Miracle-dz/UniFAR-FTUs huggingface dataset:
Mycobacterium tuberculosis induced transcription in macrophages: the role of TPL2/ERK signalling in the negative regulation of type I interferon production and implications for control of tuberculosis

Mycobacterium tuberculosis is an important global cause of mortality and morbidity. The major host cell of Mycobacterium tuberculosis is the macrophage, and Mycobacterium tuberculosis is able to subvert the macrophage response in order to survive and replicate. The majority of infected individuals mount an immune response capable of controlling Mycobacterium tuberculosis infection. This requires the cytokines IL-12, TNFα, IL-1 and IFNγ, which promote eradication or control of infection. However, other immune factors, including IL-10 and type I IFN, can inhibit this protective response. In this study we have used microarray analysis to study the temporal response of macrophages to Mycobacterium tuberculosis infection, in an unbiased fashion. In response to Mycobacterium tuberculosis infection, macrophages produced cytokines and chemokines, upregulated genes involved with major histocompatability class I antigen presentation, activated both pro- and anti-apoptotic genes and downregulated many genes involved in cell-division and metabolism. We also observed the early induction of genes regulated by the extracellular-regulated kinase (ERK) MAP kinase pathway, and the upregulation of genes known to be induced by type I IFN, leading us to further investigate the role of these pathways in the macrophage response to Mycobacterium tuberculosis. Both pathways were found to regulate the production of protective and detrimental cytokines in macrophages in response to Mycobacterium tuberculosis infection. In addition, microarray analysis found that these pathways controlled the transcription of numerous genes in response to Mycobacterium tuberculosis infection. Finally, type I IFN was found to inhibit the macrophage response to IFNγ, including IFNγ-mediated killing of Mycobacterium tuberculosis in macrophages, a crucial step in the control of Mycobacterium tuberculosis infection in vivo. We have therefore identified important regulatory mechanisms in macrophages, which are likely have an important role during Mycobacterium tuberculosis infection in vivo.
Importance of rose- grain aphid as a corn pest in Poland

(Fabricius) are major cereal aphid species of moderate climate in Europe[1, 2]. While the grain aphid is a dominant on wheat, rye and triticale, the bird cherry-oat aphid colonise mostly oat and barley, the rose-grain aphid occurs on these cereal crops in Poland only in trace amounts [3]. During the last years importance of the maize in Polish agriculture has been systematically increased. Thus knowledge on its aphid pests is extremely important for the Polish farmers. In the present paper we report on aphids occurrence on various cereal crops, and particularly for the first time present some preliminary data on performance of
People–primate interactions: implications for primate conservation

In this chapter, patterns of interactions are reviewed, from benign to mutually harmful, that characterize people–primate relationships, and the main social and ecological factors shaping people–primate coexistence are summarized. The reasons why certain primate species are better able to share landscapes with their human neighbours are examined, along with factors that influence people’s perceptions of, and attitudes, towards them. The chapter stresses how, at a local level, variations in socio-economic and cultural norms and values often underlie negative interactions between humans and primates. Lessons learned from studies to reduce negative interactions between people and primates are discussed, and broader scale landscape approaches that could facilitate effective primate conservation and human livelihood objectives examined. Finally, it is emphasized that understanding people–primate interactions requires a multifaceted approach, combining detailed understanding of the context, and needs of the different stakeholders, human and animal, and drivers of changing patterns of coexistence.
Classic Articles Published by American Scientists (1900-2014): A Bibliometric Analysis

The present study explores US independent classic articles published by American scientists from 1900 to 2014. We examined those articles that had been cited at least 1000 times since publication to the end of 2014 using the Science Citation Index Expanded in the Web of Science (WoS). We also applied a bibliometric indicator, the Y-index, to assess the contributions of the authors of these articles. The results showed that 4909 classic articles were published between 1916 and 2013, and that the most productive categories from the WoS were multidisciplinary sciences, biochemistry and molecular biology, and general and internal medicine. Science published most of these articles, and the three most productive institutions were Harvard University, Massachusetts Institute of Technology, and Stanford University. The physicist, Edward Witten was the most prolific author and an article written by the biochemist, Marion Bradford at University of Georgia in 1976 had the highest number of citations. In addition, the article by Perdew, Burke and Ernzerhof at Tulane University had the highest number of citations in 2014.
Study of the Yeast Vacuolar-type ATPase by Electron Cryomicroscopy

Study of the yeast vacuolar-type ATPase by electron cryomicroscopy Jianhua Zhao Doctor of Philosophy Graduate Department of Medical Biophysics University of Toronto 2016 Vacuolar-type ATPases (V-ATPases) are rotary enzymes that use energy from hydrolysis of adenosine triphosphate (ATP) to pump protons across membranes and control the pH of many intracellular compartments. ATP hydrolysis in the soluble catalytic region of the enzyme is coupled to proton translocation through the membrane-bound region by rotation of a rotor subcomplex. Studies of ATP synthases, V-ATPases, and vacuolar/archaeal ATPases (V/A-ATPases) have suggested that flexibility is necessary for the catalytic mechanism of rotary ATPases but the structures of different rotational states have never been observed experimentally. VATPases also serve an important role in the immune system and are targeted by intracellular pathogens. Legionella pneumophila, the causative agent of Legionnaires’ Disease, secretes a protein effector called SidK that binds and inhibits V-ATPases, preventing acidification of lysosomes and promoting survival of the bacterium inside macrophages. The mechanism of V-ATPase inhibition by SidK is not known. The structure of V-ATPases can be analyzed by single particle electron cryomicroscopy (cryo-EM), an imaging technique involving the identification of tens to hundreds of thousands of individual proteins in micrographs. A partially-automated image selection program was developed to increase particle image identification throughput. A method was also developed to correct for magnification anisotropy that was identi-
How point mutations confer resistance in BCR-ABL: a computational study

Imatinib is a first generation BCR-Abl tyrosine kinase inhibitor widely used in the treatment of CML. A significant cause of relapse in patients receiving imatinib therapy can be attributed to the development of point mutations in the BCR-Abl tyrosine kinase and resulting imatinib-resistance. Nilotinib is one of several second generation BCR-Abl tyrosine kinase inhibitors developed to treat imatinib-resistant CML. Nilotinib inhibits the majority of imatinib-resistant mutations, however mutations that are resistant to both imatinib and nilotinib persist in patients. These highly resistant mutations include compound mutants, where multiple mutations occur in the same BCR-Abl molecule. Further understanding regarding how mutations confer resistance and the ability to predict the resistance profile of a given compound mutation would enable drug design initiatives, both in CML and other cancers, to be improved in the future. In this thesis three major computational approaches; molecular dynamics, ligand docking and MM-GBSA have been applied to investigate the effects of single and compound point mutations in the BCR-Abl kinase domain. Wild-type structures of BCR-Abl were studied initially in order to validate methods and act as a benchmark for comparison against the mutant structures. A total of ten mutant structures of inactive BCR-Abl were studied; five in complex with imatinib and five with nilotinib. Using this approach we were able to rank the single mutant structures according to experimental data and test the protocol on two previously unstudied compound mutations
Isolation and Identification of Vibrio Species by Multiplex PCR and Investigation of its Prevention by Using Indian Spices

The present study focuses the incidence of Vibrio spp. in water bodies which are used by people in surroundings for their daily needs. Vibrio constitute of both pathogenic and non-pathogenic species, thus, for differentiating between them a rapid method named multiplex PCR assay has been for the study. The method used was to first determine the physical and chemical constituents of all the 15 water samples (pond water) collected from different regions of Uttar Pradesh. Isolation of bacteria was done on selective media (TCBS) which showed both green and yellow colonies. These colonies were cultured separately on non selective media. All the pure cultures obtained were thus, used to extract their DNA using Phenol chloroform method. DNA was then visualized on agarose gel and quantified using double beam spectrophotometer. Samples with higher yield of DNA were used for amplification using species specific primers by multiplex PCR. The results were documented and thus, study derived the information that most of the waterbodies showed presence of pathogenic Vibrio species while few of them showed presence of non-pathogenic Vibrio spp.
Pathogenicity by Aspergillus flavus from Gulf Coast tick cadavers (Amblyomma maculatum, Acari: Ixodidae) to any life history stage

ABSTRACT A natural aspergillosis in the Gulf Coast tick, Amblyomma maculatum, is reported for the first time. Under high relative humidity (RH) conditions, field-collected adults died and became enveloped in whitish mycelium from hyphae that protruded from their bodies. The fungus was identified as Aspergillus flavus. Laboratory-colonized eggs, larvae, nymphs, and adults displayed disease symptoms, and A. flavus was reisolated from dead individuals, about 10 days after artificial infection by submersion for 2 minutes in a 1.6 × 108 spores/ml + Tween 20 inoculum of the native A. flavus isolates. Treatment-related mortality was 87% larvae, 67% eggs, and between these extremes for nymphs and adults. Increased water loss rate was a pathogenic consequence of A. flavus infection for all stages. We conclude that A. flavus is a natural regulator of A. maculatum populations, and larvae are particularly susceptible because of their low dehydration tolerance limit.
Heritability and number of genes controlling partial resistance to Exserohilum turcicum in maize inbred H99

High levels of partial resistance are essential to manage northern corn leaf blight (NCLB) of maize, incited by the casual agent Exserohilum turcicum, in disease-prone environments. Maize inbred H99 displays high levels of partial resistance to E. turcicum and has been used as a donor line for the improvement of host resistance in susceptible temperate-adapted germplasm This study was undertaken to determine the potential of H99 as a prospective donor of partial resistance to E. turcicum in a disease-prone, mid-altitude tropical environment of East Africa. Estimates of the heritability of resistance in, and the number of genes for, resistance to E. turcicum in H99 were determined using 120 F 2:3 families and their F 2:4 progenies derived from a cross between H99 and susceptible inbred A619. The lines were evaluated in replicated field experiments at Namulonge and Kamenyamiggo, Uganda, during 1993. Disease severity was assessed by counting lesion number, visually estimating percent leaf area affected (PLAA), and calculating the area under disease progress curves (AUDPC). Heritability estimates were computed from variance component analyses and parent-offspring regressions, broad-sense heritability estimates of F 2:3 and F 2:4 lines were determined using plot-mean and family-mean bases across locations. Estimates of the number of genes controlling quantitative resistance to E. turcicum based on the Castle-Wright formula were made using the square of differences of phenotypic means of inbreds A619 and H99, and the square of the phenotypic range between the most susceptible and most resistant families in each generation, Heritability estimates for PLAA, and AUDPC based on PLAA, were higher than those for lesion number and AUDPC based on lesion number, and ranged from 0.73 to 0.78. Narrow-sense heritability estimates calculated using parent-offspring regrecsion also tended to be higher than those based on lesion number data. Gene number estimates were two to three for lesion number and four to five for PLAA based on the parental phenotypic means, Gene number estimates based on the phenotypic range of families were approximately eight for lesion number and five to seven for PLAA. Use of a modified Castle-Wright formula raised all gene number estimates.
CINÉTICA DE CRECIMIENTO DE Lactobacillus lactis Y DETERMINACIÓN DEL EFECTO PROBIÓTICO EN CEPAS PATÓGENAS

Introduction: Acid lactic bacteria have been studied for their ability to grow in harsh environments and generate antagonisms with other microorganisms. The present study sought to determine the kinetic parameters of growth of Lactobacillus lactis and its effect on Escherichia coli, Salmonella typhimurium, Clostridium perfringens and Staphylococcus aureus. Materials and Methods: The growth of the lactic strain was evaluated at concentrations of 0.5, 1 and 2% bile salts; 1 and 1.5% bile; three levels of pH (2.5, 4.5 and 7) and two temperatures (38 and 45oC). Susceptibility of all strains to Dicloxacillin, Cefepime, Cephalothin, Ciprofloxacin, Gentamicin and Penicillin was also evaluated using Kirby-Bauer technique. Inhibition of L. lactis and its supernatant in E.coli, S. typhimurium, S. aureus and C. perfringens and the following parameters were determined and estimated: growth, pH, sugar consumption, acidity and protein consumption during the kinetic fermentation in MRS. Peptides present in the L. lactis supernatant through HPLC were determined. Results: Growth of 1.2x109 and 4.1x109 CFU/ml at 1.2% bile and 0.5% bile salt was obtained; 1.1x1011, 2.1x1010 and 1.0x1010 CFU/ml for 2.5, 4.5 and 7 pH respectively; and 1.7x1013 and 1.4x1013 CFU/ml for 45 and 38oC. The lactic strain showed resistance to Cephalothin and Dicloxacilin; C. perfringens, to Penicillin and Dicloxacillin; S. typhimurium and E. coli to Cephalothin; and S. aureus, to Dicloxacillin. L. lactis inhibited E. coli and C. perfringens, and the supernatant included S. aureus. Conclusion: It is concluded that L. lactis present adequate growth in conditions in vitro and inhibited E. coli, C. perfringens and S. aureus but not S. typhimurium.
Chitinases as markers for red rot resistance in sugarcane

Red rot disease caused by Colletotrichum falcatum Went is one of the major constraints to sugarcane cultivation in India. Detailed studies were conducted on the involvement of important biochemical indices viz., pathogenesis related proteins i.e. the chitinases and phytoalexins in red rot resistance with a set of sugarcane cultivars varying in resistance. In the present investigation, quantitative as well as qualitative analyses showed that chitinases were specifically induced in disease resistant cultivars upon pathogen inoculation. Chitinases of 20, 23, 24 and 26 kDa were identified as PR-proteins specifically involved in sugarcane red rot
Oocyte In Vitro Maturation with Crude Sperm Extract Protein of Bull’s Spermatozoa

Oocyte In vitro maturation (IVM) is one of the important parts for in vitro fertilization (IVF). The success of oocyte maturation is influenced by the composit ion and the quality of IVM medium. Culture medium which used to IVM not only influences the oocyte process to reach metaphase II and proceed the fertilization, but also influences to developmental of an embryo. Crude sperm extract has high-level protein kinase and contains some sperm proteins. Crude sperm extracts expected as natural maturation medium that can increase the success of In Vitro Maturation (IVM). The characterization of crude sperm extracts profile with sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Oocyte maturation is observed in the 26 th hour from the first culture. The result of crude sperm extract characterization obtained from the protein with the molecular weight is 176.8, 63.2, 58.4, 55.3, 52.4, 49.7, 44.6, 38.02, 36.03, 34.15 and 26.8 kDa. Oocyte maturation with concentration of crude sperm extract 1.5 µg. mL -1 with 71.6% matures oocyte and oocyte maturation with concentration of crude sperm extract 2.5 µg. mL -1 with 75% matures oocyte. Keywords: Crude Sperm Extract, In Vitro Maturation, Oocyte
Cavity Occupancy by Lowland Paca (Cuniculus Paca) in the Lacandon Rainforest, Chiapas, Mexico

Habitat occupancy is a good indicator of wildlife behavior and interactions with their environment. We used camera traps to study the use of cavities by lowland paca (Cuniculus paca) in three sites in the Lacandon Rainforest of Chiapas, Mexico. To understand the biotic, environmental, physical, anthropic, and behavioral elements that affect spotted lowland paca, the cameras recorded lowland paca activity in front of 29 cavities. Monitoring occurred continuously in cavities near permanent natural water bodies, underneath roots of trees, or inside hollow logs. These cavities were more frequently found in Montes Azules Biosphere Reserve (MABR), where hunting pressure was low. The daily occupancy and permanence of lowland paca in these cavities were associated with the presence of its offspring. There were no offspring recorded in cavities alongside rivers within grazing areas. This suggests the potential existence of a sink-source type of metapopulation, where community reserves and MABR would serve as source habitat, while riparian corridors would be sink habitat for this species. Lowland pacas used these locations, which were scattered through the study area, so long as hunting was moderate and riparian corridors with safe cavities in large trees were well preserved.
Coordinate Loss of a MicroRNA Mir 145 and a Protein-Coding Gene RPS14 Cooperate in the Pathogenesis of 5q- Syndrome.

Abstract 947 Large hemizygous chromosomal deletions are among the most common molecular abnormalities in cancer, but the identification of critical haploinsufficiency disease genes within the deleted regions has been difficult. The 5q- syndrome, a subtype of myelodysplastic syndrome (MDS), is a well-studied chromosomal deletion syndrome characterized by a consistent clinical phenotype with macrocytic anemia and thrombocytosis. We have previously shown that while hemizygous loss of RPS14 recapitulates the failed erythroid differentiation seen in 5q- syndrome, it does not account for the thrombocytosis. Evaluation of the effects of all protein coding genes in the CDR on hematopoietic differentiation showed no genes other than RPS14 altered the ratio of megakaryocytic to erythroid cells, either alone or in combination with RPS14 . We therefore examined the 5q- syndrome CDR for non-coding RNAs and identified a microRNA, miR-145, which targets Fli-1, a transcriptional factor that regulates megakaryocyte development. Patients with del(5q) MDS have decreased expression of miR-145 and increased expression of Fli-1. Overexpression of miR-145 or inhibition of Fli-1 in CD34+ cells decreases megakaryocyte production, while inhibition of miR-145 or overexpression of Fli-1 has the reciprocal effect. These findings have been validated in vivo using transgenic mice. Moreover, the combined loss of miR-145 and RPS14 cooperate to alter erythroid-megakaryocytic differentiation in a manner similar to the 5q- syndrome. Taken together, these findings demonstrate for the first time that coordinate deletion of a microRNA and a protein-coding gene contributes to the phenotype of a human malignancy, the 5q- syndrome. Disclosures: No relevant conflicts of interest to declare.
Psychophysiological Effects of Orchid and Rose Fragrances on Humans

This study aimed to determine the effects of floral fragrances on human brain waves and moods. A total of 44 subjects participated in this experiment. Group 1 consisted of 11 male and 14 female college students with a mean age of 24.5 years (± 2.23) and Group 2 consisted of 10 males and 9 females with a mean age of 54.3 years (± 2.98). Subjects were exposed to floral fragrances of Rosa hybrida , ‘Hera’ (hereafter referred to as “rose”), Cymbidium faberi (hereafter referred to as “orchid”), or odorless control flowers (hereafter referred to as “control”). Experiments took place in three rooms (rose, orchid, and control). Electroencephalographs (EEGs) were recorded during exposure to the odors and the data were processed using quantitative electroencephalographic (QEEG) techniques. The changing EEG patterns were analyzed by brain mapping and compressed spectral arrays, and the subjects’ preferences (hedonic evaluations) were quantified with an A1 index. Increased activation of absolute alpha waves was verified on six of the eight EEG channels, with the right frontal and left occipital lobes exhibiting no changes and the left parietal region showing the greatest activation. According to the QEEG measurements in the electrode sites over the frontal, temporal, parietal, and occipital lobes, the strongest absolute alpha waves were induced in the parietal lobes, followed by the temporal lobes, with the other lobes showing no significant changes. On brain maps, the orchid fragrance induced greater absolute alpha and absolute mid-beta activities compared with the rose and control fragrances, and the rose fragrance induced high absolute mid-beta activation. To identify emotional responses to floral fragrances, the subjects were requested to fill in a questionnaire and the resulting odor-related emotional descriptors were analyzed using semantic differential and factor analysis. Principal component analysis identified “elegant” as the first principal component describing the floral fragrance, followed by “refreshing” and “aromatic. ” The subjects gave orchid higher scores for “elegant” and “refreshing,” while finding rose more “aromatic. ” Differences in hedonic evaluation revealed by the A1 index appeared in the 65-115 sec range of scent exposure time. The subjects with ages of around 50 years showed olfactory preferences throughout the entire experimental time of 160 sec, most markedly in the later time segment (115-165 sec), showing an increasing preference with increasing exposure time. We conclude that rose fragrance can improve concentration by creating an aromatic environment conducive to a concentrated and calm state of mind, and orchid fragrance can make people feel pampered and relaxed by creating an elegant and refreshing environment.