Allohexaploid pearl millet x elephantgrass population potential for a recurrent selection program

The objective of this work was to evaluate the potential of allohexaploid pearl millet x elephantgrass (HGL) population for a recurrent selection program through open-pollinated progenies. Seventy-eight progenies, one representative sample of the population, and two commercial cultivars, Pioneiro and Paraíso, were evaluated in a 9x9 triple lattice design, in two sites. Plant height and dry matter yield were evaluated in three and four cuts, respectively. For plant height, the 17 best progenies were similar to both commercial controls, while for dry matter yield they were higher than 'Paraíso' and lower than 'Pioneiro'. The correlation between progenies and cuts indicated that the fourth cut represents the mean of all cuts, and the possibility of using early selection. Heritability estimates considering cuts and sites were 56.9% for plant height and 58.8% for dry matter yield, and the expected response to selection was 23.4% for dry matter yield and 18.1% for plant height. These results demonstrate the promising HGL population potential for a recurrent selection program.

Glucocorticoid-induced tumor necrosis factor receptor is a p21Cip1/WAF1 transcriptional target conferring resistance of keratinocytes to UV light-induced apoptosis.

Glucocorticoid-induced tumor necrosis factor receptor (GITR) is a member of the tumor necrosis factor receptor superfamily, is expressed in T lymphocytes, and exerts an anti-apoptotic function in these cells. We reported that GITR is also highly expressed in the skin, specifically in keratinocytes, and that it is under negative transcriptional control of p21(Cip1/WAF1), independently from the cell cycle. Although GITR expression is higher in p21-deficient keratinocytes and skin, it is down-modulated with differentiation and in response to UVB. The combined analysis of keratinocytes with increased GITR expression versus normal keratinocytes and skin of mice with a disruption of the GITR gene indicates that this protein protects keratinocytes from UVB-induced apoptosis both in vitro and in vivo.

Dual inhibitors of beta-amyloid aggregation and acetylcholinesterase as multi-target anti-Alzheimer drug candidates

Notwithstanding the functional role that the aggregates of some amyloidogenic proteins can play in different organisms, protein aggregation plays a pivotal role in the pathogenesis of a large number of human diseases. One of such diseases is Alzheimer"s disease (AD), where the overproduction and aggregation of the β-amyloid peptide (Aβ) are regarded as early critical factors. Another protein that seems to occupy a prominent position within the complex pathological network of AD is the enzyme acetylcholinesterase (AChE), with classical and non-classical activities involved at the late (cholinergic deficit) and early (Aβ aggregation) phases of the disease. Dual inhibitors of Aβ aggregation and AChE are thus emerging as promising multi-target agents with potential to efficiently modify the natural course of AD. In the initial phases of the drug discovery process of such compounds, in vitro evaluation of the inhibition of Aβ aggregation is rather troublesome, as it is very sensitive to experimental assay conditions, and requires expensive synthetic Aβ peptides, which makes cost-prohibitive the screening of large compound libraries. Herein, we review recently developed multi-target anti-Alzheimer compounds that exhibit both Aβ aggregation and AChE inhibitory activities, and, in some cases also additional valuable activities such as BACE-1 inhibition or antioxidant properties. We also discuss the development of simplified in vivo methods for the rapid, simple, reliable, unexpensive, and high-throughput amenable screening of Aβ aggregation inhibitors that rely on the overexpression of Aβ42 alone or fused with reporter proteins in Escherichia coli.

The N-terminal domain of Plasmodium falciparum circumsporozoite protein represents a target of protective immunity.

The N-terminal domain of the circumsporozoite protein (CSP) has been largely neglected in the search for a malaria vaccine in spite of being a target of inhibitory antibodies and protective T cell responses in mice. Thus, in order to develop this region as a vaccine candidate to be eventually associated with other candidates and, in particular, with the very advanced C-terminal counterpart, synthetic constructs representing N- and C-terminal regions of Plasmodium falciparum and Plasmodium berghei CSP were administered as single or combined formulations in mice. We show that the antisera generated against the combinations inhibit sporozoite invasion of hepatocytes in vitro better than antisera against single peptides. Furthermore, two different P. falciparum CSP N-terminal constructs (PfCS22-110 and PfCS65-110) were recognized by serum samples from people living in malaria-endemic regions. Importantly, recognition of the short N-terminal peptide (PfCS65-110) by sera from children living in a malaria-endemic region was associated with protection from disease. Taken together, these results underline the potential of using such fragments as malaria vaccine candidates.

The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC

Positive selection is widely estimated from protein coding sequence alignments by the nonsynonymous-to-synonymous ratio omega. Increasingly elaborate codon models are used in a likelihood framework for this estimation. Although there is widespread concern about the robustness of the estimation of the omega ratio, more efforts are needed to estimate this robustness, especially in the context of complex models. Here, we focused on the branch-site codon model. We investigated its robustness on a large set of simulated data. First, we investigated the impact of sequence divergence. We found evidence of underestimation of the synonymous substitution rate for values as small as 0.5, with a slight increase in false positives for the branch-site test. When dS increases further, underestimation of dS is worse, but false positives decrease. Interestingly, the detection of true positives follows a similar distribution, with a maximum for intermediary values of dS. Thus, high dS is more of a concern for a loss of power (false negatives) than for false positives of the test. Second, we investigated the impact of GC content. We showed that there is no significant difference of false positives between high GC (up to similar to 80%) and low GC (similar to 30%) genes. Moreover, neither shifts of GC content on a specific branch nor major shifts in GC along the gene sequence generate many false positives. Our results confirm that the branch-site is a very conservative test.

Iowa Pavement Asset Management Decision-Making Framework & Pavement Treatment Selection Tool for Local Agencies, TR-651, 2015

Most local agencies in Iowa currently make their pavement treatment decisions based on their limited experience due primarily to lack of a systematic decision-making framework and a decision-aid tool. The lack of objective condition assessment data of agency pavements also contributes to this problem. This study developed a systematic pavement treatment selection framework for local agencies to assist them in selecting the most appropriate treatment and to help justify their maintenance and rehabilitation decisions. The framework is based on an extensive literature review of the various pavement treatment techniques in terms of their technical applicability and limitations, meaningful practices of neighboring states, and the results of a survey of local agencies. The treatment selection framework involves three different steps: pavement condition assessment, selection of technically feasible treatments using decision trees, and selection of the most appropriate treatment considering the return-on-investment (ROI) and other non-economic factors. An Excel-based spreadsheet tool that automates the treatment selection framework was also developed, along with a standalone user guide for the tool. The Pavement Treatment Selection Tool (PTST) for Local Agencies allows users to enter the severity and extent levels of existing distresses and then, recommends a set of technically feasible treatments. The tool also evaluates the ROI of each feasible treatment and, if necessary, it can also evaluate the non-economic value of each treatment option to help determine the most appropriate treatment for the pavement. It is expected that the framework and tool will help local agencies improve their pavement asset management practices significantly and make better economic and defensible decisions on pavement treatment selection.

14.1T magnetic resonance spectroscopic evaluation of metabolic changes in the mouse striatum following transient middle cerebral artery occlusion

Magnetic resonance imaging (MRI) and spectroscopy (MRS) allow establishing theanatomical evolution and neurochemical profiles of ischemic lesions. However onlylimited MRS studies have been reported to-date in mice due to the challenges ofMRS in small organs. The aim of the current work was to study the neurochemicaland imaging sequelae of ischemic stroke in a mouse model in a horizontal bore14.1 Tesla system.ICR-CD1 mice were subjected to 30 minute transient middle cerebral artery occlusion.The extent of the lesion was determined by MRI. The neurochemical profileconsisting of the concentrations of 22 metabolites was measured longitudinallyfollowing the recovery from ischemia at 3, 8 and 24h in the striatum.Our model produced very reproducible striatal lesions which began to appear onT2-weighted images 8h after ischemia. At 24h, they were well established andtheir size correlated with lesions measured by histology. Profound changes couldbe observed in the neurochemical profiles of the core of the striatal lesions as earlyas 3h post-ischemia, in particular, we observed elevated lactate levels, decreases inthe putative neuronal marker N-acetyl-aspartate and in glutamate, and a transienttwo-fold glutamine increase, likely linked to excitotoxic release of glutamate andconversion to glutamine. With further ischemia evolution, other changes appearedat later time-points, mainly decreases of metabolites, consistent with disruption ofcellular function. It is interesting to note that glutamine tended to return to basallevels at 24h.We conclude that early changes in markers of energy metabolism, glutamate excitotoxicityand neuronal viability can be detected with high precision non-invasively inmice following stroke. Such investigations should lead to a better understanding andinsight into the sequential early changes in the brain parenchyma after ischemia,which could be used e.g. for identifying new targets for neuroprotection.

Cross validation of experts versus registration methods for target localization in deep brain stimulation.

In the last five years, Deep Brain Stimulation (DBS) has become the most popular and effective surgical technique for the treatent of Parkinson's disease (PD). The Subthalamic Nucleus (STN) is the usual target involved when applying DBS. Unfortunately, the STN is in general not visible in common medical imaging modalities. Therefore, atlas-based segmentation is commonly considered to locate it in the images. In this paper, we propose a scheme that allows both, to perform a comparison between different registration algorithms and to evaluate their ability to locate the STN automatically. Using this scheme we can evaluate the expert variability against the error of the algorithms and we demonstrate that automatic STN location is possible and as accurate as the methods currently used.

Tenascin-C is a novel RBPJkappa-induced target gene for Notch signaling in gliomas.

Tenascin-C (TNC) expression is known to correlate with malignancy in glioblastoma (GBM), a highly invasive and aggressive brain tumor that shows limited response to conventional therapies. In these malignant gliomas as well as in GBM cell lines, we found Notch2 protein to be strongly expressed. In a GBM tumor tissue microarray, RBPJk protein, a Notch2 cofactor for transcription, was found to be significantly coexpressed with TNC. We show that the TNC gene is transactivated by Notch2 in an RBPJk-dependent manner mediated by an RBPJk binding element in the TNC promoter. The transactivation is abrogated by a Notch2 mutation, which we detected in the glioma cell line Hs683 that does not express TNC. This L1711M mutation resides in the RAM domain, the site of interaction between Notch2 and RBPJk. In addition, transfection of constructs encoding activated Notch2 or Notch1 increased endogenous TNC expression identifying TNC as a novel Notch target gene. Overexpression of a dominant negative form of the transcriptional coactivator MAML1 or knocking down RBPJk in LN319 cells led to a dramatic decrease in TNC protein levels accompanied by a significant reduction of cell migration. Because addition of purified TNC stimulated glioma cell migration, this represents a mechanism for the invasive properties of glioma cells controlled by Notch signaling and defines a novel oncogenic pathway in gliomagenesis that may be targeted for therapeutic intervention in GBM patients.

Selection strategies of segregant soybean populations for resistance to Asian rust

The objective of this work was to identify the best selection strategies for the more promising parental combinations to obtain lines with good resistance to soybean Asian rust (Phakopsora pachyrhizi). Two experiments were carried out in the field during the 2006/2007 and 2007/2008 growing seasons, to determine the percentage of infected leaf area of individual plants of five parents and their segregant F2 and F3 populations. The data obtained indicates that additive genetic variance predominates in the control of soybean resistance to Asian rust, and that the year and time of assessment do not significantly influence the estimates of the genetic parameters obtained. The narrow-sense heritability (h²r) ranged from 23.12 to 55.83%, and indicates the possibility of successful selection of resistant individuals in the early generations of the breeding program. All the procedures used to select the most promising populations to generate superior inbred lines for resistance to P. pachyrhizi presented similar results and identified the BR01-18437 x BRS 232 population as the best for inbred line selection.

Leaf plasticity in successive selection cycles of 'Saracura' maize in response to periodic soil flooding

The objective of this work was to assess the effect of successive selection cycles on leaf plasticity of 'Saracura' maize BRS-4154 under periodical flooding in field conditions. Soil flooding started at the six-leaf stage with the application of a 20-cm depth water layer three times a week. At flowering, samples of leaves were collected and fixed. Paradermic and transverse sections were observed under photonic microscope. Several changes were observed throughout the selection cycles, such as modifications in the number and size of the stomata, higher amount of vascular bundles and the resulting decrease of the distance between them, smaller diameter of the metaxylem, decrease of cuticle and epidermis thickness, decrease of number and size of bulliform cells, increase of phloem thickness, smaller sclerenchyma area. Therefore, the successive selection cycles of 'Saracura' maize resulted in changes in the leaf anatomy, which might be favorable to the plant's tolerance to the intermittent flooding of the soil.

Habitat fragmentation, ecology and sexual selection in forest bird species in Monteverde, Costa Rica

Abstract Forest fragmentation is often associated with local extinction and changes in species abundance patterns. The main topic of this thesis is the effect of forest fragmentation on birds in Monteverde, Costa Rica. This thesis also studies aspects of sexual selection and ecology of Long-tailed Manakins, Chiroxiphia Linearis. Chapter 1 investigates bird species assemblages in two degrees of forest fragmentation. It is shown that the distribution, abundance and diversity of forest bird species are strongly influenced by the amount of forest in the landscape matrix. Presence of cattle within the forest influences the presence of some bird species. The prevalence and intensity of ticks and blood parasites on birds in relation to fragmentation is described in Chapter 2. Overall tick prevalence is 3%. Understory birds are significantly more infested with ticks than species at intermediate heights. Tick prevalence on birds does not differ significantly between two degrees of forest fragmentation and individual tick loads tend to be higher in High- than in Low-fragmentation sites. Infestations by the blood parasites Haemoproteus sp. was low except in white-eared ground sparrow, Melozone leucotis, that is 28% and is significantly higher in High- than in Low-fragmentation sites. In chapter 3 results on the ecology and habitat movements of the Bare-necked Umbrellabird, Cephalopterus glabricollis, are presented. The abundance of umbrellabirds at high elevations during the breeding season coincides with the highest peak of fruit abundance. Birds leave the protected area during the non-breeding season moving to unprotected forest fragments. In chapter 4 ontogenetic changes in feather morphology through sexual maturity in Long-tailed Manakins are described. In adult males, rectrices length is positively correlated to testis volume. Changes in male morphology during ontogeny in the long-tailed manakin appear to be associated with their specific-display behaviours. Significant interpopulation differences in the morphology of Long-tailed Manakins are shown in chapter 5. These differences are more accentuated in morphological traits related to flight displays. A field experiment demonstrates that long rectrices impose flying costs for males and females. A reduction in flying ability was found to be strongest in males from a population presenting the highest degree of sexual dimorphism. Résumé La fragmentation des forêts est souvent associée avec des modifications dans l'abondance des espèces et des extinctions locales. Le thème principale de cette thèse est l'étude de l'effet de la fragmentation des forêts sur les oiseaux de Monteverde, Costa Rica. Elle décrit par ailleurs certains aspects de la sélection sexuelle et l'écologie du manakin à longue queue, Chiroxiphia linearis. Dans le Chapitre 1 je montre que la distribution, l'abondance et la diversité des assemblages d'oiseaux vivant dans la forêt sont fortement influencées pas le degré de fragmentation de celle ci. Par ailleurs, la présence ou l'absence de bétail dans les forêts influence la présence de certaines espèces d'oiseaux. Dans le chapitre 2 j'ai étudié la prévalence et l'intensité d'infestation par des tiques ainsi que la présence de parasites sanguins chez les oiseaux en relation avec la fragmentation des forêts. La prévalence globale de tiques est de 3 %, les oiseaux vivant au niveau du sol étaient plus souvent infectés par des tiques que les espèces se déplaçant à un niveau plus élevé. La prévalence de tiques sur les oiseaux n'était pas significativement différente entre les paysages avec différentes fragmentations. Les parasites sanguins du genre Haemoproteus sp. étaient présents à très basse fréquence à l'exception chez Melozone leucotis ou la prevalence était de 28% et significativement plus élevée chez les oiseaux vivant dans les forêts à forte fragmentation. Dans le Chapitre 3 je présente des résultats sur l'écologie et les mouvements entre habitats chez le "Bare-necked umbrellabird", Cephalopterus glabricollis. Cette espèce endémique du Costa Rica niche à haute altitude durant la période d'abondance des fruits et réalise une migration altitudinale vers des zones basses durant la saison de non reproduction. Dans le chapitre 4 je présente les changements ontogénétiques dans la morphologie du plumage des manakins à longue queue. Chez les mâles, les changements de morphologie semblent être associés avec leurs comportements de parade spécifiques. Dans le chapitre 5 je présente des différences morphologiques significative entre deux populations chez le manakin à longue queue et je montre que la capacité de vols chez les mâles est plus fortement influencée dans la population avec le degré de dimorphisme sexuel le plus prononcé.

Stable masking by H-2Dd cis ligand limits Ly49A relocalization to the site of NK cell/target cell contact.

Ly49A is an inhibitory receptor, which counteracts natural killer (NK) cell activation on the engagement with H-2D(d) (D(d)) MHC class I molecules (MHC-I) on target cells. In addition to binding D(d) on apposed membranes, Ly49A interacts with D(d) ligand expressed in the plane of the NK cells' membrane. Indeed, multivalent, soluble MHC-I ligand binds inefficiently to Ly49A unless the NK cells' D(d) complexes are destroyed. However, it is not known whether masked Ly49A remains constitutively associated with cis D(d) also during target cell interaction. Alternatively, it is possible that Ly49A has to be unmasked to significantly interact with its ligand on target cells. These two scenarios suggest distinct roles of Ly49A/D(d) cis interaction for NK cell function. Here, we show that Ly49A contributes to target cell adhesion and efficiently accumulates at synapses with D(d)-expressing target cells when NK cells themselves lack D(d). When NK cells express D(d), Ly49A no longer contributes to adhesion, and ligand-driven recruitment to the cellular contact site is strongly reduced. The destruction of D(d) complexes on NK cells, which unmasks Ly49A, is necessary and sufficient to restore Ly49A adhesive function and recruitment to the synapse. Thus, cis D(d) continuously sequesters a considerable fraction of Ly49A receptors, preventing efficient Ly49A recruitment to the synapse with D(d)+ target cells. The reduced number of Ly49A receptors that can functionally interact with D(d) on target cells explains the modest inhibitory capacity of Ly49A in D(d) NK cells. This property renders Ly49A NK cells more sensitive to react to diseased host cells.

In vitro negative selection of viral superantigen-reactive thymocytes by thymic dendritic cells.

Intrathymic expression of endogenous mouse mammary tumor virus (MMTV)-encoded superantigens (SAg) induces the clonal deletion of T cells bearing SAg-reactive T-cell receptor (TCR) Vbeta elements. However, the identity of the thymic antigen-presenting cells (APC) involved in the induction of SAg tolerance remains to be defined. We have analyzed the potential of dendritic cells (DC) to mediate the clonal deletion of Mtv-7-reactive TCR alphabeta P14 transgenic thymocytes in an in vitro assay. Our results show that both thymic and splenic DC induced the deletion of TCR transgenic double positive (DP) thymocytes. DC appear to be more efficient than splenic B cells as negatively selecting APC in this experimental system. Interestingly, thymic and splenic DC display a differential ability to induce CD4+ SP thymocyte proliferation. These observations suggest that thymic DC may have an important role in the induction of SAg tolerance in vivo.

Living with an imperfect cell wall: compensation of femAB inactivation in Staphylococcus aureus.

BACKGROUND: Synthesis of the Staphylococcus aureus peptidoglycan pentaglycine interpeptide bridge is catalyzed by the nonribosomal peptidyl transferases FemX, FemA and FemB. Inactivation of the femAB operon reduces the interpeptide to a monoglycine, leading to a poorly crosslinked peptidoglycan. femAB mutants show a reduced growth rate and are hypersusceptible to virtually all antibiotics, including methicillin, making FemAB a potential target to restore beta-lactam susceptibility in methicillin-resistant S. aureus (MRSA). Cis-complementation with wild type femAB only restores synthesis of the pentaglycine interpeptide and methicillin resistance, but the growth rate remains low. This study characterizes the adaptations that ensured survival of the cells after femAB inactivation. RESULTS: In addition to slow growth, the cis-complemented femAB mutant showed temperature sensitivity and a higher methicillin resistance than the wild type. Transcriptional profiling paired with reporter metabolite analysis revealed multiple changes in the global transcriptome. A number of transporters for sugars, glycerol, and glycine betaine, some of which could serve as osmoprotectants, were upregulated. Striking differences were found in the transcription of several genes involved in nitrogen metabolism and the arginine-deiminase pathway, an alternative for ATP production. In addition, microarray data indicated enhanced expression of virulence factors that correlated with premature expression of the global regulators sae, sarA, and agr. CONCLUSION: Survival under conditions preventing normal cell wall formation triggered complex adaptations that incurred a fitness cost, showing the remarkable flexibility of S. aureus to circumvent cell wall damage. Potential FemAB inhibitors would have to be used in combination with other antibiotics to prevent selection of resistant survivors.