A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software tool for their detection and reorientation

Reverse complementary DNA sequences––sequences that are inadvertently cast backward and in which all purines and pyrimidines are transposed––are not uncommon in sequence databases, where they may introduce noise into sequence-based research. We show that about 1% of the public fungal ITS sequences, the most commonly sequenced genetic marker in mycology, are reverse complementary, and we introduce an open source software solution to automate their detection and reorientation. The MacOSX/Linux/UNIX software operates on public or private datasets of any size, although some 50 base pairs of the 5.8S gene of the ITS region are needed for the analysis.     

Accumulation of low-molecular-weight organic acids in roots and leaf segments of Zea mays plants treated with cadmium and copper

Maize seedlings grown in a nutrient solution were treated with Cd (50, 100 µM) or Cu (50, 100 µM). Roots and separated leaf sections (from the youngest––basal, through the middle––mature, to the oldest––apical) were analysed. Shoot and root fresh weight, and root net growth rates were reduced significantly after Cu application in comparison to Cd. Copper (50, 100 µM) and cadmium (100 µM) decreased the sum of chlorophyll and total carotenoid pools mostly in mature and old leaf sections. The concentration of Cu and Cd increased in the old and mature leaf sections. Analysis of organic acids showed that both metals differently influenced the low-molecular-weight organic acids (LMWOAs) content in maize leaf sections. In mature sections, the excess Cu increased the succinate and tartrate contents, whereas in the young ones mainly the tartrate level was elevated. Cadmium elevated citrate accumulation in mature and old sections, compared to the control plants. Malate, the main LMWOA in maize leaves, increased only after addition of 100 µM of Cd (mature and old sections) or 50 µM of Cu (old sections). Analysis of LMWOAs in roots showed that the excess of Cd or Cu induced higher accumulation of tartrate and malate and, additionally, copper increased the citrate content.     

Common variants in the ATP2B1 gene are associated with hypertension and arterial stiffness in Chinese population

Genome-wide association studies have identified the ATP2B1 gene associated with blood pressure (BP), the evidence from large scale Chinese population was still rare. We performed the current replication study to test the association of the ATP2B1 gene and hypertension and BP in two unrelated Chinese cohorts including 2,831 unrelated individuals with hypertension and 1,987 controls in total. We also examined the influences of the ATP2B1 gene on the arterial stiffness through evaluation of carotid-femoral pulse wave velocities (cf-PWV) in 164 untreated hypertensives. The major findings of this study were that four loci––rs10858911, rs2681472, rs17249754 and rs1401982––associated with any or all of four traits: hypertension (P = 0.001–4.6E–05; odds ratio, 0.83–0.87), systolic BP (P = 0.003–0.004), diastolic BP (P = 0.002–0.003) and cf-PWV (P = 0.002–0.004). All the comparisons were adjusted for sex, age, age² and body mass index. We validated the association of the ATP2B1 gene and susceptibility to hypertension, BP traits and cf-PWV in Chinese population. In addition, further genetic and functional research was warranted to elucidate the concrete locus in the ATP2B1 gene that influenced the manifestation of BP and vascular function.     

High-Resolution Views and Transport Mechanisms of the NKCC1 and KCC Transporters

Cation-chloride cotransporters (CCCs) are responsible for the coupled co-transport of Cl^- with K⁺ and/or Na⁺ in an electroneutral manner. They play important roles in myriad fundamental physiological processes––from cell volume regulation to transepithelial solute transport and intracellular ion homeostasis––and are targeted by medicines commonly prescribed to treat hypertension and edema. After several decades of studies into the functions and pharmacology of these transporters, there have been several breakthroughs in the structural determination of CCC transporters. The insights provided by these new structures for the Na⁺/K⁺/Cl^- cotransporter NKCC1 and the K⁺/Cl^- cotransporters KCC1, KCC2, KCC3 and KCC4 have deepened our understanding of their molecular basis and transport function. This focused review discusses recent advances in the structural and mechanistic understanding of CCC transporters, including architecture, dimerization, functional roles of regulatory domains, ion binding sites, and coupled ion transport.     

Do tigers displace leopards? If so, why?

We investigated predictions concerning the competitive relationships between tigers Panthera tigris and leopards Panthera pardus in Bardia National Park, Nepal, based on spatial distributions of scats and territorial markings (sign), analyses of scat content and census of wild ungulate prey. Medium-sized ungulates, in particular chital Axis axis, was the main food of both predators, but leopards consumed significantly larger proportions of domestic animals, small mammals, and birds than tigers. Tiger sign were never found outside the park, while leopard sign occurred both inside and outside, and were significantly closer to the park border than tiger sign. Significantly higher prey densities at locations of tiger sign than that of leopards were mainly due to a preference of the latter species for the park border areas. Our results imply that interference competition––and not competition for food––was a limiting factor for the leopard population, whose distribution was restricted to the margins of the tiger territories. We suggest that the composition of the prey base is a key factor in understanding the different results and interpretations reported in studies on tiger/leopard coexistence. There are two potential mechanisms that link interference competition and prey: (1) low abundance of large ungulate prey decreases foraging efficiency of tigers, leading to increased energetic stress and aggression towards leopards; and (2) increased diet overlap due to scarcity of large prey leads to increased encounter rates and increased levels of interference competition.     

Different mechanisms of action of poly(ethylene glycol) and arginine on thermal inactivation of lysozyme and ribonuclease A

Proteins tend to undergo irreversible inactivation through several chemical modifications, which is a serious problem in various fields. We have recently found that arginine (Arg) suppresses heat‐induced deamidation and β‐elimination, resulting in the suppression of thermal inactivation of hen egg white lysozyme and bovine pancreas ribonuclease A. Here, we report that poly(ethylene glycol) (PEG) with molecular weight 1,000 acts as a thermoinactivation suppressor for both proteins, especially at higher protein concentrations, while Arg was not effective at higher protein concentrations. This difference suggests that PEG, but not Arg, effectively inhibited intermolecular disulfide exchange among thermally denatured proteins. Investigation of the effects of various polymers including PEG with different molecular weight, poly(vinylpyrolidone) (PVP), and poly(vinyl alchol) on thermoinactivation of proteins, circular dichroism, solution viscosity, and the solubility of reduced and S‐carboxy‐methylated lysozyme indicated that amphiphilic PEG and PVP inhibit intermolecular collision of thermally denatured proteins by preferential interaction with thermally denatured proteins, resulting in the inhibition of intermolecular disulfide exchange. These findings regarding the different mechanisms of the effects of amphiphilic polymers––PEG and PVP––and Arg would expand the capabilities of methods to improve the chemical stability of proteins in solution. Biotechnol. Bioeng. 2012; 109: 2543–2552. © 2012 Wiley Periodicals, Inc.     

Habitual throwing and swimming correspond with upper limb diaphyseal strength and shape in modern human athletes

Variation in upper limb long bone cross‐sectional properties may reflect a phenotypically plastic response to habitual loading patterns. Structural differences between limb bones have often been used to infer past behavior from hominin remains; however, few studies have examined direct relationships between behavioral differences and bone structure in humans. To help address this, cross‐sectional images (50% length) of the humeri and ulnae of university varsity‐level swimmers, cricketers, and controls were captured using peripheral quantitative computed tomography. High levels of humeral robusticity were found in the dominant arms of cricketers, and bilaterally among swimmers, whereas the most gracile humeri were found in both arms of controls, and the nondominant arms of cricketers. In addition, the dominant humeri of cricketers were more circular than controls. The highest levels of ulnar robusticity were also found in the dominant arm of cricketers, and bilaterally amongst swimmers. Bilateral asymmetry in humeral rigidity among cricketers was greater than swimmers and controls, while asymmetry for ulnar rigidity was greater in cricketers than controls. The results suggest that more mechanically loaded upper limb elements––unilaterally or bilaterally––are strengthened relative to less mechanically loaded elements, and that differences in mechanical loading may have a more significant effect on proximal compared to distal limb segments. The more circular humerus in the dominant arm in cricketers may be an adaptation to torsional strain associated with throwing activities. The reported correspondence between habitual activity patterns and upper limb diaphyseal properties may inform future behavioral interpretations involving hominin skeletal remains. Am J Phys Anthropol 2009. © 2009 Wiley‐Liss, Inc.     

Hypoxia–Ischemia Alters Nucleotide and Nucleoside Catabolism and Na+,K+-ATPase Activity in the Cerebral Cortex of Newborn Rats

It is well known that the levels of adenosine in the brain increase dramatically during cerebral hypoxic-ischemic (HI) insults. Its levels are tightly regulated by physiological and pathophysiological changes that occur during the injury acute phase. The aim of the present study was to examine the effects of the neonatal HI event on cytosolic and ecto-enzymes of purinergic system––NTPDase, 5′-nucleotidase (5′-NT) and adenosine deaminase (ADA)––in cerebral cortex of rats immediately post insult. Furthermore, the Na⁺/K⁺-ATPase activity, adenosine kinase (ADK) expression and thiobarbituric acid reactive species (TBARS) levels were assessed. Immediately after the HI event the cytosolic NTPDase and 5′-NT activities were increased in the cerebral cortex. In synaptosomes there was an increase in the ecto-ADA activity while the Na⁺/K⁺ ATPase activity presented a decrease. The difference between ATP, ADP, AMP and adenosine degradation in synaptosomal and cytosolic fractions could indicate that NTPDase, 5′-NT and ADA were differently affected after insult. Interestingly, no alterations in the ADK expression were observed. Furthermore, the Na⁺/K⁺-ATPase activity was correlated negatively with the cytosolic NTPDase activity and TBARS content. The increased hydrolysis of nucleotides ATP, ADP and AMP in the cytosol could contribute to increased adenosine levels, which could be related to a possible innate neuroprotective mechanism aiming at potentiating the ambient levels of adenosine. Together, these results may help the understanding of the mechanism by which adenosine is produced following neonatal HI injury, therefore highlighting putative therapeutical targets to minimize ischemic injury and enhance recovery.     

Fish genomes and their evolution under the influence of ecology

Environmental interactions and the effects of such interactions on the evolution of genome attributes is an intriguing area of ongoing research. Several earlier studies have delved into how the genome size (GS) and the guanine-cytosine content (GC) of genomes are shaped by species’ ecology while largely disregarding other genome attributes, such as number of chromosomes (CR), number of genes (GE), and protein count (PC) from such comparisons. The present study was designed at understanding the influence of ecology––climate, habitat, and depth––on genome attributes by using the most current data on 579 whole fish genomes available at NCBI. Given the diverse and intricate roles of GS and GC in species adaptations to temperature, salinity, and hydrostatic pressure, the focus was on finding if and how the genomes responded to these stressors and if any common patterns existed in the genome-level responses. Our analyses exhibited some significant and intriguing trends for fishes as a whole while indicating strong effects of ecology on GS, GC, CR, and PC. Also, some very unique trends were observed on regressing GS and GC values across temperature, salinity, and depth clines. Accordingly, a very strong decline in the GS and a concomitant increase in GC were observed in species through the tropics/sub tropics to the temperate/poles, from freshwater to the marine habitats, and from the pelagic to bathydemersal depths. Observed patterns strongly support the notion that smaller GS and larger GC are associated with species inhabiting more stable environments and vice versa. The results also signify the effect of these patterns on protein flexibility and its role in tolerating stressful conditions. Observed patterns are discussed in the light of latitudinal biodiversity gradient, habitat complexity, and energy and metabolic expenditure hypothesis.     

Flower strips increase the control of rosy apple aphids after parasitoid releases in an apple orchard

Mass releases of two parasitoid species, Aphidius matricariae and Ephedrus cerasicola, may provide an alternative measure to pesticides to control the rosy apple aphid Dysaphis plantaginea in organic apple orchards. As an exploratory study, we tested if the presence of flower strips between apple tree rows could improve the action of three early parasitoid releases––and of other naturally present aphid enemies––on the control of aphid colonies and the number of aphids per tree. Apple trees located at various distances from parasitoid release points were monitored in plots with and without flower strips in an organic apple orchard over two years, along the season of aphid infestation (March to July). Our case study demonstrated that the presence of flowering plant mixes in the alleyways of the apple orchard reduced the presence of D. plantaginea by 33.4%, compared to plots without flower strips, at the infestation peak date. We also showed a negative effect of increasing the distance to parasitoid release points on aphid control. However, our results at the infestation peak date suggest that the presence of flower strips could marginally compensate for the detrimental effect of increasing distance to the release point, probably by improving the persistence and dispersal capacities of natural enemies. Despite high variations in aphid population dynamics between years, we conclude that combining flower strips with early parasitoid releases in apple orchards is promising for biological control of the rosy apple aphid, although the method merits to be further refined.     

Demands of eicosapentaenoic acid (EPA) in <Emphasis Type="Italic">Daphnia</Emphasis>: are they dependent on body size?

Fatty acids contribute to the nutritional quality of the phytoplankton and, thus, play an important role in Daphnia nutrition. One of the polyunsaturated fatty acids (PUFAs)––eicosapentaenoic acid (EPA)––has been shown to predict carbon transfer between primary producers and consumers in lakes, suggesting that EPA limitation of Daphnia in nature is widespread. Although the demand for EPA must be covered by the diet, the demand of EPA in Daphnia that differ in body size has not been addressed yet. Here, we hypothesize that the demand for EPA in Daphnia is size-dependent and that bigger species have a higher EPA demand. To elucidate this, a growth experiment was conducted in which at 20 °C three Daphnia taxa (small-sized D. longispina complex, medium-sized D. pulicaria, and large-bodied D. magna) were fed Synechococcus elongatus supplemented with cholesterol and increasing concentrations of EPA. In addition, fatty acid analyses of Daphnia were performed. Our results show that the saturation threshold for EPA-dependent growth increased with increasing body size. This increase in thresholds with body size may provide another mechanism contributing to the prevalence of small-bodied cladocera in warm habitats and to the midsummer decline of large cladocera in eutrophic water bodies.     

What are the roles of retinoids,other morphogens,and Hox genes in setting up the vertebrate body axis?

This article is concerned with the roles of retinoids and other known anterior–posterior morphogens in setting up the embryonic vertebrate anterior–posterior axis. The discussion is restricted to the very earliest events in setting up the anterior–posterior axis (from blastula to tailbud stages in Xenopus embryos). In these earliest developmental stages, morphogen concentration gradients are not relevant for setting up this axis. It emerges that at these stages, the core patterning mechanism is timing: BMP‐anti BMP mediated time space translation that regulates Hox temporal and spatial collinearities and Hox‐Hox auto‐ and cross‐ regulation. The known anterior–posterior morphogens and signaling pathways––retinoids, FGF's, Cdx, Wnts, Gdf11 and others––interact with this core mechanism at and after space–time defined “decision points,” leading to the separation of distinct axial domains. There are also other roles for signaling pathways. Besides the Hox regulated hindbrain/trunk part of the axis, there is a rostral part (including the anterior part of the head and the extreme anterior domain [EAD]) that appears to be regulated by additional mechanisms. Key aspects of anterior–posterior axial patterning, including: the nature of different phases in early patterning and in the whole process; the specificities of Hox action and of intercellular signaling; and the mechanisms of Hox temporal and spatial collinearities, are discussed in relation to the facts and hypotheses proposed above.     

DNA interaction of europium(III) complex containing 2,2′-bipyridine and its antimicrobial activity

The interaction of native fish salmon DNA (FS-DNA) with [Eu(bpy)₃Cl₂(H₂O)]Cl, where bpy is 2,2′-bipyridine, is studied at physiological pH in Tris-HCl buffer by spectroscopic methods, viscometric techniques as well as circular dichroism (CD). These experiments reveal that Eu(III) complex has interaction with FS-DNA. Moreover, binding constant and binding site size have been determined. The value of K_b has been defined 2.46 ± .02 × 10⁵ M^?1. The thermodynamic parameters are calculated by Van’t Hoff equation, the results show that the interaction of the complex with FS-DNA is an entropically driven phenomenon. CD spectroscopy followed by viscosity as well as fluorescence and UV––Vis measurements indicate that the complex interacts with FS-DNA via groove binding mode. Also, the synthesized Eu(III) complex has been screened for antimicrobial activities.     

Odonates as Indicators of Shallow Lake Restoration by Liming: Comparing Adult and Larval Responses

Odonate assemblages were compared between replicate sets of shallow lakes that had been created and acidified by open‐cast mining across a large area (2,451 ha) of southwest France (Arjuzanx, Landes); one set of lakes (n = 5) was experimentally restored by liming with calcium carbonate, whereas another group (n = 5) was left as untreated reference lakes. Both odonate adults and exuviae were sampled bimonthly during May–August 1998. Elevated turbidity and conductivity in limed lakes were the only physicochemical measures differing between restored and reference lakes, because deacidification occurred naturally, even in reference lakes during the 17 years after the onset of restoration. Restoration by liming can apparently lead to effects on lake turbidity that might be considered adverse. Twenty‐four and 19 odonate species occurred among adults and exuviae, respectively, but there were no significant differences in richness between restored and reference sites. However, significantly, more exuviae were collected from the reference sites (588 vs. 180), where exuvial diversity and rank abundance indicated more evenly structured assemblages than those in restored lakes. Ordination showed that adult assemblages differed significantly between restored and reference lakes, and varied highly significantly with lake turbidity. This effect occurred because a small group of generally scarce adults were characteristic of reference sites (Chalcolestes viridis, Lestes virens, Cordulia aenae, Leucorrhinia albifrons, and Sympetrum sanguineum). Exuviae of these same species were less abundant at restored sites, but exuvial assemblages overall did not discriminate between restored and reference lakes. We conclude that lake restoration by liming can reduce diversity and larval numbers among odonates and subtly affects adult assemblages. In this case study, adult assemblages discriminated best between the lake types involved in the experiment, but important additional information arose from exuvial abundance and structure. This study indicates that natural recovery processes after acidification in formerly open‐cast areas––rather than chemical intervention through liming––might lead to preferable conservation outcomes.     

Ronald Brady and the cladists

Ronald Brady was the first philosopher to defend pattern cladistics as an independent scientific field. That independence was achieved through the decoupling of biological systematics from phylogenetics––that is, inferred evolutionary processes (e.g. character transformation). Brady saw parallels between biological systematics and Wolfgang von Goethe's Morphology, an empirical scientific field that incorporates human observation and perception to discover coherent morphological structures. Goethe's Morphology and pre-Darwinian systematics were independent from evolutionary narratives, a tradition that continued into the 20th Century through the work of biologists such as Agnes Arber. Most importantly, Brady provided the philosophical and historical foundations to an independent systematics by demonstrating the links between phenomenology, Goethe's Morphology and comparative biology.     

Optimization of the spray drying of a Paenibacillus polymyxa-based biopesticide on pilot plant and production scales

Spore survival and moisture content are two important properties of biopesticides, and both are related to field biocontrol efficacy and storage shelf life. In this study, Paenibacillus polymyxa (HY96-2) was spray-dried on both pilot plant and production scales, and the effects of inlet and outlet temperatures on spore survival and moisture content were investigated. The results showed that inlet temperatures ranging from 170 to 230 °C (at an outlet temperature of 80 °C) had no obvious effect on the two properties during pilot scale processing, although an inlet temperature of 230 °C resulted in higher feed speed. When the outlet temperature on the pilot scale was reduced from 100 to 80 °C, no obvious variations in spore survival and moisture content were found, while a further reduction from 80 to 65 °C resulted in a decline in spore survival from 81.0 to 67.0% and an increase in moisture content from 2.3 to 31.7%. These results indicate that both outlet temperature and moisture content have an effect on spore survival. Optimum inlet and outlet temperatures for P. polymyxa processing were 230 °C and 85–90 °C on a production scale. Under these conditions, spore survival and moisture content were 83.5–86.6% and 2.73––4.12%, respectively.     

Monophyletic classification and information content

The connection between monophyly and efficient taxonomic diagnoses is elaborated. The inefficiency of nonmonophyletic groups is shown by reconstructing data matrices from hierarchical sets of diagnoses that are derived from apomorphies and read in order from highest to lowest rank. The practice of diagnosing nonmonophyletic groups either results in omitting data, resulting in errors in reconstructed datasets, or repeating character information to make up for the implied losses. Step-by-step demonstrations with hypothetical and real data are used as guidance. Provisions are made for missing, inapplicable and polymorphic data. Slow optimization (delayed transformation) is useful for choosing a state reconstruction in order to report apomorphies completely. The diagnoses of paraphyletic groups can be expressed in different ways, including regrafting derived clades, reanalyzing data with constraints, and reading the original diagnoses in a different order––the last is the least efficient. A cladistic version of the data compression ratio is proposed to quantify the diagnostic efficiency of a cladogram.     

Sarcoptic mange vulnerability in carnivores of the Białowieża Primeval Forest,Poland: underlying determinant factors

Sarcoptic mange caused by Sarcoptes scabiei, is a highly contagious worldwide mite infection responsible for epizootic skin disease in populations of wild and domestic mammals. It causes skin disorders that may lead to severe generalized skin disease (mange). We investigated the spread and dynamics of sarcoptic mange in one of the best preserved carnivore communities in the Bia?owie?a Primeval Forest over the last 20 years. Sarcoptic mange was found in 6 of 10 investigated species. The highest percentage of infected individuals was recorded in red foxes (19 %), European badgers (9 %), grey wolves (7 %), raccoon dogs (6 %), and stone martens (5 %). Other species were not infected (least weasel, American mink, European polecat, pine marten) or infected sporadically (Eurasian lynx––1 case). Rate of infection was correlated with the sum of ecological and behavioral features, which may increase the spread of infection. Outbreaks of sarcoptic mange occurred simultaneously in several species of carnivores, which indicates the occurrence of between species transmission. We found that the source of investigated individuals (trapped, culled and found dead) may influence the results of the analysis. Our study shows that in carnivore communities such as in Bia?owie?a Forest, numerous species may serve as a reservoir of the pathogen and favor its persistence in the environment. This study indicates that sociality and use of den sites are important factors affecting sarcoptic mange spread and prevalence in wild populations of carnivores.