Molecular evolution of ribosomal intergenic spacers in Odontophrynus americanus 2n and 4n (Amphibia: Anura).

Ribosomal intergenic spacers (IGSs) of Odontophrynus americanus 2n and 4n were cloned, restriction mapped, and partially sequenced. Three distinct regions, namely alpha, beta, and delta, were identified in the IGSs. The alpha and beta regions flanked the 28S and 18S rRNA genes, respectively, conserving an identical restriction pattern at each ploidy level. The delta region, located between alpha and beta, was highly variable in size and restriction pattern, enclosing different BamHI subrepeats (B-SR), 87- to 530-bp-long. Sequence analysis showed that B-SRs were composed mainly of different arrangements of similar blocks of sequences. Another family of repetitive sequences was found in the delta region, clustered inside large BamHI fragments. These subrepeats are 189-bp-long and, although very similar in diploid and tetraploid IGSs, show a pattern of concerted evolution. A hypothetical functional role for the 189-bp repeats is discussed in view of their predicted secondary structure and presence of potential E2 binding sites inside diploid subrepeats. Although the same structural elements were present both in diploid and tetraploid IGSs, the higher level of repeatability of tetraploid IGSs suggests that common ancestor sequences have undergone several rounds of amplification after O. americanus polyploidy.     

Choosing benefits or partners: a review of the evidence for the evolution of myrmecochory

Myrmecochory, or seed dispersal by ants, is a dispersal syndrome found among several thousand plant species occupying different ecosystems and geographical regions. Typically, ants benefit from consuming a lipid-rich appendage on the seed and in return provide seed dispersal service to the plant. Several hypotheses have been proposed to explain the selective advantage for plants resulting from myrmecochory, including directed dispersal, dispersal for distance and escape from seed predators. I contrast the evidence available in the literature for these hypotheses and distinguish the studies on the basis of ecosystem and plant growth forms. The predator-avoidance and the distance dispersal hypotheses were supported in most studies that addressed them, and the directed dispersal hypothesis was supported in about half of the studies that tested it. Multiple hypotheses were supported in most studies that tested more than one hypothesis, suggesting that the various selective advantages conferred from myrmecochory are seldom exclusive. I also review evidence for the hypothesis that plants have evolved adaptations both for selecting seed dispersers and for manipulating the behavior of those dispersers. Based on this evidence, I argue that focusing future research on the evolution of partner choice by myrmecochores and its effects on the overall plant fitness will be more fruitful than putting an emphasis on classifying the selective advantage to plants into distinct categories and test for their existence separately.     

A Working Memory Deficit among Dyslexic Readers with No Phonological Impairment as Measured Using the N-Back Task: An fNIR Study

Data indicated that dyslexic individuals exhibited difficulties on tasks involving Working Memory (WM). Previous studies have suggested that these deficits stem from impaired processing in the Phonological Loop (PL). The PL impairment was connected to poor phonological processing. However, recent data has pointed to the Central Executive (CE) system as another source of WM deficit in dyslexic readers. This opened a debate whether the WM deficit stems solely from PL or can also be seen as an outcome of poor CE processing. In an attempt to verify this question, the current study compared adult skilled and compensated dyslexic readers with no impairment of phonological skills. The participants’ PL and CE processing were tested by using the fNIR device attached to the frontal lobe and measured the changes in brain oxygen values when performing N-back task. As it was previously suggested, the N = 0 represented PL and N = 1 to 3 represent CE processing. It was hypothesized that dyslexic readers who show non-impaired phonological skills will exhibit deficits mainly in the CE subsystem and to a lesser extent in the PL. Results indicated that the two reading level groups did not differ in their accuracy and reaction times in any of the N-Back conditions. However, the dyslexic readers demonstrated significant lower maximum oxyHb values in the upper left frontal lobe, mainly caused due to a significant lower activity under the N = 1 condition. Significant task effects were found in the medial left hemisphere, and the high medial right hemisphere. In addition, significant correlations between fNIR-features, reading performance and speed of processing were found. The higher oxyHb values, the better reading and speed of processing performance obtained. The results of the current study support the hypothesis that at least for the group of dyslexics with non-impaired PL, WM deficit stems from poor CE activity.     

Modelling of Thyroid Peroxidase Reveals Insights into Its Enzyme Function and Autoantigenicity

Thyroid peroxidase (TPO) catalyses the biosynthesis of thyroid hormones and is a major autoantigen in Hashimoto’s disease—the most common organ-specific autoimmune disease. Epitope mapping studies have shown that the autoimmune response to TPO is directed mainly at two surface regions on the molecule: immunodominant regions A and B (IDR-A, and IDR-B). TPO has been a major target for structural studies for over 20 years; however, to date, the structure of TPO remains to be determined. We have used a molecular modelling approach to investigate plausible modes of TPO structure and dimer organisation. Sequence features of the C-terminus are consistent with a coiled-coil dimerization motif that most likely anchors the TPO dimer in the apical membrane of thyroid follicular cells. Two contrasting models of TPO were produced, differing in the orientation and exposure of their active sites relative to the membrane. Both models are equally plausible based upon the known enzymatic function of TPO. The “trans” model places IDR-B on the membrane-facing side of the myeloperoxidase (MPO)-like domain, potentially hindering access of autoantibodies, necessitating considerable conformational change, and perhaps even dissociation of the dimer into monomers. IDR-A spans MPO- and CCP-like domains and is relatively fragmented compared to IDR-B, therefore most likely requiring domain rearrangements in order to coalesce into one compact epitope. Less epitope fragmentation and higher solvent accessibility of the “cis” model favours it slightly over the “trans” model. Here, IDR-B clusters towards the surface of the MPO-like domain facing the thyroid follicular lumen preventing steric hindrance of autoantibodies. However, conformational rearrangements may still be necessary to allow full engagement with autoantibodies, with IDR-B on both models being close to the dimer interface. Taken together, the modelling highlights the need to consider the oligomeric state of TPO, its conformational properties, and its proximity to the membrane, when interpreting epitope-mapping data.     

Tree cover at fine and coarse spatial grains interacts with shade tolerance to shape plant species distributions across the Alps

The role of competition for light among plants has long been recognised at local scales, but its importance for plant species distributions at larger spatial scales has generally been ignored. Tree cover modifies the local abiotic conditions below the canopy, notably by reducing light availability, and thus, also the performance of species that are not adapted to low‐light conditions. However, this local effect may propagate to coarser spatial grains, by affecting colonisation probabilities and local extinction risks of herbs and shrubs. To assess the effect of tree cover at both the plot‐ and landscape‐grain sizes (approximately 10‐m and 1‐km), we fit generalised linear models (GLMs) for the plot‐level distributions of 960 species of herbs and shrubs using 6935 vegetation plots across the European Alps. We ran four models with different combinations of variables (climate, soil and tree cover) at both spatial grains for each species. We used partial regressions to evaluate the independent effects of plot‐ and landscape‐grain tree cover on plot‐level plant communities. Finally, the effects on species‐specific elevational range limits were assessed by simulating a removal experiment comparing the species distributions under high and low tree cover. Accounting for tree cover improved the model performance, with the probability of the presence of shade‐tolerant species increasing with increasing tree cover, whereas shade‐intolerant species showed the opposite pattern. The tree cover effect occurred consistently at both the plot and landscape spatial grains, albeit most strongly at the former. Importantly, tree cover at the two grain sizes had partially independent effects on plot‐level plant communities. With high tree cover, shade‐intolerant species exhibited narrower elevational ranges than with low tree cover whereas shade‐tolerant species showed wider elevational ranges. These findings suggest that forecasts of climate‐related range shifts for herb and shrub species may be modified by tree cover dynamics.     

Scale‐dependent determinants of plant species richness in a semi‐arid fragmented agro‐ecosystem

Aims: (1) Understanding how the relationship between species richness and its determinants depends on the interaction between scales at which the response and explanatory variables are measured. (2) Quantifying the relative contributions of local, intermediate and large‐scale determinants of species richness in a fragmented agro‐ecosystem. (3) Testing the hypothesis that the relative contribution of these determinants varies with the grain size at which species richness is measured. Location: A fragmented agro‐ecosystem in the Southern Judea Lowland, Israel, within a desert–Mediterranean transition zone. Methods: Plant species richness was estimated using hierarchical nested sampling in 81 plots, positioned in 38 natural vegetation patches within an agricultural matrix (mainly wheat fields) among three land units along a sharp precipitation gradient. Explanatory variables included position along that gradient, patch area, patch isolation, habitat heterogeneity and overall plant density. We used general linear models and hierarchical partitioning of variance to test and quantify the effect of each explanatory variable on species richness at four grain sizes (0.0625, 1, 25 and 225 m²). Results: Species richness was mainly affected by position along a precipitation gradient and overall plant density, and to a lesser extent by habitat heterogeneity. It was also significantly affected by patch area and patch isolation, but only for small grain sizes. The contribution of each explanatory variable to explained variance in species richness varied with grain size, i.e. scale‐dependent. The influence of geographic position and habitat heterogeneity on species richness increased with grain size, while the influence of plant density decreased with grain size. Main conclusions: Species richness is determined by the combined effect of several scale‐dependent determinants. Ability to detect an effect and effect size of each determinant varies with the scale (grain size) at which it is measured. The combination of a multi‐factorial approach and multi‐scale sampling reveals that conclusions drawn from studies that ignore these dimensions are restricted and potentially misleading.     

Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes

Viruses are the most abundant and diverse genetic entities on Earth; however, broad surveys of viral diversity are hindered by the lack of a universal assay for viruses and the inability to sample a sufficient number of individual hosts. This study utilized vector-enabled metagenomics (VEM) to provide a snapshot of the diversity of DNA viruses present in three mosquito samples from San Diego, California. The majority of the sequences were novel, suggesting that the viral community in mosquitoes, as well as the animal and plant hosts they feed on, is highly diverse and largely uncharacterized. Each mosquito sample contained a distinct viral community. The mosquito viromes contained sequences related to a broad range of animal, plant, insect and bacterial viruses. Animal viruses identified included anelloviruses, circoviruses, herpesviruses, poxviruses, and papillomaviruses, which mosquitoes may have obtained from vertebrate hosts during blood feeding. Notably, sequences related to human papillomaviruses were identified in one of the mosquito samples. Sequences similar to plant viruses were identified in all mosquito viromes, which were potentially acquired through feeding on plant nectar. Numerous bacteriophages and insect viruses were also detected, including a novel densovirus likely infecting Culex erythrothorax. Through sampling insect vectors, VEM enables broad survey of viral diversity and has significantly increased our knowledge of the DNA viruses present in mosquitoes.     

Molecular Determinants of the Substrate Specificity of the Complement-initiating Protease,C1r

The serine protease, C1r, initiates activation of the classical pathway of complement, which is a crucial innate defense mechanism against pathogens and altered-self cells. C1r both autoactivates and subsequently cleaves and activates C1s. Because complement is implicated in many inflammatory diseases, an understanding of the interaction between C1r and its target substrates is required for the design of effective inhibitors of complement activation. Examination of the active site specificity of C1r using phage library technology revealed clear specificity for Gln at P2 and Ile at P1′, which are found in these positions in physiological substrates of C1r. Removal of one or both of the Gln at P2 and Ile at P1′ in the C1s substrate reduced the rate of C1r activation. Substituting a Gln residue into the P2 of the activation site of MASP-3, a protein with similar domain structure to C1s that is not normally cleaved by C1r, enabled efficient activation of this enzyme. Molecular dynamics simulations and structural modeling of the interaction of the C1s activation peptide with the active site of C1r revealed the molecular mechanisms that particularly underpin the specificity of the enzyme for the P2 Gln residue. The complement control protein domains of C1r also made important contributions to efficient activation of C1s by this enzyme, indicating that exosite interactions were also important. These data show that C1r specificity is well suited to its cleavage targets and that efficient cleavage of C1s is achieved through both active site and exosite contributions.     

The Effects of Exercise Training in Addition to Energy Restriction on Functional Capacities and Body Composition in Obese Adults during Weight Loss: A Systematic Review

Background

Obesity is associated with impairments of physical function, cardiovascular fitness, muscle strength and the capacity to perform activities of daily living. This review examines the specific effects of exercise training in relation to body composition and physical function demonstrated by changes in cardiovascular fitness, and muscle strength when obese adults undergo energy restriction.

Methods

Electronic databases were searched for randomised controlled trials comparing energy restriction plus exercise training to energy restriction alone. Studies published to May 2013 were included if they used multi-component methods for analysing body composition and assessed measures of fitness in obese adults.

Results

Fourteen RCTs met the inclusion criteria. Heterogeneity of study characteristics prevented meta-analysis. Energy restriction plus exercise training was more effective than energy restriction alone for improving cardiovascular fitness, muscle strength, and increasing fat mass loss and preserving lean body mass, depending on the type of exercise training.

Conclusion

Adding exercise training to energy restriction for obese middle-aged and older individuals results in favourable changes to fitness and body composition. Whilst weight loss should be encouraged for obese individuals, exercise training should be included in lifestyle interventions as it offers additional benefits.     

Forced activation of Stat5 subjects mammary epithelial cells to DNA damage and preferential induction of the cellular response mechanism during proliferation

Parity‐dependent adenocarcinoma tumors developed in postestropausal transgenic mice expressing a constitutively active Stat5 variant (STAT5ca) in their mammary gland. These tumors maintained elevated expression levels of genes regulating the cellular DNA damage response (DDR) mechanism, compared to the intact gland. No correlation with STAT5ca expression was observed for these genes in the established tumors. However, activated Stat5a in individual cells of the rarely and earlier developed hyperplasia was associated with induced Chk2 activity. Deregulated Stat5 may already cause DNA damage during the fertile period. This hypothesis and the specific vulnerable stage were further studied in mammary epithelial cells that were stably transfected with β‐lactoglobulin (BLG)/STAT5ca and exposed to a reproduced reproductive cycle. During the pregnancy‐like proliferative state, STAT5ca expression was induced by the added lactogenic hormones. Production of reactive oxygen species, rather than proliferation, served as the primary mediator of DNA damage and cellular DDR. Differentiated cells expressed higher levels of STAT5ca and retained the DNA nicks. However, the elevated expression of the genes involved in DDR was downregulated. Higher levels of DNA damage were also detected in the mammary gland of transgenic mice expressing the BLG/STAT5ca during pregnancy and lactation. However, the relative number of damaged cells was much lower than that in the reproduced in vitro stages and the insults were generally associated with apoptosis and DDR. This study implicates pregnancy as the vulnerable stage for deregulated Stat5 activity, and demonstrates that DNA insults in viable differentiated mammary epithelial cells are ignored by the DDR mechanism. J. Cell. Physiol. 226: 616–626, 2011. © 2010 Wiley‐Liss, Inc.