Miracle-dz/UniFAR-FTUs huggingface dataset:
eIF2B as a Target for Viral Evasion of PKR-Mediated Translation Inhibition

RNA-activated protein kinase (PKR) is one of the most powerful antiviral defense factors of the mammalian host. PKR acts by phosphorylating mRNA translation initiation factor eIF2α, thereby converting it from a cofactor to an inhibitor of mRNA translation that strongly binds to initiation factor eIF2B. To sustain synthesis of their proteins, viruses are known to counteract this on the level of PKR or eIF2α or by circumventing initiation factor-dependent translation altogether. Here, we report a different PKR escape strategy executed by sandfly fever Sicilian virus (SFSV), a member of the increasingly important group of phleboviruses. We found that the nonstructural protein NSs of SFSV binds to eIF2B and protects it from inactivation by PKR-generated phospho-eIF2α. Protein synthesis is hence maintained and the virus can replicate despite ongoing full-fledged PKR signaling in the infected cells. Thus, SFSV has evolved a unique strategy to escape the powerful antiviral PKR. ABSTRACT RNA-activated protein kinase (PKR) is a major innate immune factor that senses viral double-stranded RNA (dsRNA) and phosphorylates eukaryotic initiation factor (eIF) 2α. Phosphorylation of the α subunit converts the eIF2αβγ complex into a stoichiometric inhibitor of eukaryotic initiation factor eIF2B, thus halting mRNA translation. To escape this protein synthesis shutoff, viruses have evolved countermechanisms such as dsRNA sequestration, eIF-independent translation by an internal ribosome binding site, degradation of PKR, or dephosphorylation of PKR or of phospho-eIF2α. Here, we report that sandfly fever Sicilian phlebovirus (SFSV) confers such a resistance without interfering with PKR activation or eIF2α phosphorylation. Rather, SFSV expresses a nonstructural protein termed NSs that strongly binds to eIF2B. Although NSs still allows phospho-eIF2α binding to eIF2B, protein synthesis and virus replication are unhindered. Hence, SFSV encodes a unique PKR antagonist that acts by rendering eIF2B resistant to the inhibitory action of bound phospho-eIF2α. IMPORTANCE RNA-activated protein kinase (PKR) is one of the most powerful antiviral defense factors of the mammalian host. PKR acts by phosphorylating mRNA translation initiation factor eIF2α, thereby converting it from a cofactor to an inhibitor of mRNA translation that strongly binds to initiation factor eIF2B. To sustain synthesis of their proteins, viruses are known to counteract this on the level of PKR or eIF2α or by circumventing initiation factor-dependent translation altogether. Here, we report a different PKR escape strategy executed by sandfly fever Sicilian virus (SFSV), a member of the increasingly important group of phleboviruses. We found that the nonstructural protein NSs of SFSV binds to eIF2B and protects it from inactivation by PKR-generated phospho-eIF2α. Protein synthesis is hence maintained and the virus can replicate despite ongoing full-fledged PKR signaling in the infected cells. Thus, SFSV has evolved a unique strategy to escape the powerful antiviral PKR.
WHAT ARE THE ISSUES WITH PRESENCE–ABSENCE DATA FOR WILDLIFE MANAGERS?

Abstract Presence–absence data can be useful to wildlife managers in a wide variety of contexts, from monitoring populations at large spatial scales to identifying habitats that are of high value to specific species of conservation concern. However, a key issue is that a species may be declared “absent” from a landscape unit simply as a result of not detecting the species using the prescribed sampling methods. The effect of this imperfect detection is that parameter estimates will be biased, and any modeling of the data provides a description of the surveyors' ability to find the species on the landscape, not where the species is on the landscape. The reliability of so-called “presence–absence” data for making sound management decisions and valid scientific conclusions could therefore be questioned. However, after collecting appropriate data (i.e., repeated surveys of landscape units within a relatively short timeframe), recently developed statistical models can be used to obtain unbiased parameter estimates. Here I provide a nontechnical overview of the issues that pertain to wildlife studies or monitoring programs that seek to make reliable inference about the presence or absence of a target species.
Abundance indices: reliability testing is crucial - a field case of wild rabbit Oryctolagus cuniculus

Abstract We examined an index of abundance for rabbits Oryctolagus cuniculus involving a spotlight plot count (SPC) using capture-mark-resighting as a reference method in five study areas. In these areas, density varied over a wide range, from 0.7 to 23.4 rabbits/ha, which is representative of most European populations. The SPC precision was good, as the coefficient of variation ranged within 5-54%, the median value being 17%. We showed area and year effects on the index and a significant relationship between the SPC and ln(density) (P < 0.0001). The logarithmic relationship between density and SPC suggests a saturation of the index when density increases. Despite the fact that the SPC index was highly correlated with density, its ability to detect population changes was rather poor. This lack of sensitivity may be due to factors affecting rabbit detectability such as climatic conditions, lunar phases, observers, changes in crop rotation and, more generally, to factors affecting the number of rabbits above ground at the time of the count. The area effect means that the index is not suitable for comparing data recorded in different areas. The year effect is an actual obstacle to the use of this index since, within a defined area, the temporal changes in the index values are not related only to the estimated density. Our study highlights the necessity to validate abundance indices against reference methods so as to check their ability to detect changes in population size and their suitability for comparing data from different areas.
Changes in cytosine methylation and DNA sequence induced by ethylmethane sulfonate in rice

Although genetic mutagenicity of the chemical ethylmethane sulfonate (EMS) is well established, it remains un- clear whether and to what extent this compound is epigenetically mutagenic. This issue was studied in Oryza sativa L. (rice) by conducting a parallel investigation using two molecular markers, amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP), on two sets of EMS-treated M0 plants: phenotypically normal and altered. Although more methylation than genetic changes were induced by the EMS-treatments in both sets of plants, the greatest differences were observed in the set of plants with altered phenotypes, suggesting a role of induced epi- genetic variation in causing the phenotypic novelties. Moreover, the frequencies of the two types of instabilities induced by the EMS treatment, genetic and epigenetic, are correlated, implicating a common or overlapping mutagenic basis.
Parent‐of‐origin specific effects on the methylation of a transgene in the zebrafish, Danio rerio

We have examined the inheritance of a transgene locus in the zebrafish, Daniorerio and demonstrated that its methylation is af fected by the sex of the parent contributing the allele. This parent-of-origin effect on the zebrafish transgene appears to be identical to imprinting as seen in mammals except that in zebrafish, passage of the locus through a female tended to decreased its methylation, whereas passage through a male increased it. Methylation of the transgene in gametic tissues differed from somatic tissue with the locus being hypomethylated in sperm and hypermethylated in the unfertilized egg. The potential identification of imprinting in the zebrafish has important ramifications with respect to the evolution of the process as well as for understanding the role of imprinting in mammals. © 1995 Wiley-Liss, Inc.
A Machine Learning Approach to Objective Cardiac Event Detection

This paper presents an automated framework for the detection of the QRS complex from Electrocardiogram (ECG) signals. We introduce an artefact-tolerant pre-processing algorithm which emphasises a number of characteristics of the ECG that are representative of the QRS complex. With this processed ECG signal we train Logistic Regression and Support Vector Machine classification models. With our approach we obtain over 99.7% detection sensitivity and precision on the MIT-BIH database without using supplementary de-noising or pre-emphasis filters.
Habitat of Origin and Changes in Water Chemistry Influence Development of Western Chorus Frogs

Abstract A variety of biotic and abiotic variables have been shown to affect length of larval period and size of juveniles at metamorphosis in amphibians. However, influence of water quality on phenotypic plasticity of growth and development of tadpoles generally has received less attention. We examined how abiotic factors in the larval environment change over time and how these changes affect the growth and development of larval amphibians. Western Chorus Frogs, Pseudacris triseriata, in tallgrass prairie breed in ephemeral aquatic habitats including intermittent streams and bison wallows. Our objectives were to determine whether abiotic factors in the larval environment of P. triseriata changed predictably as pools dried and to determine whether these changes affected growth and development of tadpoles when the environment was simulated in the laboratory. In our field studies, pH increased gradually in wallows, whereas ammonium increased in streams, as each habitat dried. In the laboratory, we examined the effects of increased levels of pH and ammonium on growth and development of tadpoles collected from both wallows and streams. Tadpoles collected from streams metamorphosed significantly faster in the high ammonium treatment than tadpoles from wallows. In contrast, tadpoles from wallows metamorphosed faster in the high pH treatment than tadpoles collected from streams. Growth rates of tadpoles from streams were not significantly affected by high pH, whereas those from wallows were not significantly affected by high ammonium treatments. We suggest that changes in abiotic factors over the course of the larval period may influence developmental rate and that natal habitat may determine how tadpoles respond to changes in abiotic factors.
Feeding Response of Aedes aegypti and Anopheles dirus (Diptera: Culicidae) Using Out-of-Date Human Blood in a Membrane Feeding Apparatus

ABSTRACT: The colonization of Aedes aegypti and Anopheles dirus was performed using out-of-date human blood from a blood bank as a nutritional supply dispensed from a common artificial feeder. Preserved human blood was collected and used for feeding on days 5, 15, and 25 after date of expiration and dispensed from a common artificial feeder to rear the mosquitoes. Ae. aegypti had a feeding rate of 78.7, 62, and 18% at the respective intervals while An. dirus had a rate of 80, 56.8, and 7.3% on the same respective days. Direct feeding on live hamsters resulted in a rate of 96 and 90% for Ae. aegypti and An. dirus, respectively. Although egg production rates decreased from the day 5 feeding to the day 25 feeding, all of the developmental stages resulting from An. dirus fed at day 5 and 15 showed insignificant differences when compared with direct feeding on the blood of a hamster.
First report of endosymbionts in Dreissena polymorpha from the brackish Curonian Lagoon, SE Baltic Sea

Abstract We report the first results of a parasitological study of Dreissena polymorpha (zebra mussels) from the brackish Curonian Lagoon, SE Baltic Sea. Zebra mussels were collected monthly from May to October 2011 from a site near the mouth of the River Nemunas. Three types of endosymbionts were found in the mantle cavity and visceral mass of the molluscs during dissections, i.e. the commensal ciliate Conchophthirus acuminatus and parasitic ciliate Ophryoglena sp. , and rarely encountered, unidentified nematodes. The abundances of C. acuminatus and Ophryoglena sp. were positively associated with host shell length and water temperature, but no effect of water salinity was detected. As the endosymbionts are either highly host-specific to zebra mussels ( C. acuminatus and Ophryoglena sp.) or are probably free-living organisms that inadvertently infect the molluscs (nematodes), we conclude that the presence of D. polymorpha in the Curonian Lagoon does not pose any serious parasitological risk to native biota. We emphasize, however, that this conclusion should be treated with caution as it is based on a study conducted only at a single location. Our work extends the currently scarce records of D. polymorpha parasites and commensals from brackish waters, and adds to a better understanding of the ecological impact this highly invasive mollusc causes in the areas it has invaded.
In Vivo Replication of Recombinant Murine Cytomegalovirus Driven by the Paralogous Major Immediate-Early Promoter-Enhancer of Human Cytomegalovirus

ABSTRACT Transcription of the major immediate-early (MIE) genes of cytomegaloviruses (CMV) is driven by a strong promoter-enhancer (MIEPE) complex. Transactivator proteins encoded by these MIE genes are essential for productive infection. Accordingly, the MIEPE is a crucial control point, and its regulation by activators and repressors is pertinent to virus replication. Since the MIEPE contains multiple regulatory elements, it was reasonable to assume that specific sequence motifs are irreplaceable for specifying the cell-type tropism and replication pattern. Recent work on murine CMV infectivity (A. Angulo, M. Messerle, U. H. Koszinowski, and P. Ghazal, J. Virol. 72:8502–8509, 1998) has documented the proposed enhancing function of the enhancer in that its resection or its replacement by a nonregulatory stuffer sequence resulted in a significant reduction of infectivity, even though replication competence was maintained by a basal activity of the spared authentic MIE promoter. Notably, full capacity for productive in vitro infection of fibroblasts was restored in recombinant viruses by the human CMV enhancer. Using two-color in situ hybridization with MIEPE-specific polynucleotide probes, we demonstrated that a murine CMV recombinant in which the complete murine CMV MIEPE is replaced by the paralogous human CMV core promoter and enhancer (recombinant virus mCMVhMIEPE) retained the potential to replicate in vivo in all tissues relevant to CMV disease. Notably, mCMVhMIEPE was also found to replicate in the liver, a site at which transgenic hCMV MIEPE is silenced. We conclude that productive in vivo infection with murine CMV does not strictly depend on a MIEPE type-specific regulation.
The Interpretation of the Variations in Leaf Water Potential and Stomatal Conductance Found in Canopies in the Field

Attempts to correlate values of stomatal conductance and leaf water potential with particular environmental variables in the field are generally of only limited success because they are simultaneously affected by a number of environmental variables. For example, correlations between leaf water potential and either flux of radiant energy or vapour pressure deficit show a diurnal hysteresis which leads to a scatter diagram if many values are plotted. However, a simple model may be adequate to relate leaf water potential to the flow of water through the plant. The stomatal conductance of illuminated leaves is a function of current levels of temperature, vapour pressure deficit, leaf water potential (really turgor pressure) and ambient CO $_2$ concentration. Consequently, when plotted against any one of these variables a scatter diagram results. Physiological knowledge of stomatal functioning is not adequate to provide a mechanistic model linking stomatal conductance to all these variables. None the less, the parameters describing the relationships with the variables can be conveniently estimated from field data by a technique of non-linear least squares, for predictive purposes and to describe variations in response from season to season and plant to plant.
Deletion of the R78 G Protein-Coupled Receptor Gene from Rat Cytomegalovirus Results in an Attenuated, Syncytium-Inducing Mutant Strain

ABSTRACT The rat cytomegalovirus (RCMV) R78 gene belongs to an uncharacterized class of viral G protein-coupled receptor (GCR) genes. The predicted amino acid sequence of the R78 open reading frame (ORF) shows 25 and 20% similarity with the gene products of murine cytomegalovirus M78 and human cytomegalovirus UL78, respectively. The R78 gene is transcribed throughout the early and late phases of infection in rat embryo fibroblasts (REF) in vitro. Transcription of R78 was found to result in three different mRNAs: (i) a 1.8-kb mRNA containing the R78 sequence, (ii) a 3.7-kb mRNA containing both R77 and R78 sequences, and (iii) a 5.7-kb mRNA containing at least ORF R77 and ORF R78 sequences. To investigate the function of the R78 gene, we generated two different recombinant virus strains: an RCMV R78 null mutant (RCMVΔR78a) and an RCMV mutant encoding a GCR from which the putative intracellular C terminus has been deleted (RCMVΔR78c). These recombinant viruses replicated with a 10- to 100-fold-lower efficiency than wild-type (wt) virus in vitro. Interestingly, unlike wt virus-infected REF, REF infected with the recombinants develop a syncytium-like appearance. A striking difference between wt and recombinant viruses was also seen in vivo: a considerably higher survival was seen among recombinant virus-infected rats than among RCMV-infected rats. We conclude that the RCMV R78 gene encodes a novel GCR-like polypeptide that plays an important role in both RCMV replication in vitro and the pathogenesis of viral infection in vivo.
Transfection of 6-23 A Rat Thyroid Carcinoma Cell Line, with the Neuropeptide Y cDNA

Neuropeptide Y (NPY) is a 36 amino acid peptide found throughout the central and peripheral nervous system of rat and human. NPY has been proposed to play an important role in satiety. The aim of this study was to produce cell lines that secrete high levels of bioactive NPY. For this purpose, the complementary DNA (cDNA) that encodes NPY was isolated by PCR. The cDNA was then cloned into pCEP4, to form pCEP4NPY. 6-23 cells were transfected with pCEP4NPY by electroporation. Transfected cells were selected by the addition of hygromycin B to the culture medium. Resistant colonies were picked and transferred to 96-well plates. The medium was tested for IRNPY using a specific NPY radioimmunoassay (RIA). The IR-NPY secreted by the cells was characterized by sephadex G 50 chromatography and reversed phase fast protein liquid chromatography (FPLC). It was found to co-elute with the synthetic standard in both cases. RNA was extracted from the cells and subjected to Northern blot analysis using labeled NPY cDNA as a probe. The cells were found to express high levels of NPY at mRNA levels.
Revised diagnosis and redescription of Apistobuthus susanae (Scorpiones, Buthidae)

Abstract The scorpion Apistobuthus susanae Lourenço 1998 is redescribed based on new specimens collected from Khoozestan Province, Iran. It is distinct from A. pterygocercus Finnegan 1932 found in the dunes of Rub' al-Khali. The two species cannot be separated by previously used diagnostic characters. Instead, A. susanae is differentiated from A. pterygocercus by new characters, including more robust legs and pedipalps, shorter pectines, stronger carination, and complete fusion of central lateral and posterior median carinae of the carapace.
Polo-like kinase 1 siRNA-607 induces mitotic arrest and apoptosis in human nasopharyngeal carcinoma cells

Polo-like kinase (Plk) 1 is overexpressed in many human malignancies including nasopharyngeal carcinoma, indicating its potential as a therapeutic target. Recently, using a simple cellular morphologybased strategy, we have identified several novel effective siRNAs against Plk1 including Plk1 siRNA- 607. In this study, we further investigated the effects of Plk1 siRNA-607 in human nasopharyngeal carcinoma cell line, HNE-1. Real time RT-PCR and Western blot indicated that Plk1 siRNA-607 transfection resulted in a significant inhibition in Plk1 expression in the HNE-1 cells. Furthermore, cell cycle, cell growth and apoptosis analysis clearly indicated that Plk1 siRNA-607 caused a dramatic mitotic cell cycle arrest followed by massive apoptotic cell death, and eventually resulted in a significant decrease in growth and viability of the nasopharyngeal carcinoma cells. Given that Plk1 has been widely accepted as a novel efficient target for cancer therapy, these results suggested that Plk1 siRNA-607 could be further developed for the treatment of human nasopharyngeal carcinoma. Key words: Nasopharyngeal carcinoma, Plk1, RNA silencing, cell cycle, apoptosis.
Isolation of astaxanthin from marine yeast and study of its pharmacological activity.

The aim of the present study was to isolate and study about the antibacterial activity of astaxanthin from marine yeast. Astaxanthin a carotenoid present in marine yeast and crustaceans posses a wide range of pharmacological activity. Yeast strain was isolated from the marine sediments collected from Cochin, Kerala during the month of August 2012. The samples were collected in sterile plastic covers and brought to the laboratory without exposing to the external environment further. The marine sediment samples were directly inoculated in yeast malt. After effective screening the strains containing astaxanthin was refrigerated for further use. The strains were purified by TLC using petroleum hexane: acetone (3:1). A spectrophotometric assay was carried out by measuring absorbance at 200-500nm. The antibacterial activity was studied on several organisms like Bacillus Subtilis , Salmonella typhi , Staphylococcus aureus and Pseudomonas aeroginosa . The extracts showed excellent antibacterial activity than the standard chloramphenicol. Among this, Pseudomonas aeroginasa showed maximum inhibition. DOI: http://dx.doi. org/10.3329/icpj.v2i3. 13584 International Current Pharmaceutical Journal, February 2013, 2(3): 67-69
Isolation of an Arabidopsis thalianaMutant in Which the Multiplication of both Cucumber Mosaic Virus and Turnip Crinkle Virus Is Affected

ABSTRACT During the systemic infection of plants by viruses, host factors play an important role in supporting virus multiplication. To identify and characterize the host factors involved in this process, we isolated an Arabidopsis thaliana mutant named RB663, in which accumulation of the coat protein (CP) of cucumber mosaic virus (CMV) in upper uninoculated leaves was delayed. Genetic analyses suggested that the phenotype of delayed accumulation of CMV CP in RB663 plants was controlled by a monogenic, recessive mutation designatedcum2-1, which is located on chromosome III and is distinct from the previously characterized cum1 mutation. Multiplication of CMV was delayed in inoculated leaves of RB663 plants, whereas the multiplication in RB663 protoplasts was similar to that in wild-type protoplasts. This suggests that the cum2-1mutation affects the cell-to-cell movement of CMV rather than CMV replication within a single cell. In RB663 plants, the multiplication of turnip crinkle virus (TCV) was also delayed but that of tobacco mosaic virus was not affected. As observed with CMV, the multiplication of TCV was normal in protoplasts and delayed in inoculated leaves of RB663 plants compared to that in wild-type plants. Furthermore, the phenotype of delayed TCV multiplication cosegregated with thecum2-1 mutation as far as we examined. Therefore, thecum2-1 mutation is likely to affect the cell-to-cell movement of both CMV and TCV, implying a common aspect to the mechanisms of cell-to-cell movement in these two distinct viruses.