Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptional Regulation of Mouse δ-Opioid Receptor Gene by CpG Methylation

Opioid receptors are expressed in a cell type-specific manner. Here we show that the mouse δ-opioid receptor (mDOR) gene is regulated by promoter region CpG methylation. The mDOR promoter containing a putative CpG island is highly methylated in Neuro2A cells, correlating with the repression of this gene in these cells. This is in contrast with the unmethylated state of the mDOR promoter in NS20Y cells, which express a high level of mDOR. Repression of mDOR transcription in Neuro2A cells could be partially relieved by chemically induced demethylation with 5-aza-2′-deoxycytidine. In addition, in vitro methylation of the luciferase reporter gene driven by the mDOR promoter resulted in an inhibition of transcription in NS20Y cells. Methyl-CpG-binding protein complex 1 (MeCP1) has been implicated in methylation-mediated transcriptional repression of several genes. Electrophoretic mobility shift assays showed that fully methylated, but not unmethylated, mDOR promoter fragment formed a MeCP1-like protein complex that contained methyl-CpG-binding domain protein 2 (MBD2) and Sp3. Furthermore, the expression level of Sp3 was decreased when Neuro2A cells were demethylated with 5-aza-2′-deoxycytidine, and increasing Sp3 levels in Schneider's Drosophila line 2 cells led to the repression of mDOR promoter activity when the promoter was methylated. These results demonstrate that Sp3 and MBD2 are involved in the transcriptional repression of mDOR in Neuro2A cells through binding to the methylated CpG sites in the promoter region and may play a role in the cell type-specific expression of mDOR.
How we know II: bad dreams

dreams In my last column, we were discussing houses built on sand and the scientific method as a way of knowing. Most of us take it as given that this is a good way of knowing things about the world at large, and you and I were just about to agree completely with each other when I proposed that it is not, and that it can be a matter of life and death to argue otherwise. Well, like the Walrus and the Carpenter, let’s take a walk on the beach (need I mention that the sun is shining on the sea? ) and talk nonsense. Yes nonsense, but nonsense that is fairly recent history and of such deep importance to any of us in biomedicine that it is astonishing that it isn’t taught as essential reading in Biology 101. It isn’t, mainly because those who know about it are ashamed and don’t like to talk about it.
Genetic variability and geographical structure in partially selfing populations

In order to clarify the effect of selfing on genetic variation in geographically structured populations, Wright's island model is generalized to include; the effects of extinction, mutation, selfing, and migration of pollen and seed. The equilibrium probabilities of identity by descent for two genes are obtained. It is found that selfing causes a decrease of the variation within colonies and an increase of the variation between colonies. Our model partly explains the "heterozygosity paradox" but other factors such as selection are necessary to fully account for the paradox.
Characterization of Lupine Proteins

Proteins of eight cultivars of two lupine species (Lupinus albus and L. angustifolius) were examined by several procedures. Differences in protein solubility between the species and among varieties within a species were observed. Defatting of the lupine flour altered protein solubility. Amino acid compositions of total protein and protein fractions showed only minor differences between the species and among varieties within a species (except for cv. Kali). Sodium dodecylsulfate polyacrylamide gel electrophoresis patterns of protein fractions revealed both qualitative and quantitative differences between species and among varieties.
Complementarity in the use of nitrogen forms in a temperate broad-leaved mixed forest

Background: The complementary use of different forms of soil nitrogen (N) might lead to a higher productivity of mixed forests than monocultures, but convincing evidence for temperate mixed forests is scarce. Aims: We searched for species differences in N uptake rates and the preference for NH4+, NO3− or glycine among five temperate broad−leaved tree species (Acer pseudoplatanus, Carpinus betulus, Fagus sylvatica, Fraxinus excelsior, Tilia cordata) in a mature mixed stand. Methods: 15N tracer was added to the soil and its accumulation in fine root biomass was analysed after 10 min, 1 h and 1 d. Results: The estimated root uptake rates of the species were in the range of 5–46 µg N g−1 root h−1 for NH4+, 6–86 µg N g−1 h−1 for NO3− and 4–29 µg N g−1 h−1 for glycine during the first hour after tracer application. Carpinus, Tilia and Acer tended to prefer NH4+ over NO3−, while Fraxinus showed equal preference for both N forms and Fagus seemed to prefer NO3−. Conclusions: The five co-existing tree species differed in uptake rates and partly in their N form preference, but complementarity in the use of different N forms seems to be of minor importance in this forest because tree species appear to be rather flexible in their N form use.
Comparison of AFLPs with other markers for phylogenetic inference in wild tomatoes [Solanum L. section Lycopersicon (Mill.) Wettst.]

ac.uk Wild tomatoes (Solanum section Lycopersicon) are native to western South America. The delimitation and relationships of tomato species have differed widely depending upon whether morphological or biological species concepts are considered more important. Molecular data from mitochondrial, nuclear, and chloroplast DNA restriction fragment length polymorphisms (RFLPs), nuclear microsatellites, isozymes, and gene sequences of internal transcribed spacers of nuclear ribosomal DNA (ITS; multiple-copy), the single-copy nuclear encoded Granule-bound Starch Synthase gene (GBSSI or waxy), and morphology, have been used to examine hypotheses of species relationships. This study is a companion to the previous GBSSI gene sequence study and to the morphological study of relationships of all ten wild tomato species (including the recently described S. galapagense), with a concentration on the most widespread and variable species S. peruvianum s.l. These new AFLP data are largely concordant with the GBSSI and morphological data and in general support the species outlined in the latest treatment by C.M. Rick, but demonstrate the distinct nature of northern and southern Peruvian populations of S. peruvianum, and suggest that their taxonomy needs revision. Solanum ochranthum is supported as sister to wild tomatoes, and S. habrochaites and S. pennellii reside in a basal polytomy in the tomato clade.
The nature and physicochemical properties of histones

The electrophoretic analysis of histones extracted from the cell nuclei isolated from a number of different tissues and species has shown that, while there are some exceptions, these consist in general of three components which have been termed α-, β-, and y-histones. The α- and y-components are not, however, necessarily homogeneous proteins, for in those cases where it has been possible to fractionate the total histone either by chemical methods or by sedimentation or by a combination of both these procedures, the former has been found to consist of at least three components and the latter probably of two. The components of the a-fraction have been distinguished by the symbols a1 a2, and a3, respectively. The β-histones correspond essentially to the ‘main’, and the a- and y-fractions to the ‘subsidiary’, histones of the earlier provisional nomenclature. The β-histones possess the typical composition of traditional histones. They are further characterized by their ability to form aggregates of increasing size as the pH’s of their solutions are raised, a phenomenon brought to light by measurements of their diffusion coefficients and sedimentation constants. Subsidiary histones differ from β-histones both in amino acid composition and in physical properties. In particular, they do not exhibit the phenomenon of aggregation shown by the latter. Nevertheless, all of them resemble the β-histones in possessing strongly basic properties, a fact which is evident from their mobility-pH curves. The isoelectric points of a number of β-histones have been determined from such curves. Further evidence supporting the conception that histones are cell-specific is recorded. This has been provided mainly by a study of abnormal cells. Only small differences in isoelectric points and in electrophoretic mobilities have so far been detected between the β-histones from the liver cells and thymocytes of the ox. Examination of the histones from a number of tumours, both natural and experimental, has shown that β-histones from these sources usually differ from normal β-histones in possessing much smaller solubilities and electrophoretic mobilities and markedly greater capacities to aggregate. No combination occurs between histone and azo dye during the induction of hepatomas in rats by this carcinogen. Some dye is nevertheless bound in the nucleus during the induction period. It is presumably bound by chromosomin. It is concluded that the carcinogenic action of the dye is due to its combination with, and consequent modification or inhibition of, one or more genes. In conformity with the results of this and former investigations the terms protamin and histone have been defined more precisely than has hitherto been possible.
Ozone effects in a drier climate: implications for stomatal fluxes of reduced stomatal sensitivity to soil drying in a typical grassland species

The widely distributed temperate grassland species Dactylis glomerata was grown in competition with Ranunculus acris at two different watering regimes and exposed for 20 weeks to eight ozone treatments with mean concentrations ranging from 16.2 to 89.5 ppb, representing pre‐industrial to predicted post‐2100 ozone climates. Measurements of stomatal conductance were used to parameterize ozone flux models for D. glomerata. For the first time, a modification was made to the standard flux model to account for the observed decrease in sensitivity of stomatal conductance to reduced water availability with increasing ozone. Comparison of calculated cumulative ozone flux between the two versions of the model demonstrated that exclusion of the ozone effect on stomatal conductance in the standard flux model led to a large underestimation of ozone fluxes at mid‐ to high‐ozone concentrations. For example, at a mean ozone concentration of 55 ppb (as predicted for many temperate areas in the next few decades), the standard flux model underestimated ozone fluxes in D. glomerata by 30–40% under reduced water availability. Although the modified flux model does not markedly change the flux‐based critical level for D. glomerata, this study indicates that use of the standard flux model to quantify the risk of ozone damage to a widely distributed grassland species such as D. glomerata in areas where high ozone concentrations and reduced soil moisture coincide could lead to an underestimation of effects. Thus, this study has shown that under predicted future climate change and ozone scenarios, ozone effects on vegetation may be even greater than previously predicted in the drier areas of the world.
Localization of Carbohydrate Attachment Sites and Disulfide Bridges in Limulus α2-Macroglobulin

The primary structure determination of the dimeric invertebrate α2-macroglobulin (α2M) from Limulus polyphemus has been completed by determining its sites of glycosylation and disulfide bridge pattern. Of seven potential glycosylation sites forN-linked glycosylation, six (Asn275, Asn307, Asn866, Asn896, Asn1089, and Asn1145) carry common glucosamine-based carbohydrates groups, whereas one (Asn80) carries a carbohydrate chain containing both glucosamine and galactosamine. Nine disulfide bridges, which are homologues with bridges in human α2M, have been identified (Cys228–Cys269, Cys456–Cys580, Cys612–Cys799, Cys657–Cys707, Cys849–Cys876, Cys874–Cys910, Cys946–Cys1328, Cys1104–Cys1155, and Cys1362–Cys1475). In addition to these bridges, Limulus α2M contains three unique bridges that connect Cys361 and Cys382, Cys1370 and Cys1374, respectively, and Cys719 in one subunit with the same residue in the other subunit of the dimer. The latter bridge forms the only interchain disulfide bridge in Limulus α2M. The location of this bridge within the bait region is discussed and compared with other α-macroglobulins. Several peptides identified in the course of determining the disulfide bridge pattern provided evidence for the existence of two forms of Limulusα2M. The two forms have a high degree of sequence identity, but they differ extensively in large parts of their bait regions suggesting that they have different inhibitory spectra. The two forms (Limulus α2M-1 and -2) are most likely present in an ∼2:1 ratio in the hemolymph of each animal, and they can be partially separated on a Mono Q column at pH 7.4 by applying a shallow gradient of NaCl.
Classification Model to Estimate MIB-1 (Ki 67) Proliferation Index in NSCLC Patients Evaluated With 18F-FDG-PET/CT

Background/Aim: Proliferation biomarkers such as MIB-1 are strong predictors of clinical outcome and response to therapy in patients with non-small-cell lung cancer, but they require histological examination. In this work, we present a classification model to predict MIB-1 expression based on clinical parameters from positron emission tomography. Patients and Methods: We retrospectively evaluated 78 patients with histology-proven non-small-cell lung cancer (NSCLC) who underwent 18F-FDG-PET/CT for clinical examination. We stratified the population into a low and high proliferation group using MIB-1=25% as cut-off value. We built a predictive model based on binary classification trees to estimate the group label from the maximum standardized uptake value (SUVmax) and lesion diameter. Results: The proposed model showed ability to predict the correct proliferation group with overall accuracy >82% (78% and 86% for the low- and high-proliferation group, respectively). Conclusion: Our results indicate that radiotracer activity evaluated via SUVmax and lesion diameter are correlated with tumour proliferation index MIB-1.
Histologia da interação Stemphylium solani e tomateiro

The infection process of Stemphylium solani on resistant (Motelle) and susceptible (Moneymaker) tomato (Lycopersicon esculentum) leaflets was studied using histochemical, scanning and transmission electron microscopy techniques. No quantitative differences were found in the pre-penetration conidial events on resistant and susceptible tomatoes, indicating that resistance results from post-penetration responses. The histological studies showed that the initial infection events were similar in resistant and susceptible plants. The pathogen invaded the tomato leaf primarily through stomates and a vesicle developed inside the substomatal cavity. Secondary hyphae originated from the vesicle and within 24 and 36 h after inoculation had branched inter and intracellularly in both cultivars. Cell wall appositions in the mesophyll of resistant tomato prevented intracellular colonization.
Seasonal variation in pathways of CH4 production and in CH4 oxidation in rice fields determined by stable carbon isotopes and specific inhibitors

Flooded rice fields, which are an important source of the atmospheric methane, have become a model system for the study of interactions between various microbial processes. We used a combination of stable carbon isotope measurements and application of specific inhibitors in order to investigate the importance of various methanogenic pathways and of CH4 oxidation for controlling CH4 emission. The fraction of CH4 produced from acetate and H2/CO2 was calculated from the isotopic signatures of acetate, carbon dioxide (CO2) and methane (CH4) measured in porewater, gas bubbles, in the aerenchyma of the plants and/or in incubation experiments. The calculated ratio between both pathways reflected well the ratio determined by application of methyl fluoride (CH3F) as specific inhibitor of acetate‐dependent methanogenesis. Only at the end of the season, the theoretical ratio of acetate: H2 = 2 : 1 was reached, whereas at the beginning H2/CO2‐dependent methanogenesis dominated. The isotope discrimination was different between rooted surface soil and unrooted deep soil. Root‐associated CH4 production was mainly driven by H2/CO2. Porewater CH4 was found to be a poor proxy for produced CH4.
The Relationships between the Dictyosomes and the Forms of Endoplasmic Reticulum in Plant Cells with Different Export Programs

The relationship between dictyosomes and the endoplasmic reticulum (ER) in a variety of plant tissues was investigated by conventional and high-voltage electron microscopy. The zinc iodide/osmium tetroxide (Z10) technique was used to stain selectively the ER and cisternal membranes. No connections were observed between either the dictyosomes and the cisternal or tubular forms of the ER in the carbohydrate-secreting cells of maize root caps, bean leaf palisade tissue, and elongating bean roots. On the other hand, in the protein-secreting gland cells of Dionaea muscipula, connections between the tubular ER and dictyosome cisternae were observed across the cisternal stack. Connections between the ER and the plasmalemma of these gland cells are also reported. The results are discussed in light of recent evidence on the endomembrane concept of plant cells.
The oxidation of reduced glutathione and other sulphydryl compounds

Hopkins (1) has recently isolated a cell constituent, glutathione, which would appear to play an important part in the dynamic oxidation and reduction processes in the tissues. The substance is a dipeptide of cystein and glutaminic acid, but the exact position of the peptide linkage has not yet been determined. For convenience the formula may be written G . SH, where G represents the residue of the cystein molecule linked with glutaminic acid. On oxidation the substance is converted to the disulphide form G . S . S . G in a manner strictly analogous to the conversion of cystein to cystine.
Affinity Purification of Helicobacter pyloriUrease

A simple, reproducible and high yield method ofHelicobacter pylori urease enzyme purification was developed using a heparinoid (Cellufine sulfate) affinity gel. The purification method involved two sequential steps using the same gel that takes advantage of the differential affinity of urease to the heparinoid at two levels of hydrogen ion concentration. SDS-polyacrylamide gel electrophoresis analysis of affinity-purified urease revealed two major protein bands with about 62- and 30-kDa molecular mass. When whole cell lysates of clinical and laboratory strains of H. pylori were probed by Western blot, anti-urease hyperimmune serum produced by affinity-purified urease in rabbit recognized only the two bands corresponding to the urease A and B subunits. To probe the molecular relevance of affinity gel adherence to mucin adherence, the purified urease was derivatized withN-hydroxysuccinimidobiotin and used in adherence assays. Competitive inhibition tests revealed commonality of urease receptors among gastric mucin, heparin, and heparinoid. Composite data on adherence kinetics modulated by pH, salt, incubation time, and concentration of urease or mucin were indicative of conformation-dependent ligand-receptor interaction.
Retrieval of Associative Information Congruent with Prior Knowledge Is Related to Increased Medial Prefrontal Activity and Connectivity

We remember information that is congruent instead of incongruent with prior knowledge better, but the underlying neural mechanisms related to this enhancement are still relatively unknown. Recently, this memory enhancement due to a prior schema has been suggested to be based on rapid neocortical assimilation of new information, related to optimized encoding and consolidation processes. The medial prefrontal cortex (mPFC) is thought to be important in mediating this process, but its role in retrieval of schema-consistent information is still unclear. In this study, we regarded multisensory congruency with prior knowledge as a schema and used this factor to probe retrieval of consolidated memories either consistent or inconsistent with prior knowledge. We conducted a visuotactile learning paradigm in which participants studied visual motifs randomly associated with word–fabric combinations that were either congruent or incongruent with common knowledge. The next day, participants were scanned using functional magnetic resonance imaging while their memory was tested. Congruent associations were remembered better than incongruent ones. This behavioral finding was parallelized by stronger retrieval-related activity in and connectivity between medial prefrontal and left somatosensory cortex. Moreover, we found a positive across-subject correlation between the connectivity enhancement and the behavioral congruency effect. These results show that successful retrieval of congruent compared to incongruent visuotactile associations is related to enhanced processing in an mPFC–somatosensory network, and support the hypothesis that new information that fits a preexisting schema is more rapidly assimilated in neocortical networks, a process that may be mediated, at least in part, by the mPFC.
Promoter Use by ς38 (rpoS) RNA Polymerase

ς38 is a non-essential but highly homologous member of the ς70 family of transcription factors. In vitro mutagenesis and in vivo screening were used to identify 22 critical amino acids in the promoter interaction domain of Escherichia coliς38. Electrophoretic mobility shift assay studies showed that residues involved in duplex DNA binding largely segregated into distinct regions that coincided with those of ς70. However, the majority of these amino acids were in non-conserved positions. Analysis indicates that this region of the two ςs probably has a common overall organization but differs in how its amino acids are used to form functional open complexes. Placement of the mutations on the known ς70 holoenzyme structure shows two clusters; one appears to be used for duplex DNA recognition and the other for the subsequent isomerization events. Permanganate assays for DNA melting support this view.
Transformation of the Yeast, Saccharomyces carlsbergensis, Using an Antibiotic Resistance Marker

Transformation of the yeast, Saccharomyces carlsbergensis, with plasmids carrying the kanamycin (G418) resistance gene of Tn903 was attempted. Transformants resistant to the antibiotic, G418, were obtained from two strains of this species as well as a strain of S. cerevisiae after treatment of intact cells with lithium acetate and polyethylene glycol. The optimum period of post-incubation for expression of the kanamycin resistance gene was found to be four hours at 30°C for both S. carlsbergensis and S. cerevisiae. The transformation efficiency of S. carlsbergensis was lower than that of S. cerevisiae. The mitotic stability of the four plasmids used was determined; that of a plasmid containing the replication origin of 2 μm-DNA was lower in S. carlsbergensis than in S. cerevisiae. The mitotic stabilities of the three other plasmids containing ars 1, a centromere and ars 1, and no replication origin, respectively, in yeast cells were almost the same in S. carlsbergensis and S. cerevisiae.