Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli

Evidence is accumulating that small, noncoding RNAs are important regulatory molecules. Computational and experimental searches have led to the identification of ~60 small RNA genes in Escherichia coli. However, most of these studies focused on the intergenic regions and assumed that small RNAs were >50 nt. Thus, the previous screens missed small RNAs encoded on the antisense strand of protein-coding genes and small RNAs of <50 nt. To identify additional small RNAs, we carried out a cloning-based screen focused on RNAs of 30–65 nt. In this screen, we identified RNA species corresponding to fragments of rRNAs, tRNAs and known small RNAs. Several of the small RNAs also corresponded to 5′- and 3′-untranslated regions (UTRs) and internal fragments of mRNAs. Four of the 3′-UTR-derived RNAs were highly abundant and two showed expression patterns that differed from the corresponding mRNAs, suggesting independent functions for the 3′-UTR-derived small RNAs. We also detected three previously unidentified RNAs encoded in intergenic regions and RNAs from the long direct repeat and hok/sok elements. In addition, we identified a few small RNAs that are expressed opposite protein-coding genes and could base pair with 5′ or 3′ ends of the mRNAs with perfect complementarity.     

The fate of effector T cells in vivo is determined during activation and differs for CD4+ and CD8+ cells

Effector T cells generated in the mesenteric lymph nodes (mLN) are known to accumulate in mLN and the tissue drained by them after circulating in the blood. Their accumulation is due less to preferential entry into mLN but more to preferential proliferation within mLN. The factors regulating the proliferation of effector T cells in vivo are unclear, and it is unknown whether they are different for CD4(+) and CD8(+) effector T cells. Rat T cells from mLN or peripheral lymph nodes (pLN) were stimulated polyclonally via the TCR and CD28 and injected i.v. into congenic recipients. Using three-color flow cytometry and immunohistochemistry, they were identified in mLN, pLN, and blood over time, and proliferation was determined by measuring bromodeoxyuridine incorporation. Only effector mLN T cells showed a significantly increased proliferation rate after entry into mLN compared with that in pLN (2.4 +/- 1.8% vs 0.8 +/- 0.4%). Proliferation among the injected cells was higher when they had contact with dendritic cells within mLN (9.0 +/- 4.3%) than when they did not (4.1 +/- 2.1%). Furthermore, effector mLN T cells which were observed 56 days after injection maintained the capacity for preferential proliferation within mLN. Interestingly, CD4(+) effector mLN T cells proliferated at a higher rate (4.8 +/- 0.7%), remaining in mLN, whereas CD8(+) effector mLN T cells proliferated at a lower rate (3.3 +/- 1.0%) and were able to leave the mLN into the blood. Elucidating the factors regulating the proliferation of effector T cells in vivo will help to modify their distribution for therapeutic purposes.     

Comparison of the mutagenic activity of XAD4 and blue rayon extracts of surface water and related drinking water samples

The combination of mutagenicity tests and selective extraction methodologies can be useful to indicate the possible classes of genotoxic organic contaminants in water samples. Treated and source water samples from two sites were analyzed: a river under the influence of an azo dye-processing plant discharge and a reservoir not directly impacted with industrial discharges, but contaminated with untreated domestic sewage. Organic extraction was performed in columns packed with XAD4 resin, that adsorbs a broad class of mutagenic compounds like polycyclic aromatic hydrocarbons (PAHs), arylamines, nitrocompounds, quinolines, antraquinones, etc., including the halogenated disinfection by-products; and with blue rayon that selectively adsorbs polycyclic planar structures. The organic extracts were tested for mutagenicity with the Salmonella assay using TA98 and TA100 strains and the potencies were compared. A protocol for cleaning the blue rayon fibers was developed and the efficiency of the reused fibers was analyzed with spiked samples. For the river water samples under the influence of the azo-type dye-processing plant, the mutagenicity was much higher for both blue rayon and XAD4 extracts when compared to the water from the reservoir not directly impacted with industrial discharges. For the drinking water samples, although both sites showed mutagenic responses with XAD4, only samples from the site under the influence of the industrial discharge showed mutagenic activity with the blue rayon extraction, suggesting the presence of polycyclic compounds in those samples. As expected, negative results were found with the blue rayon extracts of the drinking water collected from the reservoir not contaminated with industrial discharges. In this case, it appears that using the blue rayon to extract drinking water samples and comparing the results with the XAD resin extracts we were able to distinguish the mutagenicity caused by industrial contaminants from the halogenated disinfection by-products generated during water treatment.     

EphB4 receptor tyrosine kinase transgenic mice develop glomerulopathies reminiscent of aglomerular vascular shunts

We have established transgenic mice over-expressing the EphB4 receptor tyrosine kinase in the kidney. The EphB4 protein was localised to the developing tubular system of both control and transgenic newborn mice. In transgenic adults, transgene expression persisted in the proximal tubules and the Bowman's capsules, structures, which were not stained in control kidneys. The glomeruli of control animals consisted of regular, round vascular baskets with clearly discernable afferent and efferent arterioles. In contrast, approximately 40% of the transgenic glomeruli had an irregular shrivelled appearance and many exhibited fused, horse shoe-like afferent and efferent arterioles bypassing the glomerulus. These abnormal glomerular structures are very reminiscent of aglomerular vascular shunts, a human degenerative glomerulopathy of unknown aetiology.     

Investigation of the immunostimulatory properties of oxihumate

A unique process has been developed to convert bituminous coal by controlled wet oxidation followed by base treatment to a water-soluble humate called oxihumate. The effects of oxihumate on the proliferative response of lymphocytes has been studied in vitro and ex vivo. Oxihumate increased the proliferative response of phytohaemagglutinin-stimulated human lymphocytes, from a concentration of 20 microg/ml and upwards. This response was even more striking in the case of lymphocytes from HIV-infected patients and was not limited to the in vitro setting since similar effects were observed ex vivo following administration of a non-toxic dosage of 4 g oxihumate per day to HIV-positive individuals for two weeks. Mechanistic studies revealed that stimulation of the proliferative response of lymphocytes by oxihumate is associated with an increased production of IL-2, as well as expression of the IL-2 receptor in the setting of decreased production of IL-10. Oxihumate therefore holds promise for the treatment of immunocompromized patients.     

Identification of calreticulin as a nuclear matrix protein associated with human colon cancer

Colon cancer is one of the most common malignancies among populations in the United States and Western Europe, and one of the leading causes of worldwide morbidity and mortality due to cancer. The early detection of colon cancer is central to the effective treatment of this disease and early detection markers are needed. We have demonstrated that high-resolution two-dimensional gel analysis of nuclear matrix proteins (NMPs) demonstrated a specific oncological fingerprint of colon cancer. Utilizing this approach, four proteins specific for colon cancer was identified. Additionally, one protein was expressed much more strongly in colon cancer compared to adjacent and normal donor tissue. The amino acid composition of this protein revealed sequence similarity with calreticulin. The multi-functional protein, calreticulin, is normally found in the lumen of the endoplasmic reticulum although some reports have described a nuclear localization of the protein. The aim of this study was to confirm the identity of the protein as calreticulin as well as to evaluate the localization of calreticulin in the nuclear matrix of colon cancer tissue.