Culture DNA Research Articles

Morphological analysis of historical landscapes based on cultural DNA approach

Recent trends in landscape architecture investigate new approaches, methods, and technologies to understand, monitor, manage, continuity, and sustainably develop heritage landscapes. Cultural DNA (CD) represents designs' transferable geometric, behavioural and functional properties. The morphological structure of Persian historical gardens possesses discoverable hidden patterns, computable through the CD's mathematical and computational models. This study aims to investigate and discover effective parameters in the spatial structure of historical Persian gardens using Space Syntax. Six Persian Gardens were surveyed, and spatial structures were analysed using DepthMap10 software. The results show that these spaces follow meaningful mathematical patterns and rules that can be formulated in the context of generative processes and generalized for the evolutionary continuity of gardens. However, further research is proposed to develop more advanced computational methods, such as artificial intelligence (AI) algorithms and AI-based decision support tools, to help to generate design scenarios and to transmit culture through the design process.

Genomic characterization of MDR/XDR-TB in Kazakhstan by a combination of high-throughput methods predominantly shows the ongoing transmission of L2/Beijing 94\u201332 central Asian/Russian clusters

BackgroundKazakhstan remains a high-burden TB prevalence country with a concomitent high-burden of multi-drug resistant tuberculosis. For this reason, we performed an in depth genetic diversity and population structure characterization of Mycobacterium tuberculosis complex (MTC) genetic diversity in Kazakhstan with both patient and community benefit.MethodsA convenience sample of 700 MTC DNA cultures extracts from 630 tuberculosis patients recruited from 12 out of 14 regions in Kazakhstan, between 2010 and 2015, was independently studied by high-throughput hybridization-based methods, TB-SPRINT (59-Plex, n = 700), TB-SNPID (50-Plex, n = 543). DNA from 391 clinical isolates was successfully typed by two methods. To resolve the population structure of drug-resistant clades in more detail two complementary assays were run on the L2 isolates: an IS6110-NTF insertion site typing assay and a SigE SNP polymorphism assay.ResultsStrains belonged to L2/Beijing and L4/Euro-American sublineages; L2/Beijing prevalence totaled almost 80%. 50% of all samples were resistant to RIF and to INH., Subtyping showed that: (1) all L2/Beijing were “modern” Beijing and (2) most of these belonged to the previously described 94–32 sublineage (Central Asian/Russian), (3) at least two populations of the Central Asian/Russian sublineages are circulating in Kazakhstan, with different evolutionary dynamics.ConclusionsFor the first time, the global genetic diversity and population structure of M. tuberculosis genotypes circulating in Kazakhstan was obtained and compared to previous local studies. Results suggest a region-specific spread of a very limited number of L2/Beijing clonal complexes in Kazakhstan many strongly associated with an MDR phenotype.

Molecular characterization of some lignicolous species from fungal culture collection

Culture collections of microorganisms, including fungi, are strain deposits recognised as Biological Resource Centers (BRCs) with a great importance in science, industry and education. Their objective is to preserve the purity, viability and genomic integrity of every single strain as a member of such collection. Since improvement of molecular methods nowadays brought many novel approaches in manipulation with strains of microorganisms, they can also be useful for characterization of existing stored strains. ITS1 region in nuclear DNA is preferred barcoding marker for taxon identification, which can be explained by its great inter-species variability. This paper presents results from analysing ITS1 region sequences (17) obtained from fungal DNA of culture collection of autochthonous, lignicolous genera Piptoporus, Pleurotus, Ganoderma and Schizophyllum cultured on malt agar plates for 14 days at 25?C. BLAST (Basic Local Alignment Search Tool) was used for comparison with online databases, while alignment of sequences was made with MEGA 5.10 software. Morphological determination of species or genus was confirmed for 13 cultures, while the others were disproved. The resulting alignment indicated small intra-species variability of ITS1 region and pointed to it as an ideal marker for verification of fungal culture collections' authenticity.

DYNAMICS OF RECOMBINANT DNA CULTURES UNDER TIME VARYING FEED CONDITIONS

This study investigates the effects of periodic perturbations on the dynamics of competition between plasmid-bearing and plasmid-free cells in recombinant DNA cultures. The model used in this numerical investigation was shown in a number of studies to be able to predict the occurrence of periodic behavior for selected growth rates of the competing populations. This research investigates the different dynamic behavior predicted by the model when the bioreactor feed conditions are periodically varied. The results show that periodic perturbations can give rise to complex dynamics that include quasi-periodic and period adding bifurcations. The effects of these parametric perturbations on the performance of the competition are also investigated. It is shown that the efficiency of the bioreactor can be substantially improved by an appropriate selection of the forcing amplitude. The effects of the position of the center of forcing on the nature of the emerging dynamic patterns are also investigated.

An operational strategy for unstable recombinant DNA cultures

A simple operational strategy is shown to offer a viable means of enhancing plasmid stability in chemostat systems where plasmid loss is a common problem. Feedback control can be used to stabilize coexistence states, which are naturally unstable in the system investigated, and thus gurantee retention of the plasmid-carrying strain. The strategy exploits the normally undesirable characteristics of substrate inhibited growth kinetics, and is illustrated with specific reference to methanolutilizing organisms. Since the methodology may be easily implemented in practice, it offers an alternative to costly environmental methods such as antibiotic addition.

A PITFALL OF LOW SPECIFIC ACTIVITY RADIOACTIVE THYMIDINE.

The action of x radiation on DNA synthesis in HeLa 53 and Chinese hamster is such that a plot of the doseresponse yields a two-component curve. In order to determine if the steep component was due to pool dilution, the effect of thymidine specific activity was investigated. Tissue cultures were irradiated with x rays and incubated with the tracer isotopes. Nucleic acids were extracted and the contents estimated by absorbancy measurements at 267 m mu . Radioactivity was determined in a spectrometer. Results show that incorporation of tritiated thymidine into DNA cultures incubated with higher concentrations (lower specific activity) of thymidine was less suppressed by the irradiation than cultures incubated with high specific activity material. Further work using granine labeled with carbon-14 failed to confirm the results. Therefore, a double labeling experiment was performed in which cells were incubated with both C/sup 14/-labeled granine and tritiated thymidine. The C/sup 14/-granine results paralleled the tritiated thymidine results. However in cultures where 4 mg/ml thymidine was used in conjunction with C/sup 14/-guanine instead of tracer thymidine, C/sup 14/ specific activity was half. It is apparent that this effect of thymidine is such that it masks the effects of x radiation on themore » DNA synthesizing system by detracting from the part of rate depression contributed by the steep component of the x-ray dose-response curve. Guanine apparently does not affect DNA synthesis rate. (H.M.G.)« less