Miracle-dz/UniFAR-FTUs huggingface dataset:
Strain-Specific Single-Nucleotide Polymorphism Assays for the Bacillus anthracis Ames Strain

ABSTRACT Highly precise diagnostics and forensic assays can be developed through a combination of evolutionary analysis and the exhaustive examination of genomic sequences. In Bacillus anthracis, whole-genome sequencing efforts revealed ca. 3,500 single-nucleotide polymorphisms (SNPs) among eight different strains and evolutionary analysis provides the identification of canonical SNPs. We have previously shown that SNPs are highly evolutionarily stable, and the clonal nature of B. anthracis makes them ideal signatures for subtyping this pathogen. Here we identified SNPs that define the lineage of B. anthracis that contains the Ames strain, the strain used in the 2001 bioterrorist attacks in the United States. Sequencing and real-time PCR were used to validate these SNPs across B. anthracis strains, including (i) 88 globally and genetically diverse isolates; (ii) isolates that were shown to be genetic relatives of the Ames strain by multiple-locus variable number tandem repeat analysis (MLVA); and (iii) several different lab stocks of the Ames strain, including a clinical isolate from the 2001 letter attack. Six SNPs were found to be highly specific for the Ames strain; four on the chromosome, one on the pX01 plasmid, and one on the pX02 plasmid. All six SNPs differentiated the B. anthracis Ames strain from the 88 unique B. anthracis strains, while five of the six separated Ames from its close genetic relatives. The use of these SNPs coupled with real-time PCR allows specific and sensitive (<100 fg of template DNA) identification of the Ames strain. This evolutionary and genomics-based approach provides an effective means for the discovery of strain-specific SNPs in B. anthracis.
Rifampin-resistant mutants of Myxococcus xanthus defective in development

Rifampin, an antibiotic which is known to bind to and inhibit RNA polymerase, was used to probe the molecular regulation of development in Myxococcus xanthus. Rifampin-resistant mutants were screened for defects in fruiting-body formation. About 20% of the isolates in the initial screenings showed major defects in developmental aggregation or sporulation. Eleven independent mutants with wild-type growth rates and stable phenotypes were analyzed by transduction. In these strains, the rifampin-resistant and nonfruiting phenotypes showed cotransduction frequencies equal to or greater than 99.0 to 99.9%. The RNA polymerase activities were resistant to rifampin in vitro, indicating that the RNA polymerase is altered in these strains. Although their fruiting phenotypes are heterogeneous, these strains can be divided into two classes based on the level of aggregation. The results suggest that RNA polymerase plays a significant role in the regulation of development in M. xanthus since mutations which cause no apparent changes in vegetative growth result in striking defects in fruiting-body formation.
Hierarchy of polyadenylation site usage by bovine papillomavirus in transformed mouse cells

The great majority of viral mRNAs in mouse C127 cells transformed by bovine papillomavirus type 1 (BPV) have a common 3' end at the early polyadenylation site which is 23 nucleotides (nt) downstream of a canonical poly(A) consensus signal. Twenty percent of BPV mRNA from productively infected cells bypasses the early polyadenylation site and uses the late polyadenylation site approximately 3,000 nt downstream. To inactivate the BPV early polyadenylation site, the early poly(A) consensus signal was mutated from AAUAAA to UGUAAA. Surprisingly, this mutation did not result in significant read-through expression of downstream RNA. Rather, RNA mapping and cDNA cloning experiments demonstrate that virtually all of the mutant RNA is cleaved and polyadenylated at heterogeneous sites approximately 100 nt upstream of the wild-type early polyadenylation site. In addition, cells transformed by wild-type BPV harbor a small population of mRNAs with 3' ends located in this upstream region. These experiments demonstrate that inactivation of the major poly(A) signal induces preferential use of otherwise very minor upstream poly(A) sites. Mutational analysis suggests that polyadenylation at the minor sites is controlled, at least in part, by UAUAUA, an unusual variant of the poly(A) consensus signal approximately 25 nt upstream of the minor polyadenylation sites. These experiments indicate that inactivation of the major early polyadenylation signal is not sufficient to induce expression of the BPV late genes in transformed mouse cells.
Inhibition of the autophagic flux by salinomycin in breast cancer stem-like/progenitor cells interferes with their maintenance

Breast cancer tissue contains a small population of cells that have the ability to self-renew; these cells are known as cancer stem-like cells (CSCs). We have recently shown that autophagy is essential for the tumorigenicity of these CSCs. Salinomycin (Sal), a K+/H+ ionophore, has recently been shown to be at least 100 times more effective than paclitaxel in reducing the proportion of breast CSCs. However, its mechanisms of action are still unclear. We show here that Sal blocked both autophagy flux and lysosomal proteolytic activity in both CSCs and non-CSCs derived from breast cancer cells. GFP-LC3 staining combined with fluorescent dextran uptake and LysoTracker-Red staining showed that autophagosome/lysosome fusion was not altered by Sal treatment. Acridine orange staining provided evidence that lysosomes display the characteristics of acidic compartments in Sal-treated cells. However, tandem mCherry-GFP-LC3 assay indicated that the degradation of mCherry-GFP-LC3 is blocked by Sal. Furthermore, the protein degradation activity of lysosomes was inhibited, as demonstrated by the rate of long-lived protein degradation, DQ-BSA assay and measurement of cathepsin activity. Our data indicated that Sal has a relatively greater suppressant effect on autophagic flux in the ALDH+ population in HMLER cells than in the ALDH− population; moreover, this differential effect on autophagic flux correlated with an increase in apoptosis in the ALDH+ population. ATG7 depletion accelerated the proapoptotic capacity of Sal in the ALDH+ population. Our findings provide new insights into how the autophagy-lysosomal pathway contributes to the ability of Sal to target CSCs in vitro.
Dengue virus up‐regulates expression of notch ligands Dll1 and Dll4 through interferon‐β signalling pathway

The Notch signalling pathway is involved in multiple cellular processes and has been recently indicated to modulate the host immune response. However, the role of the Notch pathway in dengue virus (DENV) infection remains unknown. Our study has screened the expression profile of Notch receptors, ligands and target genes in human monocytes, macrophages and dendritic cells in response to DENV infection. The real‐time PCR data showed that Notch ligand Dll1 was significantly induced in DENV‐infected monocytes; and receptor Notch4, ligands Dll1 and Dll4, and target Hes1 were dramatically enhanced in DENV‐infected macrophages and dendritic cells. In macrophages, induction of Dll1 and Dll4 mediated by DENV2 was increased by treatment with interferon‐β (IFN‐β), and was impaired by neutralization of IFN‐β. The DENV‐induced Dll1 and Dll4 expression level was decreased by silencing key innate immune molecules, including Toll‐like receptor 3 (TLR3), MyD88, RIG‐I and IPS‐I. In IFN‐receptor‐depleted macrophages, the Dll1 and Dll4 induction was significantly alleviated. Functionally, activation of Notch signalling by Dll1 in CD4+ T cells enhanced the expression of a T helper type 1 (Th1) cytokine IFN‐γ, while Notch activation in macrophages had no direct effect on replication of DENV. Our data revealed that the expressions of Notch ligands in antigen‐presenting cells were differentially induced by DENV via innate immune signalling, which is important for Th1/Th2 differentiation during adaptive immune response.
Skin autofluorescence is elevated in neovascular age-related macular degeneration

Background/aims Skin autofluorescence (AF) is a non-invasive marker for advanced glycation endproducts (AGE) in tissues, making use of their characteristic AF pattern. The aim of this study was to investigate whether skin AF is increased in patients with neovascular age-related macular degeneration (AMD) compared with healthy controls. Methods Skin AF was assessed in 73 consecutive patients with active and documented neovascular AMD without evidence for diabetic or hypertensive retinopathy and in 31 healthy age-matched controls. Exclusion criteria were: known renal disease, current inflammatory or malignant disease, or skin type V or VI. Skin AF was measured on the forearm and was calculated as a ratio of mean intensities detected from the skin between 420–600 and 300–420 nm. Student t test and χ2 test were used to compare differences between groups. Results Skin AF was increased in neovascular AMD compared with controls (2.57±0.68 vs 2.23±0.63 arbitrary units × 10−2; p=0.018). In patients without vascular risk factors or cardiovascular disease, skin AF was not significantly higher than that of the controls. Skin AF correlated with age in both patients and controls. Conclusion Skin AF is increased in patients with neovascular AMD, suggesting that AMD is accompanied by enhanced systemic AGE accumulation, which may indicate a role in the pathophysiology of AMD.
Phosphorylation of Specific Serine Residues in the PKR Activation Domain of PACT Is Essential for Its Ability to Mediate Apoptosis*

Activation of the latent protein kinase, PKR, by extracellular stresses and triggering of resultant cellular apoptosis are mediated by the protein, PACT, which itself gets phosphorylated in stressed cells. We have analyzed the underlying biochemical mechanism by carrying out alanine-scanning mutagenesis of the PKR activation domain of PACT. Among the indispensable residues identified were two serine residues, whose phosphorylation was essential for the cellular actions of PACT. Two-dimensional gel analysis, Western analysis using phosphoamino acid-specific antiserum, and in vivo 32P labeling of PACT demonstrated that constitutive phosphorylation of one of the two residues, Ser246, was required for stress-induced phosphorylation of the other, Ser287. Substitution of either of them by threonine or aspartic acid, but not alanine, was tolerated. Substitution of both residues with the phosphoserine mimetic, aspartic acid, produced a mutant PACT that, unlike the wild-type protein, caused PKR activation and apoptosis, even in unstressed cells. These results indicate that phosphorylation of specific serine residues in the activation domain of PACT is the major mode of transmission of cellular stress response to PKR.
Dynamics of Production of Sexual Forms in Aphids: Theoretical and Experimental Evidence for Adaptive “Coin‐Flipping” Plasticity

The best strategy for an organism to deal with unpredictable environmental conditions is a stochastic one, but it is not easy to distinguish it from nonadaptive randomness in phenotype production, and its convincing demonstrations are lacking. Here we describe a new method for detection of adaptive stochastic polyphenism and apply it to the following problem. In fall, each female of the bird cherry–oat aphid, Rhopalosiphum padi, faces a decision either to produce sexuals, which mate and lay cold‐tolerant eggs, or to continue production of cold‐sensitive parthenogenetic females, which potentially yields a higher population growth rate but is risky because a cold winter can kill all of her descendants. Using a simulation model, we show that global investment in sexual reproduction should be proportional to winter severity and that variance in the peak date of production of sexual individuals should depend on climate predictability. Both predictions are validated against standardized trap data on aphid flight accompanied by meteorological data, and the predictions support adaptive phenotypic plasticity.
Urine Proteome Analysis Reflects Atherosclerotic Disease in an ApoE−/− Mouse Model and Allows the Discovery of New Candidate Biomarkers in Mouse and Human Atherosclerosis*

Noninvasive diagnosis of atherosclerosis via single biomarkers has been attempted but remains elusive. However, a previous polymarker or pattern approach of urine polypeptides in humans reflected coronary artery disease with high accuracy. The aim of the current study is to use urine proteomics in ApoE−/− mice to discover proteins with pathophysiological roles in atherogenesis and to identify urinary polypeptide patterns reflecting early stages of atherosclerosis. Urine of ApoE−/− mice either on high fat diet (HFD) or chow diet was collected over 12 weeks; urine of wild type mice on HFD was used to exclude diet-related proteome changes. Capillary electrophoresis coupled to mass spectrometry (CE-MS) of samples identified 16 polypeptides specific for ApoE−/− mice on HFD. In a blinded test set, these polypeptides allowed identification of atherosclerosis at a sensitivity of 90% and specificity of 100%, as well as monitoring of disease progression. Sequencing of the discovered polypeptides identified fragments of α1-antitrypsin, epidermal growth factor (EGF), kidney androgen-regulated protein, and collagen. Using immunohistochemistry, α1-antitrypsin, EGF, and collagen type I were shown to be highly expressed in atherosclerotic plaques of ApoE−/− mice on HFD. Urinary excretion levels of collagen and α1-antitrypsin fragments also significantly correlated with intraplaque collagen and α1-antitrypsin content, mirroring plaque protein expression in the urine proteome. To provide further confirmation that the newly identified proteins are relevant in humans, the presence of collagen type I, α1-antitrypsin, and EGF was also confirmed in human atherosclerotic disease. Urine proteome analysis in mice exemplifies the potential of a novel multimarker approach for the noninvasive detection of atherosclerosis and monitoring of disease progression. Furthermore, this approach represents a novel discovery tool for the identification of proteins relevant in murine and human atherosclerosis and thus also defines potential novel therapeutic targets.
Determining the structural relaxation times deep in the glassy state of the pharmaceutical Telmisartan

By using the dielectric relaxation method proposed recently by Casalini and Roland (2009 Phys. Rev. Lett. 102 035701), we were able to determine the structural α-relaxation times deep in the glassy state of the pharmaceutical, Telmisartan. Normally, deep in the glassy state τα is so long that it cannot be measured but τβ, which is usually much shorter, can be directly determined. The method basically takes advantage of the connection between the α-relaxation and the secondary β-relaxation of the Johari–Goldstein kind, including a relation between their relaxation times τα and τβ, respectively. Thus, τα of Telmisartan were determined by monitoring the change of the dielectric β-loss, ε′′, with physical aging time at temperatures well below the vitrification temperature. The values of τα were compared with those expected by the coupling model (CM). Unequivocal comparison cannot be made in the case of Telmisartan because its β-loss peak is extremely broad, and the CM predicts only an order of magnitude agreement between the primitive relaxation frequency and the β-peak frequency. We also made an attempt to analyze all isothermal and aging susceptibility data after transformation into the electric modulus representation. The τα found in the glass state by using the method of Casalini and Roland in the modulus representation are similar to those obtained in the susceptibility representation. However, it is remarkable that the stretching parameter βKWW − M = 0.51 in the electric modulus representation gives more precise fits to the aging data than in the susceptibility representation with βKWW = 0.61. Our results suggest that the electric modulus representation may be useful as an alternative to analyze aging data, especially in the case of highly polar glassformers having a large ratio of low frequency and high frequency dielectric constants, such as the Telmisartan studied.
Genetic variation and significant association of polymorphism rs7700944 G>A of TIM‐4 gene with rheumatoid arthritis susceptibility in Chinese Han and Hui populations

The T‐cell immunoglobulin and mucin domains 1 (TIM‐1) and 3 (TIM‐3) have been shown to be associated with susceptibility to rheumatoid arthritis (RA) in many ethnicities. In this study, we investigated the rs7700944 polymorphism of the intron region of TIM‐4 gene in Chinese Han and Hui populations, with and without RA in Ningxia Hui Autonomous Region of China. Our results demonstrated genetic variations of the TIM‐4 gene, along with significantly different distributions of genotypes and alleles at rs7700944 site in these two populations, with or without RA (P < 0.01). In addition, a strong association between the polymorphism with RA susceptibility was found in the studies of Chinese Han and Hui ethnic groups (P < 0.01), although the risk genotype contributed to RA susceptibility was different between the Han and Hui groups (P < 0.01). The AG was the risk genotype for RA in Han population, while GG was the risk genotype at rs7700944 site of TIM‐4 gene in Hui ethnicity. In addition to the genotype, the risk alleles of this single nucleotide polymorphism for RA in these two populations were also different, individuals with A allele was more susceptible to RA in Chinese Han [odds ratio (OR) = 1.930; 95% CI 1.412, 2.636; P < 0.01], but the risk allele in Hui was G in this study (OR = 1.823; 95% CI 1.330, 2.498; P < 0.01). These findings strongly suggest that polymorphism of rs7700944 of TIM‐4 may be a potential genetic variant among distinguished populations, as well as an important genetic factor associated with the RA susceptibility in many ethnicities.
Comparative study of asymmetric bridge and split AC supply converter for switched reluctance motor

The popularity of the Switched Reluctance Motors (SRMs) increases gradually due to its advantages such as low weight, less cost, high efficiency, high starting torque and rugged construction as compared to conventional motors. The overall cost reduction of SRM drive can be done with minimum switching devices in power converter. The ac split supply converter is best alternative for asymmetric bridge converter. This paper deals with the performance of ac split converter and asymmetric bridge converter with 8/6 SRM motor using MATLAB simulation. The 8/6 SRM motor parameter is determined with Ansys / Rmxprt. This paper discusses split ac supply converter has low cost and better efficiency.
Association between plasma viscosity and all‐cause mortality: results from the MONICA–Augsburg Cohort Study 1984–92

Several studies have reported a strong association between various markers of the acute‐phase response and death from cardiovascular diseases and all‐cause mortality. Inflammation at a low level of intensity may be a common phenomenon associated with the majority of causes of death owing to chronic diseases. We sought to investigate the association of plasma viscosity with all‐cause mortality in a cohort of apparently healthy men. The study population consisted of 964 men aged 45–64 years at entry, randomly selected from the general population and taking part in the first MONICA–Augsburg survey 1984–85. The main outcome measure was all‐cause mortality. During 8 years of follow‐up, there were 81 deaths (37 cardiovascular deaths, 23 deaths from cancer and 21 deaths from other causes). There was a strong positive and statistically significant age‐adjusted relationship between plasma viscosity and all‐cause mortality. The relative risk of death for a one standard deviation increase in plasma viscosity (0·070 mPa/s) was 1·45 [95% confidence interval (CI) 1·19–1·76]. After further adjusting for smoking, total cholesterol, body mass index, blood pressure and education, a relative risk of 1·41 (95% CI 1·14–1·74) resulted. Other risk variables had only negligible confounding effects. The relative risk of the median of the top quintile of the plasma viscosity distribution compared with the median of the bottom quintile, computed from the adjusted model, was 2·68 (95% CI 1·63–4·42). These findings suggest that plasma viscosity may have considerable potential to predict death from all causes in middle‐aged men.
Effects of Fatigue and Sleep Deprivation on Microvascular Anastomoses

AbstractPrevious studies have investigated the effects of various human-based factors, such as tremor, exercise, and posture, on microsurgical performance. In this study, the authors investigated the effects of sleep deprivation and fatigue on microsurgery. A total of 48 Wistar Hannover rats were divided into 3 groups (16 anastomoses in each group) to be operated on at 3 different times: in the morning at 08:00 hours (group I), at night on the same day (01:00 h, group II), and the next morning at 09:00 hours (group III) following a night with no sleep. The blindly evaluated parameters were anastomotic times, error score (ES), global rating scale (GRS), autopsy scores (ASs), and patency. There was progressive decrease in the anastomosis times between the groups (P > 0.05). The patency rates were 93% in group I, 81% in group II, and 81% in group III (P > 0.05). The ES (P < 0.01), AS (P < 0.001), and GRS (P < 0.001) revealed significant results. Comparison between the groups showed that other than the anastomosis time, the night group (group II) showed a significant drop when compared with the preceding morning group (group I) (ES P < 0.01, AS P < .001, and GRS P < 0.001). In most of the parameters, the errors occurred with fatigue after the day and reached a maximum at the end of the day (group II). This study provides valuable data that might have significant medicolegal implications for controversial issues. More studies, however, including multiple surgeons with different experience levels, might be required to fully elucidate the overall effects of fatigue and sleep deprivation on microsurgery.
Monitoring Cumulative Long-Term Vegetation Changes Over the Athabasca Oil Sands Region

This study uses two remotely sensed vegetation indices to investigate cumulative long-term changes of undisturbed vegetation in the Athabasca Oil Sands region of Alberta, Canada, between 1984 and 2012. The Normalized Difference Vegetation Index (NDVI) and the Normalized Difference Wetness Index (NDWI) were derived from both Landsat and MODIS time series, for comparative purposes and to increase confidence in detected trends. Trend analysis of undisturbed forest areas, i.e., area without abrupt changes revealed a consistent decrease in vegetation condition, quantified by an average reduction of 18.6% (SD=5.02% ) in NDVI and of 31.0% (SD=10.06%) in NDWI, over the 28-year period. The study does not conclusively associate the trends with any single stressor, but seeks to quantify the spatial and temporal distribution of cumulative effects resulting from a variety of natural and anthropogenic causes. Examination of the temporal pattern of trends showed an increase in the occurrence of decreasing trends in the last 10 years. The decreasing trends were more frequent closer to mining developments for both the Landsat and MODIS time series. Climate change was not considered a major causal factor as climate normalized trends had little effect on the results. The trend analysis undertaken can be used to enhance in situ monitoring programs for site selection of additional monitoring facilities particularly regarding potential cumulative effects, provide an indication of likely future short-term changes in the region, and to aid in the development of mitigation measures.