Miracle-dz/UniFAR-FTUs huggingface dataset:
Sidebar: IR-4 Project targets specialty crops

P applications for “minor” or “specialty” crops — typically those grown on less than 300,000 acres nationwide — often do not get the full support of product registrants because the potential economic benefits are perceived as much more limited than for applications targeting crops grown on large acreages, such as soybeans and field corn. The IR-4 Project is a unique partnership of researchers, producers, the crop-protection industry and federal agencies designed to increase pest-management options for specialty crops, which include vegetables, fruits, nuts, herbs, nursery crops and flowers. (Most of the crops grown in California fit into this category.) With funding from the U.S. Department of Agriculture, state agencies, commodity groups and other industry sources, IR-4 researchers and cooperators generate field and laboratory residue data, which are submitted to the U.S. Environmental Protection Agency (EPA) to secure regulatory clearances for using safer pest-control techniques on specialty crops. Projects are prioritized based on requests from growers, commodity groups, and USDA and land-grant university researchers. Since 1963, IR-4 has contributed to more than 7,300 regulatory clearances for specialty crops.
Resistance of exotic collections of gerbera (Gerbera jamesonii) against whitefly (Bemisia tabaci) and thrips (Thrips palmi) under polyhouse conditions.

An experiment was conducted during 2003-04 to study the resistance of 16 exotic collections of gerbera (Gerbera jamesonii Bolus ex. Hooker F.) against whitefly (Bemisia tabaci Genn.) and thrips (Thrips palmi Karney) under polyhouse conditions at Bangalore. Of the 16 collections screened, 2 varieties 'Eva', and 'Carocci' showed combined resistance to both whitefly and thrips while 3 varieties 'Alberino' 'Dil', and 'Cassiona' were highly susceptible to both the pests. Varietal reactions were also studied in relation to flower structure type and colour. It was found that double types were least susceptible (38.26%) to thrips damage compared to single (56.48%) and semi-double types (75.38%). Among flower colours, red colour attracted highiest thrips incidence (77.89%), followed by yellow (59.61%) while pink varieties had significantly less damage (34.37%).
A Systems Genetics Approach to the Identification of Causal Genes in Heart Failure Using a Large Mouse Panel

Heart failure (HF) accounts for 1 in 9 deaths in the United States and is the leading cause of hospitalization for people over the age of 65 and the incidence of HF is predicted to rise over the coming years. The complexity which underlies common forms of HF has hindered the study of the disease in humans, and approaches, such as genome-wide association studies (GWAS), have had only modest success in identifying genes which are related to this disease. Here we describe the use of a panel of mice to facilitate the study of this complex disorder, reducing heterogeneity and facilitating systems-level approaches.We used the beta-adrenergic agonist isoproterenol to induce HF in 105 unique strains drawn from the Hybrid Mouse Diversity Panel, a novel mouse resource population for the analysis of complex traits. Our first study reports the results of a GWAS on heart weights, cardiac fibrosis and other surrogate traits relevant to HF. Among the 32 significant loci, we identified several strong candidates which had previously been shown to contribute to mendelian forms of cardiomyopathy. We were also able to validate two novel candidate genes, the orphan transporter Abcc6, and the long noncoding RNA Miat, using gene targeting, transgenic and in vitro approaches.As part of our systems genetics approach, we developed a novel gene network construction algorithm, which improves on prior methods by allowing non-linear interactions and the ability for genes to operate in multiple modules at once. We were able to demonstrate using previously published data that our results either matched or exceeded another well-known network construction algorithm. In a subsequent study, we applied this method to transcriptomes taken from the HF study. We identified a module of 41 genes which significantly regulates the response of the heart to isoproterenol and HF and which contains several genes of interest such as Lgals3, a diagnostic marker for human HF.Our results provide a valuable resource toward a better understanding of the pathways and gene-by-environment interactions influencing heart failure.
Estimation of swell index of fine grained soils using regression equations and artificial neural networks.

The swell index which is the slope of the rebound curve of void ratio versus the logarithm of the effective pressure curve is used to estimate the consolidation settlement of overconsolidated fine grained soils. Because determination of swell index from oedometer tests takes a relatively long time, empirical equations involving index soil properties, are needed to estimate it for preliminary calculations and to control the validity of consolidation tests. Geotechnical engineering literature involves empirical equations for the estimation of compression and swell indexes. In this study the performance of widely used empirical equations were assessed using a database consisting of 42 test data. In addition to this, new empirical relationships with single and multiple dependent variables were developed with better estimation capability. An artificial neural network (ANN) which has two input variables, one hidden layer and eight hidden layer nodes was also developed to estimate swell index. It was concluded that the performance of the ANN is better than empirical equations. Key words: Swell index, clay soils, regression analyses, artificial neural networks.
Genomic characterization of ETV6/RUNX1-positive acute lymphoblastic leukemia

The t(12;21) translocation generates the ETV6/RUNX1 fusion gene, present in 25% of childhood acute lymphoblastic leukemia. This fusion gene is important for leukemia development but is not sufficient for leukemia to arise. Hence, the additional genetic changes present in leukemic ETV6/RUNX1-positive cells give important clues regarding the history of the leukemia. The aim of this thesis has been to characterize thoroughly the genetic changes present in ETV6/RUNX1-positive ALL. In Article I, seventeen ETV6/RUNX1-positive ALLs were characterized using array CGH. This revealed that gain of Xq material, present in six cases, was the most common copy number aberration (CNA). A large number of genes was present in the commonly gained region but the high and specific expression of SPANXB identified this gene as a likely target of the gain. In Article II, 24 ALLs were analyzed using 500K single nucleotide polymorphism arrays. The data from these ALLs were combined with previously published external SNP array data from 140 ETV6/RUNX1-positive ALLs. A high number of recurrent CNAs could be identified in this dataset. The recurrent CNAs were further analyzed using hierarchical clustering, connected pair analysis, and oncogenetic tree models. These analyzes revealed that the majority of cases had acquired a unique set of recurrent CNAs, indicating that the process of acquiring CNAs is unique for each ALL. In Article III, exome sequencing was used to sequence all protein coding genes in two ETV6/RUNX1-positive ALLs. Seven somatic single nucleotide mutations were present in each ALL, six of these were in genes previously implicated in cancer. (Less)
Morphometric and Genetic Variation in Three Populations of Indian Salmon (Polydactylus plebeius)

Morphometric character analyses and RAPD was used to discriminate and ratify the status of three populations of Indian salmon, Polydactylus plebeius along the coromandel coast of India. Morphometric analyses showed a clear pattern of differentiation between the stocks and revealed the discreteness of two groups, southern stock (Pazhayar) and northern stock (Cuddalore). The univariate analysis of variance showed significant differences between means of the samples for most morphometric descriptors. A total of 1077 scorable bands were produced using all ten arbitrary primers in three populations. An un-weighted pair-group method with arithmetic mean (UPGMA) dendrogram was constructed based on genetic values to show the genetic relationship among the three populations. The genetic diversity (H) of P. plebeius in Cuddalore was more (0.0733 ± 0.0648) than Pazhayar (0.0609 ± 0.0416) and Vellar (0.0613 ± 0.0344) populations. All the three populations had significantly (p<0.001) higher interpopulation genetic distance value than the intrapopulation value. Further molecular studies, comprising more markers and populations are still required to precisely evaluate the genetic structure of threadfin fishes throughout the Indian coast.
Effets des arbres d’ombrage sur les bioagresseurs de Coffea Arabica

The coffee tree is a shade tolerant plant originating from Africa. Its cultivation however developed mainly apart from its zone of origin, particularly in Latin America, with intensive systems in full sun. With the extension of the zones of cultivation, certain traditional pests and diseases of the coffee tree, such as the coffee berry borer, also colonized new territories while others, such as the agent of the coffee berry disease Colletotrichum kahawae, remained on the continent of origin. During the extension of its zone of cultivation, the coffee tree encountered other pests and diseases which were already adapted to the new zones. The cultivation in full sun facilitates high production but requires more inputs, particularly pesticides. Today, the association of the coffee tree with shade trees in agroforestry systems is being studied from the point of view of greater crop and environmental sustainability. This paper presents an overview of the impact of shade trees on several important pests and diseases of the coffee tree. Various mechanisms, such as the barrier effect or the microclimate modification, will be discussed using examples. Lastly, recommendations will be proposed according to the pest and disease existing in the cultivation zones. The use of shade trees is particularly recommended in zones where the coffee berry disease prevails and agroforestry systems are especially recommended for use in these areas.
Ageing in the mammalian brain

With a globally ageing population diseases associated with this natural process are becoming major issues worldwide. Research into the process of ageing and its concomitant issues is rapidly expanding; the need for new tools and models to investigate this rapidly expanding arena of research is paramount. The discovery of a spontaneous mutation in the AS rat strain which introduces a premature stop mutation into the gene encoding protein kinase C  (PKC lead to the development of a model for one such age related disorder, Parkinson‟s disease. Consequently, this model has been selected to investigate age related changes in specific areas of the brain (the cerebellum, basal ganglia, cerebral cortex and brainstem). These regions were selected because they have previously been shown to demonstrate changes with age (cerebellum, cerebral cortex and basal Ganglia), they show differences between the AS and AS/AGU strains (basal ganglia) or they show differences in PKC knockout models (cerebellum). The Brainstem was selected as it shows little change due to age and shows no differences in PKC knockouts or AS/AGU rats. This study used established qPCR methods to measure a validated biomarker of ageing, CDKN2A (the transcript for p16INK4a) in the brains of these rats to determine whether this model is in fact a genuine model for accelerated ageing. This thesis demonstrates that CDKN2A expression, in combination with senescence-associated -galactosidase staining, provides clear evidence of accelerated ageing in the brains of AS/AGU rats when compared with the parent AS strain. These investigations were furthered by an investigation of members of the Sirtuin family of proteins. The changes in expression of these Sirtuins indicates that there may be increased levels of cellular stress, disruption of metabolism and DNA damage in the AS/AGU rats, this would be congruent with the accelerated ageing phenotype present in this strain. Furthermore, the levels of these Sirtuins were in line with the predictions from the MTR trinity in regards to the accelerated ageing phenotype. Whilst some of the changes in senescence and metabolic disruption may be attributable to the PKC mutation in the AS/AGU rats, it would appear that there is some element of accelerated ageing that is independent of this mutation.
Drug clearance pathway prediction based on semi-supervised learning

It is necessary to confirm that a new drug can be appropriately cleared from the human body. However, checking the clearance pathway of a drug in the human body requires clinical trials, and therefore requires large cost. Thus, computational methods for drug clearance pathway prediction have been studied. The proposed prediction methods developed previously were based on a supervised learning algorithm, which requires clearance pathway information for all drugs in a training set as input labels. However, these data are often insufficient because of the high cost of their acquisition. In this paper, we propose a new drug clearance pathway prediction method based on semisupervised learning, which can use not only labeled data but also unlabeled data. We evaluated the effectiveness of our method, focusing on the cytochrome P450 2C19 enzyme, which is involved in one of the major clearance pathways.
The biocalcification of mollusk shells and coral skeletons: Integrating molecular, proteomics and bioinformatics methods

The research described in this thesis is focused on biominerals of calcium carbonate, in particular the organic matrix embedded in the mineral phase of mollusk shells and corals skeletons, which directly controls the biocalcification process in these organisms. In this scope, the organic matrix proteins are considered as key components of the biological control over mineralization. Since the first report by Miyamoto and co-workers of a protein (Nacrein) from the mollusk shell of the pearl oyster in 1996, many proteins in shells and other mineralized structures were identified by a one-per-one approach using classical molecular biology and biochemistry techniques. Until recently, the existing information was manageable and consisting of some proteins with very specific signatures: secretion signals, acidic domains, carbonic anhydrases, low complexity regions, and not much else. With the entrance in the post-‘omic’ era, the fields of genomics, proteomics and transcriptomics also reached the biomineralization field and have allowed the scientific community to discover a much wider range of proteins taking part in the control of biocalcification mechanisms. These large newly identified protein datasets, are often difficult to interpret in light of the current models of calcification. The main goal of this dissertation is to give a contribution in this context. Apart from identifying several new proteins by means of high-throughput technologies, we present a careful analysis of the results and further interpretation from functional and evolutionary perspectives.
21 Regulation of Translation Elongation and the Cotranslational Protein Targeting Pathway

The factors involved in translation elongation are subject to sophisticated control mechanisms that come into play under a wide variety of conditions. Even though translation is most frequently controlled during the initiation phase (Chapter 1) and the regulatory mechanisms impinging on the initiation steps have received considerable attention (reviewed in several chapters of this book), accumulating information points to the elongation phase as a target for controls under defined circumstances. In this chapter, we focus on recent developments in understanding the control of elongation in mammalian cells. As a special case, we also discuss cotranslational protein targeting, a cellular process involving the control of elongation on an important class of mRNAs. REGULATION OF TRANSLATION ELONGATION The mechanism of peptide-chain elongation and the functions of translation elongation factors are described in Chapters 2 and 3. In addition, detailed aspects of the structure and function of eukaryotic elongation factor 2 (eEF2) are the subject of a recent informative review (Jorgensen et al. 2006). eEF2 is a phosphoprotein in mammalian cells, and most of the recent advances relate to the regulation of eEF2 and its cognate kinase, eEF2 kinase. eEF1A and eEF1B also are phosphoproteins and have been discussed in earlier reviews on this subject (Proud 2000; Traugh 2001; Browne and Proud 2002; Le Sourd et al. 2006). Significance of eEF2 Phosphorylation for the Control of Protein Synthesis Under a diverse range of conditions, the phosphorylation state of eEF2 changes in directions consistent with its having a role in regulating protein synthesis; i.e.,.
MODELING, DYNAMICS AND OPTIMAL CONTROL OF WEST NILE VIRUS WITH SEASONALITY

West Nile virus (WNv) is a mosquito-borne disease which arrived in Canada in 2001. It has kept spreading across the country and still remains a threat to public health. In this dissertation, we formulate dynamical models and apply theory of dynamical systems to investigate the behavior of the transmission of WNv in the mosquito-bird cycle and humans. In the first part, we propose a system of ordinary differential equations to model the role of corvids and non-corvids birds in the transmission of WNv in the mosquito-bird cycle in a single season and proved the existence of backward bifurcation in the model. In the second part, we consider another deterministic model to study the impact of seasonal variations of the mosquito population on the transmission dynamics of WNv. We prove the existence of periodic solutions under specific conditions. As for the third part, the latter model is extended to assess the impact of some anti-WNv control measures; by re-formulating the model as an optimal control problem. For mosquito-borne diseases, it is essential to access and forcast the virus risk. Therefore in the final part, we generalize the risk index, minimum infection rate (MIR) by using a compartment model for WNv, ii to define a dynamical minimum infection rate (DMIR) for assessing risk of WNv. By using the data from Peel region, we test and forecast the weekly risk of WNv which can help identify the optimal mitigation strategies.
The biology and control of Riccadoella limacum (Schrank), a mite pest of farmed snails.

The differences between the similar species, Riccardoella limacum and Riccardoella oudemansi we're examined using SEM techniques. The two species may be separated by differences in setal structure and number. The internal anatomy of R. limacum was examined using plastic sections for light microscopy and found to be similar to previous descriptions. Computer-aided three dimensional reconstruction was carried out on serial sections and the relative positions of various organs noted. The life cycle of R. limacum was confirmed as having a hexapod larva and three nymphal stages. The occurrence of an overwintering egg was observed in hibernating snail hosts and there was no relationship between hatching and snail hibernation. No such egg is present in R oudemansi, perhaps related to the death of their hosts during the winter. Mites were found to spread rapidly to colonise a new host and quickly laid numerous eggs, large numbers of mites have been seen to build up inside a snail. R. limacum was found to contain a substance which reacted with keyh6le limpet haemocyanin antibodies, this was likely to be haernocyanin. The mite obtains haemocyanin as a form of nourishment from the hosts blood, though the possibility that mucus is also a source of food cannot be eliminated in this study. The effect of different mite numbers on the snail was examined. High mite infestations cause poor quality shells, slow growth and delayed reproductive maturation. A low number of mites can be tolerated seemingly with little in effect except on reproduction. The concentration of proteins and glycogen/free glucose in the snail tissues was the same in snails with and without mites. However, as the final weights of snails were dramatically different, the total amount of protein and glycogen/free glucose in each snail was also different. Some interest in R. limacum was shown by the predatory mite, Macrocheles muscaedomesticae though it is not certain whether deaths of R. firnacum can be attributed to the predator. R. limacum is attracted to certain stimuli more than others, snail odour being the preferred stimulus. In the light of the present study recommendations for controlling R. limacum on a commercial snail farm have been made.
Scavenging of Hydrogen Peroxide in Prokaryotic and Eukaryotic Algae: Acquisition of Ascorbate Peroxidase during the Evolution of Cyanobacteria

Cyanobacteria can be divided into two groups, those that has and those that lacks AsA peroxidase. The first group scavenges hydrogen peroxide with the peroxidase using a photoreductant as the electron donor, and the second group only scavenges hydrogen peroxide with catalase
The use of otolith microstructure in resolving issues of ageing and growth of young Micropogonias furnieri from southern Brazil

Abstract The corvina Micropogonias furnieri is a long-lived coastal sciaenid fish that sustains an important demersal fishery from southern Brazil to northern Argentina. The ageing of young corvinas in the Patos Lagoon estuary has been controversial. In former studies, up to six thin opaque bands in their otolith sections were considered annuli, supporting the hypothesis of slow growth and long permanence in the lagoon. However, corvinas caught in coastal waters with the same number of annuli were much larger. This fact raised doubts regarding the periodicity of the band formation in the otoliths of lagoon specimens. To better understand the growth of young corvinas, we examined the microstructure of otoliths. First, we validated the daily periodicity of growth increments using an oxytetracycline marking experiment. Second, 130 wild specimens were aged: 88 from the lagoon (30–285 mm TL, 51–678 days) and 42 from adjacent marine waters (133–275 mm TL, 212–514 days). The thin opaque bands were found to be formed on an average of 159, 269, 341, 418, 477 and 547 days and their number was higher in those corvinas remaining in the lagoon. Specimens of a similar size were older in the lagoon, suggesting slower growth than those that move to the marine environment around the first year of life. These differences may be due to growth constraints on those juveniles that remain in the more variable estuarine environment in the lagoon, or to a larger food supply in the more stable coastal environment.
Avaliação de Ribózio em Cornição em solo ácido

Foram testadas 16 estirpes de Rhizobium loti em cornichao, (Lotus corniculatus L.) cv. Sao Gabriel, em casa de vegetacao, num solo da unidade de mapeamento Vacaria (Haplo-humox). O solo, apos a calagem, mostrava pH de 5,1, 6,5 ppm de P e 0,9 meq/100 g de Al. Em laboratorio, 14 estirpes foram testadas quanto ao crescimento em meio liquido, sob dois niveis de pH (4,9 e 4,5) e cinco niveis de Al (0, 50, 100, 150 e 300 g). As estirpes EEL 3484, EEL 11184 e EEL 17384 foram as mais susceptiveis ao Al nos pHs 4,9 e 4,5. Estas tres estirpes tambem foram as menos eficientes no solo em casa de vegetacao, tanto em producao de materia seca como em N total no tecido da parte aerea. As estirpes EEL 13484, EEL 13584 e EEL 17384 foram as de melhor desempenho em producao de materia seca, embora nao tendo diferido estatisticamente das testemunhas SEMIA 806 e SEMIA 816.