Miracle-dz/UniFAR-FTUs huggingface dataset:
Purification and characterization of enterocin 62-6, a two-peptide bacteriocin produced by a vaginal strain of Enterococcus faecium: Potential significance in bacterial vaginosis

A bacteriocin produced by a vaginal isolate of Enterococcus faecium strain 62-6, designated enterocin 62-6, was characterized following purification and DNA sequence analysis and compared to previously described bacteriocins. Enterocin 62-6 was isolated from brain heart infusion (BHI) culture supernatants using ammonium sulfate precipitation followed by elution from a Sepharose cation exchange column using a continuous salt gradient (0.1–0.7 M NaCl). SDS-PAGE of an active column fraction resulted in an electrophoretically pure protein, which corresponded to the growth inhibition of the sensitive Lactobacillus indicator strain in the gel overlay assay. Purified enterocin 62-6 was shown to be heat- and pH-stable, and sensitive to the proteolytic enzymes α-chymotrypsin and pepsin. Results from mass spectrometry suggested that it comprised two peptides of 5206 and 5219±1 Da, which was confirmed by DNA sequence analysis. The characteristics of enterocin 62-6 as a small, heat- and pH-stable, cationic, hydrophobic, two-peptide, plasmid-borne bacteriocin, with an inhibitory spectrum against a broad range of Gram-positive but not Gram-negative bacteria, were consistent with its classification as a class IIc bacteriocin. Furthermore, its wide spectrum of growth inhibitory activity against Gram-positive bacteria of vaginal origin including lactobacilli, and stability under the acidic conditions of the vagina, are consistent with our hypothesis that it could have potential significance in disrupting the ecology of the vaginal tract and pave the way for the establishment of the abnormal microbiota associated with the vaginal syndrome bacterial vaginosis. This is the first class IIc bacteriocin produced by a strain of E. faecium of vaginal origin to be characterized.
Serum S100β increases in marathon runners reflect extracranial release rather than glial damage

The contribution of extracranial tissue damage to serum S100β increases was examined in 18 marathon runners without clinical or laboratory signs of brain damage. Postrace serum S100β and creatine kinase (CK) concentrations increased (p < 0.001), and areas under the curve were highly correlated (p = 0.001). To conclude, serum S100β increases after running originate from extracranial sources. CK determination may improve specificity of S100β as a marker of brain tissue damage in acute trauma.
Cellular Distribution of 6‐Phosphofructo‐1‐Kinase Isoenzymes in Rat Brain

Abstract: In the brain, all three isoenzyme types [muscle (M), liver (L), and brain (C)] of 6‐phosphofructo‐1‐kinase (PFK; EC 2.7.1.11) occur, forming a complex mixture of homo‐ and heterotetramers. The PFK isoenzyme pattern of the different brain cell types is yet unknown. In the present study, we investigated the distribution of the PFK isoenzyme subunits in primary and secondary cell cultures and in bulk‐isolated cells of rat brain by means of sodium dodecyl sulfate‐polyacrylamide gel electrophoresis and western blotting. All three PFK isoenzymes are present in all cell types but in different proportions. The cellular distribution of the PFK isoenzymes in situ was studied immunohistochemically with different polyclonal antisera against purified rat PFKs. The monospecific antibody against M‐type PFK stained preferentially the perinuclear areas of neurons and glial cells. The antibodies that in immunoblots detected mainly the L‐type PFK showed a characteristic staining in only the cytoplasma and the processes of cells, whereas the C‐type antibodies almost homogeneously stained whole cell bodies as well as large dendrites. Because the PFK isoenzymes differ with respect to their allosteric properties, their differential distribution in different brain cells might be of importance for the regulation of brain glycolysis in the different cellular compartments of the brain.
A kernel prototype-based clustering algorithm

One-class SVM is a kernel-based method which utilizes the kernel trick for data clustering. However it is only able to detect one cluster of non-convex shape. In this study, we propose a strategy using one-class SVM to calculate the centroid of the sphere for each cluster in feature space. In addition, a mechanism is provided to control the position of the cluster centroid in feature space to work against outliers. We compare our method with other kernel prototype-based clustering algorithms, like KKM and KFCM, on two synthetic data sets and four UCI real data sets, the results indicate that our method outperforms KKM and KFCM.
Aspartate Residue 142 Is Important for Catalysis by ADP-glucose Pyrophosphorylase from Escherichia coli *

Structural prediction of several bacterial and plant ADP-glucose pyrophosphorylases, as well as of other sugar-nucleotide pyrophosphorylases, was used for comparison with the three-dimensional structures of two crystallized pyrophosphorylases (Brown, K., Pompeo, F., Dixon, S., Mengin-Lecreulx, D., Cambillau, C., and Bourne, Y. (1999) EMBO J. 18, 4096–4107; Blankenfeldt, W. , Asuncion, M. , Lam, J. S. , and Naismith, J. H. (2000)EMBO J. 19, 6652–6663). This comparison led to the discovery of highly conserved residues throughout the superfamily of pyrophosphorylases despite the low overall homology. One of those residues, Asp142 in the ADP-glucose pyrophosphorylase fromEscherichia coli, was predicted to be near the substrate site. To elucidate the function that Asp142 might play in the E. coli ADP-glucose pyrophosphorylase, aspartate was replaced by alanine, asparagine, or glutamate using site-directed mutagenesis. Kinetic analysis in the direction of synthesis or pyrophosphorolysis of the purified mutants showed a decrease in specific activity of up to 4 orders of magnitude. Comparison of other kinetic parameters, i.e. the apparent affinities for substrates and allosteric effectors, showed no significant changes, excluding this residue from the specific role of ligand binding. Only the D142E mutant exhibited altered K m values but none as pronounced as the decrease in specific activity. These results show that residue Asp142 is important in the catalysis of the ADP-glucose pyrophosphorylase from E. coli.
Immuno-Northern Blotting: Detection of RNA Modifications by Using Antibodies against Modified Nucleosides

The biological roles of RNA modifications are still largely not understood. Thus, developing a method for detecting RNA modifications is important for further clarification. We developed a method for detecting RNA modifications called immuno-northern blotting (INB) analysis and herein introduce its various capabilities. This method involves the separation of RNAs using either polyacrylamide or agarose gel electrophoresis, followed by transfer onto a nylon membrane and subsequent immunoblotting using antibodies against modified nucleosides for the detection of specific modifications. We confirmed that INB with the antibodies for 1-methyladenosine (m1A), N6-methyladenosine (m6A), pseudouridine, and 5-methylcytidine (m5C) showed different modifications in a variety of RNAs from various species and organelles. INB with the anti-m5C antibody revealed that the antibody cross-reacted with another modification on DNA, suggesting the application of this method for characterization of the antibody for modified nucleosides. Additionally, using INB with the antibody for m1A, which is a highly specific modification in eukaryotic tRNA, we detected tRNA-derived fragments known as tiRNAs under the cellular stress response, suggesting the application for tracking target RNA containing specific modifications. INB with the anti-m6A antibody confirmed the demethylation of m6A by the specific demethylases fat mass and obesity-associated protein (FTO) and ALKBH5, suggesting its application for quantifying target modifications in separated RNAs. Furthermore, INB demonstrated that the knockdown of FTO and ALKBH5 increased the m6A modification in small RNAs as well as in mRNA. The INB method has high specificity, sensitivity, and quantitative capability, and it can be employed with conventional experimental apparatus. Therefore, this method would be useful for research on RNA modifications and metabolism.
Economic crisis, austerity and the Greek public health system.

For 2 years the Greek financial crisis has captured global attention. In return for loans from the International Monetary Fund (IMF) and European institutions, Greece agreed on harsh across-the-board austerity measures, yet most commentators offer little hope for recovery, at least in the short run. The economy is expected to contract by a further 6.1% in 2011 and 3% in 2012, while unemployment is projected to reach 18.5% in 2012 up from 7.7% in 2008. The Greek health-care system has been accumulating structural problems for a decade1 that have been exacerbated by the economic crisis. In terms of expenditure, a failure to contain costs, in part due to an absence of explicit funding criteria, created budget deficits for sickness funds. Although the system is highly centralized, resource allocation suffers from a lack of planning and coordination, weak managerial and administrative capacity, and underdeveloped mechanisms for assessing needs and setting priorities. In addition, an oversupply of specialist physicians coexists with an undersupply of general practitioners and nurses. The combination of an absence of a functioning referral system and irrational pricing and reimbursement mechanisms leads to poor coordination of care, large out-of-pocket payments and a sizable black economy, impeding the system's ability to deliver equitable financing and access to services. Since the onset of the crisis, …
Structure of the linkage region between the polysaccharide and protein parts of Saccharomyces cerevisiae mannan.

Abstract An oligosaccharide fragment corresponding to the linkage region between the polysaccharide and protein parts of Saccharomyces cerevisiae X2180 yeast mannan has been isolated. This was accomplished by the combined action of a bacterial endo-α(1→6)mannanase and an endo-β-N-acetylglucosaminidase on the mutant mannan from S. cerevisiae X2180-1A-5 that has an unbranched polysaccharide outer chain. The mannanase removed the unbranched mannan outer chain and the glucosaminidase apparently split a di-N-acetylchitobiose unit at the point of attachment of the polysaccharide to asparagine in the protein part. This order of degradation is assumed from the facts that wild type mannan with a branched outer chain was not attacked whereas ovalbumin was degraded with the release of the expected oligosaccharide fragment terminated by N-acetylglucosamine at the reducing end. Thus, the glucosaminidase was able to act only on a partially degraded mannan chain. The linkage fragment was composed of about 12 mannose units and a single N-acetylglucosamine which was found at the reducing end. The attachment of mannose to N-acetylglucosamine was by a β(1→4) linkage as in other glycoproteins. Acetolysis of the oligosaccharide yielded mannose, mannobiose αMan(1→2)Man and αMan(1→3)Man, mannotriose with both 1→2 and 1→3 linkages, and mannotetraose, probably αMan(1→3)αMan(1→2)αMan(1→3)Man. These fragments were interlinked by α(1→6) bonds, and the oligosaccharide was attached to the N-acetylglucosamine. Another acetolysis fragment isolated, αMan(1→3)αMan(1→2)αMan(1→3)βMan(1→4)GNAc, is common to other glycoproteins. The observation that this kind of branched inner core structure is made in a yeast mutant that forms an unbranched outer chain demonstrates that the formation of these two parts of the molecule is regulated in part by different enzymes and may serve different functions in the translocation of the mannan proteins and their organization in the cell wall.
Mitochondria-Dependent Reactive Oxygen Species-Mediated Programmed Cell Death Induced by 3,3′-Diindolylmethane through Inhibition of F0F1-ATP Synthase in Unicellular Protozoan Parasite Leishmania donovani

Mitochondria are the principal site for the generation of cellular ATP by oxidative phosphorylation. F0F1-ATP synthase, a complex V of the electron transport chain, is an important constituent of mitochondria-dependent signaling pathways involved in apoptosis. In the present study, we have shown for the first time that 3,3′-diindolylmethane (DIM), a DNA topoisomerase I poison, inhibits mitochondrial F0F1-ATP synthase of Leishmania donovani and induces programmed cell death (PCD), which is a novel insight into the mechanism in protozoan parasites. DIM-induced inhibition of F0F1-ATP synthase activity causes depletion of mitochondrial ATP levels and significant stimulation of mitochondrial reactive oxygen species (ROS) production, followed by depolarization of mitochondrial membrane potential (ΔΨm). Because ΔΨm is the driving force for mitochondrial ATP synthesis, loss of ΔΨm results in depletion of cellular ATP level. The loss of ΔΨm causes the cellular ROS generation and in turn leads to the oxidative DNA lesions followed by DNA fragmentation. In contrast, loss of ΔΨm leads to release of cytochrome c into the cytosol and subsequently activates the caspase-like proteases, which lead to oligonucleosomal DNA cleavage. We have also shown that mitochondrial DNA-depleted cells are insensitive to DIM to induce PCD. Therefore, mitochondria are necessary for cytotoxicity of DIM in kinetoplastid parasites. Taken together, our study indicates for the first time that DIM-induced mitochondrial dysfunction by inhibition of F0F1-ATP synthase activity leads to PCD in Leishmania spp. parasites, which could be exploited to develop newer potential therapeutic targets.
Estimates of Critical Power and Anaerobic Work Capacity from a Single, All-Out Test of Less than 3-Min

The purpose of this study was to determine if Critical Power (CP) and Anaerobic Work Capacity (AWC) could be estimated from a single, all-out test of less than 3-min. Twenty-eight subjects (mean ± SD: age 23.3 ± 3.3 years, body mass 71.6 ± 16 kg) performed an incremental cycle ergometer test to exhaustion to determine peak oxygen consumption rate and heart rate peak. The 3-min all-out test was used to determine the criterion and six estimated values of CP and AWC. The criterion critical power (CP180) and anaerobic work capacity (AWC180) values were determined from the 3-min all-out test and were expressed as 30-s averages (155-180-s). The six estimated CP and AWC values were calculated from 30-s averages at decreasing 10-s intervals from 145 to 170-s (CP170 and AWC170), 135 to 160-s (CP160 and AWC160), 125 to 150-s (CP150 and AWC150), 115 to 140-s (CP140 and AWC140), 105 to 130-s (CP130 and AWC130), and 95 to 120-s (CP120 and AWC120). Mean differences, total error, constant error, standard error of the estimate, and correlations were used to compare the criterion to the estimated CP and AWC values. The results of the present study indicated that 150-s was the shortest test duration that resulted in non-significant differences between the criterion (CP180 and AWC180) and estimated CP (CP150) and AWC (AWC150) values. The subsequent validation analyses showed that there were close agreements for the estimated CP150 and AWC150 versus the criterion (CP180 and AWC180) values. Therefore, the current findings indicated that estimates of CP and AWC were not affected by shortening the test by 30-s. Reducing the length of the test to 2.5 minutes provides a less strenuous, yet valid protocol for estimating CP and AWC.
A Transcriptional Regulatory Role of the THAP11–HCF-1 Complex in Colon Cancer Cell Function

ABSTRACT The recently identified Thanatos-associated protein (THAP) domain is an atypical zinc finger motif with sequence-specific DNA-binding activity. Emerging data suggest that THAP proteins may function in chromatin-dependent processes, including transcriptional regulation, but the roles of most THAP proteins in normal and aberrant cellular processes remain largely unknown. In this work, we identify THAP11 as a transcriptional regulator differentially expressed in human colon cancer. Immunohistochemical analysis of human colon cancers revealed increased THAP11 expression in both primary tumors and metastases. Knockdown of THAP11 in SW620 colon cancer cells resulted in a significant decrease in cell proliferation, and profiling of gene expression in these cells identified a novel gene set composed of 80 differentially expressed genes, 70% of which were derepressed by THAP11 knockdown. THAP11 was found to associate physically with the transcriptional coregulator HCF-1 (host cell factor 1) and recruit HCF-1 to target promoters. Importantly, THAP11-mediated gene regulation and its chromatin association require HCF-1, while HCF-1 recruitment at these genes requires THAP11. Collectively, these data provide the first characterization of THAP11-dependent gene expression in human colon cancer cells and suggest that the THAP11–HCF-1 complex may be an important transcriptional and cell growth regulator in human colon cancer.
The annual number of breeding adults and the effective population size of syntopic newts (Triturus cristatus, T. marmoratus)

Pond‐breeding amphibians are deme‐structured organisms with a population genetic structure particularly susceptible to demographic threats. We estimated the effective number of breeding adults (Nb) and the effective population size (Ne) of the European urodele amphibians Triturus cristatus (the crested newt) and T. marmoratus (the marbled newt), using temporal shifts in microsatellite allele frequencies. Eight microsatellite loci isolated from a T. cristatus library were used, five of which proved polymorphic in T. marmoratus, albeit with high frequencies of null alleles at two loci. Three ponds in western France were sampled, situated 4–10 kilometres apart and inhabited by both species. Parent–offspring cohort comparisons were used to measure Nb; samples collected at time intervals of nine or 12 years, respectively, were used to measure Ne. The adult population census size (N) was determined by mark–recapture techniques. With one exception, genetic distances (FST) between temporal samples were lower than among populations. Nb ranged between 10.6 and 101.8 individuals, Ne ranged between 9.6 and 13.4 individuals. For the pond where both parameters were available, Nb/N (overall range: 0.10–0.19) was marginally larger than Ne/N (overall range: 0.09–0.16), which is reflected in the temporal stability of N. In line with the observed differences in reproductive life‐histories between the species, Nb/N ratios for newts were about one order of magnitude higher than for the anuran amphibian Bufo bufo. Despite of the colonization of the study area by T. cristatus only some decades ago, no significant genetic bottleneck could be detected. Our findings give rise to concerns about the long‐term demographic viability of amphibian populations in situations typical for European landscapes.
Prion Protein-Deficient Cells Show Altered Response to Oxidative Stress Due to Decreased SOD-1 Activity

The cellular function of the prion protein (PrPc), a cell surface glycoprotein expressed in neurones and astrocytes, has not been elucidated. Cell culture experiments reveal that cerebellar cells lacking PrPc are more sensitive to oxidative stress and undergo cell death more readily than wild-type cells. This effect is reversible by treatment with vitamin E. In vivo studies show that the activity of Cu/Zn superoxide dismutase is reduced in Prnp gene-ablated (Prnp0/0) mice. Constitutively high Mn superoxide dismutase activity in these animals may compensate for this loss of responsiveness to oxidative stress. These findings suggest that PrPc may influence the activity of Cu/Zn superoxide dismutase and may be important for cellular resistance to oxidative stress.
Current status of hyperthermic limb perfusion for in-transit melanoma

In-transit disease is a unique form of regional lymphatic spread of melanoma that is considered an infrequent event although certain high-risk subgroups have been identified with higher incidence rates. Although this disease entity is associated with a high risk for distant relapse, regionally focused treatment of disease is important due to the high morbidity associated with in-transit disease. Isolated limb perfusion has been a utilized method of regional treatment since the 1950's. The technical aspects, indications, historical results, and toxicity of limb perfusion are reviewed. Finally, perfusion based treatment of in-transit melanoma is an excellent model for studying novel agents and regimens in both the pre-clinical and patient care setting.
Cloud property datasets retrieved from AVHRR, MODIS, AATSR and MERIS in the framework of the Cloud_cci project

Abstract. New cloud property datasets based on measurements from the passive imaging satellite sensors AVHRR, MODIS, ATSR2, AATSR and MERIS are presented. Two retrieval systems were developed that include components for cloud detection and cloud typing followed by cloud property retrievals based on the optimal estimation (OE) technique. The OE-based retrievals are applied to simultaneously retrieve cloud-top pressure, cloud particle effective radius and cloud optical thickness using measurements at visible, near-infrared and thermal infrared wavelengths, which ensures spectral consistency. The retrieved cloud properties are further processed to derive cloud-top height, cloud-top temperature, cloud liquid water path, cloud ice water path and spectral cloud albedo. The Cloud_cci products are pixel-based retrievals, daily composites of those on a global equal-angle latitude–longitude grid, and monthly cloud properties such as averages, standard deviations and histograms, also on a global grid. All products include rigorous propagation of the retrieval and sampling uncertainties. Grouping the orbital properties of the sensor families, six datasets have been defined, which are named AVHRR-AM, AVHRR-PM, MODIS-Terra, MODIS-Aqua, ATSR2-AATSR and MERIS+AATSR, each comprising a specific subset of all available sensors. The individual characteristics of the datasets are presented together with a summary of the retrieval systems and measurement records on which the dataset generation were based. Example validation results are given, based on comparisons to well-established reference observations, which demonstrate the good quality of the data. In particular the ensured spectral consistency and the rigorous uncertainty propagation through all processing levels can be considered as new features of the Cloud_cci datasets compared to existing datasets. In addition, the consistency among the individual datasets allows for a potential combination of them as well as facilitates studies on the impact of temporal sampling and spatial resolution on cloud climatologies. For each dataset a digital object identifier has been issued: Cloud_cci AVHRR-AM: https://doi.org/10.5676/DWD/ESA_Cloud_cci/AVHRR-AM/V002 Cloud_cci AVHRR-PM: https://doi.org/10.5676/DWD/ESA_Cloud_cci/AVHRR-PM/V002 Cloud_cci MODIS-Terra: https://doi.org/10.5676/DWD/ESA_Cloud_cci/MODIS-Terra/V002 Cloud_cci MODIS-Aqua: https://doi.org/10.5676/DWD/ESA_Cloud_cci/MODIS-Aqua/V002 Cloud_cci ATSR2-AATSR: https://doi.org/10.5676/DWD/ESA_Cloud_cci/ATSR2-AATSR/V002 Cloud_cci MERIS+AATSR: https://doi.org/10.5676/DWD/ESA_Cloud_cci/MERIS+AATSR/V002