Sources of Variability in a Synthetic Gene Oscillator

Synthetic gene oscillators are small, engineered genetic circuits that produce periodic variations in target protein expression. Like other gene circuits, synthetic gene oscillators are noisy and exhibit fluctuations in amplitude and period. Understanding the origins of such variability is key to building predictive models that can guide the rational design of synthetic circuits. Here, we developed a method for determining the impact of different sources of noise in genetic oscillators by measuring the variability in oscillation amplitude and correlations between sister cells. We first used a combination of microfluidic devices and time-lapse fluorescence microscopy to track oscillations in cell lineages across many generations. We found that oscillation amplitude exhibited high cell-to-cell variability, while sister cells remained strongly correlated for many minutes after cell division. To understand how such variability arises, we constructed a computational model that identified the impact of various noise sources across the lineage of an initial cell. When each source of noise was appropriately tuned the model reproduced the experimentally observed amplitude variability and correlations, and accurately predicted outcomes under novel experimental conditions. Our combination of computational modeling and time-lapse data analysis provides a general way to examine the sources of variability in dynamic gene circuits.     

Nucleosome-like complex of the histone from the hyperthermophile Methanopyrus kandleri (MkaH) with linear DNA

The MkaH protein from the archaeon Methanopyrus kandleri, an unusual assembly of two histone-fold domains in a single polypeptide chain, demonstrates high structural similarity to eukaryal histones. We studied the DNA binding and self-association properties of MkaH by means of the electrophoretic mobility shift assay (EMSA), electron microscopy (EM), chemical cross-linking, and analytical gel filtration. EMSA showed an increased mobility of linear DNA complexed with MkaH protein with a maximum at a protein-DNA weight ratio (R(w)) of approximately 3; the mobility decreased at higher protein concentration. EM of the complexes formed at Rw or=9) thickened compact nucleoprotein structures were observed; no individual loops were seen within the complexes. Gel filtration chromatography and chemical fixation indicated that in the absence of DNA the dominant form of the MkaH in solution, unlike other archaeal histones, is a stable dimer (pseudo-tetramer of the histone-fold domain) apparently resembling the eukaryal (H3-H4)(2) tetramer. Similarly, dimers are the dominant form of the protein interacting with DNA. The properties of MkaH supporting the assignment of its intermediate position between other archaeal and eukaryal histones are discussed.     

State of gonads in juvenile triploid trout <Emphasis Type=Italic>Oncorhynchus mykiss</Emphasis> under conditions of South Vietnam after artificial sex inversion

Gonad morphology and structure of sex cells in juvenile triploid trout Oncorhynchus mykiss of the Donaldson breed incubated and reared at a trout plant under climatic conditions of South Vietnam have been studied. Anomalies in the structure of sex gonads and oocyte structure were found, and partial resorption of sex cells was detected. It was shown that sex inversion in triploid (unisexual) fingerlings of rainbow trout passed successfully on the whole since many sex gonads of these fish simultaneously had both female and male sex cells and sometimes were sterile. The connection of anomalies found in the structure of sex system of trout with species rearing under unusual for it climatic conditions and artificial sex inversion is discussed.     

Modulation of TNF release by choline requires alpha7 subunit nicotinic acetylcholine receptor-mediated signaling

The alpha7 subunit-containing nicotinic acetylcholine receptor (alpha7nAChR) is an essential component in the vagus nerve-based cholinergic anti-inflammatory pathway that regulates the levels of TNF, high mobility group box 1 (HMGB1), and other cytokines during inflammation. Choline is an essential nutrient, a cell membrane constituent, a precursor in the biosynthesis of acetylcholine, and a selective natural alpha7nAChR agonist. Here, we studied the anti-inflammatory potential of choline in murine endotoxemia and sepsis, and the role of the alpha7nAChR in mediating the suppressive effect of choline on TNF release. Choline (0.1-50 mM) dose-dependently suppressed TNF release from endotoxin-activated RAW macrophage-like cells, and this effect was associated with significant inhibition of NF-kappaB activation. Choline (50 mg/kg, intraperitoneally [i.p.]) treatment prior to endotoxin administration in mice significantly reduced systemic TNF levels. In contrast to its TNF suppressive effect in wild type mice, choline (50 mg/kg, i.p.) failed to inhibit systemic TNF levels in alpha7nAChR knockout mice during endotoxemia. Choline also failed to suppress TNF release from endotoxin-activated peritoneal macrophages isolated from alpha7nAChR knockout mice. Choline treatment prior to endotoxin resulted in a significantly improved survival rate as compared with saline-treated endotoxemic controls. Choline also suppressed HMGB1 release in vitro and in vivo, and choline treatment initiated 24 h after cecal ligation and puncture (CLP)-induced polymicrobial sepsis significantly improved survival in mice. In addition, choline suppressed TNF release from endotoxin-activated human whole blood and macrophages. Collectively, these data characterize the anti-inflammatory efficacy of choline and demonstrate that the modulation of TNF release by choline requires alpha7nAChR-mediated signaling.     

Shunt in the diagnosis of initial lung lesion in smokers

Cigarette smoking is an important risk factor for all respiratory tract diseases. Unfortunately, the symptoms develop slowly, thus patients feel the consequences of the slowly developing inflammation too late. The inflammation first develops in the area of respiratory bronchioles. In this stage, the disease is asymptomatic. The study included a sample of 31 smokers, mean age 36.38 years, with normal spirometry indices, acid-base status and arterial blood gases. The mean smoking index was 11.28 smoking/years. All subjects were healthy, without any subjective health problems or disease indicators. The aim was to define dead lung area (V/Q) as an early indicator of changes in smokers. Study results demonstrated the mean shunt value in smokers of 8.25%, which showed positive correlation with smoking. The shunt size yielded negative correlation with the forced expiratory volume in one second and midexpiratory flow in smokers. In conclusion, determination of lung shunt is a simple method that is sensitive enough in the diagnosis of initial lung lesion due to cigarette smoking.     

Substrate specificity of nonribosomal peptide synthetase modules responsible for the biosynthesis of the oligopeptide moiety of cephabacin in Lysobacter lactamgenus

Lysobacter lactamgenus produces cephabacins, a class of beta-lactam antibiotics which have an oligopeptide moiety attached to the cephem ring at the C-3 position. The nonribosomal peptide synthetase (NRPS) system, which comprises four distinct modules, is required for the biosynthesis of this short oligopeptide, when one takes the chemical structure of these antibiotics into consideration. The cpbI gene, which has been identified in a region upstream of the pcbAB gene, encodes the NRPS - polyketide synthase hybrid complex, where NRPS is composed of three modules, while the cpbK gene -- which has been reported as being upstream of cpbI-- comprises a single NRPS module. An in silico protein analysis was able to partially reveal the specificity of each module. The four recombinant adenylation (A) domains from each NRPS module were heterologously expressed in Escherichia coli and purified. Biochemical data from ATP-PPi exchange assays indicated that L-arginine was an effective substrate for the A1 domain, while the A2, A3 and A4 domains activated L-alanine. These findings are in an agreement with the known chemical structure of cephabacins, as well as with the anticipated substrate specificity of the NRPS modules in CpbI and CpbK, which are involved in the assembly of the tetrapeptide at the C-3 position.     

Downstream migration in ammocoetes of the Arctic lamprey <Emphasis Type="Italic">Lethenteron camtschaticum</Emphasis> in some Kamchatka rivers

This paper considers the major patterns of downstream migration in Arctic lamprey ammocoetes in Kamchatka rivers. Ammocoetes of different age groups are shown to be constantly noted in the composition of the migrant part of a river community. The greatest intensity of downstream migration in ammocoetes of the age class 0+ is noted in the period of their primary dispersion in late July-early August. The ammocoetes of the age groups 1+ and older migrate from spring to late autumn, but their concentrations are not high. The significant similarity of such a biologic feature as downstream migration in ammocoetes and juvenile salmonids serves as an example of ecological analogy.     

Fast recycling of Escherichia coli ribosomes requires both ribosome recycling factor (RRF) and release factor RF3.

A complete translation system has been assembled from pure initiation, elongation and termination factors as well as pure aminoacyl-tRNA synthetases. In this system, ribosomes perform repeated rounds of translation of short synthetic mRNAs which allows the time per translational round (the recycling time) to be measured. The system has been used to study the influence of release factor RF3 and of ribosome recycling factor RRF on the rate of recycling of ribosomes. In the absence of both RF3 and RRF, the recycling time is approximately 40 s. This time is reduced to approximately 30 s by the addition of RF3 alone and to approximately 15 s by the addition of RRF alone. When both RF3 and RRF are added to the translation system, the recycling time drops to <6 s. Release factor RF3 is seen to promote RF1 cycling between different ribosomes. The action of RRF is shown to depend on the concentration of elongation factor-G. Even in the presence of RRF, ribosomes do not leave the mRNA after termination, but translate the same mRNA several times. This shows that RRF does not actively eject mRNA from the terminating ribosome. It is proposed that terminating ribosomes become mobile on mRNA and ready to enter the next translation round only after two distinct steps, catalysed consecutively by RF3 and RRF, which are slow in the absence of these factors.     

Hormonal stimulation of maturation and ovulation of oocytes in Zebrasoma scopas (Acanthuridae)

The experiments were carried out on hormonal stimulation of oocyte maturation in Zebrasoma scopas from the South China Sea, Vietnam. Three variants of surfagon injections were studied: 1—double injections (5 + 20 μg/kg of fish body weight); 2—double injections (2 + 8 μg/kg); and 3—single injections (20 μg/kg). The time interval between two injections comprised 15–24 h. Ovulation of oocytes in variants 1 and 2 was observed in most (67%) females 33–47 h after the first injection. The increase of the time interval between injections I and II was followed by the decrease of the interval between injection II and ovulation. In variant 3, oocytes ripened but ovulation was absent. The oocytes possessed with the competence for maturation are always present in the ovaries because of a continuous type of oogenesis. The morphological changes in oocytes in the process of maturation were observed. Ovulated oocytes could be stored in the ovary cavity no more than 4 h; the number of embryos with normal cleavage decreased during this time from 90 to 53%.     

Screening of population genetic SCAR markers for mykiss <Emphasis Type="Italic">Parasalmo</Emphasis> (<Emphasis Type="Italic">Oncorhynchus</Emphasis>) <Emphasis Type="Italic">mykiss</Emphasis> from Kamchatka

Using AP-PCR, the genome of Kamchatka mykiss (Parasalmo (O.) mykiss) was examined. Polymorphic fragments, implying geographic differences among the samples, were selected, cloned, and sequenced. Based on these sequences, longer, specific SCAR primers were selected and constructed. Using the BLAST software program, the sequences were analyzed for analogy to those from the GenBank database. It seemed likely that all sequences obtained belonged to earlier unexamined repeated sequences, variable in the populations of the species of interest. A total of seven SCAR markers, characterized by population-significant variability of the DNA products in Kamchatka geographic group of rainbow trout were constructed. These markers can be used for further investigation of the species Parasalmo (O.) mykiss. The SCAR marker sequences were deposited in GenBank under the accession numbers EU805500 to EU805506.