A practical algorithm for reconstructing level-1 phylogenetic networks

Recently, much attention has been devoted to the construction of phylogenetic networks which generalize phylogenetic trees in order to accommodate complex evolutionary processes. Here, we present an efficient, practical algorithm for reconstructing level-1 phylogenetic networks--a type of network slightly more general than a phylogenetic tree--from triplets. Our algorithm has been made publicly available as the program LEV1ATHAN. It combines ideas from several known theoretical algorithms for phylogenetic tree and network reconstruction with two novel subroutines. Namely, an exponential-time exact and a greedy algorithm both of which are of independent theoretical interest. Most importantly, LEV1ATHAN runs in polynomial time and always constructs a level-1 network. If the data are consistent with a phylogenetic tree, then the algorithm constructs such a tree. Moreover, if the input triplet set is dense and, in addition, is fully consistent with some level-1 network, it will find such a network. The potential of LEV1ATHAN is explored by means of an extensive simulation study and a biological data set. One of our conclusions is that LEV1ATHAN is able to construct networks consistent with a high percentage of input triplets, even when these input triplets are affected by a low to moderate level of noise.     

Night shift work and osteoporosis: evidence and hypothesis

Osteoporosis is an important public health problem worldwide. Among the countries with a very high population risk of fractures, there are those with the highest level of economic development. Osteoporotic fractures are the main cause of disability among elderly people, and the resultant disabilities require particularly large financial support associated not only with the direct treatment of the fracture but also with the necessity for long-term rehabilitation and care for the disabled person. Many well-established factors can have impact on bone mass and fracture risk. Recently, it has been hypothesized that working during nighttime which leads to endocrine disorders may have an indirect impact on bone physiology among night shift workers. Therefore, it can be presumed that the night shift work may contribute to the etiology of osteoporosis. The aim of our work was to make a review of the epidemiological evidence on the association between night shift work and bone mineral density or fracture risk as well as to discuss the potential biological mechanisms linking the work under this system with the development of osteoporosis. We have identified only four studies investigating the association between system of work and bone mineral density or fracture risk among workers. The findings of three out of four studies support the hypothesis. None of the studies has investigated a potential relationship between night shift work and bone turnover markers. Given that there have been no epidemiological studies in European countries that would concern working populations and the noticeable difference in the risk of osteoporosis between communities, further studies are warranted to elucidate the problem. It is presumed that further in-depth studies will not only identify the underlying factors of the disease but also contribute to developing guidelines for policy makers and employers for primary prevention of osteoporosis in workplace.     

The image of motor units architecture in the mechanomyographic signal during the single motor unit contraction: in vivo and simulation study

The mechanomyographic (MMG) signal analysis has been performed during single motor unit (MU) contractions of the rat medial gastrocnemius muscle. The MMG has been recorded as a muscle surface displacement by using a laser distance sensor. The profiles of the MMG signal let to categorize these signals for particular MUs into three classes. Class MMG-P (positive) comprises MUs with the MMG signal similar to the force signal profile, where the distance between the muscle surface and the laser sensor increases with the force increase. The class MMG-N (negative) has also the MMG profile similar to the force profile, however the MMG is inverted in comparison to the force signal and the distance measured by using laser sensor decreases with the force increase. The third class MMG-M (mixed) characterize the MMG which initially increases with the force increases and when the force exceeds some level it starts to decrease towards the negative values. The semi-pennate muscle model has been proposed, enabling estimation of the MMG generated by a single MU depending on its localization. The analysis have shown that in the semi-pennate muscle the localization of the MU and the relative position of the laser distance sensor determine the MMG profile and amplitude. Thus, proposed classification of the MMG recordings is not related to the physiological types of MUs, but only to the MU localization and mentioned sensor position. When the distance sensor is located over the middle of the muscle belly, a part of the muscle fibers have endings near the location of the sensor beam. For the MU MMG of class MMG-N the deflection of the muscle surface proximal to the sensor mainly influences the MMG recording, whereas for the MU MMG class MMG-P, it is mainly the distal muscle surface deformation. For the MU MMG of MMG-M type the effects of deformation within the proximal and distal muscle surfaces overlap. The model has been verified with experimental recordings, and its responses are consistent and adequate in comparison to the experimental data.     

Body fatness and its social and lifestyle determinants in young working males from Cracow, Poland

The aim of this study was to determine the degree to which general body fatness variation, presented by body mass index (BMI), the sum of the three skinfold thicknesses (TST) (triceps, subscapular, abdominal) and percentage of body fat (%FAT), can be explained by socioeconomic status (SES) and lifestyle. The cross-sectional, population-based survey was of 259 healthy working males aged 20-30 from the city of Cracow, Poland. Objective anthropometric measurements, bioelectrical impedance analysis, the results of motor fitness tests and social and lifestyle data from a questionnaire were analysed. The independent variables were: age, socioeconomic status (birthplace, place of residence until the age of 14, social class, educational level and the type of work done) and lifestyle elements (smoking habits, dietary habits, family obesity resemblance, sport activity in the past, leisure time physical activity and level of motor fitness). Three separate full models were created using stepwise straightforward regression with BMI, TST and %FAT as dependent variables. The highest autonomous influence on BMI and %FAT was ascribed to age and family obesity resemblance, whereas variation in TST was explained by level of motor fitness, age, city as a place of residence until the age of 14 and family obesity resemblance. Although the analysed variables explained only from 8% (BMI) to 13% (TST) of body fatness variation, indicating at the same time that most variations are explained by other variables, the impact of lifestyle family-shared factors on body fatness seems to be significant.     

Effects of different dietary fatty acids profiles on the growth performance and body composition of juvenile tench (<Emphasis Type="Italic">Tinca tinca</Emphasis> (L.))

Juvenile tench (initial weight of about 57 g) were fed feed supplemented with fish oil (group FO), linseed oil (group LO), peanut oil (group PO), or rapeseed oil (group RO) containing 47% protein and 12% fat for 55 days. The inclusion of the tested oils was 50 g kg⁻¹ (42% total crude lipids in diets). No significant differences were noted in the fish growth performance. The proximate composition of the whole fish bodies and the viscera (water, protein, fat, ash) was similar in all the dietary treatments (P > 0.05). Differences were noted only with regard to the ash content of the fillets (P < 0.05). The analysis of the fatty acids profiles of tench (whole fish) indicated there were significant differences in the total content of monoenoic and polyenoic (PUFA) acids. Significant differences were also noted with regard to n-3 PUFA and n-6 PUFA. Consequently, the ratio of n-3/n-6 acids ranged from 1.6 (group PO) to 2.08 (group LO; P < 0.05). The feed applied was not confirmed to have had an impact on the fatty acids profile of the tench fillets. There was a statistically significant intergroup difference in the content of saturated fatty acids (SFA) in tench viscera. In the fish fed vegetable oils supplemented diets, the level of SFA was lower (P < 0.05).     

Vesicle transmembrane potential is required for translocation to the cytosol of externally added FGF-1

Externally added fibroblast growth factor-1 (FGF-1) is capable of crossing cellular membranes to reach the cytosol and the nucleus in a number of cell types. We have monitored the translocation of the growth factor by two methods: phosphorylation of FGF-1, and prenylation of an FGF-1 mutant that contains a C-terminal prenylation signal. Inhibition of endosomal acidification by ammonium chloride or monensin did not block the translocation of FGF-1, whereas bafilomycin A1, a specific inhibitor of vacuolar proton pumps, blocked translocation completely. A combination of ionophores expected to dissipate the vesicular membrane potential (valinomycin plus monensin) also fully inhibited the translocation. The inhibition of translocation by bafilomycin A1 was overcome in the presence of monensin or nigericin, while ouabain blocked translocation under these conditions. The data indicate that translocation of FGF-1 to cytosol occurs from the lumen of intracellular vesicles possessing vacuolar proton pumps, and that a vesicular membrane potential is required. Apparently, activation of vesicular Na+/K+-ATPase by monensin or nigericin generates a membrane potential that can support translocation when the proton pump is blocked.     

E2F-1 is essential for normal epidermal wound repair.

E2F factors are involved in proliferation and apoptosis. To understand the role of E2F-1 in the epidermis, we screened wild type and E2F-1(-/-) keratinocyte mRNA for genes differentially expressed in the two cell populations. We demonstrate the reduced expression of integrins alpha(5), alpha(6), beta(1), and beta(4) in E2F-1(-/-) keratinocytes associated with reduced activation of Jun terminal kinase and Erk upon integrin stimulation. As a consequence of altered integrin expression and function, E2F-1(-/-) keratinocytes also show impaired migration, adhesion to extracellular matrix proteins, and a blunted chemotactic response to transforming growth factor-gamma1. E2F-1(-/-) keratinocytes, but not dermal fibroblasts, exhibit altered patterns of proliferation, including significant delays in transit through both G(1) and S phases of the cell cycle. Recognizing that proliferation and migration are key for proper wound healing in vivo, we postulated that E2F-1(-/-) mice may exhibit abnormal epidermal repair upon injury. Consistent with our hypothesis, E2F-1(-/-) mice exhibited impaired cutaneous wound healing. This defect is associated with substantially reduced local inflammatory responses and rates of re-epithelialization. Thus, we demonstrate that E2F-1 is indispensable for a hitherto unidentified cell type-specific and unique role in keratinocyte proliferation, adhesion, and migration as well as in proper wound repair and epidermal regeneration in vivo.     

Three dimensional tissue and organ models in vitro: their application in basic and practical research

Good and reliable three dimensional biomodel in vitro should mimic the in vivo structure and function of investigated tissue or organ. This can be achieved through the interaction of various cell types and the environment (extracellular matrix, as well as spatial cell contacts). While designing such a model it is necessary to find best nutritive and adhesive factors, to allow access to components of optimal matrix and to enable cell contacts in three dimensions. The response and function of such models reminds physiological function of tissue of origin. Over several years there has been an increasing number of experiments and publications reporting research involving spatial cell models. This model and its structural and molecular analysis clearly showed, that in comparison with conventional cultures, mainly monocultures grown as monolayers, spatial cultures resemble the in vivo situation with regard to cell shape and biological behaviour. Spatial arrangement of cells and the environment can direct tissue differentiation. Interesting example of the importance of the environment for the latter, is the finding that the ectopic implantation of embryonic cells transforms them into malignant tissue while the same cells located in the uterus undergo normal embryogenesis. The present review describes several three-dimensional models in vitro and their application in basic and practical studies. It is especially interesting and important in the light of developments of tissue modeling to obtain in vitro substitutes of damaged or impaired tissues and organs. Other demands come from animal protectionists who suggest replacement of experimental animals with cultures and tissue models in bio-, pharmacological, and toxicological assays. In response, European Union legislation introduces increasing restrictions on animal experiments. At last, researchers seek in vitro models which would enable avoiding discrepancies between in vitro and in vivo results.