Miracle-dz/UniFAR-FTUs huggingface dataset:
Fluorescence Cross-Correlation Spectroscopy for Real-Time Monitoring of Exogenous DNA Behavior in Living Cells

Many kind of DNA transfection techniques have been developed and widely used in the field of biochemical assay (Boussif et al., 1995, Chu et al., 1987, Felgner et al., 1987). Since recent development of fluorescent proteins such as green fluorescent protein (GFP), its variants and bio sensors, DNA transfection techniques play a greater role in the field of cell biology especially in bioimaging studies. DNA transfection is also used as a key technology to gene therapy (Selkirk, 2004, Schaffert et al., 2008). Thus the development of gene delivery vector with high efficiency is expected. Gene delivery systems with artificial nonviral vectors are widely used in the research field of cell biology and also in the clinical field as gene therapy to promote exogenous gene expression or inhibit production of a target protein. Nonviral vectors have advantages such as a low immune response and no risk of a disorder, which might be caused by native viral vector genome integration (Thomas et al., 2003). However, nonviral vectors need to overcome the disadvantage of low gene expression efficiency compared with native viral vectors (Luo et al., 2000). To increase the expression efficiency, it is needed to know gene delivery mechanisms. In general, complexes of exogenous DNAs and a cationic polymer or cationic lipid, commonly used as nonviral vectors, are internalized to target cells by endocytosis. Then a sequential process progresses spontaneously with escape from endosomes, dissociation of complexes, and diffusion of naked DNAs in the cytoplasm to the nucleus (Fig. 1) (Elouahabi et al., 2005). However, such dynamic properties of transfected DNAs are not yet clearly distinguished because of the lack of suitable technique to observe intracellular DNA behavior. Fluorescence correlation spectroscopy (FCS) is a method based on observation of fluorescence intensity fluctuations that is the result of single fluorescent molecules diffuse in and out of small detection area (Fig. 2A, B) (Eigen et al., 1994). FCS technique can be applied for quantification of the absolute number of fluorescently labeled particles and measuring the molecular weight or size with extremely high sensitivity in a small sample volume, and a physical separation procedure is not needed. Therefore, FCS has currently employed to investigate molecular size or interactions in vitro and in vivo (Kinjo et al., 1995, Kitamura et al., 2006, Remaut et al., 2007, Kinjo et al., 2010). Dual color fluorescence cross-correlation spectroscopy (FCCS), an extended technique of FCS, can monitor molecular interactions directly in addition to parameters given from FCS measurements (Saito et al., 2004, Kogure et al., 2006, Bacia et al., 2007, Kim et al., 2007).
Four o'clock pollination biology: nectaries, nectar and flower visitors in Nyctaginaceae from southern South America

Floral nectary structure and nectar sugar composition were investigated in relation to other floral traits and flower visitors in contrasting species of Nyctaginaceae from southern South America, representing four tribes (Bougainvilleeae, Colignonieae, Nyctagineae, Pisoneae). Our comparative data will aid in the understanding of plant–pollinator interactions and in the development of hypotheses on the origin of floral and reproductive characters in this family. The nectaries are located on the inner side of the staminal tube. The nectariferous tissue is composed of an epidermis and three to ten layers of secretory parenchymal cells, supplied indirectly by the filament vascular bundles. Stomata appear to be associated with nectar secretion. For the first time in Nyctaginaceae, nectary ultrastructure is described in Boerhavia diffusa var. leiocarpa. Nectary parenchyma cells are densely cytoplasmic and contain numerous starch grains. Plasmodesmata connect the nectariferous cells. Flowers of Nyctaginaceae secrete a small volume of nectar of variable concentration (10–47%). Nectar is dominated by hexoses, but Mirabilis jalapa showed a balanced proportion of sucrose and hexoses. Hymenoptera are the most common visitors for most species; nocturnal Lepidoptera are the most common visitors for M. jalapa and Bougainvillea stipitata. We found relatively low variation in the nectary characteristics of Nyctaginaceae compared with broad variation in flower structure, shape, colour and nectar traits. © 2013 The Linnean Society of London
The complementary structure of the superficial and deep surfaces of the cells lof the stratum corneum of the hard palate in the rat

The supeerficial and deep surfaces of the cells of the stratum corneum from the hard palate of the rat were examined in the scanning electron mictroscope. The appearances were compared with those seen in thin sections. In the scanning electron microscope, the superficial surface of each epithelial cell, whether it was situated on the exposed surface or more deepley within the epithelium, had a honeycomb surface pattern of inteerconnecting ridges surrounding depressions. Lateral cell boundaries consisted of two ridges separated by a gap, and the imprints of the edges of the overlying cells were formed by single raised ridges which crossed on to adjacent cells. The deep surface of the cells was covered by microvilli, a deepo groove separated teh margins of adjacent cells, and the imprints of the cell boundaries of the underlying cells were formed by shallower grooves which also crossed on to adjacet cells, The sectionaal appearance of the stratum corneum, as seen in the transmissison electron microscope, confirmed that the cells at different levels overlapped. It also confirmed that the microvilli and grooves on teh deepo surface of the cells were truly complementary and intimately related to the depressions and ridges on the superficial surfaces of opposing cells.
Rôle des topoisomérases de type IA dans la ségrégation des chromosomes chez Escherichia coli

E. coli possesses two type IA topoisomerases (topos), namely topo I (topA) and topo III (topB). The major function of topo I is the relaxation of excess negative supercoiling. Much less is known about the function of topo III. Cells lacking both type IA topos suffer from severe chromosome segregation and growth defects. We show that these defects are mostly related to the presence of gyrase mutations that prevent excess negative supercoiling in topA null mutants. Indeed, increasing gyrase activity by spontaneous mutations, by substituting a gyrB(Ts) allele for a wild-type one or by exposing cells carrying the gyrB(Ts) allele to permissive temperatures, significantly corrected the growth and segregation defects of cells lacking type IA topo activity. We also found that topB mutants are hypersensitive to novobiocin due to gyrase inhibition. Our data also suggest that unregulated replication occurring in the absence of topA and rnhA (RNase HI) exacerbates the need for topo III activity. Moreover, when topA and rnhA were absent, we found that topo III overproduction reduced the extensive DNA degradation that took place in the absence of recA (RecA). All together, our results lead us to propose a role for topo III in chromosome segregation when gyrase activity is suboptimal, thus reducing replication forks collapse, especially when replication is unregulated due to the absence of topo I and RNase HI.
Induction of somatic embryogenesis and organogenesis from hypocotyl of muskmelon (Cucumis melo L.)

to genotypes and inoculation medium. Culture medium MSD.5B (MS + 1. 0 mg. l -1 2,4-D + 0. 5 mg. l -1 BA + 30.0 g. l -1 sucrose + 7.5 g.l -1 agar) induced direct somatic embryogenesis (21.77%) in higher frequencies. Average number of somatic embryo(s) per explant in higher number (s) (25.16) was induced by induction medium MS2D.5B (MS + 2. 0 mg. l -1 2, 4-D + 0.
What defines mast seeding? Spatio‐temporal patterns of cone production by whitebark pine

1. Synchronous, episodic mast seeding is common in plant populations, and is thought to increase plant fitness through economies of scale, such as satiating seed predators, attracting seed dispersers and enhancing pollination success. Although mast seeding is easy to conceptualize, it has been quantified using a number of different metrics that reflect different features of pulsed reproduction.
Studies into host macrophage transcriptional control by the African Swine Fever Virus protein A238L

The African swine fever virus A238L protein inhibits calcineurin phosphatase activity and activation of NF-κB and p300 co-activator. An 82 amino acid domain containing residues 157 to 238 at the C-terminus of A238L was expressed in E. coli and purified. This purified A238L fragment acted as a potent inhibitor of calcineurin phosphatase in vitro with an IC50 of approximately 70 nM. Two putative nuclear localisation signals were identified between residues 80 to 86 (NLS-1) and between residues 203 to 207 overlapping with the N-terminus of the calcineurin docking motif (NLS-2). Mutation of these motifs independently did not reduce nuclear localisation compared to the wild type A238L protein, whereas mutation of both motifs significantly reduced nuclear localisation of A238L. Mutation of the calcineurin docking motif resulted in a dramatic increase in the nuclear localisation of A238L provided an intact NLS was present. We propose that binding of calcineurin to A238L masks NLS-2 contributing to the cytoplasmic retention of A238L. Crown Copyright © 2008 Published by Elsevier Inc. All rights reserved.
α‐Synuclein–synaptosomal membrane interactions

α-Synuclein exists in two different compartments in vivo– correspondingly existing as two different forms: a membrane-bound form that is predominantly α-helical and a cytosolic form that is randomly structured. It has been suggested that these environmental and structural differences may play a role in aggregation propensity and development of pathological lesions observed in Parkinson's disease (PD). Such effects may be accentuated by mutations observed in familial PD kindreds. In order to test this hypothesis, wild-type and A53T mutant α-synuclein interactions with rat brain synaptosomal membranes were examined. Previous data has demonstrated that the A30P mutant has defective lipid binding and therefore was not examined in this study. Electron microscopy demonstrated that wild-type α-synuclein fibrillogenesis is accelerated in the presence of synaptosomal membranes whereas the A53T α-synuclein fibrillogenesis is inhibited under the same conditions. These results suggested that subtle sequence changes in α-synuclein could significantly alter interaction with membrane bilayers. Fluorescence and absorption spectroscopy using environment sensitive probes demonstrated variations in the inherent lipid properties in the presence and absence of α-synuclein. Addition of wild-type α-synuclein to synaptosomes did not significantly alter the membrane fluidity at either the fatty acyl chains or headgroup space, suggesting that synaptosomes have a high capacity for α-synuclein binding. In contrast, synaptosomal membrane fluidity was decreased by A53T α-synuclein binding with concomitant packing of the lipid headgroups. These results suggest that alterations in α-synuclein–lipid interactions may contribute to physiological changes detected in early onset PD.
Understanding active abl kinase conformations: Application to discovery of small molecule allosteric modulators

The c-Abl protein-tyrosine kinase regulates diverse cellular signaling pathways involved in cell growth, adhesion, and responses to genotoxic stress. Abl is well known in the context of Bcr-Abl, the active fusion tyrosine kinase, which causes chronic myelogenous leukemia (CML) and other leukemias. The tyrosine kinase activity of Abl is tightly regulated by auto-inhibitory interactions involving its non-catalytic SH3 and SH2 domains. Mutations that perturb these intramolecular interactions result in kinase activation. This study examined the effect of activating mutations on the biochemistry and solution structure of Abl core proteins. In an active myristic acid-binding pocket mutant (A356N), the relative positions of the regulatory N-cap, SH3 and SH2 domains were virtually identical to those of the assembled wild-type core despite differences in catalytic activity and thermal stability. In contrast, a dramatic structural rearrangement in an active gatekeeper mutant (T315I) was observed with the positions of the SH2 and SH3 domains reversed relative to wild-type. These results show that Abl kinases can adopt multiple conformations in solution and kinase activation does not necessarily require destabilization of the assembled core structure. Small molecules that allosterically regulate Abl kinase activity through its non-catalytic domains may represent selective probes of Abl function. I developed a screening assay to identify chemical modulators of Abl kinase activity that either disrupt or stabilize the regulatory interaction of the SH3 domain with the SH2-kinase linker. This fluorescence polarization (FP) assay is based on a recombinant Abl protein containing the regulatory domains (Ncap-SH3-SH2-linker, N32L) and a short fluorescein-labeled probe peptide that binds the SH3 domain. The probe peptide binds the recombinant Abl N32L protein in vitro producing a robust FP signal. Mutation of the SH3 binding site (W118A) or introduction of a high-affinity linker both resulted in loss of the FP signal. Pilot screens were performed with two chemical libraries (2800 compounds total), and thirteen compounds were found to specifically inhibit the FP signal. Secondary assays showed that one of these hit compounds enhances Abl kinase activity in vitro. These results show that screening assays based on the regulatory domains of Abl can identify allosteric modulators of kinase function.
Geographic Variations and Taxonomic Status of Myotis myotis (Borkhausen,1797) in Turkey ( Chiroptera: Vespertilionidae)

This study is a taxonomical evaluation of 146 specimens of Myotis myotis (Borkhausen, 1797) collected in Turkey between 1974 and 1994. Turkish Myotis myotis were compared with records from the Palaearctic Region. It was determined that both Myotis myotis myotis and Myotis myotis macrocephalicus are distributed in Turkey. The diagnostic characters, habitat, pelage colour, external and cranial measurements and distribution of each taxon were recorded.
Role of HIV-1 Vpr on Host-Cellular Functions: Cell-Specific Analysis in Productively-Infected Macrophages

Progression of human immunodeficiency virus type 1 (HIV-1) pathogenesis impedes on the patient’s ability to combat foreign pathogens by infecting immune cells, a disease commonly referred to as acquired immunodeficiency syndrome (AIDS). In addition to the onset of AIDS, HIV-1 is known to cause other health issues over time, including cardiovascular disease, premature aging, neurocognitive impairment, and dementia. The quality of life for HIV-1-positive patients has drastically increased with the introduction of highly active anti-retroviral therapies (HAART). Though the use of HAART treatments lower the incidence of HIV-1-associated comorbidities, including dementia, more understanding on HIV-1-associated comorbidities is necessary to help further improve the quality of life for HIV-1-positive patients, which is of considerable public health significance. This study focuses on the role of the HIV-1 accessory protein viral protein R (Vpr) in HIV-1 pathogenesis. Previous studies in our laboratory have established a role for Vpr in HIV-1 immunopathogenesis and neuropathogenesis, particularly in the modulation of cytokines and chemokines, including IL-8 and IL-1β, in monocyte-derived macrophages and dendritic cells. These proinflammatory cytokines were additionally found to cause immune dysregulation and neuronal injury. As a result, this study focuses on understanding the origin of these cytokines within subpopulations of monocyte-derived macrophages: productively-infected macrophages that are actively producing virions and non-productively-infected macrophages, which include latently-infected macrophages, uninfected macrophages, and macrophages exposed to virus particles and viral proteins. In order to distinguish between the two groups, reporter viruses were created that are capable of infecting macrophages and expressing the enhanced green fluorescence protein (EGFP) upon replication. Productively-infected macrophages were successfully identified from non-productively-infected macrophages by utilizing EGFP expression, which allowed for cell-specific analysis of cytokine expression within the macrophage subpopulations. Productively-infected macrophages yielded a decrease in IL-8 and IL-1β when infected with Vpr-deficient (∆Vpr) reporter viruses, while non-productively-infected and exposed macrophages showed no noticeable difference. Similarly, a virion association defective mutant of Vpr (Vpr-A30L) resulted in lower amounts of IL-8 expression. These results elucidate the distinct role of Vpr in IL-1β and IL-8 expression in the virion-associated forms and during de novo synthesis in productively-infected macrophages.
Comparative study of Aspergillus niger and Penicillium sp. in the biodegradation of automotive gas oil (AGO) and premium motor spirit (PMS)

The comparative study of Aspergillus niger and Penicillium sp. in the biodegradation of automotive gas oil (AGO) and premium motor spirit (PMS) was carried out to ascertain the effectiveness of using these microorganisms in cleaning and restoring the ecosystem when polluted by petroleum products. These fungi were observed to grow at all concentrations of the petroleum products (pollutant) used, but the growth on AGO was considerably reduced compared to the growth on PMS. The mycelia growth of A. niger was observed to be faster in PMS than in AGO. The ability of A. niger and Penicillium sp. to tolerate these pollutants and grow on them, suggest that they can be employed as bioremediation agents and can be used in restoring the ecosystem when contaminated by these pollutants.
The computational power of optimization in online learning

We consider the fundamental problem of prediction with expert advice where the experts are “optimizable”: there is a black-box optimization oracle that can be used to compute, in constant time, the leading expert in retrospect at any point in time. In this setting, we give a novel online algorithm that attains vanishing regret with respect to N experts in total O(√N) computation time. We also give a lower bound showing that this running time cannot be improved (up to log factors) in the oracle model, thereby exhibiting a quadratic speedup as compared to the standard, oracle-free setting where the required time for vanishing regret is Θ(N). These results demonstrate an exponential gap between the power of optimization in online learning and its power in statistical learning: in the latter, an optimization oracle—i.e., an efficient empirical risk minimizer—allows to learn a finite hypothesis class of size N in time O(logN). We also study the implications of our results to learning in repeated zero-sum games, in a setting where the players have access to oracles that compute, in constant time, their best-response to any mixed strategy of their opponent. We show that the runtime required for approximating the minimax value of the game in this setting is Θ(√N), yielding again a quadratic improvement upon the oracle-free setting, where Θ(N) is known to be tight.
Efficacy of different entomopathogenic fungi against cowpea aphid, Aphis craccivora Koch under laboratory and field condition.

Cowpea aphid, Aphis craccivora Koch is an important pest of wide range of leguminous crops such as cowpea, groundnut, pigoenpea, chickpea, peas, mungbean and urdbean. Both nymphs and adults infest all the stages of crop growthby sucking cell sap from tender shoots, flower stalks and pods resulting in stunting of plant growth and can cause yield loss of 20-40 per cent (Singh and Allen, 1980) due to transmission of virus diseases such as rosette, mottles, stunt and stripe (Porter et al., 1984). It is a difficult pest to control with insecticides because of its polyphagous nature with very short life cycle and high reproduction rates. Fungi have been considered the principal group of aphid pathogens, the most prevalent and widely encountered species belonging to the order Entomopthorales (Zygomycetes). In particular environments (green house/tropical regions) Deutermycetous species also significantly reduce aphid numbers. V. lecanii is a well documented, extremely wide spread entomopathogen and spectacular epizootics are observed on its most common hosts viz., aphids and scales in tropical and sub tropical region (Hall, 1980). In this context efforts have been made to evaluate efficacy of fungal entomopathogens on cowpea aphids under laboratory and field conditionss.
Response of prilled and neem extract coated urea application timings to rice (Oryza sativa).

The application of neem extract coated urea (NCU) 50% basal + 25 % at tillering + 25% at panicle initiation (PI) stage recorded the maximum grain and straw yield. N concentration and uptake, nitrogen use efficiency and nitrogen recovery. The application of 30% NEU as basal + priDed urea (PU) 40% at tiDering and 30% at PI stage or NCU 75% basal and 25% at PI stage performed as good as application of NCU 50% basal + 25 at tillering + 25% at PI stage for grain yield, N concentration and N uptake of rice.
Who Trusts? Ethnicity, Integration, and Attitudes Toward Elected Officials in Urban Nigeria

In the developing world, politicians often use public office to redistribute resources to their core constituencies. This form of clientelistic exchange motivates ethnic voting in Africa and may also shape broader attitudes toward the state. But does clientelism retain its power as cross-ethnic contact increases, or might new forms of political linkage emerge? This article uses public opinion data from urban Nigeria to investigate how social position affects trust in elected local officials. The article finds that local ethnic minorities are less trusting of local officials, but this trust deficit does not diminish as cross-ethnic contact rises. For members of locally dominant ethnic groups, however, greater cross-ethnic contact and lessened ethnic attachment dampen expressed trust in local elected officials. The article argues that ethnic clientelism is resilient in urban contexts but that scholarship must take a more nuanced approach to assessing membership in clientelistic coalitions.
Effects of transport distance and the season of the year on death rates among hens and roosters in transport to poultry processing plants in the Czech Republic in the period from 1997 to 2004

Poor welfare is the cause of high mortality among hens and roosters transported to poultry processing plants. In the Czech Republic, death rates among hens and roosters in transport to poultry slaughter plants were monitored between 1997 and 2004, and their total mortality rate was in the 0.925% ± 0.479% range. Death rates among hens and roosters were influenced by the transport distance to poultry processing plants. The percentage of dead birds increased from 0.592% ± 0.575% at transport distances up to 50 km to 1.638% ± 0.952% at transport distances up to 300 km. The bird mortality was also influenced by the season of the year. Higher mortality rates were ascertained during the cold months of the year, specifically in October through to April.