Contribution of STAT4 gene single-nucleotide polymorphism to systemic lupus erythematosus in the Polish population

The STAT4 has been found to be a susceptible gene in the development of systemic lupus erythematosus (SLE) in various populations. There are evident population differences in the context of clinical manifestations of SLE, therefore we investigated the prevalence of the STAT4 G > C (rs7582694) polymorphism in patients with SLE (n = 253) and controls (n = 521) in a sample of the Polish population. We found that patients with the STAT4 C/G and CC genotypes exhibited a 1.583-fold increased risk of SLE incidence (95 % CI = 1.168-2.145, p = 0.003), with OR for the C/C versus C/G and G/G genotypes was 1.967 (95 % CI = 1.152-3.358, p = 0.0119). The OR for the STAT4 C allele frequency showed a 1.539-fold increased risk of SLE (95 % CI = 1.209-1.959, p = 0.0004). We also observed an increased frequency of STAT4 C/C and C/G genotypes in SLE patients with renal symptoms OR = 2.259 (1.365-3.738, p = 0.0014), (p (corr) = 0.0238) and in SLE patients with neurologic manifestations OR = 2.867 (1.467-5.604, p = 0.0016), (p (corr) = 0.0272). Moreover, we found a contribution of STAT4 C/C and C/G genotypes to the presence of the anti-snRNP Ab OR = 3.237 (1.667-6.288, p = 0.0003), (p (corr) = 0.0051) and the presence of the anti-Scl-70 Ab OR = 2.665 (1.380-5.147, p = 0.0028), (p (corr) = 0.0476). Our studies confirmed an association of the STAT4 C (rs7582694) variant with the development of SLE and occurrence of some clinical manifestations of the disease.     

P2 nucleotide receptors on C2C12 satellite cells

In developing muscle cells environmental stimuli transmitted by purines binding to the specific receptors are crucial proliferation regulators. C2C12 myoblasts express numerous purinergic receptors representing both main classes: P2X and P2Y. Among P2Y receptors we have found the expression of P2Y(1), P2Y(2), P2Y(4), P2Y(6) and P2Y(12) family members while among P2X receptors P2X(4), P2X(5) and P2X(7) were discovered. We have been able to show that activation of those receptors is responsible for ERK class kinase activity, responsible for regulation of cell proliferation pathway. We have also demonstrated that this activity is calcium dependent suggesting Ca(2+) ions as secondary messenger between receptor and kinase regulatory system. More specifically, we do suspect that in C2C12 myoblasts calcium channels of P2X receptors, particularly P2X(5) play the main role in proliferation regulation. In further development of myoblasts into myotubes, when proliferation is gradually inhibited, the pattern of P2 receptors is changed. This phenomenon is followed by diminishing of the P2Y(2)-dependent Ca(2+) signaling, while the mRNA expression of P2Y(2) receptor reminds still on the high level. Moreover, P2X(2) receptor mRNA, absent in myoblasts appears in myotubes. These data show that differentiation of C2C12 cell line satellite myoblasts is accompanied by changes in P2 receptors expression pattern.     

Fhit proteins can also recognize substrates other than dinucleoside polyphosphates

We show here that Fhit proteins, in addition to their function as dinucleoside triphosphate hydrolases, act similarly to adenylylsulfatases and nucleoside phosphoramidases, liberating nucleoside 5'-monophosphates from such natural metabolites as adenosine 5'-phosphosulfate and adenosine 5'-phosphoramidate. Moreover, Fhits recognize synthetic nucleotides, such as adenosine 5'-O-phosphorofluoridate and adenosine 5'-O-(gamma-fluorotriphosphate), and release AMP from them. With respect to the former, Fhits behave like a phosphodiesterase I concomitant with cleavage of the P-F bond. Some kinetic parameters and implications of the novel reactions catalyzed by the human and plant (Arabidopsis thaliana) Fhit proteins are presented.     

Structural heterogeneity of linear habitats positively affects Barred Warbler Sylvia nisoria,Common Whitethroat Sylvia communis and Lesser Whitethroat Sylvia curruca in farmland of Western Poland

Capsule Structural heterogeneity was the most important factor influencing the distribution of Barred Warbler Sylvia nisoria, Common Whitethroat S. communis and Lesser Whitethroat S. curruca in linear habitats in farmland of Western Poland.

Aims To investigate the occurrence of three species of Sylvia warblers in relation to the spatial structure of linear habitats in the agricultural landscape of Western Poland where, in contrast to Western Europe, field boundaries are not managed in terms of their size or spatial structure.

Methods In 2008, the distribution of breeding territories of Sylvia warblers in linear habitats was estimated in farmland of Western Poland. Redundancy detrended analysis was used to assess the relationship between bird abundance and seven linear habitat variables in ninety-four 150?m sections.

Results Sylvia warblers differed in habitat requirements, however heterogeneity affected their distribution to the greatest extent. In addition, Barred Warbler preferred high shrub volume and wider sections, whereas Common Whitethroat was attracted by brambles and nettles and Lesser Whitethroat favoured shrubs. All species avoided a high proportion of low vegetation.

Conclusion Structural heterogeneity resulted in highly preferred linear habitats for Sylvia warblers. Thus, maintaining or increasing structural heterogeneity of linear habitats may be a very effective tool for the conservation of farmland bird populations.     

Characterization of Phages Virulent for <Emphasis Type="Italic">Robinia pseudoacacia</Emphasis> Rhizobia

Three lytic phages (ΦRP1, ΦRP2, and ΦRP3) specific for Robinia pseudoacacia rhizobia were isolated from the soil under black locust. They were characterized by their morphology, host range, and some other properties including DNA molecular weights. Studied phages have been found to belong to Siphoviridae family that comprises viruses with long, and noncontractile tails. They had broad host ranges and effectively lysed not only Robinia pseudoacacia microsymbionts but also different Mesorhizobium species. The phages were homogenous in latent periods (300 min) but heterogeneous in burst sizes (100–200 phage particles per one infected cell) and rise periods (90–120 min). They showed a distinct adsorption rate to Robinia pseudoacacia rhizobia (70.4–93.94%). The molecular weights of phage DNAs estimated from restriction enzyme digests were in the range from ca. 82 kb to ca. 105 kb.     

Assembly of Helicobacter pylori Initiation Complex Is Determined by Sequence-Specific and Topology-Sensitive DnaA–oriC Interactions

In bacteria, chromosome replication is initiated by binding of the DnaA initiator protein to DnaA boxes located in the origin of chromosomal replication (oriC). This leads to DNA helix opening within the DNA-unwinding element. Helicobacter pylori oriC, the first bipartite origin identified in Gram-negative bacteria, contains two subregions, oriC1 and oriC2, flanking the dnaA gene. The DNA-unwinding element region is localized in the oriC2 subregion downstream of dnaA. Surprisingly, oriC2–DnaA interactions were shown to depend on DNA topology, which is unusual in bacteria but is similar to initiator–origin interactions observed in higher organisms. In this work, we identified three DnaA boxes in the oriC2 subregion, two of which were bound only as supercoiled DNA. We found that all three DnaA boxes play important roles in orisome assembly and subsequent DNA unwinding, but different functions can be assigned to individual boxes. This suggests that the H. pylori oriC may be functionally divided, similar to what was described recently for Escherichia coli oriC. On the basis of these results, we propose a model of initiation complex formation in H. pylori.     

Relationship between the percentage of body fat and surrogate indices of fatness in male and female Polish active and sedentary students

Background

Limited data have indicated that body mass index (BMI), waist circumference (WC), waist to hip ratio (WHR) and waist to height ratio (WHtR) of athletes and young adults provide misleading results concerning body fat content. This study was aimed at the evaluation of the relationship between different surrogate indices of fatness (BMI, WC, WHR, WHtR and body adiposity index (BAI)) with the percentage of body fat in Polish students with respect to their sex and physical activity.

Methods

A total of 272 students volunteered to participate in the study. Of these students, 177 physical education students (90 males and 87 females) were accepted as active (physical activity of 7 to 9 hours/week); and 95 students of other specializations (49 males and 46 females) were accepted as sedentary (physical activity of 1.5 hours/week). Weight, height, waist and hip circumferences were measured, and BMI, WHR, WHtR and BAI were calculated. Body fat percentage was assessed using four skinfold measurements.

Results

Classification of fatness according to the BMI and the percentage of body fat have indicated that BMI overestimates fatness in lean subjects (active men and women, sedentary men), but underestimates body fat in obese subjects (sedentary women). In all groups, BMI, WHR, WHtR and BAI were significantly correlated with the percentage of body fat (with the exception of WHR and hip circumference in active and sedentary women, respectively). However, coefficients of determination not exceeding 50% and Lin’s concordance correlation coefficients lower than 0.9 indicated no relationship between measured and calculated body fat.

Conclusion

The findings in the present study support the concept that irrespective of physical activity and sex none of the calculated indices of fatness are useful in the determination of body fat in young adults. Thus, it seems that easily calculated indices may contribute to distorted body image and unhealthy dietary habits observed in many young adults in Western countries, but also in female athletes.     

Locus-aware decomposition of gene trees with respect to polytomous species trees

Background

Horizontal gene transfer (HGT), a process of acquisition and fixation of foreign genetic material, is an important biological phenomenon. Several approaches to HGT inference have been proposed. However, most of them either rely on approximate, non-phylogenetic methods or on the tree reconciliation, which is computationally intensive and sensitive to parameter values.

Results

We investigate the locus tree inference problem as a possible alternative that combines the advantages of both approaches. We present several algorithms to solve the problem in the parsimony framework. We introduce a novel tree mapping, which allows us to obtain a heuristic solution to the problems of locus tree inference and duplication classification.

Conclusions

Our approach allows for faster comparisons of gene and species trees and improves known algorithms for duplication inference in the presence of polytomies in the species trees. We have implemented our algorithms in a software tool available at https://github.com/mciach/LocusTreeInference.