Correlation approach to identify coding regions in DNA sequences.

Recently, it was observed that noncoding regions of DNA sequences possess long-range power-law correlations, whereas coding regions typically display only short-range correlations. We develop an algorithm based on this finding that enables investigators to perform a statistical analysis on long DNA sequences to locate possible coding regions. The algorithm is particularly successful in predicting the location of lengthy coding regions. For example, for the complete genome of yeast chromosome III (315,344 nucleotides), at least 82% of the predictions correspond to putative coding regions; the algorithm correctly identified all coding regions larger than 3000 nucleotides, 92% of coding regions between 2000 and 3000 nucleotides long, and 79% of coding regions between 1000 and 2000 nucleotides. The predictive ability of this new algorithm supports the claim that there is a fundamental difference in the correlation property between coding and noncoding sequences. This algorithm, which is not species-dependent, can be implemented with other techniques for rapidly and accurately locating relatively long coding regions in genomic sequences.     

Mycoplasma capricolum membranes induce tumor necrosis factor α by a mechanism different from that of lipopolysaccharide

Summary Heat-inactivated (60°C, 45 min)Mycoplasma capricolum strain JR cells activate murine macrophages to secrete high levels of tumór necrosis factor (TNF) and to lyse tumor target cells efficiently. Fractionation of the intactM. capricolum cells, obtained from cells harvested at the exponential phase of growth, shows that their capacity to induce TNF secretion by macrophage resides exclusively in the membrane fraction. The macrophage-mediated cytolysis following activation byM. capricolum membranes was significantly inhibited by specific anti-recombinant murine TNF antibodies.M. capricolum membranes are a potent inducer of TNF as the commonly used bacterial lipopolysaccharide, indicated by their doseresponse curve for macrophage activation. Our study further showed thatM. capricolum membranes and lipopolysaccharide synergize to augment TNF secretion by C57BL/6-derived macrophages markedly. Moreover, lipopolysaccharide-unresponsive C3H/HeJ-derived macrophages, were pronouncedly activated byM. capricolum membranes, which do not contain lipopolysaccharide. These findings suggest that the mechanism by whichM. capricolum membranes activate macrophages differs from that of lipopolysaccharide. Results of preliminary experiments show that human monocytes as well secrete TNF following activation byM. capricolum membranes. Thus, in contrast with the prohibitive toxicity of lipopolysaccharide to animals and humans,M. capricolum membranes, which contain no lipopolysaccharide and are nontoxic in nature, may be of therapeutic value in the treatment of cancer.This study was supported by the Ernst David Bergmann Fund of the Hebrew University, Jerusalem, the Concern II Foundation for Cancer Research, Los Angeles, and the Society of Research Associates of the Lautenberg Center     

In vitro exposure of nasal epithelial cells to atmospheric dust

Dust storms are common phenomena in many parts of the world, and significantly increase the level of atmospheric particulate matter (PM). The soil-derived dust is a mixture of organic and inorganic particles and even remnants of pesticides from agricultural areas nearby. The risk of human exposure to atmospheric dust is well documented, but very little is known on the impact of inhaled PM on the biological lining of the nasal cavity, which is the natural filter between the external environment and the respiratory tract. We developed a new system and methodology for in vitro exposure of cultured nasal epithelial cells (NEC) to atmospheric soil-dust pollutants under realistic and controlled laboratory simulations that mimic nasal breathing. We exposed cultured NEC to clean and dust-polluted airflows that mimic physiological conditions. The results revealed that the secretion of mucin and IL-8 from the NEC exposed to clean and dust-polluted airflows was less than the secretion at static conditions under clean air. The secretion of IL-8 from NEC exposed to dust-polluted air was larger than that of clean air, but not larger than in the static case. The experiments with dust air pollution that also contained agricultural pesticides did not reveal differences in the secretion of mucin and IL-8 as compared to the same pollution without pesticides.     

TLR3 and TLR9 Agonists Improve Postexposure Vaccination Efficacy of Live Smallpox Vaccines

Eradication of smallpox and discontinuation of the vaccination campaign resulted in an increase in the percentage of unvaccinated individuals, highlighting the need for postexposure efficient countermeasures in case of accidental or deliberate viral release. Intranasal infection of mice with ectromelia virus (ECTV), a model for human smallpox, is curable by vaccination with a high vaccine dose given up to 3 days postexposure. To further extend this protective window and to reduce morbidity, mice were vaccinated postexposure with Vaccinia-Lister, the conventional smallpox vaccine or Modified Vaccinia Ankara, a highly attenuated vaccine in conjunction with TLR3 or TLR9 agonists. We show that co-administration of the TLR3 agonist poly(I:C) even 5 days postexposure conferred protection, avoiding the need to increase the vaccination dose. Efficacious treatments prevented death, ameliorated disease symptoms, reduced viral load and maintained tissue integrity of target organs. Protection was associated with significant elevation of serum IFNα and anti-vaccinia IgM antibodies, modulation of IFNγ response, and balanced activation of NK and T cells. TLR9 agonists (CpG ODNs) were less protective than the TLR3 agonist poly(I:C). We show that activation of type 1 IFN by poly(I:C) and protection is achievable even without co-vaccination, requiring sufficient amount of the viral antigens of the infective agent or the vaccine. This study demonstrated the therapeutic potential of postexposure immune modulation by TLR activation, allowing to alleviate the disease symptoms and to further extend the protective window of postexposure vaccination.     

Establishment of functional human pituitary tumor cell cultures

Summary Five primary human pituitary tumor cell cultures were initiated from adenoma fragments obtained from patients with prolactin-secreting adenomas and acromegaly. Functional cell cultures were maintained and propagated in monolayer or suspension culture for up to 9 months. Optimal cell viability and growth were achieved using Ham’s F10 medium enriched with 20% fetal bovine serum, although cells from a patient with acromegaly also grew in serum-free, defined, hormone-containing medium. Bromocriptine (100 ng/ml) did not alter the growth curve of replicating cells derived from a patient with acromegaly. These cells initially secreted 5.5 μg human growth hormone/10⁶ cells, and hormone production diminished after 6 wk. Prolactin secretion by cells derived from prolactinomas (0.5 to 1.3 μg/10⁶ cells/24 h) was stimulated by thyrotropin-releasing hormone (10 ng/ml) in two of the cultures. Both dopamine (10 ng/ml) and nickel chloride (1 mM) suppressed PRL secretion. These studies demonstrate that responsive human pituitary tumor cell cultures can be initiated and maintained. This research was supported by VA Medical Research Funds and NIH Grant HD 7181.     

Long-Range Correlations and Memory in the Dynamics of Internet Interdomain Routing

Data transfer is one of the main functions of the Internet. The Internet consists of a large number of interconnected subnetworks or domains, known as Autonomous Systems (ASes). Due to privacy and other reasons the information about what route to use to reach devices within other ASes is not readily available to any given AS. The Border Gateway Protocol (BGP) is responsible for discovering and distributing this reachability information to all ASes. Since the topology of the Internet is highly dynamic, all ASes constantly exchange and update this reachability information in small chunks, known as routing control packets or BGP updates. In the view of the quick growth of the Internet there are significant concerns with the scalability of the BGP updates and the efficiency of the BGP routing in general. Motivated by these issues we conduct a systematic time series analysis of BGP update rates. We find that BGP update time series are extremely volatile, exhibit long-term correlations and memory effects, similar to seismic time series, or temperature and stock market price fluctuations. The presented statistical characterization of BGP update dynamics could serve as a basis for validation of existing and developing better models of Internet interdomain routing.