Mesenchymal stromal/stem cell separation methods: concise review

Mesenchymal stem (stromal) cells (MSCs) possess unique biological characteristics such as plasticity, long term self-renewal, secretion of various bioactive molecules and ability of active migration to the diseased tissues that make them unique tool for regenerative medicine, nowadays. Until now MSCs were successfully derived from many tissue sources including bone marrow, umbilical cord, adipose tissue, dental pulp etc. The crucial step prior to their in vitro expansion, banking or potential clinical application is their separation. This review article aims to briefly describe the main MSCs separations techniques currently available, their basic principles, as well as their advantages and limits. In addition the attention is paid to the markers presently applicable for immunoaffinity-based separation of MSCs from different tissues and organs.     

Hyperfractionated high-dose rate brachytherapy in the treatment of oral tongue cancer

Background

Low-dose rate brachytherapy is a well established treatment modality of oral cancer. Data about high-dose rate (HDR) brachytherapy are still sparse with various fractionation schedules and heterogeneous results.

Aim

The aim of our retrospective study was to evaluate the results of HDR brachytherapy with doses of 3 Gy twice daily.

Patients and methods

Twenty patients with squamous cell tongue cancer were treated in the years 2001–2009 by exclusive HDR BT 18 × 3 Gy twice daily. The plastic tube technique was used. Median follow up was 47 months (7.8–118) since brachytherapy.

Results

The local and locoregional control was 85% and 68%, respectively. Bone necrosis developed in one case treated without mandibular shielding and soft tissue necrosis in 2 cases.

Conclusion

It can be concluded that HDR brachytherapy with 18 × 3 Gy twice daily is safe with promising local control. The risk of nodal recurrences is substantial.     

Light utilization efficiency in photosynthetic microbial mats

Based on combined microsensor measurements of irradiance, temperature and O(2) , we compared light energy budgets in photosynthetic microbial mats, with a special focus on the efficiency of light energy conservation by photosynthesis. The euphotic zones in the three studied mats differed in their phototrophic community structure, pigment concentrations and thickness. In all mats, < 1% of the absorbed light energy was conserved via photosynthesis at high incident irradiance, while the rest was dissipated as heat. Under light-limiting conditions, the photosynthetic efficiency reached a maximum, which varied among the studied mats between 4.5% and 16.2% and was significantly lower than the theoretical maximum of 27.7%. The maximum efficiency correlated linearly with the light attenuation coefficient and photopigment concentration in the euphotic zone. Higher photosynthetic efficiency was found in mats with a thinner and more densely populated euphotic zone. Microbial mats exhibit a lower photosynthetic efficiency compared with ecosystems with a more open canopy-like organization of photosynthetic elements, where light propagation is not hindered to the same extent by photosynthetically inactive components; such components contributed about 40-80% to light absorption in the investigated microbial mats, which is in a similar range as in oceanic planktonic systems.     

On parameter synthesis by parallel model checking

An important problem in current computational systems biology is to analyze models of biological systems dynamics under parameter uncertainty. This paper presents a novel algorithm for parameter synthesis based on parallel model checking. The algorithm is conceptually universal with respect to the modeling approach employed. We introduce the algorithm, show its scalability, and examine its applicability on several biological models.     

The spliceosome-associated protein Nrl1 suppresses homologous recombination-dependent R-loop formation in fission yeast

The formation of RNA–DNA hybrids, referred to as R-loops, can promote genome instability and cancer development. Yet the mechanisms by which R-loops compromise genome instability are poorly understood. Here, we establish roles for the evolutionarily conserved Nrl1 protein in pre-mRNA splicing regulation, R-loop suppression and in maintaining genome stability. nrl1Δ mutants exhibit endogenous DNA damage, are sensitive to exogenous DNA damage, and have defects in homologous recombination (HR) repair. Concomitantly, nrl1Δ cells display significant changes in gene expression, similar to those induced by DNA damage in wild-type cells. Further, we find that nrl1Δ cells accumulate high levels of R-loops, which co-localize with HR repair factors and require Rad51 and Rad52 for their formation. Together, our findings support a model in which R-loop accumulation and subsequent DNA damage sequesters HR factors, thereby compromising HR repair at endogenously or exogenously induced DNA damage sites, leading to genome instability.     

Construction of conditional analog-sensitive kinase alleles in the fission yeast Schizosaccharomyces pombe

Reversible protein phosphorylation is a major regulatory mechanism in a cell. A chemical-genetic strategy to conditionally inactivate protein kinases has been developed recently. Mutating a single residue in the ATP-binding pocket confers sensitivity to small-molecule inhibitors. The inhibitor can only bind to the mutant kinase and not to any other wild-type kinase, allowing specific inactivation of the modified kinase. Here, we describe a protocol to construct conditional analog-sensitive kinase alleles in the fission yeast Schizosaccharomyces pombe. This protocol can be completed in about 3 weeks and should be applicable to other organisms as well.     

Two-dimensional mapping of photopigment distribution and activity of Chloroflexus-like bacteria in a hypersaline microbial mat

Pigment analysis in an intact hypersaline microbial mat by hyperspectral imaging revealed very patchy and spatially uncorrelated distributions of photopigments Chl a and BChl a/c, which are characteristic photopigments for oxygenic (diatoms and cyanobacteria) and anoxygenic phototrophs (Chloroflexaceae). This finding is in contrast to the expectation that these biomarker pigments should be spatially correlated, as oxygenic phototrophs are thought to supply the Chloroflexaceae members with organic substrates for growth. We suggest that the heterogeneous occurrence is possibly due to sulfide, whose production by sulfate-reducing bacteria may be spatially heterogeneous in the partially oxic photic zone of the mat. We furthermore mapped the near-infra-red-light controlled respiration of Chloroflexaceae under light and dark conditions and found that Chloroflexaceae are responsible for a major part of oxygen consumption at the lower part of the oxic zone in the mat. The presence of Chloroflexaceae was further confirmed by FISH probe and 16S rRNA gene clone library analysis. We assume that species related to the genera Oscillochloris and 'Candidatus Chlorothrix', in contrast to those related to Chloroflexus and Roseiflexus, depend less on excreted photosynthates but more on the presence of free sulfide, which may explain their presence in deeper parts of the mat.     

DNA sequence analysis of the tellurite-resistance determinant from clinical strain of Escherichia Coli and identification of essential genes

The tellurite-resistant Escherichia coli strain KL53 was found during testing of the group of clinical isolates for antibiotics and heavy metal ion resistance (Burian et al. 1990). Determinant of the tellurite resistance of the strain was located on the large conjugative plasmid pTE53 and cloned into pACYC184. Three different Te^r clones harboring pLK2, pLK18 and pLK20 were isolated (Burian et al. 1998). The smallest functional Te^r clone harboring pLK18 was chosen for further analysis. Plasmid pLK18 have been subcloned to obtain convenient DNA fragments for sequencing of tellurite-resistance determinant. Sequencing of this DNA fragments provided complete DNA sequence of the determinant, 5250 bp in size. The sequence has been compared with nucleotide and protein databank (BLAST programs) and significant homology with the three known operons coding for tellurite resistance has been found (determinat on plasmid pR478 from Serratia marcescens, on plasmid pMER610 from Alcaligenes sp. and chromosomal tellurite resistance genes from Proteus mirabilis). We identified 5 ORFs coding for 5 genes named terB to terF. The clone harboring pLK18 was subjected to the transposition with Tn1737Km to disrupt determinant of the tellurite resistance. Plasmid DNA of several clones containing pLK18 with Tn1737Km was isolated to locate the target site of Tn1737Km. Analyses showed, the genes terB, terC, terD and terE are essential for conservation of the resistance whereas the gene terF is not important in this respect.