Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterisation of antagonist binding sites on chemokine receptor CCR4

CCR4 is a chemokine receptor notably expressed on T helper 2 and regulatory T cells. CCR4 binds the chemokines CCL17 and CCL22. These are involved in T cell homeostasis and inflammatory diseases including asthma and atopic dermatitis, making CCR4 a potential therapeutic target. Previous studies suggested that CCL22 is dominant over CCL17 with respect to ligand-induced internalisation and desensitisation of CCR4. The biology of CCR4 was investigated in this project using point mutational studies. A C-terminal lysine within the conserved helix VIII region was determined to be dispensable for CCL22-induced chemotaxis but required for CCL17-induced chemotaxis, suggesting that the two chemokines stabilised distinct receptor conformations. The highly conserved GluVII:06 of helix VII was shown to be critical for chemokine binding and receptor function. Seven small molecule allosteric antagonists of CCR4, supplied by GlaxoSmithKline, were hypothesised to bind either a classical intrahelical site (site 1) within the receptor or a novel intracellular site (site 2). 22 amino acids were predicted to be involved in the binding of the antagonists. Antagonist binding was indirectly investigated by inhibiting either function or chemokine binding of the receptor mutants. Mutation of leucine 118 in transmembrane helix III significantly reduced CCR4 sensitivity to site 1 antagonism in chemotaxis and chemokine-binding assays. Mutants of phenylalanine 305 and leucine 307 at the end of transmembrane helix VII also showed a reduction in antagonist 2 sensitivity. Direct investigation of the effects of mutation on antagonist binding was performed using tritium-labelled antagonists. Mutation of GluVII:06 prevented site 1 antagonist binding to CCR4. Further investigation of site 1 antagonist binding was hindered by high non-specific binding of the compounds. A low-affinity site for the tritium-labelled site 2 antagonist was identified on untransfected cells, possibly within endogenously expressed chemokine receptors. This antagonist therefore may have potential as a broad-spectrum chemokine receptor inhibitor.
Circulating tumor DNA and its clinical applications

Tumor-derived genetic changes and epigenetic alterations have been found in the serum and plasma of cancer patients. The alterations found in the blood mimic the alterations found in the primary tumor with a 71% of similarity. Moreover, these alterations are not found in normal tissues of healthy controls. These findings have important consequences for the detection, monitoring, prognosis, and early diagnosis of cancer. In this work, we will revisit anecdotal but repetitive observations of these possibilities that have been made during the last decade. New studies should be undertaken in order to ascertain the applicability of these observations, and their use in clinics. Sensitivity and specificity must be improved, and clinical and epidemiological studies should incorporate this technology to enable proper conclusions. DNA nowotworu kra˝ace w osoczu/surowicy i jego zastosowania kliniczne W surowicy i osoczu chorych na nowotwory z∏oEliwe mo˝na stwierdzic zmiany genetyczne i przemiany epigenetyczne, wywo∏ane sama obecnoEcia guza nowotworowego. Przemiany, stwierdzane we krwi, naEladuja przemiany obecne w pierwotnym
Microwave Assisted Synthesis and Microbial Screening of Novel Amino-pyrimidine Derivatives using Bis-chalcones

A simple and clean one pot method for the preparation of amino-pyrimidine derivatives using chalcones of cyclic imides and guanidine nitrate in presence of neutral alumina under microwave supported solvent free condition is described. Some of the synthesized amino-pyrimidines showed synergistic significant activities against Candida albicans and Aspergillus niger fungal strains.
FASCIATED MUTANT INDUCED BY THE COMBINED TREATMENT OF GAMMA RAYS AND SODIUM AZIDE (20 KR + 0.10% SA) IN LINUM USITATISSIMUM L.

The present investigation provides the effect of combined treatment of gamma rays and SA (Sodium Azide) on the morphology of Linum usitatissimum. Fasciated plants were obtained in M2 and M3 generation. Various widened and flattened organs were found such as fasciated stems, abnormal branches arising from fasciated stems, broad and abnormal leaves. The enhanced activity of apical meristem and cambium resulted in a significantly increased circumference of the stem resulting into increasing number of leaves, buds, flowers, fruits and seeds. Moreover the size of fruits and seeds were much bigger than control.
Methanogenic abundance and changes in community structure along a rice soil chronosequence from east China

Changes in abundance, community structure and activity of archaea were investigated for rice paddy soil under long‐term cultivation along a chronosequence that spans 700 years in a coastal area of east China. Topsoil samples were analysed for archaeal abundance and community structures, which were determined with archaeal 16S rRNA and methanogenic mcrA genes. Methane production potential (MPP) was evaluated concurrently with a laboratory anaerobic incubation of treated topsoil samples. Gene abundance of archaea and methanogenic archaea increased from 6.70 × 106 and 1.53 × 105 copies g−1 in marsh to 2.89 × 108 and 2.73 × 107 copies g−1 in rice soil cultivated for seven centuries, respectively. Compared with the uncultivated marsh, diversity indices for both archaea and methanogenic archaea increased markedly with rice cultivation. Methanogenic archaeal community structure was dominated by Methanosarcinales and changed to a lesser extent after 100 years. The measured MPP varied over a range from 241.3 to 301.1 µg CH4 g−1 for the rice soil, whereas it was 101.3 µg CH4 g−1 for the uncultivated marsh soil. Therefore, gene abundance of both archaea and methanogenic archaea appeared to increase with the accumulation of organic matter following long‐term rice cultivation. The changes in MPP and community structure, however, were independent of differences in archaeal abundance. This suggests a complex interaction of soil organic matter, archaeal abundance and community structure, which could change the potential methanogenic activity in rice soil with long histories of rice cultivation.
Resistance Management: Slowing Pest Adaptation to Transgenic Crops

Transgenic crops that are genetically modified to produce insecticidal proteins from the common bacterium Bacillus thuringiensis (Bt) can help to control pests while reducing reliance on insecticide sprays. So far, no insects have evolved resistance in the field to Bt transgenic crops. However, diamondback moth populations have evolved resistance to Bt sprays in the field and many pests have evolved resistance to Bt toxins in the laboratory. To delay resistance, the refuge strategy provides host plants that do not produce Bt toxins, thereby promoting survival of susceptible pests. In Arizona, Bt cotton has been extremely effective in controlling the pink bollworm (Pectinophora gossypiella), a major pest. Despite a surprisingly high frequency of resistance in 1997, resistance did not increase in Arizona field populations of pink bollworm from 1997 to 1999. Nonetheless, pink bollworm and other insects will eventually evolve resistance, so any particular transgenic crop variety is not a permanent solution to pest problems. Instead, transgenic crops can be used in harmony with other tactics as part of integrated pest management. Evaluations of transgenic crops should consider their advantages and disadvantages compared with alternatives. If transgenic crops can greatly reduce use of hazardous insecticides, as achieved in Arizona cotton, great benefits may occur.
[Study of gene polymorphism responsible for metabolism of proton pump inhibitors in children with H. pylori infection: is there a correlation with efficacy of eradication treatment?].

UNLABELLED: THE AIM of this study was to determine the effects of CYP2C19 polymorphism on H. pylori eradication in pediatric population in the Republic of Bashkortostan. METHODS: Fifty-nine children were entered into the study (age range: 12 to 17; 22 female). All the patients were infected with H. pylori and received the combination of omeprazole (1 mg/kg/day), furazolidone (10 mg/kg/day) and amoxicilline (25 mg/kg/day) or clarithromycin (7.5 mg/kg/day) for 10 days. The participants were classified into 3 groups according to CYP2C19 genotype; rapid metabolizers (RM) (54.2%), intermediate metabolizers (IM) (35.6%) and poor metabolizers (PM) (10.2%). H. pylori infection status was assessed before and after the treatment. RESULTS: The eradication rate was 65.6% for RM, 71.4% for IM, and 83.3% for PM. CONCLUSION: The present study confirmed the low eradication rate for RM and for the IM groups. Alternative regimens expected to be with a higher eradication rate should be recommended (rabeprazole-based treatment).
Revealing kleptoparasitic and predatory tendencies in an African mammal community using camera traps: a comparison of spatiotemporal approaches

Camera trap data are increasingly being used to characterise relationships between the spatiotemporal activity patterns of sympatric mammal species, often with a view to inferring inter-specific interactions. In this context, we attempted to characterise the kleptoparasitic and predatory tendencies of spotted hyaenas Crocuta crocuta and lions Panthera leo from photographic data collected across 54 camera trap stations and two dry seasons in Tanzania's Ruaha National Park. We applied four different methods of quantifying spatiotemporal associations, including one strictly temporal approach (activity pattern overlap), one strictly spatial approach (co-occupancy modelling), and two spatiotemporal approaches (co-detection modelling and temporal spacing at shared camera trap sites). We expected a kleptoparasitic relationship between spotted hyaenas and lions to result in a positive spatiotemporal association, and further hypothesised that the association between lions and their favourite prey in Ruaha, the giraffe Giraffa camelopardalis and the zebra Equus quagga, would be stronger than those observed with non-preferred prey species (the impala Aepyceros melampus and the dikdik Madoqua kirkii). Only approaches incorporating both the temporal and spatial components of camera trap data resulted in significant associative patterns. The latter were particularly sensitive to the temporal resolution chosen to define species detections (i.e. occasion length), and only revealed a significant positive association between lion on spotted hyaena detections, as well as a tendency for both species to follow each other at camera trap sites, during the dry season of 2013, but not that of 2014. In both seasons, observed spatiotemporal associations between lions and each of the four herbivore species considered provided no convincing or consistent indications of any predatory preferences. Our study suggests that, when making inferences on inter-specific interactions from camera trap data, due regards should be given to the potential behavioural and methodological processes underlying observed spatiotemporal patterns.
Oxidative enzymatic gelation of sugar beet pectin for emulsion stabilization

(18/10/2019) Oxidative enzymatic gelation of sugar beet pectin for emulsion stabilization Pectin from sugar beet is derived from the sugar beet pulp residue which results when sugar beets are processed for sucrose extraction. The sugar beet pectin has poor gelationability by the classic divalentcation molecular mechanism because of a relatively high acetylation degree and short polygalacturonate backbone chain length. However, due to the feruloyl-substitutions on the side chains, the sugar beet pectic polysaccharides can be cross-linked via enzyme catalyzed oxidation. The enzyme kinetics and functionality of such oxidativelycross-linked sugar beet pectin, in relation to stabilizing emulsions has recently been investigated in model food emulsions. This paper reviews the pectin chemistry, enzymatic oxidative gelation mechanisms, interaction mechanisms of the sugar beet pectin with the emulsion droplets and explores how the gelation affects the rheology and stability of emulsion systems. The applied biotechnology concept of enzymatic gelation provides an array of opportunities for upgrading of low-value pectins for new food and non-food uses.
Technology for Automation of Weed Control in Specialty Crops

Specialty crops, like flowers, herbs, and vegetables, generally do not have an adequate spectrum of herbicide chemistries to control weeds and have been dependent on hand weeding to achieve commercially acceptable weed control. However, labor shortages have led to higher costs for hand weeding. There is a need to develop labor-saving technologies for weed control in specialty crops if production costs are to be contained. Machine vision technology, together with data processors, have been developed to enable commercial machines to recognize crop row patterns and control automated devices that perform tasks such as removal of intrarow weeds, as well as to thin crops to desired stands. The commercial machine vision systems depend upon a size difference between the crops and weeds and/or the regular crop row pattern to enable the system to recognize crop plants and control surrounding weeds. However, where weeds are large or the weed population is very dense, then current machine vision systems cannot effectively differentiate weeds from crops. Commercially available automated weeders and thinners today depend upon cultivators or directed sprayers to control weeds. Weed control actuators on future models may use abrasion with sand blown in an air stream or heating with flaming devices to kill weeds. Future weed control strategies will likely require adaptation of the crops to automated weed removal equipment. One example would be changes in crop row patterns and spacing to facilitate cultivation in two directions. Chemical company consolidation continues to reduce the number of companies searching for new herbicides; increasing costs to develop new herbicides and price competition from existing products suggest that the downward trend in new herbicide development will continue. In contrast, automated weed removal equipment continues to improve and become more effective.
Analysis of Promoter Hypermethylation of p16 Gene and DAPK Gene in Sera from Primary Liver Cancer Patients

Objective To analyze the aberrant methylation of p16 gene and DAPK gene in sera from primary liver cancer patients and to evaluate the clinical significance. Methods A methylation-specific PCR was performed for the detection of promoter hypermethylation of p16 gene and DAPK gene in blood DNA from 64 cases of PLC patients. The relation of the aberrant methylation of p16 gene and DAPK gene and the clinical pathological data was analyzed. Results 76.6%(49/64)of the sera from 64 cases of PLC patients showed hypermethylation for p16 promoter and 40.6%(26/64)the same for DAPK promoter, whereas no methylated p16 gene and DAPK gene were found in sera from liver benign diseases patients and normal control. Methylated p16 gene and DAPK gene promoters in sera did not strongly correlate with HBsAg, stage ,metastasis and differentiation in PLC;but strongly correlated with AFP. Conclusion Detection of the aberrant methylation of p16 and DAPK gene in serum from PLC patients might offer an effective method for the earlier auxiliary diagnosis of the malignancy.
Functional Analysis of Human and Mouse Splenic B cells

of a dissertation at the University of Miami. Dissertation supervised by Professor Wasif N. Khan. No. of pages in text. (113) T-cell independent (TI) antibodies may be critical in closing the gap between early innate and late adaptive immune responses against bacterial pathogens. In the mouse, innate marginal zone (MZ) B cells rapidly produce these antibodies. In humans, the characterization of a MZ B cell equivalent to that of mice is controversial because of phenotypic differences between the two species. Studies suggest that TLR activation upregulate BAFF receptors, TACI and BR3 in mouse splenic B. Upregulation of BAFF receptors is important because the ligands for these receptors, BAFF and APRIL, are critical in the regulation of humoral immune responses and immunoglobulin (Ig) isotype class switching in the context of TI antigens. By comparison of human splenic MZ B cells (MZ) with their well characterized mouse counterparts we investigated a role for innate TLRs and BAFF receptors (BR3 and TACI) in TI antibody responses. I show in this dissertation that among splenic B cells, the bulk of TI antibodies are produced by MZ B cells relative to follicular I and II B cells (FOBI and FOBII) both in human and mouse. Although MZ B cells were most responsive to TLR stimulation in both species, they differed qualitatively in the regulation of BAFF receptors. Human MZ B cells increased TACI, but not BR3. Once the TACI was increased, human MZ B cells produced more IgM and switched to IgA and to a lesser extent to IgG1 in the presence of BAFF or APRIL. Bruton’s tyrosine kinase (Btk) was found to be required to mediate TLR signaling that enhanced expression of antibody regulators, TACI and an atypical I B, NFBid. Together these results suggest that like mouse, human splenic MZ B cells are the major responders to TLR ligand containing TI antigens and require Btk signaling for these TLR driven TI antibody responses.
Isolation, Characterization, and Expression Analysis of the MaMDH Gene in Banana

A full-length cDNA isolated from banana (Musa acuminata L. AAA group) fruit was named MaMDH, containing an open reading frame encoding 332 amino acids that represents the gene for cytoplasmic malic dehydrogenase (MDH). Sequence analysis showedthatMaMDHshareshigh similarity with MDHs from castor bean (XP_002533463), tobacco (CAC12826), peach (AAL11502), and chickpeas (CAC10208). Real-time quan- titative polymerase chain reaction (PCR) analysis of MaMDH spatial expression showed that it was expressed in all organs examined: roots, rhizomes, leaves, flowers, and fruits. The expression was the highest in flowers followed by the fruits and roots, whereas the rhizomes and leaves displayed the lowest expression levels. Real-time quantitative PCR revealed that MaMDH exhibited differential expression patterns in post-harvest banana fruits correlating with ethylene biosynthesis. In naturally ripened banana fruits, MaMDH expression was in accordance with ethylene biosynthesis. In accordance, for banana fruits treated with the ethylene analog 1-methylclopropene (1-MCP), MaMDH expression levels were inhibited and remained constant. After treatment with ethylene, MaMDH expression in banana fruits significantly increased with ethylene biosynthesis and peaked 3 days after harvest, which was 11 days earlier than that in naturally ripened banana fruits. These results suggest that MaMDH expression is induced by ethylene to regulate post-harvest banana fruits ripening.
USO DE LA TÉCNICA DE LA BOLSA DE NYLON MOVIL PARA MEDIR DIGESTIBILIDAD IN SITU DE ALGUNOS INSUMOS Y AGUACATE EN CERDOS

The mobile nylon bag technique was used for measuring in situ digestibility of conventional feeds and avocado (Persea americana Mills) products in three 70 kg pigs fitted with a simple cannula in duodenum. One 3x3 Latin square was used for determining in situ digestibility of soybean, maize and sorghum meal and another 3x3 Latin square for measuring in situ digestibility of seed, peel plus seed meal and the entire Nayaritean avocado fruit of Hass type, as well as of the commercial diet given ad libitum to animals. In a preliminary test conducted with only bags containing a commercial feedstuff, it was found that in situ digestibility of DM was on average 73.01%. In conventional feeds, soybean meal samples showed higher (P<0.05) in situ digestibility values for DM, NDF and N, than those of maize and sorghum. Among avocado products, the seeds showed a higher nutritive value than peels plus seeds, whereas the entire fruit had higher (P<0.05) in situ digestibility for DM and NDF than the other two avocado products. There were not significant differences (P>0.05) for N digestibility among avocado products, which was generally low (between 28.02 and 34.58%). In situ organic matter digestibility was linked to that of MS (r = 0.915; P<0.001), both in percent, in 42 examined samples, by the following found equation: y = 2.076 + 0.926 x. The herein described studies concerning the utilization of the mobile bag showed that it is possible to obtain a fast response in connection to the nutritive value of non conventional, tropical alimentary resources for pigs. On the other hand, the continuation of studies relative to the nutritive value of avocado products for pigs is highly recommended.
ABC proteins : from bacteria to man

Preface. Introduction. PART 1-PHYLOGENY AND EVOLUTION OF ABC-TRANSPORTERS Phylogenetic and Functional Classification of ABC (ATP-binding cassette) Systems Membrane Topology of the Human ABC Transporter Proteins Human and Drosophila ABC-Proteins PART 2-FUNDAMENTAL ASPECTS OF THE MECHANISM OF ACTION OF ABC-TRANSPORTERS Structure and Modular Organization of ABC-Transporters Substrate Binding Sites in ABC-Transporters Probing of Conformational Changes,Catalytic Cycle and ABC-Transporters Function X-ray Structure of an Intact ABC-Transporter, MsbA PART 3-PROKARYOTE ABC-TRANSPORTERS Introduction to Bacterial ABC-Transport Systems Import of Solutes by ABC-Transporters-The Maltose System Crystal Structures of Periplasmic Solute Binding Proteins in ABC-Transport Complexes Illuminate their Function Bacterial ABC-Transporters Involved in Protein Translocation Bacterial Multidrug Resistance Mediated by ABC-Transporters Structure and Function of Osmoregulated ABC Transporters PART 4 -NON-MAMMALIAN EUKARYOTE ABC-TRANSPORTERS Inventory & Evolution of Fungal ABC Protein Genes. Fungal ABC Proteins in Clinical Drug Resistance & Cellular Detoxification Drug Resistance Mediated by ABC Transporters in Parasites of Humans The Plant ABC Transporter Superfamily: the Functions of a Few and Identities of Many PART 5-MAMMALIAN MULTIDRUG RESISTANCE ABC-TRANSPORTERS Solving the Problem of Multidrug Resistance: ABC Transporters in Clinical Oncology Multidrug Resistance Protein 1 (ABCC1) MRP2, the Apical Export Pump for Anionic Conjugates The Multidrug Resistance Proteins 3-7 Lipid Transport by ABC Transporters Role of ABCA1 in Cell Turnover and Lipid Homeostasis Peroxisome ABC-Transporters ABC-Transporters in Mitochondria The Transporter Associated with Antigen Processing (TAP): A Peptide Transport and Loading Complex Essential for Cellular Immune Responses The Sulphonylurea Receptor: an ABCC Transporter that Acts as an Ion Channel Regulator ABC-Transporters and Human Eye Disease Structure Function Analysis of CFTR
Wood anatomy of six species of Lycium, with comments on fibriform vessel elements

The study of wood anatomy of 6 species of Lycium L. was made. These species share an homogeneous structure. The essential wood characteristics are: dendritic distribution, presence of spiral thickness in the secondary wall of vascular elements and tracheids, apotracheal and paratracheal axial parenchyma, radial heterogeneous, and libriform fibres. The presence of fibriform vessel elements is described in 6 six species of Lycium for the first time.