Miracle-dz/UniFAR-FTUs huggingface dataset:
Mapping multiple QTL by combining linkage disequilibrium/linkage analysis in outbred populations

INTRODUCTION Based on a model for Marker-Assisted-BLUP breeding value estimates (Fernando and Grossman, 1989; Goddard, 1992), Grignola et al. (1996 a,b) developed a variance component mapping method for QTL. The method uses Residual Maximum likelihood (REML, Patterson and Thompson 1971) to estimate the QTL position, and assumes an infinite number of QTL alleles, but a simulation study showed that the method was robust to the actual number of alleles at the QTL (Grignola et al. 1996b). Variance component mapping uses a matrix of IBD probabilities between the QTL alleles as a correlation matrix to estimate the variance associated with the QTL and the (Residual) likelihood of the QTL model. Flanking markers were used to predict the IBD probabilities, where the base-population-alleles, i.e. the alleles of animals that had no parents in the data, were assumed unrelated (non-IBD). This method utilises linkage analysis.
A Role for Late Meristem Identity2 in the Reproductive Development of Arabidopsis

The switch from producing vegetative structures--branches and leaves--to producing reproductive structures-flowers--is a crucial developmental transition that significantly affects the reproductive success of flowering plants. In Arabidopsis thaliana , this transition is in large part controlled by the meristem identity regulator LEAFY (LFY) and the LFY direct target APETALA1 (AP1 ). The molecular mechanisms by which LFY orchestrates a precise and robust switch to flower formation is not well understood. Here we show that the R2R3 MYB transcription factor and direct LFY target LATE MERISTEM IDENTITY2 ( LMI2 ) plays a role in the meristem identity transition. Like LFY, LMI2 directly activates AP1 ; moreover LMI2 and LFY physically interact. LFY, LMI2 and AP1 are connected in a feed-forward and positive feedback loop network. We propose that these intricate regulatory interactions direct not only the precision of this critical developmental transition, but also contribute to its robustness and irreversibility. Subsequent to the meristem identity transition floral primordia undergo a growth period prior to floral organogenesis. This growth phase is maintained in part by the flowering-time genes SHORT VEGETATIVE PHASE (SVP), AGAMOUS-LIKE24 (AGL24) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1). Eventually, these flowering-time genes are downregulated by AP1. This downregulation results in the termination of meristematic activity and the onset of floral differentiation. In the absence of AP1, ectopic expression of SVP, AGL24 and SOC1 prevents differentiation and leads to the development of floral meristems in the axils of the first whorl organs. These floral meristems give rise to "branched" flowers. Here we present a possible role for LMI2 during floral primordia growth. Similar to SVP, AGL24 and SOC1, AP1 downregulates LMI2 in young flower primordia thus preventing the development of branched flowers. LMI2 acts in the same pathway as SVP, AGL24 and SOC1 and the similar expression patterns of LMI2 and SVP as well as the direct binding of LMI2 to SVP suggests a link between LMI2 and the pathways that maintain primordia growth during early flower development. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Biology First Advisor Doris Wagner
Understanding Osmoregulation and Immunity in Heteromyid Rodents Through Insights Gained from RNA-Seq

Marra, Nicholas J. Ph.D., Purdue University, December 2013. Understanding Osmoregulation and Immunity in Heteromyid Rodents Through Insights Gained from RNA-Seq. Major Professor: Dr. J. Andrew DeWoody. Understanding the genetic basis of adaptation is one of the central questions of evolutionary genetics. In the face of selective pressure, individuals with adaptive phenotypes survive and pass on their beneficial alleles that conferred this fitness advantage. Over sufficient time scales and under strong selection, differences accumulate between taxa in the form of physical and/or behavioral traits that have been shaped differently. By looking at the transcriptomes of related taxa we can identify sequence and regulatory differences that represent molecular signatures of these different selection regimes. When we study these differences between taxa that have evolved under opposing selective forces we can identify the genetic underpinnings of adaptation to those conditions. Species from the Heteromyidae form an exemplary system for studying the genetics of adaptation in a comparative framework. This new world family of rodents is comprised of three subfamilies (the Dipodomyinae, Perognathinae, and Heteromyinae) that range from the temperate/arid habitat of the southwestern United States down through Mexico and the mesic habitat of Central America into northern South America.
The effects of host response and vaccine design on early signaling profiles of MUC1-specific T cells

Vaccines are beginning to be explored for cancer prevention. Since the time between vaccination and determination of efficacy is long, there is a need for predictive early biomarkers. Immunological endpoints that are determined weeks or months post vaccination are currently being evaluated as biomarkers of vaccine efficacy to replace disease outcome that could take years to assess. However, when multiple vaccines are available, waiting for the development of humoral and cellular immunity could still cause delays while an earlier assessment would allow a timely change to a more effective prevention modality. We hypothesize that early activation of signaling networks within T cells in response to immunization predicts the outcome of the immune response and may be used as a biomarker of vaccine efficacy. Applying the phospho-flow technique to primary T cells, we examined phosphorylation of proteins that shape activation, proliferation, and differentiation of MUC1 tumor antigen-specific CD4 T cells within the first 24 hours post immunization as candidate biomarkers. Previously, our lab has shown that a vaccine composed of a MUC1 peptide loaded on DC is more effective in eliciting T cell immunity than a vaccine composed of the same peptide plus adjuvant. Furthermore, both vaccines stimulate T cells more effectively in wildtype (WT) compared to MUC1.Tg mice. We examined if signaling events downstream of the TCR or through various cell proliferation and survival pathways could predict differential potential of these two vaccines in two different hosts as early as 3, 6, 12, and 24 hours post immunization. Signaling signatures obtained reflect primarily differences between vaccines rather than between the hosts. We demonstrate the feasibility of using this approach to evaluate a vaccine’s potential to elicit a desired response leading to better vaccine design.
The effectiveness of micronized powder and crumb rubbers as fine aggregates replacement in ultra-high performance concrete

Ultra-high performance concrete (UHPC) is a relatively new class of advanced construction material and has superior strength. Nowadays, the need to incorporate recycled or waste product as alternative materials in concrete mixture is become interests and great potential to be explored. Previous researches have been studied on the effectiveness of using recycled waste tyres as replacement materials in conventional and high strength concretes. In comparison with previous studies, micro-waste rubber powder (micro WRP) was used as fine aggregate to replace the-conventional sand. As a consequence, this study was focused on the effect of using crumb rubber and microWRP in UHPC mixture. The levels replacement of crumb rubber and micro WRP comprises of 0%, 10%, 20%, 30%, 40% and 50% from the weight of fine aggregate used. To fulfil the utilization of crumb and micro WRP in UPHC, the workability properties and compressive strength of UPHC and a series of UHPC incorporating crumb rubber and miro WRP (rubberized-UHPC) was examined. The compressive strength of UHPC and rubberized-UHPC was tested for 7, 14 and 28 days of curing days. Further, the expected outcome of this study will correlate the effectiveness of incorporating different levels of crumb rubber and microWRP with subjected to the workability properties and compressive strength of rubberized-UHPC has been reviewed. The experiment results revealed that the incorporation of crumb rubber and micro WRP into UHPC mix was leaded to the reduction of workability and compressive strength. In this study found that the increasing the percentage of crumb rubber and micro WRP as partial replacement of sand, decrease the flowabilty of concrete. It can observed that percentage of crumb rubber and micro WRP as replacement of sand are increase, the compressive strength of rubberized are decreasing.
Application of protein misfolding cyclic amplification for the rapid diagnosis of acquired Creutzfeldt-Jakob disease

The susceptibility, clinical phenotype, and pathology of Creutzfeldt-Jakob disease (CJD) depends on both a methionine (M) /valine (V) polymorphism at codon 129 of the PRNP gene and the type of abnormal isoform of prion protein (PrPSc), either type 1 or type 2. The majority of CJD is sporadic CJD (sCJD) or genetic CJD, while CJD can be transmitted resulting in acquired CJD. It has been reported that dura mater graft-associated CJD (dCJD) with methionine homozygosity at codon 129 could be divided into distinct two phenotypes, namely the non-plaque-type of dCJD (np-dCJD) or the plaque-type of dCJD (p-dCJD). The cause of these two distinct phenotypes of dCJD was clarified by animal transmission studies using PrP-humanized mice based on the susceptibility and neurological or biochemical features in the mice inoculated with PrPSc from each dCJD subgroup. It is now likely that np-dCJD is associated with sCJD-MM1 or -MV1, the most common forms of sCJD (denoted as M1 strain in transmission studies), while p-dCJD is associated with sCJD-VV2 or -MV2, the second most common forms of sCJD (denoted as V2 strain). Although animal transmission studies are the most useful tool for identifying such atypical CJDs, relying exclusively on animal transmission studies may not be feasible due to the enormous cost and time. Therefore, we reported a method that can more easily and rapidly distinguish between M1-derived and V2-derived acquired CJDs using the protein misfolding cyclic amplification (PMCA) technique. Here, we describe the advantages of PMCA as a diagnostic tool for acquired CJD based on a comparison with those of conventional animal transmission studies.
Linear evaluation of the type of Holstein-Friesian bull dams.

The objective of this research was to calculate main type values of heads of cattle in nucleus herd of bull dams, using linear method of evaluation. Research included 224 cows of Holstein-Friesian breed selected as bull dams on the territory of Central Serbia. For all studied traits basic variation-statistical parameters were calculated: arithmetic mean, standard deviation, variation coefficient, standard error and variation interval. Average values of the evaluation of Holstein-Friesian bull dams were following: body height 7.11, strength and capacity 7.34, milk traits 7.23, pelvis width 6.31, position of pelvis 5.29, position of hind legs 5.10, fore udder attachment 6.69, height of rear udder 6.95, width of rear udder 7.31, udder depth 6.70, central ligament 6.85, udder balance 5.17, teat position 5.96, teat length 5.23. Evaluation/score of type and body development are very important indicators of production performance of cows, their ability to consume sufficient quantities of food, produce technologically high quality milk, reduce consumption of energy in production and remain in exploitation as long as possible.
ROLE DES OSTENSIFS DANS LES TECHNIQUES DE TYPE DE TACHES RELEVANT DU CHAMP ADDITIF.

Une tâche qui releve du champ additif peut etre traitee par differentes techniques. Nous employons ici tâche et technique au sens de la Theorie Anthropologique du Didactique (TAD) (Chevallard, 1999). Notre objectif est de comprendre comment ces techniques sont introduites et mises en place dans des institutions qui visent l'etude de l'operation d'addition. Pour cela, on considere comme element fondamental de cette analyse les notions d'ostensif et de non-ostensif (Bosch, M. et Chevallard, Y. 1999). Les ostensifs constituent la partie visible de l'activite mathematique tandis que les non-ostensifs vivent dans le domaine des idees. Ainsi, la mise en oeuvre d'une technique se traduit par la manipulation d'ostensifs controles par des non ostensifs. Dans notre communication nous presenterons des resultats d'une recherche que nous avons menee sur le champ additif dans des manuels du systeme educatif bresilien. Nous avons analyse et decrit l'evolution des techniques depuis les premieres rencontres avec des types de tâches qui mobilisent la notion d'addition jusqu'a l'institutionnalisation de l'algorithme usuel. Pour l'analyse nous avons cherche a identifier des liens entre les techniques et les ostensifs. Nous mettrons ainsi en evidence l'importance des ostensifs et leurs differents roles dans l'etude de cette evolution. En particulier, on etudiera l'usage de quelques ostensifs, comme signes, discours oral, doigts, droite numerique et materiel de numeration.
Antioxidant activity in commonly grown and consumed vegetables: a screening survey

A diet rich in fruits and vegetables is associated with a reduced risk of developing cardiovascular diseases and certain types of cancer. This positive effect is related to bioactive phytochemicals found in plants. The vegetables were grown in the field or in greenhouses at the Norwegian University of Life Sciences (59o40’N) during the years 2000-2002. The vegetables were harvested at commercial maturity and analysed for dry matter and antioxidant activity assessed by the FRAP (Ferric Reducing Ability of Plasma) assay. There was a large variation in antioxidant activity both between and within different species. The highest antioxidant activity was observed in kale, red cultivars of cabbage and table beet. The lowest antioxidant activity was observed in lettuce, cucumber, carrots and tomato. The vegetables possessing a red colour showed higher antioxidant activity with the exception of carrots and tomatoes.
Interactions between elevated atmospheric CO2 and defoliation on North American rangeland plant species at low and high N availability

Although common disturbances of grazing lands like plant defoliation are expected to affect their sensitivity to increasing atmospheric CO2 concentration, almost no research has been conducted to evaluate how important such effects might be on the direct responses of rangelands to CO2. This growth chamber experiment subjected intact plant–soil cylinders from a Wyoming, USA, prairie to a 3-way factorial of CO2 (370 vs. 720 μL L−1), defoliation (non-clipped vs. clipped) and soil nitrogen (control vs. 10 g m−2 added N) under simulated natural climatic conditions. Above- and below-ground biomass and N dynamics of the functional groups C3 grasses, C4 grasses and forbs were investigated. CO2 and defoliation had independent influences on biomass and N parameters of these rangeland plants. Growth under CO2-enriched conditions enhanced above-ground biomass 50% in C3 grasses alone, while shoot N concentration declined 16% in both C3 and C4 grasses. Plant-soil 15N uptake was unaffected by CO2 treatment. In contrast, defoliation had no effect on biomass, but increased tissue N concentration 29% across all functional groups. Without additional N, forage quality, which is in direct relation to N concentration, will decline under increasing atmospheric CO2. Increased dominance of C3 grasses plus reduced forage quality may necessitate changes in grazing management practices in mixed-species rangelands.
Ingénierie d'états quantiques multimodes avec des impulsions femtosecondes

Cette these a pour ambition de preparer des etats de la lumiere dotes de caracteristiques nouvelles et desirables en utilisant les proprietes des peignes de frequences appliquees a l'optique quantique multimode. Un des avantages de l'optique femtoseconde vient du caractere hautement multimode des peignes de frequence, qui permet notamment de creer du vide comprime multimode. La repartition des ressources quantiques entre ces differents modes etant d'importance, nous avons etudie une maniere de la controler grâce a une mise en forme spectrale du faisceau de pompe de l'oscillateur parametrique optique. Nous montrons qu'une detection homodyne multipixel est un outil d'analyse indispensable. Pour une repartition modale donnee, il est possible de modifier l'etat quantique qui la peuple. Une modification desirable est la degaussification de la fonction de Wigner, que nous implementons au moyen d'une soustraction de photon. Outre la possibilite de degaussifier l'etat dans un mode, notre dispositif permet egalement de soustraire un photon dans une superposition coherente de supermodes, ce qui est nouveau. De plus, nous pouvons choisir librement le mode dans lequel la soustraction a lieu. Cette versatilite permet de creer de nouveaux types d'etats, par exemple lorsque l'on soustrait dans les nœuds d'un canevas quantique (aussi appele etat cluster). En particulier, nous pouvons creer des etats presentant de l'intrication inherente entre les modes, c'est-a-dire une intrication qui ne peut pas etre defaite par changement de base.
Gonadotrophic and morphogenetic effects of a juvenile hormone analog treatment and ovary presence on last instar male and female Diploptera punctata (Blattaria: Blaberidae)

Application of the juvenile hormone analog, 7S-hydroprene, to last instar female larvae of the viviparous cockroach Diploptera punctata on day 1 resulted in vitellogenesis in the basal oocytes of the larval ovary, a peak of juvenile hormone synthesis not seen in controls, as well as maintenance of juvenile characteristics in the instar following the molt. To investigate whether juvenile hormone analog and/or the developing ovary was responsible for such changes in juvenile hormone synthesis, the present study used 7S-hydroprene treatment on intact and ovariectomized last instar females and on last instar males with or without an adult or last instar larval ovary. In last instar males, 400 µg of this JH analog was found to promote vitellogenin synthesis by the male fat body and its uptake by an implanted adult ovary for up to 10 days following treatment.The metamorphic outcome following these treatments shows that hydroprene treatment in the presence of a larval ovary in females and an adult ovary in males resulted in a greater number of supernumerary larval molts than hydroprene treatment alone. This indicates that the ovary did contribute to higher juvenile hormone titers. However, hydroprene treatment did not result in a peak of juvenile hormone synthesis in females or males either with or without ovaries. Hydroprene treatment did result in vitellogenin in hemolymph and uptake in the ovary when a rapidly growing ovary was present.
Activation of SPS from darkened spinach leaves by an endogenous protein phosphatase

Sucrose-phosphate synthase from darkened spinach leaves has a low activation state but can undergo a time-dependent activation in desalted leaf extracts that is inhibited by Pi, molybdate, okadaic acid and vanadate, but stimulated by fluoride. SPS labeled in vivo with ({sup 32}P)Pi in excised leaves in the dark loses incorporated {sup 32}P with time when extracts are incubated at 25{degree}C. This loss is largely prevented by vanadate, suggesting that an endogenous protein phosphatase can use SPS as substrate. Changes in phosphorylation state are closely paralleled by changes in SPS activation state. The spontaneous activation achieved in the extracts can be reversed by addition of 2 mM MgATP. Feeding okadaic acid to darkened leaves prevents light activation of SPS suggesting that the endogenous protein phosphatase is similar to the type-1 enzyme of animal tissues. Overall, the results are consistent with the notion that light activation of SPS involves dephosphorylation of inhibitory phosphorylation site(s). Regulation of the protein phosphatase by Pi may be of physiological significance.
Genetic diversity of high and low molecular weight glutenin subunits in Saharan bread and durum wheats from Algerian Oases.

Saharan wheats have been studied particularly from a botanical viewpoint. Genotypic identifica - tion, classification and genetic diversity studies to date were essentially based on the morphology of the spike and grain. For this, the allelic variation at the glutenin loci was studied in a set of Saharan bread and durum wheats from Algerian oases where this crop has been traditionally cultivated. The high molecular weight and low molecular weight glutenin subunit composition of 40 Saharan bread and 30 durum wheats was determined by SDS-PAGE. In Saharan bread wheats 32 alleles at the six glutenin loci were detected, which in combination resulted in 36 different patterns including 17 for HMW and 23 for LMW glutenin subunits. For the Saharan durum wheats, 29 different alleles were identified for the five glutenin loci studied. Altogether, 29 glutenin pat - terns were detected, including 13 for HMW-GS and 20 for LMW-GS. Three new alleles were found in Saharan wheats, two in durum wheat at the Glu-B1 and Glu-B3 loci, and one in bread wheat at the Glu-B1 locus. The mean indices of genetic variation at the six loci in bread wheat and at the five loci in durum wheat were 0.59 and 0.63, respectively, showing that Saharan wheats were more diverse. This information could be useful to select Saharan varieties with improved quality and also as a source of genes to develop new lines when breeding for quality.
Ticks and other bloodsucking arthropods as urban pests inside and outside dwellings.

The first case of hard ticks, Dermacentor reticulatus (F.) and Ixodes ricinus (L.), as well as mites, Ornithonyssus bacoti (Hirst), and rat lice living in the ground floor office of an apartment building of the city of Minsk, Byelorussia is described. Ectoparasites appeared in the end of November in a house situated 300 m away from the nearest homestead as a result of rat immigration from incompletely destroyed houses nearby, coupled with insufficient disinfestation. Climate warming could have caused I. ricinus ticks appearing in the city parks of Vilnius, Lithuania very early in the season, first collected on April 15, 2005. Ticks collected by flagging totaled 23 nymphs, 39 adults. Among adults, 47.2% specimens showed exoskeleton anomalies; ten of 36 PCR-tested ticks were infected by tick-borne pathogens. Borrelia afzelii, Borrelia garinii and Ehrlichia muris were revealed, Borrelia burgdorferi sensu lato was identified twice while in seven ticks live spirochetes not belonging to the B. burgdorferi s.l. group were found. Dually (two species of Borrelia simultaneously) and triple infected ticks were detected. Multi-infected ticks prevailed among the specimens with exoskeleton abnormalities. Ticks in dwellings, near suburbs and parks infected ixodids are found, indicate that entry of tick-borne infection inside them can not be completely ruled out.