Miracle-dz/UniFAR-FTUs huggingface dataset:
Chromatin dynamics at the Saccharomyces cerevisiae PHO5 promoter

Chromatin Dynamics at the Saccharomyces cerevisiae PHO5 Promoter. (December 2004) Walter Joseph Jessen, B.S., Purdue University Chair of Advisory Committee: Dr. Michael Kladde In eukaryotes, the organization of DNA into chromatin is a primary determinant of gene expression. Positioned nucleosomes in promoter regions are frequently found to regulate gene expression by obstructing the accessibility of cis-regulatory elements in DNA to trans-factors. This dissertation focuses on the chromatin structure and remodeling program at the S. cerevisiae PHO5 promoter, extending the use of DNA methyltransferases as in vivo probes of chromatin structure. Our studies address the diversity of histone-DNA interactions in vivo by examining nucleosome conformational stabilities at the PHO5 promoter. We present high-resolution chromatin structural mapping of the promoter, required to relate in vivo site accessibility to nucleosome stability and show that the PHO5 promoter nucleosomes have different accessibilities. We show a correlation between DNA curvature and nucleosome positioning, which is consistent with the observed differences in accessibility/stability. Kinetic analyses of the chromatin remodeling program at PHO5 show that nucleosomes proximal to the enhancer are disrupted preferentially and prior to those more distal, demonstrating bidirectional and finite propagation of chromatin remodeling from bound activators and providing a novel mechanism by which transactivation at a distance occurs.
Synaptonemal Complex Analysis of Spermatocytes in Hybrids of Silver Fox and Blue Fox.

Investigations of male meiosis in silver fox x blue fox hybrids have revealed meiotic arrest at the first prophase stage. Synaptonemal complex analysis using light and electron microscopy demonstrated the occurrence of multivalents, bivalentlike structures, and unpaired axes. We conclude that the sterility of male hybrid foxes probably is due to pairing problems of chromosomes caused by extensive karyotypical differences of the two species, resulting in unpaired chromosomes, chromosome segments, and broken chromosomes.
Plant adaptation to climate change—Where are we?

Climate change poses critical challenges for population persistence in natural communities, for agriculture and environmental sustainability, and for food security. In this review, we discuss recent progress in climatic adaptation in plants. We evaluate whether climate change exerts novel selection and disrupts local adaptation, whether gene flow can facilitate adaptive responses to climate change, and whether adaptive phenotypic plasticity could sustain populations in the short term. Furthermore, we discuss how climate change influences species interactions. Through a more in‐depth understanding of these eco‐evolutionary dynamics, we will increase our capacity to predict the adaptive potential of plants under climate change. In addition, we review studies that dissect the genetic basis of plant adaptation to climate change. Finally, we highlight key research gaps, ranging from validating gene function to elucidating molecular mechanisms, expanding research systems from model species to other natural species, testing the fitness consequences of alleles in natural environments, and designing multifactorial studies that more closely reflect the complex and interactive effects of multiple climate change factors. By leveraging interdisciplinary tools (e.g., cutting‐edge omics toolkits, novel ecological strategies, newly developed genome editing technology), researchers can more accurately predict the probability that species can persist through this rapid and intense period of environmental change, as well as cultivate crops to withstand climate change, and conserve biodiversity in natural systems.
Mitochondrial dysfunction and loss of Parkinson's disease‐linked proteins contribute to neurotoxicity of manganese‐containing welding fumes

Welding generates complex metal aerosols, inhalation of which is linked to adverse health effects among welders. An important health concern of welding fume (WF) exposure is neurological dysfunction akin to Parkinson's disease (PD), thought to be mediated by manganese (Mn) in the fumes. Also, there is a proposition that welding might accelerate the onset of PD. Our recent findings link the presence of Mn in the WF with dopaminergic neurotoxicity seen in rats exposed to manual metal arc‐hard surfacing (MMA‐HS) or gas metal arc‐mild steel (GMA‐MS) fumes. To elucidate the molecular mechanisms further, we investigated the association of PD‐linked (Park) genes and mitochondrial function in causing dopaminergic abnormality. Repeated instillations of the two fumes at doses that mimic ~1 to 5 yr of worker exposure resulted in selective brain accumulation of Mn. This accumulation caused impairment of mitochondrial function and loss of ty‐rosine hydroxylase (TH) protein, indicative of dopa‐minergic injury. A fascinating finding was the altered expression of Parkin (Park2), Uchll (Park5), and Dj1 (Park7) proteins in dopaminergic brain areas. A similar regimen of manganese chloride (MnCl2) also caused extensive loss of striatal TH, mitochondrial electron transport components, and Park proteins. As mutations in PARK genes have been linked to early‐onset PD in humans, and because welding is implicated as a risk factor for parkinsonism, PARK genes might play a critical role in WF‐mediated dopaminergic dysfunction. Whether these molecular alterations culminate in neurobehavioral and neuro‐pathological deficits reminiscent of PD remains to be ascertained. —Sriram, K. , Lin, G. X. , Jefferson, A. M. , Roberts, J. R. , Wirth, O. , Hayashi, Y. , Krajnak, K. M. , Soukup, J. M. , Ghio, A. J., Reynolds, S. H. , Castranova, V. , Munson, A. E. , Antonini, J. M. Mito‐chondrial dysfunction and loss of Parkinson's disease‐linked proteins contribute to neurotoxicity of manganese‐containing welding fumes. FASEB J. 24, 4989–5002 (2010). www.fasebj. org
Ticks and tick-borne diseases

s of these presentations are included in this publication to inform other research groups of these activities, which were not yet at the stage where formal publication of results was possible. Participants divided into four groups after each field had been covered. They evaluated the data available and made recommendations on future research priorities, with emphasis on the following areas: (I) specific field problems to be studied; (2) modelling needs (needs of users and of modellers); (3) data requirements for process-based models; (4) data requirements for defining the field situation.
Effect of weightlessness on cytoskeleton architecture and proliferation of human breast cancer cell line MCF‐7

Because cells are sensitive to mechanical forces, weightlessness might act on stress‐dependent cell changes. We hypothesized that the integration of environmental factors might induce specific cytoskeletal architecture patterns, characterized by quantitative image analysis. Human breast cancer cells MCF‐7, flown in space in a photon capsule, were fixed after 1.5, 22, and 48 h in orbit. Cells subjected to weightlessness were compared with 1 g in‐flight and ground controls. Postflight, fluorescent labelings were performed to visualize cell proliferation (Ki‐67), signal transduction (phosphotyrosine), three cytoskeleton components (microtubules, microfilaments, and intermediate filaments), and chromatin structure. Confocal microscopy and image analysis were used to quantify cycling cells and mitosis, modifications of the cytokeratin network, and chromatin structure. In weightlessness, phosphotyrosine signal transduction was lower, more cells were cycling, and mitosis was prolonged. Finally, cell proliferation was reduced as a consequence of a cell‐cycle blockade. Microtubules were altered in many cells. The perinuclear cytokeratin network was more loosely ‘woven’, and chromatin structure was modified. The prolongaion of mitosis can be explained by an alteration of microtubule self‐organization in weightlessness, involving reaction‐diffusion processes. The loosening of the perinuclear cytokeratin network and modification of chromatin distribution are in agreement with basic predictions of cellular tensegrity.
Infundibular Lesion and Pars Intermedia Activity in the Tadpole

Vunder 1 reported that the transplantation of a single hypophysis into an hypophysectomized Axolotl led to an excessive development of pigmentation. He ascribed this result to traumatic stimulation in the operation and supported his view by showing that the same result followed pricking the gland with a needle. In connection with the development of anterior lobe function in the tadpole, one of us 2 has confirmed and extended Vunder's findings. His interpretation, however, seemed unacceptable since it was there found that transplantation of even primordia into the embryo led to the development of the pigmentation weeks later and also because the effect often persisted as long as the animal could be kept, in many cases over 4 months. In a brief report of some of this material 3 it was suggested that the pituitary is under some restraint in its normal site, from which it is released on transplantation. It was further suggested that the source of this inhibition might be the nerve tract from the hypothalamus to the pars nervosa and intermedia. This tract usually called the supra-optico-hypophyseal tract has been found by the authors in the frog. Recently we have been able to put this theory to a test through having developed an operative approach to the tadpole's pituitary. The operation was performed in Rana sylvatica tadpoles by exposing the entire dorsum of the brain, cutting the olfactory and one or both optic nerves and lifting the brain out sufficiently to make possible the manipulation of the infundibulum by the anterior approach. In the experimental animals the infundibulum was partly or completely destroyed by pinching with fine forceps and where possible plucking out part of the tissue. In the controls the infundibulum was merely slightly manipulated though the rest of the operation was carried out as in the experimentals.
Protection against leishmaniasis by DNA injection of a plasmid encoding the Leishmania major Cpn60 gene

The leishmaniases are parasitic protozoan infections caused by members of the genus Leishmania. Injection of Leishmania major into various strains of inbred mice cause disease symptoms which mimic the symptoms of a human leishmanial infection. Protection against an L. major infection in BALB/c mice depends on the generation of a macrophage-activating CD4 + Thl immune response with production of IL-2 and IFNy, but not IL-4, a Th2 cytokine that results in disease exacerbation. Immunization using DNA vaccines is a promising new approach for the prevention of diseases caused by intracellular pathogens. The antigen of interest encoded in the plasmid is transcribed and translated by the host cellular machinery and presented to the immune system inducing specific cell-mediated and humoral immune responses against the encoded protein. In this study a eukaryotic expression vector, pcDNA3.1 encoding the L. major chaperonin 60 (Cpn60) was constructed and tested in vitro to confirm that the mammalian translational machinery could synthesize the protein. Cell-free coupled transcription/translation using rabbit reticulocyte lysate and transfection studies using COS-7 cells were carried out by SDS-PAGE and western blot analysis of protein products. A single protein of the correct size was produced in vaccine samples but not in the Controls. To test the vaccine efficacy, BALB/c mice were immunized with either the vaccine construct, empty plasmid control or PBS, and boosted twice two weeks apart. Spleen cells from mice immunized with the vaccine construct did not produce significant amounts of the Thl cytokines interleukin-2 (IL-2) or gamma interferon (IFN-y), or the
A New Genus and a New Species of Braconinae (Hymenoptera, Braconidae) from China

In this paper, a new genus and a new species of Braconinae (Hymenoptera, Braconidae) are described and illustrated from China, i. e. Platybracon gen. nov. and Platybracon sinicus sp. nov. The type specimens are deposited in the Benificial Insects Lab, College of Plant Protection, Fujian Agriculture and Forestry University, China.
Correlations between Vitelline Membrane Strength and Selected Physical Parameters of Poultry Eggs

Abstract The aim of this study was to evaluate the strength of vitelline membrane and its correlation with other morphological traits and the viscosity of egg yolk of different poultry species: goose, turkey, Muscovy duck, chicken, guinea fowl and Japanese quail. Vitelline membrane strength (VMS) was defined as work and force after the deformation of yolk at 6 mm. Bird species affected the VMS of egg yolk. The lowest strength was measured for the vitelline membrane of goose egg yolk. There were no apparent differences in the strength of vitelline membrane for ducks, guinea fowl, chickens and Japanese quail. In contrast, the vitelline membrane of turkey egg yolk appeared to be of the highest strength. Statistically significant positive correlations were observed between VMS and yolk index, while there was no correlation between the weight of the eggs and egg yolk. The work deformation of yolk was positively correlated with the viscosity of poultry egg yolk.
On the proposal of a GO phase and the restriction point

Zetterberg and Larsson proposed that the restriction point divides the G1 phase into two parts. Cells before this point are able to leave the division cycle and enter a GO phase; cells past this point are unaffected by a short period of low serum. Additional results of Zetterberg and Larsson—1) cycloheximide treatment affects cells in the same way as low serum, and 2) a delay in the second division after serum starvation in the cells not initially affected in their first division—indicate that their experiments are consistent with serum removal affecting cells in all phases of the cell cycle equally. Their experiments are consistent with the continuum model of the mammalian division cycle. There is no need to postulate a restriction point or a GO phase to explain the serum starvation results. —Cooper, S. On the proposal of a GO phase and the restriction point. FASEB J. 12, 367–373 (1998)
Term Development and Increases Placental Weight in Mice 1 2

1 This study investigated the effects on fertilized embryo development of somatic 2 cytoplasm after its injection into intact mouse oocytes. Mature oocytes collected from female 3 B6D2F1 mice were injected with cumulus cell cytoplasm of different volumes and from different 4 mouse strains (B6D2F1, ICR, C57BL/6), or with embryonic cytoplasm. After culture for 1 h, 5 B6D2F1 sperm were injected into those oocytes by ICSI. The oocytes were examined for pre6 and postimplantation developmental competence. Increases in the volume of the somatic 7 cytoplasm from onefold to fourfold resulted in an impairment of blastocyst development and 8 full-term development (28% and 7%, respectively, vs. 96% and 63%, respectively, in the control 9 group; P < 0.01). An increase in the volume of somatic cytoplasm reduced the expression of 10 POU5F1 (more commonly known as OCT4) in expanded blastocysts. The frequency of embryos 11 that developed to the blastocyst stage did not differ when B6D2F1 or ICR somatic cytoplasm 12 was injected, but injection of C57BL/6 somatic cytoplasm induced a two-cell block in embryo 13 development. Injection of the cytoplasm from fertilized embryos did not reduce the frequency of 14 embryos attaining full-term development. Interestingly, somatic cytoplasm significantly 15 increased the placental weight of ICSI embryos, even the injection of onefold cytoplasm (0.2002 16 ± 0.02 [n = 32] vs. 0.1198 ± 0.02 in the control group [n = 87]; P < 0.01). These findings indicate 17 that the injection of somatic cytoplasm into oocytes before ICSI causes a decrease in 18 preimplantation development, clearly impairs full-term development, and causes placental 19 overgrowth in fertilized embryos. To our knowledge, placental overgrowth phenotypes are only 20 caused by interspecies hybridization and cloning, and in genetically modified mice. Here, we 21 report for the first time that somatic cytoplasm causes abnormal placentas in fertilized embryos. 22 This study suggests that somatic cell cytoplasmic material is one cause of the low rate of full23 term development in cloned animals. 24
Identification of the human analog of SR‐BI and LOX‐1 as receptors for hypochlorite‐modified high‐density lipoprotein on human umbilical venous endothelial cells

As HOCl‐modified (lipo)proteins colocalize with endothelial cells in viivo, the interaction of HOCl‐modified high‐density lipoprotein (HOCl‐HDL3) with human umbilical venous endothelial cells (HUVECs) was studied. HUVECs have much higher binding capacity and holoparticle turnover for HOCl‐HDL3 than for HDL3. The cholesterylester (CE)‐uptake from HDL3 and HOCl‐HDL3 in excess of holoparticle uptake suggested involvement of the human analog of scavenger receptor class B, type I (hSR‐BI). hSR‐BI could be identified by RT‐PCR and Northern and Western blots on HUVECs. Also, CHO‐cells overexpressing SR‐BI revealed high‐affinity binding and pronounced increase in selective CE‐uptake from HDL3 and HOCl‐HDL3. However, that intracellular degradation of HOCl‐HDL3 by HUVECs increased with degree of HOCl‐modification (which could partially be inhibited by chloroquine) pointed towards another pathway that involves receptor‐mediated endocytosis. We identified in ligand blots a single binding protein for HOCl‐HDL3 comigrating with lectin‐like oxidized‐LDL receptor (LOX‐1). Preincubation of nitrocellulose strips with anti‐LOX‐1 IgG revealed pronounced inhibition of HOCl‐HDL3 binding. Competition studies with known ligands performed on intact cells corroborated involvement of LOX‐1 in binding of HOCl‐HDL3. We conclude that hSR‐BI and LOX‐1 act in concert, with the first primarily mediating selective CE‐uptake and the latter responsible for holoparticle uptake and lysosomal degradation of HOCl‐HDL3.
Uses and properties of Citrus flavonoids

Flavonoids are a widely distributed group of polyphenolic compounds with health-related properties, which are based in their antioxidant activity. These properties have been found to include anticancer, antiviral, antiinflammatory activities, effects on capillary fragility, and an ability to inhibit human platelet aggregation. The antioxidant capacity of any flavonoid will be determined by a combination of the O-dihydroxy structure in the B-ring, the 2,3-double bond in conjugation with a 4-oxo function and the presence of both hydroxyl groups in positions 3 and 5. Flavanones, flavones, and flavonols are the flavonoids present in Citrus, and although flavones and flavonols have been found in low concentrations in Citrus tissues, in relationship to flavanones, these types of compounds have been show to be powerful antioxidants and free radical scavengers. Some Citrus flavonoids can be used directly as repellents or toxins or be used in plant improvement programs to obtain more resistant crops. In addition, .
The disabled dendritic cell

Dendritic cells are important antigen‐presenting cells of the immune system that induce and modulate immune responses. They interact with T and B lymphocytes as well as with natural killer cells to promote activation and differentiation of these cells. Dendritic cells generated in vitro from monocytes by use of the cytokines GM‐CSF and IL‐4 are increasingly used clinically to enhance antitumor immunity in cancer patients. However, recent studies revealed that the functional repertoire of monocyte‐derived dendritic cells may be incomplete. Important functions of monocyte‐derived dendritic cells such as migration or the ability to induce natural killer cell activation or type 2 T helper cell differentiation appear to be impaired. We propose that all these deficiencies relate to a single biochemical deficiency of monocyte‐derived dendritic cells. IL‐4, which is used to generate monocyte‐derived dendritic cells, suppresses phospholipase A2, the enzyme that liberates arachidonic acid from membrane phospholipids and contributes to the synthesis of platelet‐activating factor. Monocyte‐derived dendritic cells must therefore fail to generate platelet‐activating factor as well as arachidonic acid derivatives such as prostaglandins, leukotrienes, and lipoxins, collectively referred to as eicosanoids. Since eicosanoids and platelet‐activating factor are known to play an important role in processes such as leukocyte migration, natural killer cell activation, and type 2 T helper cell differentiation, the deficiency in eicosanoid and platelet‐activating factor biosynthesis may be responsible for the observed handicaps of monocyte‐derived dendritic cells. —Thumher, M. , Zelle‐Rieser, C. , Ramoner, R. , Bartsch, G. , Höltl, L. The disabled dendritic cell. FASEB J. 15, 1054–1061 (2001)
Host-plant-mediated interactions between a generalist folivore and its tachinid parasitoid

We investigated the consequences of feeding on different species of host-plants on the performance of a generalist lepidopteran larva (Platyprepia virginalis (Bvd.) Arctiidae) and its interactions with a tachinid fly parasitoid (Thelairia bryanti Curran). Growth rate of P. virginalis was not different for larvae reared individually on either poison hemlock, Conium maculatum L. , bush lupine, Lupinus arboreus Sims, or fiddle neck, Amsinckia menziesii (Lehm.) under laboratory conditions. 3. Further, larvae caged in the field on either hemlock or lupine did not differ in developmental rates or pupal mass. In 1 of 2 years survivorship was higher for moth larvae caged on hemlock
Influence of Service Quality of E-Commerce Websites on Customers’ Trust, Commitment and Loyalty: A Case of Indian Customers

: Introduction: The e-commerce providers inevitably need to deliver high quality services to create an admirable customer experience and gain customer trust, commitment and loyalty. In the present times of web based businesses and shifting customer loyalties, identification of service quality gaps are of prime importance to e-businesses. Objective: The objective of the research paper is to measure the influence of service quality on selected e-commerce websites on customer trust, commitment and loyalty. This objective examines the influence of the different dimensions of the service quality on the selected e-commerce websites on the trust, commitment and loyalty of the Indian consumers for the respective online shopping websites. Methodology: This research study is descriptive and causal in nature. The judgmental sampling method is used to select sample units from the target population. The data is collected from 400 customers having experience of e commerce i.e. buying the products from the e commerce websites. The primary data is collected from the selected customers with the help of a questionnaire developed for the purpose. The SEM approach is used in order to achieve the objective. Findings: Different dimensions of service quality in case of e commerce websites are found to have significant positive impact on the customer trust, loyalty and commitment. It influences the customer trust positively as it diminishes perceptions of uncertainty and perceived risk. It is found to have a substantial positive impact on the consumer loyalty. Lastly it is found to influence consumer commitment and leads to a successful long-term relationship between buyer and seller. Originality/Value