Assessment of movements and habitat use of <Emphasis Type="Italic">Salmo opimus</Emphasis> in Fırnız stream,river Ceyhan of Turkey using radio telemetry techniques

This study was carried out to provide information about movement and habitat use by an endemic Salmonid species (Salmo opimus Turan et al. Ichthyol Explor Freshw 23: 219–236, Turan et al. 2012) in F?rn?z Stream, a tributary of River Ceyhan in Turkey, using manual tracking as a radio telemetry technique. During the study, 19 of the 23 tagged trout were relocated by eight to 20 times (mean: 15 relocations per fish) in F?rn?z Stream. The time between the tracking surveys and relocations varied from 21 to 44 days (mean: 30 days) and the mean distance between relocations was 151 m (26 to 881 m). Tagged trout showed a distribution within a distance of 9350 m in F?rn?z Stream. 95% of the relocations clustered at a distance of 4500 m, while 75 and 50% of them were distributed at a distance of 1935 m and 1488 m, respectively. The linear home range of the individual ranged from 199 to 5087 m (mean 792 m), whereas mean 95% Kernel Density Home Range (KDHR), 75% KDHR, and mean core range (50% KDHR), were 632 m, 477 m and 290 m, respectively. The depths and velocities of the locations where tagged trout occurred varied from 20 to 185 cm (mean depth: 43 cm) and 11 to 240 cm/s (mean velocity: 45.9 cm/s). There was no correlation between fish size and depth and fish size and velocity. Hydropower stations and trout farms negatively affected movement of the brown trout in the stream. The fish passage in F?rn?z Hydropower Station (HPP) is inefficient due to low water mark downstream. Thus, all the obstructions that prevent fish movements must be arranged to enable fish passage in F?rn?z Stream in order to preserve the brown trout population in the stream.     

Estimating changes of isotopic fractionation based on chemical kinetics and microbial dynamics during anaerobic methane oxidation: apparent zero- and first-order kinetics at high and low initial methane concentrations

Changes in natural isotopic composition may be used to reveal metabolic pathways of substrate transformation by microbial communities (Vavilin in Ecol Model 240:84–92, 2012b). Anaerobic oxidation of methane (AOM) by sulfate has been described using a mathematical model based on chemical kinetics, microbial dynamics and equations for ¹³C isotope accumulation in products as well as their redistribution between substrate and products. Experimental data for two batch cultures that originated from microbial mats covering methane seep chimneys in the Black Sea, previously obtained by Seifert et al. (Org Geochem 37:1411–1419, 2006) and Holler et al. (Env Microbiol Reports 1(5):370–376, 2009), were used to model AOM. During long-time incubation, changes of isotope signatures in CH₄ showed that in the Seifert et al. batch tests (low methane concentration), in contrast to the Holler et al. batch tests (high methane concentration), methane production occurred along with methane oxidation. In accordance with the model, apparent zero and first-order kinetics of methane oxidation were valid for the Holler et al. and Seifert et al. batch tests, respectively. The observed change of $ \delta {}^{13}{\text{CH}}_{4} $ was explained by microbial kinetics reflecting that the rate is lower for heavy substrate microbial utilization when compared to light substrate microbial utilization. The model showed that small amounts of methanogenesis will change the carbon isotopic composition of methane because biogenic methane has a distinct isotopic composition and due to the large difference between the maximum specific rates of methane oxidation and production. The estimated biomass doubling time of methane-oxidizers for high and low methane concentration was 408/126 days and 4640/1160 days, respectively, depending on the value of the half-saturation constant K _S (5 and 20 mM).     

Quantitative Analysis of Porcine Endogenous Retroviruses in Different Organs of Transgenic Pigs Generated for Xenotransplantation

The pig appears to be the most promising animal donor of organs for use in human recipients. Among several types of pathogens found in pigs, one of the greatest problems is presented by porcine endogenous retroviruses (PERVs). Screening of the source pig herd for PERVs should include analysis of both PERV DNA and RNA. Therefore, the present study focuses on quantitative analysis of PERVs in different organs such as the skin, heart, muscle, and liver and blood of transgenic pigs generated for xenotransplantation. Transgenic pigs were developed to express the human α-galactosidase, the human α-1,2-fucosyltransferase gene, or both genetic modifications of the genome (Lipinski et al., Medycyna Wet 66:316–322, 2010; Lipinski et al., Ann Anim Sci 12:349–356, 2012; Wieczorek et al., Medycyna Wet 67:462–466, 2011). The copy numbers of PERV DNA and RNA were evaluated using real-time Q-PCR and QRT-PCR, respectively. Comparative analysis of all PERV subtypes revealed the following relationships: PERV A > PERV B > PERV C. PERV A and B were found in all samples, whereas PERV C was detected in 47 % of the tested animals. The lowest level of PERV DNA was shown in the muscles for PERV A and B and in blood samples for PERV C. The lowest level of PERV A RNA was found in the skin, whereas those of PERV B and C RNA were found in liver specimens. Quantitative analysis revealed differences in the copy number of PERV subtypes between various organs of transgenic pigs generated for xenotransplantation. Our data support the idea that careful pig selection for organ donation with low PERV copy number may limit the risk of retrovirus transmission to the human recipients.     

Chemical inactivation of Pat1

Comment on: Guerra-Moreno A, et al. Cell Cycle 2012; 11:1621-5 and Cipak L, et al. Cell Cycle 2012; 11:1626-33     

A critical role for TORC1 in cellular senescence

Comment on: Kolesnichenko M, et al. Cell Cycle 2012; 11:2391-401 and Pospelova TV, et al. Cell Cycle 2012; 11:2402-407.     

p53 and cancer stem cells: The mevalonate connexion

Comment on: Freed-Pastor WA, et al. Cell 2012; 148:244-58 and Ginestier C, et al. Stem Cells 2012; 1327-37.     

CTGF-mediated autophagy-senescence transition in tumor stroma promotes anabolic tumor growth and metastasis

Comment on: Capparelli C, et al. Cell Cycle 2012; 11:2272-84 and Capparelli C, et al. Cell Cycle 2012; 11:2285-302.     

Cancers co-opt cohabitants’ catabolism

Comment on: Capparelli C, et al. Cell Cycle 2012; 11:2272-84 and Capparelli C, et al. Cell Cycle 2012; 11:2285-302.     

Dissecting the role of mTOR complexes in cellular senescence

Comment on: Kolesnichenko M, et al. Cell Cycle 2012; 11:2391-401. and Pospelova TV, et al. Cell Cycle 2012; 11:2402-407.     

Dissecting the role of mTOR complexes in cellular senescence

Comment on: Kolesnichenko M, et al. Cell Cycle 2012; 11:2391-401. and Pospelova TV, et al. Cell Cycle 2012; 11:2402-407.     

Aurora-C: The youngest of "The Three (Aurora kinase) Tenors" of mitotic symphony

Comment on: Slattery SD, et al. Cell Cycle 2009; 8:2984-94.     

Brain fingerprinting: let’s focus on the science—a reply to Meijer, Ben-Shakhar, Verschuere, and Donchin

Farwell in Cogn Neurodyn 6:115–154, (2012) reviewed all research on brainwave-based detection of concealed information published in English, including the author’s laboratory and field research. He hypothesized that specific methods are sufficient to obtain less than 1 % error rate and high statistical confidence, and some of them are necessary. Farwell proposed 20 brain fingerprinting scientific standards embodying these methods. He documented the fact that all previous research and data are compatible with these hypotheses and standards. Farwell explained why failure to meet these standards resulted in decrements in performance of other, alternative methods. Meijer et al. criticized Farwell in Cogn Neurodyn 6:115–154, (2012) and Farwell personally. The authors stated their disagreement with Farwell’s hypotheses, but did not cite any data that contradict the three hypotheses, nor did they propose alternative hypotheses or standards. Meijer et al. made demonstrable misstatements of fact, including false ad hominem statements about Farwell, and impugned Farwell’s motives and character. We provide supporting evidence for Farwell’s three hypotheses, clarify several issues, correct Meijer et al.’s misstatements of fact, and propose that the progress of science is best served by practicing science: designing and conducting research to test and as necessary modify the proposed hypotheses and standards that explain the existing data.     

Prevalence of pink-footed goose grubbing in the arctic tundra increases with population expansion

In the high-arctic archipelago of Svalbard, the pink-footed goose (Anser brachyrhynchus) population has increased dramatically over the last decades. The population increase and the corresponding range expansion suggest a substantial increase in the potential for disturbance of the tundra caused by goose herbivory. In this study, we used surveys of pink-footed goose grubbing from two separate years (2007 and 2012) to examine the temporal changes in the prevalence of grubbing in central Spitsbergen. During this time period, the Svalbard-breeding pink-footed goose population had increased from 56,400 to 80,000 individuals. We compared grubbing prevalence between the 2 years, standardising the comparison by using a published model of habitat suitability for grubbing (Speed et al. in Ecosystems 12:349-359, 2009) as a covariate. Habitat suitability was a significant predictor of grubbing prevalence across both years, with higher grubbing probability in habitats predicted to be more suitable for grubbing. The probability of grubbing was on average 4 times higher in 2012 than in 2007. In 2007, all tundra habitats had a probability of <27 % of being grubbed whilst in 2012, there was a probability for being grubbed of more than 34 % in the least suitable habitat and around 59 % in the most suitable habitat. The increase in grubbing prevalence demonstrates a great need for monitoring the expanding pink-footed goose population and its impact on the tundra landscape.     

Epigenetic Variations in Plant Hybrids and Their Potential Roles in Heterosis

Heterosis,one of the most important biological phenomena,refers to the phenotypic superiority of a hybrid over its genetically diverse parents with respect to many traits such as biomass,growth rate and yield.Despite its successful application in breeding and agronomic production of many crop and animal varieties,the molecular basis of heterosis remains elusive.The classic genetic explanations for heterosis centered on three hypotheses:dominance (Davenport,1908;Bruce,1910;Keeble and Pellew,1910;Jones,1917),overdominance (East,1908;Shull,1908) and epistasis (Powers,1944;Yu et al.,1997).However,these hypotheses are largely conceptual and not connected to molecular principles,and are therefore insufficient to explain the molecular basis of heterosis (Birchler et al.,2003).Recently,many studies have explored the molecular mechanism of heterosis in plants at a genome-wide level.These studies suggest that global differential gene expression between hybrids and parental lines potentially contributes to heterosis in plants (e.g.,Swanson-Wagner et al.,2006;Zhang et al.,2008;Wei et al.,2009;Song et al.,2010).Research suggests that genetic components,including cis-acting elements and trans-acting factors,are critical regulators of differential gene expression in hybrids (Hochholdinger and Hoecker,2007;Springer and Stupar,2007;Zhang et al.,2008).However,other research indicates that epigenetic components,the regulators of chromatin states and genome activity,also have the potential to impact heterosis (e.g.,Ha et al.,2009;He et al.,2010;Groszmann et al.,2011;Barber et al.,2012;Chodavarapu et al.,2012;Greaves et al.,2012a;Shen et al.,2012).     

Some progress in the study of plant–soil interactions in China

Plants and soil are the base for sustainably surviving human beings on the globe as the role of materials, energy, resources and environment (Shao & Chu 2008; Shao et al. 2008, 2009, 2010, 2012a,b; Liu & Shao, 2010; Ruan et al. 2010; Xu et al. 2010, 2012; Shao 2012; Huang et al. 2013). This topic has been extensively investigated for 100 years with more achievements in many sectors and practical significance in conducting high-efficient agriculture and eco-environmental construction. The plant–soil interaction is the core issue of this topic, which has been given much attention for the past 30 years (Wu et al. 2007, 2010; Zhang et al. 2011, 2013; Xu et al. 2012, 2013).     

Detection of Legionella spp. and Legionella pneumophila in water samples of Spain by specific real-time PCR

Legionella pneumophila is the primary cause of the legionellosis diseases (90 %) (Yu et al. in J Infect Dis 186:127–128, 2002; Doleans et al. in J Clin Microbiol 42:458–460, 2004; Den Boer et al. in Clin Microbiol Infect 14:459–466, 2008). In this study, methodologies based on molecular biology were developed in order to provide a quick diagnosis of the bacterial presence in water samples of Spain. Multiplex real-time polymerase chain reaction assays were realized to target the 16S rRNA and macrophage infectivity potentiator (mip) genes of, respectively, Legionella spp. and L. pneumophila including in the design of an internal control. The results obtained by the culture and the gene amplification methods agreed in 94.44 % for the 16S rRNA gene, and a concordance of 66.67 % of the cases was obtained for the mip gene.     

Immune plexins and semaphorins: old proteins,new immune functions

Plexins and semaphorins are a large family of proteins that are involved in cell movement and response. The importance of plexins and semaphorins has been emphasized by their discovery in many organ systems including the nervous (Nkyimbeng-Takwi and Chapoval, 2011; McCormick and Leipzig, 2012; Yaron and Sprinzak, 2012), epithelial (Miao et al., 1999; Fujii et al., 2002), and immune systems (Takamatsu and Kumanogoh, 2012) as well as diverse cell processes including angiogenesis (Serini et al., 2009; Sakurai et al., 2012), embryogenesis (Perala et al., 2012), and cancer (Potiron et al., 2009; Micucci et al., 2010). Plexins and semaphorins are transmembrane proteins that share a conserved extracellular semaphorin domain (Hota and Buck, 2012). The plexins and semaphorins are divided into four and eight subfamilies respectively based on their structural homology. Semaphorins are relatively small proteins containing the extracellular semaphorin domain and short intracellular tails. Plexins contain the semaphorin domain and long intracellular tails (Hota and Buck, 2012). The majority of plexin and semaphorin research has focused on the nervous system, particularly the developing nervous system, where these proteins are found to mediate many common neuronal cell processes including cell movement, cytoskeletal rearrangement, and signal transduction (Choi et al., 2008; Takamatsu et al., 2010). Their roles in the immune system are the focus of this review.     

Curcumin attenuates oxidative damage in animals treated with a renal carcinogen, ferric nitrilotriacetate (Fe-NTA): implications for cancer prevention

Curcumin (diferuloylmethane), a biologically active ingredient derived from rhizome of the plant Curcuma longa, has potent anticancer properties as demonstrated in a plethora of human cancer cell lines/animal carcinogenesis model and also acts as a biological response modifier in various disorders. We have reported previously that dietary supplementation of curcumin suppresses renal ornithine decarboxylase (Okazaki et al. Biochim Biophys Acta 1740:357–366, 2005) and enhances activities of antioxidant and phase II metabolizing enzymes in mice (Iqbal et al. Pharmacol Toxicol 92:33–38, 2003) and also inhibits Fe-NTA-induced oxidative injury of lipids and DNA in vitro (Iqbal et al. Teratog Carcinog Mutagen 1:151–160, 2003). This study was designed to examine whether curcumin possess the potential to suppress the oxidative damage caused by kidney-specific carcinogen, Fe-NTA, in animals. In accord with previous report, at 1 h after Fe-NTA treatment (9.0 mg Fe/kg body weight intraperitoneally), a substantial increased formation of 4-hydroxy-2-nonenal (HNE)-modified protein adducts in renal proximal tubules of animals was observed. Likewise, the levels of 8-hydroxy-2′-deoxyguanosine (8-OHdG) and protein reactive carbonyl, an indicator of protein oxidation, were also increased at 1 h after Fe-NTA treatment in the kidneys of animals. The prophylactic feeding of animals with 1.0% curcumin in diet for 4 weeks completely abolished the formation of (i) HNE-modified protein adducts, (ii) 8-OHdG, and (iii) protein reactive carbonyl in the kidneys of Fe-NTA-treated animals. Taken together, our results suggest that curcumin may afford substantial protection against oxidative damage caused by Fe-NTA, and these protective effects may be mediated via its antioxidant properties. These properties of curcumin strongly suggest that it could be used as a cancer chemopreventive agent.     

Improving efficiency of a regional stand alone bone bank

The introduction of a stand-alone Bone Bank in our Regional Orthopaedic Hospital has improved the availability of femoral head allograft. Benninger et al. (Bone Joint J 96-B:1307–1311, 2014), demonstrated their institutions bank to be cost effective despite a 30 % discard rate for harvested allograft. We sought to audit our own discard rates and subsequent cost-effectiveness of our bone bank. Donor recruitment. Before approaching a potential donor, our establishment’s nurse specialists review their clinical notes and biochemical laboratory results, available on a regional Electronic Care Records. They view femoral head architecture on radiographs against set criteria, Patient Archive and Communication system (SECTRA, Sweden). In total 1383 femoral heads were harvested, 247 were discarded giving an overall rate of 17.9 %. The most common reasons for discard of harvested graft was a positive microbiology/bacteriology result, n = 96 (38.9 %). After a rise in discard rates in 2007, we have steadily reduced our discard rates since 2006/2007 (28.2 %), 2008/2009 (17 %), 2010/2011 (14.8 %), and finally to 10.3 % in 2012/2013. In the current financial year, our cost to harvest, test, store and release a femoral head is £610. With a structured donor recruitment process and unique pre-operative radiographic analysis we have successfully reduced our discard rates bi-annually making our bone bank increasingly cost-effective.     

Wavelength-dependent photodamage to <Emphasis Type="Italic">Chlorella</Emphasis> investigated with a new type of multi-color PAM chlorophyll fluorometer

A new type of multi-color PAM chlorophyll fluorometer (Schreiber et al. 2012) was applied for measurements of photodamage to photosystem II (PS II) in optically thin suspensions of Chlorella (200 μg Chl l^?1) in the presence of 1 mM lincomycin. An action spectrum of the relative decrease of F _v/F _m in the 440–625 nm range was measured, which not only showed the expected high activity in the blue, but at a lower level also substantial activity above 540 nm. With the same dilute suspension, a PS II absorption spectrum was derived via measurements of the O-I₁ rise kinetics induced by differently colored strong light at defined incident quantum flux densities. After normalization of the two spectra at 625 nm, the relative extent of photodamage at 440–480 nm proved substantially higher than absorption by PS II, whereas the two spectra were close to identical in the 540–625 nm range. Hence, overall photodamage to PS II appears to consist of two components, one of which is due to light absorbed by PS II pigments, whereas the other one is likely to involve direct light absorption by Mn in the oxygen-evolving complex (Hakala et al. Biochim Biophys Acta 1706:68–80, 2005). Based on this rationale, an action spectrum of the Mn mechanism of photodamage was deconvoluted from the overall action spectrum, declining steeply above 480 nm. An almost identical Mn-spectrum was derived by another approach with the PAR of the various colors being adjusted to give identical rates of PS II turnover, PAR _II. The tentative, basic assumption of negligibly small contribution of the Mn mechanism to photodamage above 540 nm was supported by supplementary measurements using an external 665 nm lamp. 665 nm not only gave about two times PS II turnover as compared to 625 nm, but also about two times photodamage.