Miracle-dz/UniFAR-FTUs huggingface dataset:
Selection of Core SSR Loci by Using Chinese Autumn Soybean

In this study Chinese autumn soybean were used as materials, and their genomic DNAs were analyzed with SSR markers. The objective was to obtain a set of representative SSR loci for analysis of genetic diversity and DNA fingerprinting in Chinese soybean germplasm. Therefore, it will be useful for enhancing management and utilization of Chinese soybean germplasm resources. Ninety six loci from 200 loci were screened out by resolving alleles with agarose gels, and then detected alleles with silver stained polyarylamide gels. A set of 60 representative SSR loci was obtained which had following characteristics:(1) they distributed on 20 integrated linkage groups with an average of 50 cM genetic distances between two adjacent loci,including 5 loci on each of C 2 and O, 2 loci on each of G,K and M,and 3 loci on each of the other 15 linkage groups;(2) Defined the relationship among Chinese autumn soybeans were greatly significant correlation with that using 96 loci(r= 0.910 *);(3)They showed a higher level of polymorphism with an average of 8.8 alleles and 0.773 value of polymorphism informative content (PIC) per locus detected in the 80 autumn soybeans;(4) Each of them had single loci in majority of the 80 autumn soybeans and exhibited specificity;(5)Different alleles per locus were easy to discriminate and revealed approximately uniform amplified intensity under the same PCR conditions. This set of core SSR loci will play a very important role in establishment of Chinese soybean core collection.
The effects of salinity and flooding on Phragmites australis

1. Phragmites australis buds with attached rhizomes were planted in PVC tubes and grown under various salinity and flooding conditions in a greenhouse for one growing season. 2. P. australis buds did not emerge from cores flooded to the soil surface, regardless of salinity, indicating a possible lack of oxygen transport to below-ground structures. 3. Density, height and biomass were all negatively affected by increasing salinity (0, 15 and 30 g l1), as were recoverable underground reserves (RUR) and rhizome non-structural carbohydrate concentration (RNCC). 4. Height, biomass, RUR and RNCC decreased with increased flooding level (20 and 10 cm of the core above water level). 5. Cutting and flooding P. australis plants also reduced growth and survival in a separate outdoor experiment. When plants were cut and the stubble flooded with brackish (salinity 10gl-') water, there was no further above-ground growth for 18 months, i.e. all plants apparently died. 6. The results suggest that it may be possible to control P. australis stands in marshes by controlling water tables/flooding and salinity levels.
Planning High-Level Paths in Hostile, Dynamic, and Uncertain Environments

This paper introduces and studies a graph-based variant of the path planning problem arising in hostile environments. We consider a setting where an agent (e.g. a robot) must reach a given destination while avoiding being intercepted by probabilistic entities which exist in the graph with a given probability and move according to a probabilistic motion pattern known a priori. Given a goal vertex and a deadline to reach it, the agent must compute the path to the goal that maximizes its chances of survival. We study the computational complexity of the problem, and present two algorithms for computing high quality solutions in the general case: an exact algorithm based on Mixed-Integer Nonlinear Programming, working well in instances of moderate size, and a pseudo-polynomial time heuristic algorithm allowing to solve large scale problems in reasonable time. We also consider the two limit cases where the agent can survive with probability 0 or 1, and provide specialized algorithms to detect these kinds of situations more efficiently.
A NEW SPECIES OF PSEUDOTRAPELUS (AGAMIDAE, SAURIA) FROM DHOFAR, OMAN

A new species of Pseudotrapelus from Dhofar, Oman is described. It differs morphologically from P. sinaitus in that its 3rd toe is much longer than its 4th one (11–13 lamellae under the 4th toe), from P. aqabensis and P. neumanni in that it has one row of 6 – 8 unseparated precloacal pores in males. This new species also has 15% genetic divergence from P. sinaitus and 10% from P. aqabensis (COI). Taxonomic relationships of Arabian Peninsula Pseudotrapelus need further investigations.
Virulence of the entomopathogenic fungus Lecanicillium longisporum against the greenhouse whitefly, Trialeurodes vaporariorum and its parasitoid Encarsia formosa

ABSTRACT Understanding the interactions among biological control agents, such as competition for the same host in intraguild predation, is a key component for successful biological control strategies. The pathogenic ability of Lecanicillium longisporum (Petch) Zare and Gams (Ascomycota: Clavicipitaceae) against the greenhouse whitefly, Trialeurodes vaporariorum (Westwood) (Hemiptera: Aleyrodidae) and its parasitoid, Encarsia formosa Gahan (Hymenoptera: Aphelinidae) was assessed. Treatment with six serial deposition rates of fungal conidia on cucumber leaf surface indicated that whitefly mean mortalities for isolates LRC190, LRC216 and LRC229 reached 61, 79 and 54% at 2.6 × 107 conidia/mm2, respectively. Median lethal time (LT50) values for isolates LRC190, LRC216 and LRC229 were 6.2, 4.9 and 6.9 days, and median lethal dose (LD50) values were 1.2 × 106, 2.9 × 105 and 6.9 × 106 conidia/mm2, respectively. The number of surviving parasitoid larvae, pupae and adults decreased with increasing concentrations of fungus, and earlier developmental stages of parasitoid were affected negatively by fungal treatment. Reproductive capacity and longevity of female parasitoid emerging from fungus-treated hosts were not affected by fungus treatment. These results indicate that correct timing of fungal and parasitoid application may mitigate the negative effects due to direct competition for the same host. In this regard, treatment with fungi in later immature stages of the parasitoid was generally positive with minimum risks of deleterious effects.
A Study showing antagonistic effect of Lactobacilli casei and Lactobacilli sporogenesis against some common pathogens- in vitro

Microorganisms that beneficially affect the host are called probiotics. Lactobacilli are the most widely distributed probotic strains within the Lactic acid bacteria (LAB) group. Lactobacillus sp. are Gram positive bacilli that are catalase negative and believed to be safe because they have been established as the normal flora in fermented food for a long time, so they have great potential to be used as a bio preservative and these preserving effects of lactic acid bacteria are due to the production of antimicrobial agents such as such as diacetyl, hydrogen peroxide, bacteriocins lactic and other organic acids and other related substances (Desmazeaud and Cogan, 1996; Cocolin et al., 2007; Quwehand and Vesterlund, 2004 ). Several Lactobacillus strains are in important dairy culture starter and used for the manufacture of fermented food (Fitzsimmons et al., 1999; Badis et al., 2004). The antimicrobial effects of Lactobacilli lead to inhibition of the growth of potential pathogens through a variety of mechanisms including their capacity to decrease luminal pH and secrete bactericidal proteins and inhibit bacterial adhesion to epithelial cells. Lactobacillus casei is a species of genus Lactobacilli found in the human intestine and mouth. ISSN: 2319-7706 Volume 4 Number 6 (2015) pp. 36-40 http://www.ijcmas. com
Ubiquitylation regulates CD4+ T cell activation and effector differentiation to shape the immune response

Ubiquitylation of cellular proteins alters protein function and half-life to impact cell signaling and fate decisions. In T cells, ubiquitylation events, mediated by substrate-specific E3 ubiquitin ligases and deubiquitylating enzymes, can promote or limit T cell activation and alter function. For example, the catalytic E3 ligase Nedd4 is required for robust T cell activation, while a related Nedd4 family member, Itch, negatively regulates T cell signaling. Several Nedd4 family ligases are activated by binding Nedd4 family interacting protein 1 (Ndfip1) and/or Ndfip2. I have determined that ligase activity depends non-redundantly on both Ndfip1 and Ndfip2. Unlike Ndfip1, Ndfip2 is not a prominent negative regulator of T cell activation or TH2 polarization. However, loss of Ndfip2 in Ndfip1 deficient cells leads to a T cell-intrinsic expansion of pathogenic TH2 effector cells. Defining substrates of critical ubiquitylation events in activated T cells can enhance our understanding of T cell function in both health and disease. Thus, I took a targeted approach to identify new substrates of Nedd4 family catalytic E3 ligases in activated T cells, developing a proteomics workflow for unbiased quantification of differential ubiquitylation in T cells. I identified Jak1 as a substrate for Ndfip-dependent E3 ligases, and determined that Ndfip-mediated Jak1 degradation limits cytokine signaling during TCR engagement. Having successfully used proteomics for substrate-identification, I considered the utility of quantitative proteomics in globally assessing ubiquitylation in T cells. I developed a mass spectrometry-based approach pairing immunoprecipitation of “ubiquitin remnant” peptides (with di-glycine modified lysine residues) and whole proteome analysis to quantify changes in protein-specific ubiquitylation in activated CD4+ T cells. I observed dynamic changes in ubiquitylation of hundreds of proteins, including key signal transducers, during TCR stimulation. Comparing changes in ubiquitylation with changes in protein abundance in stimulated CD4+ T cells I propose to identify proteins for which ubiquitylation is tightly linked to protein abundance and/or function in a signal-dependent manner. This profiling effort, in combination with targeted studies similar to those undertaken to identify substrates of Ndfip-dependent E3 ligases, will facilitate a more global understanding of how ubiquitylation events in activated T cells finely tune the T cell response. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Paula M. Oliver
The Exxon Valdez oil spill disrupted the breeding of black oystercatchers

I evaluated the effects of the Exxon valdez oil spill on black oystercatchers (Haematopus bachmani) by comparing the breeding success of pairs inhabiting oiled and unoiled islands in Prince William Sound, Alaska. I hypothesized that direct and indirect consequences of shoreline oiling would disrupt the breeding and foraging behavior of oystercatchers. Fewer pairs occupied (36%) or maintained nests on (34%) oiled Green Island after the spill in 1989 than in 1991, whereas the number of pairs and nests remained similar on unoiled Montague Island during the same period. In 1989, chicks disappeared from nests at a greater rate (42%) on Green Island than from nests on Montague Island; disturbance associated with cleanup operations also reduced productivity on Green Island in 1990. By 1991, productivity on Green Island (1.3 chicks/pair) exceeded that on Montague Island (0.6 chicks/pair). In 1989, mortality of bay mussels (Mytilus trossulus) was significantly higher (P = 0.003), and feeding rates of oystercatchers were significantly lower (P = 0.0002), on Green Island than on Montague Island. I concluded that the breeding of black oystercatchers was disrupted during 1989 and 1990 but had substantially recovered by 1991. Additional, intensive restoration actions probably are not needed for black oystercatchers to recover in areas affected by the spill.
House Fly Sex Pheromone: Enhancement of Mating Strike Activity by Combination of ( Z )-9-tricosene with Branched Saturated Hydrocarbons

The pheromone of the female house fly, Musca dornestica L. , that causes male flies to initiate copulation appears to be a mixture of unsaturated and saturated hydrocarbons. The most active unsaturated hydrocarbon among the ( Z )-9-alkenes present on the female was ( Z )-9-tricosene (muscalure). Methyl- and dimethyl-branched C27 and C29 alkanes were responsible for the activity in the saturated hydrocarbons. When synthetic branched alkanes were combined with ( Z )-9-tricosene, 13-methylnonacosane, and 4,8-dimethylheptacosane produced the greatest amount of mating strike response.
What Parasitic Gaps Reveal about Overlapping Paths and Multiple Specifier Formation0

This paper investigates sentences in which A′-movement paths overlap. I argue that the behavior of parasitic gaps in such contexts, when examined in terms of predictions from Nissenbaum (2000), reveals evidence for the following generalization: If two A′moving phrases XP1 and XP2 form specifiers of a phase YP such that XP1 c-commands XP2, then XP1 c-commands XP2 in all subsequent positions these phrases occupy. I argue that this result emerges from a theory in which cross-phasal movement is constrained by cyclic spell-out and linearization preservation, with consequences for topics such as the path containment condition and the nature of multiple specifier formation.
Spatial structure and development of Paspalum vaginatum (Poaceae): an architectural approach

Paspalum vaginatum Sw. is a perennial grass originating from tropical and subtropical regions worldwide that plays important ecological and utilitarian roles such as dune stabilisation and erosion control, and is used as a lawn and forage plant. The vegetative morphology of shoots was studied using an architectural approach with the aim of identifying constant features that characterise the architectural unit of this species, describing its developmental dynamics, and exploring the morphological basis of its extraordinary plasticity and adaptability to multiple ecological conditions. Plants of two ecotypes were cultivated in pots outdoors during two consecutive summers, and axes of different branching order were marked for periodical observations. Leaf typology, orientation and position of branches and occurrence and position of reproductive axes were considered. The basic growth pattern arises as a result of extensive plagiotropic growth of axes up to fourth branching order, which initially behave as stolons but can become rhizomes insofar the soil cover increases. Orthotropic floriferous axes up to fifth order develop at the axils of stolons, which can form ‘daughter’ clumps by basal tillering. Despite quantitative differences, both ecotypes share similar architectural features. Architectural analysis provides the basis to predict space occupation dynamics under different environmental conditions of growth.
Climate-Dependent Groundwater Discharge on Semi-Arid Inland Ephemeral Wetlands: Lessons from Holocene Sediments of Lagunas Reales in Central Spain

Wetlands are environments whose water balance is highly sensitive to climate change and human action. This sensitivity has allowed us to explore the relationships between surface water and groundwater in the long term as their sediments record all these changes and go beyond the instrumental/observational period. The Lagunas Reales, in central Spain, is a semi-arid inland wetland endangered by both climate and human activity. The reconstruction of the hydroclimate and water levels from sedimentary facies, as well as the changes in the position of the surface water and groundwater via the record of their geochemical fingerprint in the sediments, has allowed us to establish a conceptual model for the response of the hydrological system (surface water and groundwater) to climate. Arid periods are characterized by low levels of the deeper saline groundwater and by a greater influence of the surface freshwater. A positive water balance during wet periods allows the discharge of the deeper saline groundwater into the wetland, causing an increase in salinity. These results contrast with the classical model where salinity increases were related to greater evaporation rates and this opens up a new way of understanding the evolution of the hydrology of wetlands and their resilience to natural and anthropogenic changes.
RNA-seq analysis reveals distinct splenic response of two chickens lines to Newcastle disease virus

Leghorn 2 dpi Leghorn 6 dpi Jibin Zhang1, Michael G. Kaiser, Melissa S. Herrmann 1, Rodrigo A. Gallardo2, David A. Bunn3, Huaijun Zhou3, Susan J Lamont1 1 Department of Animal Science, Iowa State University, Ames, IA 50010 USA 2 Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616 3 Department of Animal Science, University of California, Davis, CA 95616
Biogeography of two southwest American oaks in relation to atmospheric dynamics

A causal relationship between Holocene patterns of plant distributions in the American Southwest and shifts in atmospheric flow structure has been inferred, but has yet to be demonstrated. To investigate this inferred relationship, seedlings of Quercus gambelii were transplanted along various local microhabitat gradients and regional air mass gradients and assessed for patterns of seedling establishment. The primary cause of seedling mortality appeared to be summer drought stress, which paralleled the latitudinal gradient of the 'Arizona monsoon'. The 'Arizona monsoon' air mass gradient produces an increasing probability of summer drought stress with increasing latitude, while the 'polar front' air mass gradient produces an increasing probability of winter and spring cold stress with increasing latitude. We hypothesize that the two gradients produce, as a function of increasing latitude, convergent upper and lower elevational limits of Q. gambelii. The results of this elevational convergence appear to be a virtual absence of oak seedling establishment near the species' northern limits and a gradual senescence of long-lived clones from spring freeze stress when followed by summer drought stress. These conclusions have been extended to the biogeography of Q. turbinella through growth chamber experiments on the comparative drought physiology of seedlings of the two species and through previous work on their associated biogeographic patterns. Thus, the northern ecotones of Q. gambelii and Q. turbinella, appear to be primarily caused by the combination of spring freeze stress and summer moisture stress, rather than freeze stress alone, as previously proposed. We report systematic temporal and spatial shifts in the two air mass gradients, between warming and cooling trends, which can account for the Holocene biogeographic history of the two oak species and, in part, the observed spatial and temporal variations in oak morphology and oak/pine community structure.
Investigation of mesenchymal stem cell response to bioactive nanotopography

Mesenchymal stem cells (MSC) are multipotent stem cells that have much potential for application in regenerative medicine, with their ability to self-renew and to undergo differentiation into several lineages, including those that comprise fat, bone, and cartilage. Studies on MSCs have mainly focused on exploiting their capacity to differentiate, rather than self-renewal, yet understanding of the latter process is pivotal for the expansion of these cells to sufficient numbers for use in future clinical treatments. Aspects of MSC behaviour can be induced by culture on nanopatterned substrates, known as nanotopography. Use of established nanopit features, in arrangements known to maintain MSC multipotency over long periods in culture (SQ), in addition to an osteogenic promoting arrangement (NSQ), were used as a tool to study self-renewal in MSCs, and begin to elucidate some of the potential mechanisms underlying the effects of the nanotopographies on stem cell fate. This study utilised patient-specific primary MSCs derived from bone marrow, which were optimised in terms of initial seeding density, to make efficient use of our nanotopographies. Once the fundamental details pertaining to optimal conditions for use of the substrates and cells were established, exploration of changes in metabolism, cell cycle and gene expression were carried out. Results indicated that MSCs on SQ contained more unsaturated metabolites, and that cell cycle may be altered, which warranted further investigation. Further study identified some differences in cell cycle regulatory proteins when compared to NSQ and flat controls. Further inferences were achieved by analysis of transcript abundances and differential expression, supporting the hypothesis of a heterogeneous population existing on NSQ, and activation of pathways linked to differentiation, consistent with previous work. A greater percentage of MSCs on SQ were shown to be in the early G0/G1 stages of the cell cycle in comparison to those on flat, suggesting that cell cycle is altered and further establishes a link between self-renewal and cell cycle regulation. Nanotopography was assessed for a novel application, namely the potential of SQ to reprogram differentiating MSCs. Nanotopography was used to induce and reverse the onset of osteogenic differentiation, and evaluated in conjunction with the addition of an epigenetic modifier, valproic acid. Results did not indicate that nanotopographical cues were able to reprogram MSCs. However, promising indications that stem cell marker STRO-1 levels increased, is consistent with SQ being a surface that maintains ‘stemness’ and multipotency of MSCs with culture in vitro.
A STUDY OF LETHAL EFFECT OF PURE N_2 ATMOSPHERE TO STOSTORED GRAIN INSECT

This study conducted a bioassay to major stored grain pests under extreme pure N2,30℃±1℃ and 75%±5%RH atmosphere.LT50 values of maize weevil(Sitophilus zeamais Motschulsky),rice weevil(Sitophilus oryzae(Linnaeus)),large grain borer(Rhyzopertha dominica(Fabricius)),red flour beetle(Tribolium castaneum(Herbst))(Zhongshan strain),confused flour beetle(Tribolium confusum Jacquelin du Val),red flour beetle(Tribolium castaneum(Herbst))(Yiyang strain),book louse(Liposcelis bostrychophila Badonnel) and saw flour beetle(Oryzaephilus surinamensis(Linnaeus)) are 34.0h、32.5h、32.5h、13.9h、13.4h、12.5h、5.4h and 5.1h. Which mean a great variety of tolerance of different insects to this low O2 atmosphere.
Optimal Regulation of Variable Speed Pumps in Sewer Systems

In this work, the optimal regulation of variable speed pump (VSP) was solved by means of two optimization algorithms: a mixed-integer optimizer based on the BONMIN (Basic Open-Source Nonlinear Mixed Integer Programming) package, and an original hybrid genetic algorithm (GA) called GA–Powell’s direction set method (PDSM), which employs a derivative free inner optimizer, that is, the Powell’s direction set method (PDSM). The obtained results show how the use of a strategy based on the optimal regulation of VSP allows to obtain huge energy cost savings. The analysis of the results shows that the regulation of the plant does not apparently follow a general rule.