Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic and biochemical analysis of Victoria blight : identification of AFLP markers and purification and characterization of the oat saspase

approved: J. Wiolpert Victoria blight of oats (Avena sativa) is caused by the fungus, Cochliobolus victoriae, which produces the toxin, victorin. Victorin production is required for pathogenicity of the fungus. In oats, sensitivity to the toxin and susceptibility to the pathogen is conditioned by a dominant allele at the 1'b locus, while oats with a homozygous recessive allele are insensitive to victorin and resistant to the fungus. Vb is either tightly linked to or the same gene as Pc-2, a gene that confers crown rust resistance in oats. Therefore, the same gene may provide resistance to one pathogen while conferring susceptibility to another. To better understand the interaction of victorin with oats, genetic markers linked to the Vb locus were identified and proteases involved in victorin-induced programmed cell death (PCD) were purified and characterized. Amplified fragment length polymorphism (AFLP) technology was used to identify two genetic markers that flank the Vb locus. We produced an F2 population segregating for victorin sensitivity. Over 51,000 markers generated by 512 different AFLP primer pairs were screened for polymorphisms between victorin-sensitive and insensitive genotypes. These results facilitated the production of a genetic map of the Vb locus. Redacted for Privacy Victorin induces a response in oats that has been characterized as a fonn of programmed cell death (PCD). One biochemical feature of victonn-induced PCD is the proteolytic cleavage of ribulose1 ,5-bisphosphate carboxylase/oxygenase (rubisco). Rubisco proteolysis had previously been shown to be inhibited by general protease inhibitors. Here, we describe inhibition of rubisco proteolysis by caspase-specific inhibitors and present evidence for a protease cascade. The first protease from plants that exhibits caspase specificity and involvement with PCD was purified and characterized. This protease, we have termed a "saspase", contains amino acid sequence homology to plant subtilisin-like serine proteases and is found in the extracellular fluid (ECF) after victorin treatment. Heat shock-induced PCD is also described and displays characteristics similar to victorin-induced PCD, including DNA laddering, rubisco proteolysis, and localization of the saspase in the ECF. © Copyright by Warren C. Coffeen May 16, 2003 All Rights Reserved Genetic and Biochemical Analysis of Victona Blight: Identification of AFLP Markers and Purification and Characterization of the Oat Saspase by Warren C. Coffeen
AVIAN DIVERSITY IN THE MOSKITIA REGION OF HONDURAS

The Moskitia region of northeastern Honduras has long been suspected of supporting high avian diversity, due to the diversity and large expanse of habitats, some with little or no known history of large-scale human disturbance. We have drawn on recent field studies combined with historic data to report on 358 species for this region, more than twice the number of species previously reported. This number represents half the total number of bird species found in Honduras. A total of 65 species are restricted to mature lowland broadleaf forest and susceptible to habitat loss throughout Central America. Five species are recognized as deserving conservation concern and one is regionally range-restricted (endemic). We include a complete list of reported species giving the residency status, threatened status, fre- quency of observation, and method of substantiation. A second list includes 145 species that likely occur in the Honduran Moskitia but have not yet been reported. We conclude that the Honduran Moskitia is especially important for conserving regional biodiversity. Meanwhile, much additional fieldwork is needed to understand the status and abundance of birds in northeastern Honduras. Accepted 31 July 2004.
Chemomechanical regulation of integrin activation and cellular processes in acidic extracellular pH

It is well established that extracellular pH (pHe) becomes acidic in several important physiological and pathological contexts, including the tumor and wound microenvironments. Although it is known that acidic pHe can have profound effects on cell adhesion and migration processes integral to tumor progression and wound healing, the molecular mechanisms underlying the cellular responses to acidic pHe are largely unknown. Transmembrane integrin receptors form a physical linkage between cells and the extracellular matrix, and are thus capable of modulating cell adhesion and migration in response to extracellular conditions. In this thesis, computational and experimental approaches are used to investigate the role of acidic extracellular pH in regulating activation and binding of integrin v3, and to characterize the consequences for downstream subcellularand cellular-scale processes. Molecular dynamics simulations demonstrate that opening of the integrin v3 headpiece occurs more frequently in acidic pHe than in normal pHe, and that this increased headpiece opening can be partially attributed to protonation of ASP127 in acidic pHe. These computational data indicate that acidic pHe can promote activation of integrin v3. This is consistent with flow cytometry and atomic force microscope-enabled molecular force spectroscopy experiments, which demonstrate that there are more activated v3 receptors on live v3 CHO-B2 cell surfaces at acidic pHe than at normal pHe 7.4. Put together, these atomisticand molecular-level data suggest a novel mechanism of outsidein integrin activation regulation by acidic extracellular pH. Next, the consequences of acid-induced integrin activation for subcellularand cellular-scale processes are investigated. Kymography experiments show that v3 CHO-B2 cell membrane protrusion lifetime is increased and protrusion velocity is decreased for cells in pHe 6.5, compared to cells in pHe 7.4. Furthermore, v3 CHO-B2 cells in pHe 6.5 form more actin-integrin adhesion complexes than cells in pHe 7.4, and acidic extracellular pH results in increased cell area and decreased cell circularity. Cell migration measurements demonstrate that v3 CHO-B2 cells in pHe 6.5 migrate slower than cells in pHe 7.4, and that the fibronectin ligand density required for peak migration speed is lower for cells in pHe 6.5. Together, these data show that acidic pHe affects subcellularand
Topics in random matrices and statistical machine learning

This thesis consists of two independent parts: random matrices, which form the first one-third of this thesis, and machine learning, which constitutes the remaining part. The main results of this thesis are as follows: a necessary and sufficient condition for the inverse moments of $(m,n,\beta)$-Laguerre matrices and compound Wishart matrices to be finite; the universal weak consistency and the strong consistency of the $k$-nearest neighbor rule in metrically sigma-finite dimensional spaces and metrically finite dimensional spaces respectively. In Part I, the Chapter 1 introduces the $(m,n,\beta)$-Laguerre matrix, Wishart and compound Wishart matrix and their joint eigenvalue distribution. While in Chapter 2, a necessary and sufficient condition to have finite inverse moments has been derived. In Part II, the Chapter 1 introduces the various notions of metric dimension and differentiation property followed by our proof for the necessary part of Preiss' result. Further, Chapter 2 gives an introduction to the mathematical concepts in statistical machine learning and then the $k$-nearest neighbor rule is presented in Chapter 3 with a proof of Stone's theorem. In chapters 4 and 5, we present our main results and some possible future directions based on it.
Une solution informatisée à l'analyse de sensibilité d'Electre III

La methode multicritere Electre III permet d’etablir un classement parmi des actions susceptibles d’apporter une solution a un probleme de decision et ce, en se basant sur plusieurs criteres. La complexite de cette methode rend fastidieuse l’eventuelle analyse de sensibilite qu’on voudrait en faire. Cette note detaille un algorithme iteratif mis en œuvre dans un logiciel Electre III preexistant et permettant donc d’effectuer cette analyse de facon automatisee.
The Bent Pyramid and the Major Lunar Standstill

Here it is given a discussion about the orientation of the causeway which is linking the Bent Pyramid to its Valley Temple. Using mooncalc.org software we can see that the causeway has an orientation that could have been determined according to the northernmost direction of the moonrise, which happens on a major lunar standstill. By means of the simulation, we can also see that, at the latitude of Dahshur, on such a major lunar standstill in the northernmost direction, the moon reaches an altitude of 89 degrees, having therefore a passage close to the zenith of the sky. Using software Stellarium, we can see that an orientation of the causeway to the rising of Capella is also possible. However, I consider more plausible an orientation to the northernmost direction of the moonrise.
Direct and indirect effects in herbivore - periphyton interactions

In this article we review the indirect interactions prevailing in littoral communities and compare their importance to direct trophic interactions. We focus on the interaction between benthic algae and their herbivorous consumers, i. e. invertebrate grazers and herbivorous fish. In addition to the effects of grazers on periphyton biomass and production, we categorise and describe the types of indirect interactions observed and we present a quantitative meta-analysis to compare the effect magnitude of indirect and direct effects. Our review shows that herbivore-plant interactions comprise considerable complexity beyond consumption. We identify and review three different indirect interactions, which play important roles for periphyton-grazer interactions in benthic food webs. These are keystone predation, trophic cascading and habitat facilitation. Direct negative effects were stronger than indirect positive effect, because grazing leads in almost all studies to a decrease in algal biomass. We found positive effects of grazing on algal nutrient content, biomass-specific productivity and evenness. We found negative overall effects on species richness and area-specific productivity. Moreover, spatial heterogeneity was on average increased by grazing. The magnitudes of direct and indirect effects were often correlated
The HLA System: A New Approach

This is an edited collection of papers based on a conference exploring the most recent research on HLA, the field of histocompatibility and its medical implications. Since HLA is moving from a major serological technique into oligonucleotide testing, one chapter describes the area of molecular biology. Another chapter is devoted to bone marrow transplantation. While concentrating mainly on the fields of blood transfusion rather than covering every aspect of HLA, one section contains an intensive set of studies on the antigen frequencies of HLA for Caucasian, black and oriental populations. This data can be used for any aspect of study requiring control data for HLA, such as disease association studies, paternity testing and human genetics.
Can Hydraulic Barriers Stop the Spread of the Round Goby

Abstract : The round goby, Neogobius melanostomus, a native of Eurasia, is spreading throughout the waters of North America. Native to the Black Sea and Caspian Sea systems, the round goby appeared in the St. Clair River, ONT-MI in 1990, and subsequently in the Great Lakes during 1993-1996 (Charlebois et al. 1997). Particular concern exists for the population in southern Lake Michigan and the Calumet River, which is spreading west via the Cal-Sag Channel towards the Des Plaines River (Moy 1997). Penetration by the round goby into the Mississippi River system, or any large river system, would allow virtually unlimited spread throughout large geographic areas. Its high rate of dispersal (e.g., all five Great Lakes in only 5 years) is particular cause for concern (Jude 1997). This benthic species, although small, is highly aggressive toward native fishes, especially the moffled sculpin (Cottus bairdi), which is unable to effectively defend the cavities it normally inhabits from gobies (Dubs and Corkum 1996). The round goby is also aggressive towards larger, pelagic species such as rock bass (Ambloplites rupestris) and smallmouth bass (Micropterus dolomieui) (Wickett and Corkum 1998), as well as smaller, benthic species like darters, Etheostoma spp. (Jude 1997). Containment of the round goby has been identified as a priority by several agencies, including the U.S. Army Corps of Engineers and the U.S. Fish and Wildlife Service. The round goby could be contained by use of ichthyocides, electricity, or by hydraulics. The last of these is environmentally benign and safe, but efficacy is unknown.
Pseudomonas aeruginosa AlgZR two-component system : expression, responsiveness, control of iron acquisition and impact on virulence

Pseudomonas aeruginosa virulence components are subject to complex regulatory control primarily through two-component regulatory systems that allow for sensing and responding to environmental stimuli. In this study, the expression and regulation of the P. aeruginosa AlgZR two-component regulatory system were examined. Two transcriptional initiation sites were identified for algR within the algZ coding region, and two additional start sites were identified upstream of the algZ coding region. The two algR transcriptional start sites, RT1 and RT2, are directly regulated by the alternative sigma factor AlgU consistent with previous reports of increased algR expression in mucoid backgrounds, and the alternative sigma factor RpoS additionally plays a role in algR transcription. The expression of the first algZ promoter, ZT1, is entirely dependent upon the transcriptional regulator Vfr for expression whereas neither Vfr, RpoS or AlgU regulate the second algZ promoter, ZT2. The algZ and algR genes are also co-transcribed, in both nonmucoid and mucoid backgrounds. Furthermore, algZR was found to be co-transcribed with hemCD. Taken together these results indicate that algZR transcription involves multiple factors at multiple start sites that control individual gene expression as well as co-expression of this two-component system with heme biosynthetic genes.
Human natural killer cell responses to tumour-priming

As one of the central components of host anti-tumour immunity, natural killer (NK) cells exert cellular cytotoxicity against tumour cells and secrete a milieu of immunoregulatory cytokines to inhibit tumour progression. NK cell-mediated cytotoxicity requires successful progression through discrete activation events that begin with NK cell adhesion to a target cell and culminate in the polarized release of cytotoxic granules into the immunological synapse. These activation events are tightly regulated by a complex array of signalling molecules, the engagement of which by ligands on target cells can determine susceptibility to NK cell-mediated killing. Resistance to NK cell cytotoxicity can be attributable to a deficiency in any of the signalling requirements for the events leading to granule exocytosis. Tumour resistance to NK cell lysis may be overcome by priming of NK cells with cytokines or by binding of NK cell activating receptors to ligands expressed on target cells. Here, the activation profiles of normal, freshly isolated human peripheral blood NK cells upon tumour-priming with the NK-resistant leukemic cell line, CTV-1 are defined, and candidate NK cell receptors involved in the delivery of the tumour-priming signal are identified. Results from this study demonstrate that NK cell responses to tumour-priming are distinct from those induced by the gold standard in immunotherapy, cytokine-priming. Tumour-priming of NK cells resulted in a significant downregulation of various activating NK cell receptors including CD16, NKp46, NK group 2, member D (NKG2D), and intracellular adhesion molecule (ICAM)-1. Tumour-primed NK cells (TpNKs) also exhibited a strong pro-inflammatory profile marked by ample secretion of macrophage inflammatory protein (MIP)-1α, MIP-1β, regulated on activation normal T cell expressed and secreted (RANTES), tumour necrosis factor (TNF)-α and interferon (IFN) -γ after short incubations with CTV-1. Their secretory profiles were distinct from the profiles of NK cells stimulated with exogenous cytokines or the NK-sensitive target cell line, K562. Collectively, data from this study demonstrates that NK cell responses can differ according to the type of stimulus, as well as the ligand combination presented by the target cell. The co-engagement of NK cell receptors LFA-1 and CD2 by their respective ligands on CTV-1 cells, ICAM-1 and CD15, seems to play an important role in the delivery of the tumour- priming signal.
The Life Cycles of Mayflies of the Eastern Ukraine. Subfamily Baetinae (Ephemeroptera, Baetidae)

Abstract The life cycle types of mayflies of the subfamily Baetinae in Eastern Ukraine are determined. The scheme for identification of larval age structure is given. The age structure changes of Baetis braaschi, B. nexus and Alainites muticus larvae during the year are described in detail. The flight periods of imagoes throughout the studied region are delimited for almost all species of the subfamily. B. braaschi is shown to have the bivoltine life cycle, with its populations overwintering as the larval stage (MBws) independently on temperature conditions in the water body. The peculiarities of oviposition are described for this species. The following aspects of life cycles were revealed: nymphs, subimagoes and imagoes of different generations of B. braaschi differ considerably in size; the voltinity of B. vernus in the region can vary (Us and/or MBss), mainly due to temperature conditions of the water bodies, where its development takes place; geographically isolated populations of A. muticus in the Eastern Ukraine reproduce only by thelytoky Установлены типы жизненных циклов представителей подсемейства Baetinae, которые они демонстрируют в пределах Восточной Украины. Подана схема определения возрастной структуры личинок. Детально описано изменение возрастной структуры личинок Baetis braaschi, B. nexus и Alainites muticus на протяжении года. Приведены периоды лёта имаго в регионе практически для всех видов подсемейства. Установлено, что независимо от температурного режима водотока B. braaschi имеет бивольтинный жизненный цикл с зимовкой на стадии личинки (MBws). Описаны особенности откладки яиц данным видом. Выявлены следующие аспекты жизненных циклов: нимфы, субимаго и имаго разных генераций B. braaschi существенно отличаются размерами; вольтинность B. vernus в регионе может варьировать (Us и/или MBss) главным образом в зависимости от температурного режима водного объекта, в котором проходит его развитие; географически изолированные популяции A. muticus Восточной Украины размножаются исключительно при помощи телитокии.
Crystallographic Analysis and Kinetic Studies of HIV-1 Protease and Drug-Resistant Mutants

HIV-1 protease is the most effective target for drugs to treat AIDS, however, the long-term therapeutic efficiency is restricted by the rapid development of drug resistant variants. To better understand the molecular basis of drug resistance, crystallographic and kinetic studies were applied to wild-type HIV-1 protease (PR) and drug-resistant mutants, PRV82A, and PRI84V, in complex with substrate analogs, the current drug saquinavir and the new inhibitor UIC-94017 (TMC-114). UIC-94017 was also studied with mutants PRD30N and PRI50V. The drug-resistant mutations V82A, I84V, D30N and I50V participate in substrate binding. Eighteen crystal structures were refined at resolutions of 0.97-1. 60Å. The high accuracy of the atomic resolution crystal structures helps understand the reaction mechanism of HIV-1 PR. Different binding modes are observed for different types of inhibitors. The substrate analogs have more extended interactions with PR subsites up to S5-S5’, while the clinical inhibitors maximize the contacts within S2-S2’. Hydrophobic interactions are the major force for saquinavir binding since it was designed with enhanced hydrophobic groups based on substrate side-chains. In contrast, the new clinical inhibitor UIC-94017 was designed to mimic the hydrogen bonds between substrates and PR. UIC-94017 forms polar interactions with the PR main-chain atoms of Asp29/30, which have been proposed to be critical for its potency against resistant HIV. The mutants showed different structural and kinetic effects, depending on the inhibitor and location of the mutations. The observed structural changes were consistent with the relative inhibition data. Both PRI84V and PRI50V lost favorable hydrophobic interactions with inhibitor compared with PR. Similarly, in PRD30N the UIC-94017 had a water-mediated interaction with the side-chain of Asn30 rather than the direct interaction observed in PR. However, PRV82A compensated for the mutation by shifts of the backbone of Ala82. Furthermore, the complexes of PRV82A showed smaller shifts relative to PR, but more movement of the peptide analog, compared to complexes with clinical inhibitors. The structures suggest that substrate analogs have more flexibility than the drugs to accommodate the structural changes caused by mutation, which may explain how HIV can develop drug resistance while retaining the ability of PR to hydrolyze natural substrates. INDEX WORDS: HIV-1 protease, drug resistance, V82A, I84V, D30N, I50V, substrate analog, UIC-94017, TMC-114, saquinavir, crystal structure, kinetics. CRYSTALLOGRAPHIC ANALYSIS AND KINETIC STUDIES OF HIV-1 PROTEASE AND DRUG-RESISTANT MUTANTS
The assessment of vegetation seasonal dynamics using multitemporal NDVI and EVI images derived from modis

O objetivo deste trabalho foi caracterizar a dinâmica sazonal do cerrado, floresta estacional semidecidual e decidual no norte do estado de Minas Gerais, Brasil. Series multitemporais dos indices de vegetacao NDVI (indice de vegetacao da diferenca normalizada) e EVI (indice de vegetacao melhorado) derivados do sensor MODIS, foram comparadas analisando o perfil temporal e os resultados de classificacao das imagens. Os resultados mostraram que: (1) Os indices de vegetacao estudados refletiram o padrao sazonal das fisionomias, diferenciando os periodos chuvosos e os periodos de seca; (2) a fisionomia floresta estacional decidual apresentou menores valores dos indices e maior variacao; (3) as fisionomias cerrado e floresta estacional semidecidual apresentaram alto valores dos indices e baixa variacao; (4) de acordo com os resultados das classificacoes o melhor indice para o mapeamento das fisionomias na area de estudo foi o NDVI, porem ambos podem ser usados para avaliar a dinâmica sazonal da vegetacao; e (5) estudos precisam ser realizados explorando algoritmos de extracao de feicoes para melhorar a acuracidade do mapeamento das fisionomias cerrado, floresta decidua e semidecidua na area de estudo.