Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization

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GFP markers for studying D. melanogaster spermatogenesis

Localization of a set of chimeric GFP proteins in D. melanogaster spermatogenesis has been studied. In the collection used, the proteins with detectable germ-line expression frequently occur to be involved in mRNA maturation. According to the cellular localization, proteins fall into three groups, namely, the protein Rtc1, involved in splicing, displays an exclusively nuclear localization; the proteins Squid (splicing and mRNA transport), Pabp2 (polyadenylation), and Hrb98DE (splicing and mRNA transport) change their localization during germ-line development; and the protein Imp (mRNA localization) is located exclusively in the cytoplasm. The distribution of Rtc1, Squid and Hrb98DE in the spermatocyte nuclei is morphologically similar to the distribution of splicing bodies, the so-called splicing factor compartments. The proteins Imp and Hrb98DE at the stage of elongation are localized to a specialized structure in the caudal region of cyst; this region corresponds to the site of the highest synthetic activity in the cyst cells at this developmental stage.     

Intercontinental spread of promiscuous mercury-resistance transposons in environmental bacteria

We demonstrate that horizontal spread of mer operons similar to worldwide spread of antibiotic-resistance genes in medically important bacteria occurred in bacteria found in ores, soils and waters. The spread was mediated by different transposons and plasmids. Some of the spreading transposons were damaged in different ways but this did not prevent their further spread. Certain transposons are mosaics composed of segments belonging to distinct sequence types. These mosaics arose as a result of homologous and site-specific recombination. Our data suggest that the mercury-resistance operons of Gram-negative environmental bacteria can be considered as a worldwide population composed of a relatively small number of distinct recombining clones shared, at least partially, by environmental and clinical bacteria.     

A dose-sensitive modifier of the of Drosophila melanogaster ectopic eye

Ectopic eyes induced in a wing serve as a system for studying developmental plasticity in Drosophila. We used a set of chromosome deficiencies covering the second chromosome to ask whether there are dose-sensitive modifiers of the process. We identified three overlapping deletions showing the enlargement of ectopic eyes. The study of the genes localized in the region of interest suggests that the mutation in the sxc (super sex combs) gene (PcG group) is responsible for the observed phenotype.     

Does extirpation of the primary breast tumor give boost to growth of metastases? Evidence revealed by mathematical modeling

A comprehensive mechanistic model of cancer natural history was utilized to obtain an explicit formula for the distribution of volumes of detectable metastases in a given secondary site at any time post-diagnosis. This model provided an excellent fit to the volumes of n = 31, 20 and 15 bone metastases observed in three breast cancer patients 8 years, 5.5 years and 9 months after primary diagnosis, respectively. The model with optimal parameters allowed us to reconstruct the individual natural history of cancer for the first patient. This gave definitive answers, for the patient in question, to the following three questions of major importance in clinical oncology: (1) How early an event is metastatic dissemination of breast cancer? (2) How long is the metastasis latency time? and (3) Does extirpation of the primary breast tumor accelerate the growth of metastases? Specifically, according to the model applied to the first patient, (1) inception of the first metastasis occurred 29.5 years prior to the primary diagnosis; (2) the expected metastasis latency time was about 79.5 years; and (3) resection of the primary tumor was followed by a 32-fold increase in the rate of metastasis growth. The model and our conclusions were validated by the results for the two other patients.     

Overexpression of inhA,but not kasA,confers resistance to isoniazid and ethionamide in Mycobacterium smegmatis,M. bovis BCG and M. tuberculosis

The inhA and kasA genes of Mycobacterium tuberculosis have each been proposed to encode the primary target of the antibiotic isoniazid (INH). Previous studies investigating whether overexpressed inhA or kasA could confer resistance to INH yielded disparate results. In this work, multicopy plasmids expressing either inhA or kasA genes were transformed into M. smegmatis, M. bovis BCG and three different M. tuberculosis strains. The resulting transformants, as well as previously published M. tuberculosis strains with multicopy inhA or kasAB plasmids, were tested for their resistance to INH, ethionamide (ETH) or thiolactomycin (TLM). Mycobacteria containing inhA plasmids uniformly exhibited 20-fold or greater increased resistance to INH and 10-fold or greater increased resistance to ETH. In contrast, the kasA plasmid conferred no increased resistance to INH or ETH in any of the five strains, but it did confer resistance to thiolactomycin, a known KasA inhibitor. INH is known to increase the expression of kasA in INH-susceptible M. tuberculosis strains. Using molecular beacons, quantified inhA and kasA mRNA levels showed that increased inhA mRNA levels corre--lated with INH resistance, whereas kasA mRNA levels did not. In summary, analysis of strains harbouring inhA or kasA plasmids yielded the same conclusion: overexpressed inhA, but not kasA, confers INH and ETH resistance to M. smegmatis, M. bovis BCG and M. tuberculosis. Therefore, InhA is the primary target of action of INH and ETH in all three species.     

Pharmacokinetics, safety and inducible cytokine responses during a phase 1 trial of the oral histone deacetylase inhibitor ITF2357 (givinostat)

ITF2357 (givinostat) is a histone deacetylase inhibitor with antiinflammatory properties at low nanomolar concentrations. We report here a phase I safety and pharmacokinetics trial in healthy males administered 50, 100, 200, 400 or 600 mg orally. After 50 mg, mean maximal plasma concentrations reached 104 nmol/L 2 h after dosing, with a half-life of 6.9 h. After 100 mg, maximal concentration reached 199 nmol/L at 2.1 h with a half-life of 6.0 h. Repeat doses for 7 consecutive days of 50, 100 or 200 mg resulted in nearly the same kinetics. There were no serious adverse effects (AEs) and no organ toxicities. However, there was a dose-dependent but transient fall in platelets. After 7 daily doses of 50 or 100 mg, the mean decrease in platelets of 17 and 25% was not statistically significant and returned to baseline within 14 d. Blood removed from the subjects after oral dosing was cultured ex vivo with endotoxin, and the release of tumor necrosis factor (TNF)-α, interleukin (IL)-1β, IL-6, IL-1Ra, interferon (IFN)-γ and IL-10 was determined. Maximal reduction in IL-1β, TNFα, IL-6 and IFNγ was observed 4 h after dosing but returned to baseline at 12 h. There was no significant reduction in IL-1Ra or IL-10. With daily dosing, the fall in cytokine production in blood cultures observed on day 7 was nearly the same as that of the first day. We conclude that dosing of 50 or 100 mg ITF2357 is safe in healthy humans and transiently but repeatedly reduces the production of proinflammatory cytokines without affecting production of antiinflammatory cytokines.     

Virus variation resources at the National Center for Biotechnology Information: dengue virus

Background  

There is an increasing number of complete and incomplete virus genome sequences available in public databases. This large body of sequence data harbors information about epidemiology, phylogeny, and virulence. Several specialized databases, such as the NCBI Influenza Virus Resource or the Los Alamos HIV database, offer sophisticated query interfaces along with integrated exploratory data analysis tools for individual virus species to facilitate extracting this information. Thus far, there has not been a comprehensive database for dengue virus, a significant public health threat.     

Brightness of yellow fluorescent protein from coral (zFP538) depends on aggregation

The yellow fluorescent protein from coral (zFP538) forms aggregates in water solutions. According to dynamic light scattering and gel filtration data, the aggregation number is approximately 1000-10000 at pH 8-9 and protein concentration 1 mg/mL. Gel filtration demonstrated that dissociation of the aggregates takes place upon dilution, and the molecular weight of the aggregates decreases with pH. Atomic force microscopy (AFM) and near-field scanning optical microscopy (NSOM) were used to obtain images of zFP538 in the solid state. It was shown that protein films are comprised of fluorescent ellipsoidal granules with a 50-300 nm major axis and a 30-130 nm minor axis. The dependence of zFP538 fluorescence on protein concentration between 1.2 x 10(-)(9) and 5.5 x 10(-)(7) M can be divided in two linear regions with different slopes indicating the existence of at least two different forms of zFP538. The fluorescence of zFP538 decreases with time upon acidification, and the decrease depends on pH and protein concentration. Between pH 3.5 and pH 5.5, relative residual fluorescence is higher for concentrated zFP538 solutions (about 10(-)(6) M) as compared with diluted ones (10(-)(7) M and below). Aggregation makes zFP538 more stable against fluorescence quenching upon acidification: the decrease in zFP538 fluorescence at protein concentration 1 mg/mL is completely reversible, unlike that observed for less concentrated solutions. This phenomenon may be due to the decrease in the freedom of chromophore mobility in zFP538 aggregates.