Scale‐dependent intraspecific competition of Taurus cedar (Cedrus libani A. Rich.) saplings in the Southern Turkey

Better understanding of the competitive interaction at the early development stages of the stand is crucial to help schedule silvicultural treatments for young stands and for the better management of the future stands. We used scale‐dependent analysis to improve our understanding of sapling dynamics in the pure Taurus cedar (Cedrus libani A. Rich.) stands in Southern Turkey. Using data from nine plots established at the western Taurus Mountains, diameter, height, and crown radii of saplings were compared, and spatial point pattern analyses were performed. We found significant differences for the mean diameter and height, and crown radii of saplings among the plots. Univariate pair correlation function showed that sapling pattern was regular only at small scales (r < 0.4 m) but was predominantly random. Bivariate pair correlation function revealed no evidence of spatial interaction between tall saplings and short saplings. Univariate mark correlation function revealed that strong intraspecific competition was detected at small scales (up to 0.55 m). This distance is reasonable for the juvenile age tending of Taurus cedar saplings and should be under consideration during silvicultural treatments to use the site productivity more efficiently.     

Interleukin-10-1082 gene polymorphism is associated with papillary thyroid cancer

The etiopathogenesis of thyroid cancer has not been clearly elucidated although the role of chronical inflammation and the imbalance between pro- and anti-inflammatory cytokines may play a role in the etiology. The aim of the present study was to investigate whether cytokine gene polymorphisms are associated with papillary thyroid cancer (PTC), and to evaluate the relationship between genotypes and clinical/laboratory manifestation of PTC. Tumor necrosis factorα (TNFα) G-308A (rs 1800629), interleukin-6 (IL-6) G-174C (rs 1800795) and IL-10 A-1082G (rs 1800896) single nucleotide polymorphisms in DNA from peripheral blood leukocytes of 190 patients with thyroid cancer and 216 healthy controls were investigated by real-time PCR combined with melting curve analysis. There was no notable risk for PTC afflicted by TNFα-308 and IL-6-174 alone. However, IL-10-1082 G allele frequency were higher among PTC patients than healthy controls (p = 0.009). The patients with IL-10-1082 GG geotype have twofold increased risk of developing thyroid cancer according to AA genotype (OR 2.07, 95 % CI 1.21–3.55). In addition, the concomitant presence of IL-10-1082 G allele (GG + AG genotypes) together with IL-6 -174 GG genotype has a nearly twofold increased risk for thyroid cancer (OR 1.75 with 95 % CI 1.00–3.05, p = 0.049). We suggest that IL-10-1082 G allele is associated with an increased risk of PTC. The polymorphism of IL-10 gene can improve our knowledge about the pathogenesis of PTC, and could provide to estimate people at the increased risk for PTC.     

The <Emphasis Type="Italic">VKORC1</Emphasis> Asp36Tyr variant and <Emphasis Type="Italic">VKORC1</Emphasis> haplotype diversity in Ashkenazi and Ethiopian populations

The vitamin K epoxide reductase (VKORC1) is a key enzyme in the vitamin K cycle impacting various biological processes. VKORC1 genetic variability has been extensively studied in the context of warfarin pharmacogenetics revealing different distributions of VKORC1 haplotypes in various populations. We previously identified the VKORC1 Asp36Tyr mutation that was associated with warfarin resistance and with distinctive ethnic distribution. In this study, we performed haplotype analysis using Asp36Tyr and seven other VKORC1 markers in Ashkenazi and Ethiopian-Jewish and non-Jewish individuals. The VKORC1 variability was represented by nine haplotypes (V1-V9) that could be grouped into two distinct clusters (V1-V3 and V4-V9) with intra-cluster difference limited to two nucleotide changes. Phylogeny analysis suggested that these haplotypes could have developed from an ancestral variant, the common V8 haplotype (40 % in all population samples), after ten single mutation events. Asp36Tyr was exclusive to the V5 haplotype of the second cluster. Two haplotypes V5 and V4, distinguished only by Asp36Tyr, were prevalent in both Ethiopian population samples. The V2 haplotype, belonging to the first cluster, was the second most prevalent haplotype in the Ashkenazi population sample (15.8 %) but relatively uncommon in the Ethiopian origin (4.5-4.7 %). We discuss the genetic diversity among studied populations and its potential impact on warfarin-dose management in certain populations of African and European origin.     

Combined pharmacological therapy of the acute radiation disease using a cyclooxygenase-2 inhibitor and an adenosine A3 receptor agonist

Combined approaches to the treatment of acute radiation disease are preferred to single-agent therapies due to proven or anticipated better outcomes comprising increased therapeutic efficacy and decreased incidence of undesirable side effects. Our studies on post-exposure treatment of mice irradiated by sublethal or lethal doses of ionizing radiation included testing the effectiveness of meloxicam, a cyclooxygenase-2 inhibitor, and IB-MECA, an adenosine A3 receptor agonist. The efficacy of meloxicam and IB-MECA to positively influence the progress of the acute radiation disease has been tested in situations of their combined administration with granulocyte colony-stimulating factor (G-CSF) or with each other. The results of our studies revealed a significantly improved regeneration of hematopoietic cell populations ranging from the bone marrow progenitor cells to mature blood cells following combined treatments. Also, survival of mice exposed to lethal radiation doses was highest in the animals treated with a combination of the two drugs. It can be inferred from the results that if the drug combinations employed were used in humans, e.g. in the treatment of victims of radiation accidents, a better therapeutic outcome could be expected. Therefore, further studies directed at clinical applications of meloxicam and IB-MECA in radiation victims is recommended.     

DDX21 is a p38-MAPK-sensitive nucleolar protein necessary for mouse preimplantation embryo development and cell-fate specification

Successful navigation of the mouse preimplantation stages of development, during which three distinct blastocyst lineages are derived, represents a prerequisite for continued development. We previously identified a role for p38-mitogen-activated kinases (p38-MAPK) regulating blastocyst inner cell mass (ICM) cell fate, specifically primitive endoderm (PrE) differentiation, that is intimately linked to rRNA precursor processing, polysome formation and protein translation regulation. Here, we develop this work by assaying the role of DEAD-box RNA helicase 21 (DDX21), a known regulator of rRNA processing, in the context of p38-MAPK regulation of preimplantation mouse embryo development. We show nuclear DDX21 protein is robustly expressed from the 16-cell stage, becoming exclusively nucleolar during blastocyst maturation, a localization dependent on active p38-MAPK. siRNA-mediated clonal Ddx21 knockdown within developing embryos is associated with profound cell-autonomous and non-autonomous proliferation defects and reduced blastocyst volume, by the equivalent peri-implantation blastocyst stage. Moreover, ICM residing Ddx21 knockdown clones express the EPI marker NANOG but rarely express the PrE differentiation marker GATA4. These data contribute further significance to the emerging importance of lineage-specific translation regulation, as identified for p38-MAPK, during mouse preimplantation development.     

Phycobilisome Mobility and Its Role in the Regulation of Light Harvesting in Red Algae

Red algae represent an evolutionarily important group that gave rise to the whole red clade of photosynthetic organisms. They contain a unique combination of light-harvesting systems represented by a membrane-bound antenna and by phycobilisomes situated on thylakoid membrane surfaces. So far, very little has been revealed about the mobility of their phycobilisomes and the regulation of their light-harvesting system in general. Therefore, we carried out a detailed analysis of phycobilisome dynamics in several red alga strains and compared these results with the presence (or absence) of photoprotective mechanisms. Our data conclusively prove phycobilisome mobility in two model mesophilic red alga strains, Porphyridium cruentum and Rhodella violacea. In contrast, there was almost no phycobilisome mobility in the thermophilic red alga Cyanidium caldarium that was not caused by a decrease in lipid desaturation in this extremophile. Experimental data attributed this immobility to the strong phycobilisome-photosystem interaction that highly restricted phycobilisome movement. Variations in phycobilisome mobility reflect the different ways in which light-harvesting antennae can be regulated in mesophilic and thermophilic red algae. Fluorescence changes attributed in cyanobacteria to state transitions were observed only in mesophilic P. cruentum with mobile phycobilisomes, and they were absent in the extremophilic C. caldarium with immobile phycobilisomes. We suggest that state transitions have an important regulatory function in mesophilic red algae; however, in thermophilic red algae, this process is replaced by nonphotochemical quenching.Photosynthetic light reactions are mediated by pigment-binding protein complexes located either inside the thylakoid membrane (e.g. chlorophyll-binding proteins of both photosystems) or associated on the membrane surface (e.g. phycobilisomes [PBsomes] in cyanobacteria and red algae). Recent progress in structural biology has allowed the construction of high-resolution structural models of most photosynthetic protein complexes (for review, see Fromme, 2008) together with their large-scale organization into supercomplexes (for review, see Dekker and Boekema, 2005). However, the dynamics of these supercomplexes and the mobility of particular light-harvesting proteins in vivo are still poorly understood (for review, see Mullineaux, 2008a; Kaňa, 2013; Kirchhoff, 2014) The importance of protein mobility in various photosynthetic processes, like nonphotochemical quenching and state transitions, has been explored mostly based on indirect in vitro experiments, including single-particle analysis (Kouřil et al., 2005), or by biochemical methods (Betterle et al., 2009; Caffarri et al., 2009). Recent studies on the mobility of light-harvesting proteins using live-cell imaging (for review, see Mullineaux, 2008a; Kaňa, 2013) have elucidated the importance of protein mobility for photosynthetic function (Joshua and Mullineaux, 2004; Joshua et al., 2005; Goral et al., 2010, 2012; Johnson et al., 2011). In addition, the redistribution of respiratory complexes in cyanobacterial thylakoid membranes plays an essential role in controlling electron flow (Liu et al., 2012).It is generally accepted that the mobility of most of the transmembrane photosynthetic proteins is very restricted in the thylakoid. The typical effective diffusion coefficient of photosynthetic proteins is somewhere between 0.01 and 0.001 μm⁻² s⁻¹ (Kaňa, 2013). A similar restriction in membrane protein mobility has also been described for bacterial membranes (Dix and Verkman, 2008; Mika and Poolman, 2011). In fact, this is very different in comparison with what we know for other eukaryotic membranes (e.g. plasma membrane and endoplasmic reticulum), where membrane-protein diffusion can be faster by 1 or 2 orders of magnitude (Lippincott-Schwartz et al., 2001). Therefore, macromolecular crowding of proteins has been used to rationalize the restricted protein mobility in thylakoid membranes of chloroplasts (Kirchhoff, 2008a, 2008b). Indeed, atomic force microscopy studies have shown that there is a dense packing and interaction of complexes in the photosynthetic membranes (Liu et al., 2011). Therefore, the diffusion of photosynthetic proteins in the thylakoid membrane is rather slow, and it increases only in less crowded parts of thylakoids (Kirchhoff et al., 2013). The current model of photosynthetic protein mobility thus proposes the immobility of protein supercomplexes, such as PSII (Mullineaux et al., 1997; Kirchhoff, 2008b), with only a small mobile fraction of chlorophyll-binding proteins represented by external antennae of photosystems, including light harvesting complex of PSII in higher plants (Consoli et al., 2005; Kirchhoff et al., 2008) or iron stress-induced chlorophyll-binding protein A in cyanobacteria (Sarcina and Mullineaux, 2004).The restricted mobility of internal membrane supercomplexes (photosystems) contrasts with the relatively mobile PBsomes (Mullineaux et al., 1997; Sarcina et al., 2001). PBsomes are sizeable biliprotein supercomplexes (5–10 MD) attached to the thylakoid membrane surface with dimensions of approximately 64 × 42 × 28 nm (length × width × height; Arteni et al., 2008; Liu et al., 2008a). PBsomes are composed of chromophore-bearing phycobiliproteins and colorless linker polypeptides (Adir, 2005; Liu et al., 2005). They serve as the main light-harvesting antennae in various species, including cyanobacteria, red algae, glaucocystophytes, and cryptophytes. Although a single PBsome is composed of hundreds of biliproteins, absorbed light energy is efficiently transferred toward a specific biliprotein that functions as a terminal energy emitter (Glazer, 1989). From there, energy can be transferred to either PSI or PSII and used in photosynthesis (Mullineaux et al., 1990; Mullineaux, 1992, 1994). In typical prokaryotic cyanobacteria and eukaryotic red algae, PBsomes are composed of two main parts: (1) allophycocyanin (APC) core proteins adjacent to the thylakoid membrane; and (2) peripheral rod proteins made from phycocyanin only or from a combination of phycocyanin together with phycoerythrin. Such complex and modular composition allows for different spectroscopic properties of PBsomes and thus their complementary absorption in the spectral region that is not covered by chlorophyll-binding proteins.PBsome mobility has been studied only in a few types of cyanobacteria (for review, see Kaňa, 2013). PBsomes have been recognized as a mobile element with an effective diffusion coefficient of about 0.03 μm² s⁻¹ for Synechococcus sp. PCC 7942 (Mullineaux et al., 1997; Sarcina et al., 2001). The effective diffusion coefficient value depends on lipid composition, temperature, and the size of the PBsome (Sarcina et al., 2001). The diffusion coefficient reflects PBsome mobility, but it is not affected singularly by physical diffusion processes, and the role of PBsome-photosystem interaction is an open question (Kaňa, 2013). PBsome mobility seems to be related to the requirement of light-induced PBsome redistribution during state transitions (Joshua and Mullineaux, 2004). The mechanism of state transitions in cyanobacteria is still rather questionable (for review, see Kirilovsky et al., 2014). As PSII seems to be immobile, it has been suggested that PBsomes interact with photosystems only transiently and that physical redistribution (diffusion) of PBsomes is crucial for the state transition (Mullineaux et al., 1997). The importance of such long-distance diffusions, however, should be tested experimentally in more detail (Kaňa, 2013), as an alternative theory of the state transition proposed only slight PBsome movement (shifting) between photosystems (McConnell et al., 2002). However, in both cases, PBsome mobility (i.e. the PBsome’s ability to move) is required (Kaňa, 2013).Red algae are the eukaryotic representatives of phototrophs containing PBsomes (Su et al., 2010). They represent the ancestor of photosynthetic microorganisms from the red clade of photosynthesis (Yoon et al., 2006; Wang et al., 2013), which includes various model organisms such as diatoms, chromerids, or dinoflagellates. Red algae contain a unique combination of antennae systems on their membrane surfaces, which are formed mostly by hemispherical PBsomes (Mimuro and Kikuchi, 2003; Arteni et al., 2008). Red algae also contain transmembrane light-harvesting antennae (Vanselow et al., 2009; Neilson and Durnford, 2010; Green, 2011) associated mostly with PSI (Wolfe et al., 1994). Therefore, red algae represent a functionally important eukaryotic model organism; however, few facts are known about the regulation of its light-harvesting efficiency, although it seems to be connected with photoprotection in the reaction center (Delphin et al., 1996, 1998; Krupnik et al., 2013). The presence of photoprotective NPQ in PBsomes of prokaryotic cyanobacteria has been conclusively proven (Kirilovsky et al., 2014); however, this mechanism seems to be missing in eukaryotic phycobiliproteins of cryptophytes (Kaňa et al., 2012b) and red algae. Moreover, the presence (or absence) of PBsome mobility has not been confirmed conclusively (Liu et al., 2009).Therefore, we carried out a detailed study of PBsome mobility in red algal chloroplasts to determine the role of mobility in the regulation of light-harvesting efficiency. We found that red alga PBsomes are a mobile protein complex with effective diffusion coefficient between 2.7 × 10⁻³ and 13 × 10⁻³ μm⁻² s⁻¹ in all studied mesophilic strains. It contrasted with PBsomes in extremophilic red algal strains (Cyanidium caldarium), where PBsome mobility under physiological conditions was highly restricted (effective diffusion coefficient of approximately 0.6 × 10⁻³ μm⁻² s⁻¹). The restriction of PBsome mobility in extremophilic C. caldarium was due to a tight interaction of PBsomes with both photosystems and not to changes in lipid desaturation, an effect typical for extremophiles. The PBsome-photosystem interaction was weakened for C. caldarium grown at suboptimal temperatures, resulting in a pronounced increase in PBsome mobility thanks to PBsome decoupling from the photosystem. This result shows that PBsome mobility in this strain is limited by the strength of the PBsome-photosystem interaction rather than by the restriction of diffusion by factors such as macromolecular crowding. Moreover, our study allows us to describe two different models of light-harvesting antenna regulation in red algae. In mesophilic strains (Porphyridium cruentum and Rhodella violacea), absorbed light is redistributed between photosystems in a process of state transition that requires PBsome mobility. On the contrary, in extremophilic C. caldarium, PBsome are strongly coupled to photosystems and excess light is dissipated by a process of nonphotochemical quenching, as has been described recently (Krupnik et al., 2013).     

Cerebrospinal fluid and serum prealbumin (transthyretin) in patients with multiple sclerosis (MS): Comparison of particular subgroups of MS patients

The levels of prealbumin (PAB, transthyretin) were determined and evaluated in the cerebrospinal fluid (CSF) and serum in various subgroups of the multiple sclerosis (MS) patients. In severely disabled patients, serum PAB was elevated more frequently. CSF and serum PAB concentrations were higher in treated than in nontreated patients; the values above the upper reference limits were also more frequently found in treated patients. PAB index showed a tendency to decrease during the course of the disease. The routine determination of PAB in CSF and serum is, therefore, recommended to be recognized in MS patients as a substantial clinical value and, thus, be comprised, including also immunoglobulins and other parameteres, into the spectrum of characteristics in Protein Pannel.     

Cytokine responses of bovine macrophages to diverse clinical Mycobacterium avium subspecies paratuberculosis strains

Background  

Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of Johne's disease (JD) persistently infects and survives within the host macrophages. While it is established that substantial genotypic variation exists among MAP, evidence for the correlates that associate specific MAP genotypes with clinical or sub-clinical disease phenotypes is presently unknown. Thus we studied strain differences in intracellular MAP survival and host responses in a bovine monocyte derived macrophage (MDM) system.     

CLAGen: a tool for clustering and annotating gene sequences using a suffix tree algorithm

Most multiple gene sequence alignment methods rely on conventions regarding the score of a multiple alignment in pairwise fashion. Therefore, as the number of sequences increases, the runtime of sequencing expands exponentially. In order to solve the problem, this paper presents a multiple sequence alignment method using a linear-time suffix tree algorithm to cluster similar sequences at one time without pairwise alignment. After searching for common subsequences, cross-matching common subsequences were generated, and sometimes inexact matching was found. So, a procedure aimed at masking the inexact cross-matching pairs was suggested here. In addition, BLAST was combined with a clustering tool in order to annotate the clusters generated by suffix tree clustering. The proposed method for clustering and annotating genes consists of the following steps: (1) construction of a suffix tree; (2) searching and overlapping common subsequences; (3) grouping subsequence pairs; (4) masking cross-matching pairs; (5) clustering gene sequences; (6) annotating gene clusters by the BLAST search. The performance of the proposed system, CLAGen, was successfully evaluated with 42 gene sequences in a TCA cycle (a citrate cycle) of bacteria. The system generated 11 clusters and found the longest subsequences of each cluster, which are biologically significant.     

Water-splitting manganese complex controls light-induced redox changes of cytochrome <Emphasis Type="Italic">b</Emphasis><Subscript>559</Subscript> in Photosystem II

The effect of water-splitting Mn complex on light-induced redox changes of cytochrome b ₅₅₉ (cyt b ₅₅₉) was studied in spinach photosystem II (PSII) membranes. Photoreduction of the heme iron in the intact PSII membranes was completely suppressed by DCMU, whereas photoreduction and photooxidation of the heme iron in the Mn-depleted PSII membranes were unaffected by DCMU. Interesingly, photoreduction and photooxidation of the heme iron in the Mn-depleted PSII membranes were completely diminished by exogenous superoxide dismutase (SOD), whereas no effect of SOD on photoreduction of the heme iron was observed in the intact PSII membranes. The current work shows that the light-induced redox changes of cyt b ₅₅₉ proceed via a different mechanism in the both types of PSII membranes. In the intact PSII membranes, photoreduction of the heme iron is mediated by plastoquinol. However, in the Mn-depleted PSII membranes, photoreduction and photooxidation of the heme iron are mediated by superoxide anion radical formed in PSII.