs, and the current therapy means have limited success. One of the documented risk factors for developing pancreatic adenocarcinoma is chronic pancreatitis. It is postulated that a chronic inflammatory disease has a potential of evolving toward neoplasia, a fact that could account for a percentage of the pancreatic cancers. Starting from this assumption, we intended to analyze the serum reflection of some molecules with proinflammatory roles, and compare them in healthy individuals, in patients with chronic pancreatitis and with pancreatic adenocarcinoma. Additionally, we performed a biochemical and hematological assessment of the study groups, and compared the results with the immunological parameters analyzed in the same subjects. We found significantly higher levels of Tumor Necrosis Factor-alpha and Interleukin 6 in chronic pancreatitis and pancreatic adenocarcinoma sera (with higher levels in the pancreatitis group than in the cancer group), compared to healthy controls. Additionally, we found significantly higher levels of interleukin 8 and Macrophage Inflammatory Protein-3 alpha in pancreatic cancer, compared to chronic pancreatitis and controls. We also identified numerous correlations between the abovementioned cytokines/chemokines and biochemical parameters, not very much studied before. Our results plead for a pathogenic role of chronic inflammation in pancreatic carcinogenesis, thus offering a potential tool for earliy diagnose or targets for therapy.     

Ammonia excretion increased and urea excretion decreased in urine of a new world nectarivorous bat with decreased nitrogen intake

We determined the effect of water and nitrogen intake on nitrogenous waste composition in the nectarivorous Pallas's long-tongued bat Glossophaga soricina (Phyllostomidae) to test the hypothesis that bats reduce excretion of urea nitrogen and increase the excretion of ammonia nitrogen as nitrogen intake decreases and water intake decreases. Because changes in urine nitrogen composition are expected only in animals whose natural diets are low in nitrogen and high in water content, we also measured maintenance nitrogen requirements (MNR). We hypothesized that, similar to other plant-eating vertebrates, nectarivorous bats have low MNR. Our nitrogen excretion hypothesis was partly proved correct. There was an increase in the proportion of N excreted as ammonia and a decrease in the proportion excreted as urea in low-nitrogen diets. The proportion of N excreted as ammonia and urea was independent of water intake. Most individuals were ureotelic (n = 28), and only a few were ureo-ammonotelic (n = 3) or ammonotelic (n = 2). According to our nitrogen requirement hypothesis, apparent MNR (60 mg kg(-0.75) d(-1)) and truly digestible MNR (54 mg N kg(-0.75) d(-1)) were low. A decrease in urea excretion in low-nitrogen diets may result from urea recycling from liver to the gut functioning as a nitrogen salvage system in nectarivorous bats. This mechanism probably contributes to the low MNR found in Pallas's long-tongued bats.     

Phosphorylation of eukaryotic translation initiation factor 4E is critical for growth

Eukaryotic translation initiation factor 4E (eIF4E) binds to the cap structure at the 5' end of mRNAs and is a critical target for the control of protein synthesis. eIF4E is phosphorylated in many systems in response to extracellular stimuli, but biochemical evidence to date has been equivocal as to the biological significance of this modification. Here we use a genetic approach to this problem. We show that, in Drosophila melanogaster, homozygous eIF4E mutants arrest growth during larval development. In Drosophila eIF4EI, Ser251 corresponds to Ser209 of mammalian eIF4E, which is phosphorylated in response to extracellular signals. We find that, in vivo, eIF4EI Ser251 mutants cannot incorporate labeled phosphate. Furthermore, transgenic Drosophila organisms expressing eIF4E(Ser251Ala) in an eIF4E mutant background have reduced viability. Escapers develop more slowly than control siblings and are smaller. These genetic data provide evidence that eIF4E phosphorylation is biologically significant and is essential for normal growth and development.     

BRCA1 supports XIST RNA concentration on the inactive X chromosome

BRCA1, a breast and ovarian tumor suppressor, colocalizes with markers of the inactive X chromosome (Xi) on Xi in female somatic cells and associates with XIST RNA, as detected by chromatin immunoprecipitation. Breast and ovarian carcinoma cells lacking BRCA1 show evidence of defects in Xi chromatin structure. Reconstitution of BRCA1-deficient cells with wt BRCA1 led to the appearance of focal XIST RNA staining without altering XIST abundance. Inhibiting BRCA1 synthesis in a suitable reporter line led to increased expression of an otherwise silenced Xi-located GFP transgene. These observations suggest that loss of BRCA1 in female cells may lead to Xi perturbation and destabilization of its silenced state.     

Extracellular calcium does not contribute to cryopreservation-induced cytotoxicity

Summary The possible role of extracellular calcium ([Ca⁺²]e) in cryopreservation-induced cytotoxicity was tested using Madin-Darby canine kidney (MDCK) cells and a fluorescent multiple endpoint assay. MDCK cells maintained in 2 mM [Ca⁺²]e and treated with the calcium ionophore, ionomycin, increased their intracellular calcium ([Ca⁺²]i) as revealed by the calcium indicator dye, Fluo3 and the bottom-reading spectrofluorometer, CytoFluor 2300. The addition of 10 mM [ethylene bis (oxyethylenenitrilo)]-tetraacetic acid (EGTA) to the extracellular medium before treatment with ionomycin blocked this ionomycin-dependent increase in [Ca⁺²]i. A number of site and activity-specific fluorescent probes were surveyed to determine which indicator dye might best reveal the ionomycin-induced cytotoxic events during this increase in [Ca⁺²]i. Although most dyes changed their emission profiles in response to calcium, neutral red was found to best reflect the loss of [Ca⁺²]i homeostasis. The NR50 for a 15-min exposure to ionomycin in the presence of 2 mM [Ca⁺²]e was approximately 2μM ionomycin, but ionomycin had little apparent effect on neutral red retention when 10 mM EGTA was added to the extracellular medium. Thus it was clear that an increase in [Ca⁺²]i could be cytotoxic to MDCK cells and that neutral red could monitor this cytotoxic episode. To test if [Ca⁺²]e was similarly cytotoxic during cryopreservation, MDCK cells were subjected to cryopreservation in the presence of dimethylsulfoxide (DMSO). In contrast to previous studies, plasma membrane integrity, not lysosomal function, seemed to best correlate with cell survival subsequent to cryopreservation. In addition, decreasing [Ca⁺²]e had no discernable effect on the retention of plasma membrane indicator dyes, neutral red, or cell survival. It is concluded that a) plasma membrane indicator dyes, not neutral red, might be better indicators of cytotoxicity occurring during cryopreservation; b) DMSO might be toxic to lysosomes during cryopreservation of cultured cells; and c) although [Ca⁺²]e can contribute to cytotoxicity, the presence of [Ca⁺²]e might not influence cryopreservation-induced cytotoxicity.