Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding the Interactions of Developing Thymocytes and Antigen Presenting Cells in the Thymic Medulla

The contribution of thymic APC subsets in selecting a self-tolerant T cell population remains unclear. We show that BM APCs and mTECs played non-overlapping roles in shaping the TCR repertoire by deletion and Treg cell selection of distinct TCRs. Aire, which induces tissue-specific-antigen expression in mTECs, affected the TCR repertoire in a manner distinct from mTEC presentation. Approximately half of Aire-dependent deletion or Treg cell selection utilized a pathway dependent on antigen presentation by BM APCs. Batf3-dependent CD8α DCs were the crucial BM APC for Treg cell selection via this pathway, showing enhanced ability to present antigens from stromal cells. These results demonstrate the division of function between thymic APCs in shaping the self-tolerant TCR repertoire, and reveal an unappreciated cooperation between mTECs and CD8α DCs for presentation of Aire-induced self-antigens to developing thymocytes.
Chapter 3:Drug Molecules and Biology: Network and Systems Aspects

Complex biological networks are strikingly robust to deletion or interruption of their components. This robustness may be mediated by network features that we can now target specifically through network analysis. Network components (‘nodes’) differ greatly in importance depending upon the extent to which a node is connected to other nodes (‘degree’), the extent to which a node connects otherwise unconnected clusters (‘betweenness’) and the extent to which there are alternative pathways through a network (‘redundancy’). While networks are highly robust to random deletions of nodes, they are much more susceptible to targeted deletions prioritised by network properties such as degree and betweenness. A small number of combinations of, for example, five proteins can have a very great impact on network integrity in most biological networks. The strategy of network pharmacology-based approaches such as combinatorial network impact analysis is to find these very few high impact protein combinations that should be addressed simultaneously in order to yield high therapeutic efficacy.
Bacillus spp. or Bacillus spp.-Derived Membrane Vesicles Induce the Intrinsic Pathways of Apoptosis of Human Colon Cancer Cell Lines

The striking increase in colorectal cancer (CRC) has shown the great fatality in Korea for more than 15 years. The leading edge of this rising incidence rate is mainly due to the people"s dietary changes in Korea. Some studies have reported that the dietary fiber does not have significant cytotoxic effects on CRC cells, which contrasts to the effects of probiotics. It gives a positive evaluation that the nonpathogenic spore-forming Bacillus species among the probiotics including fermented bacteria might have optimistic effects on CRC incidence rate. Recently, we isolated Bacillus lentus (BL) from Korean soybean fermented food. BL showed the cytotoxic effect on human colon carcinoma cell lines HCT116 and SW480. Interestingly, BL did not have effect on human dermal fibroblast cells and human hepatoma cell line HepG2. It suggested that BL has the target cell-specific cytotoxicity toward human colon carcinoma cells. To clarify the death signaling pathway underlying the BL-induced apoptosis in cancer cells, we analyzed the expression of caspases, Bax and Bcl-2 by western blotting. The apoptotic effects by cytotoxic elements were executed by direct BL contact or membranederived vesicles isolated from BL. Treatment of HCT116 with BL activated caspase-9, -3 and increased cleavage form of poly (ADP-ribose) polymerase (PARP). However, caspase-8 activity was not increased by BL. BL-activated intrinsic pathway increased the pro-apoptotic Bax, decreased the anti-apoptotic Bcl-2 proteins on mitochondria, disrupted the mitochondrial membrane potential, and then released the cytochrome c from mitochondria. The membrane-derived vesicles (MVs) from BL induced apoptosis of the HCT116. Here, we propose that BL as a strong candidate for the development of apoptosis-specific anti-tumor agent will give great contribution to the understandings of the tumor-microbe interdisciplinary areas.
Système de reproduction et adaptation à la toxicité du sol chez la Brassicacée pseudo-métallophyte Noccaea caerulescens

Je m’interesse a l’ecologie evolutive et en particulier a l’evolution des systemes de reproduction, a l’adaptation et aux interactions de ces deux processus. En effet, les modeles theoriques ainsi qu’un certain nombre d’observations en populations naturelles soulignent que le systeme de reproduction devrait avoir un effet majeur sur les processus evolutifs et demographiques en populations naturelles. Lors de ma these, j’aborde ces themes sous divers angles a partir d’une Brassicacee tolerante et hyper-accumulatrice aux metaux lourds, Noccaea caerulescens, et a partir de modeles theoriques. Dans un premier temps, je m’interesse a la variation du systeme de reproduction en populations naturelles. Comment s’organisent les flux de genes entre populations ou sous-populations, et entre individus d’une meme population ? Je me suis particulierement interessee a l’influence de la pollution des sols sur le taux d’autofecondation chez N. caerulescens, aux flux de genes entre populations vivant dans les mines et populations vivant sur des sols non contamines, et a la structure a l’interieur des populations. Afin de mieux comprendre les facteurs influencant le systeme de reproduction, j’ai ensuite teste l’effet de la densite en plantes sur le taux d’autofecondations en populations naturelles. Dans un second temps, je teste les interactions existant entre adaptation a des milieux potentiellement tres toxiques et systeme de reproduction. Plus specifiquement, je teste si la depression de consanguinite depend du niveau de stress que subissent les populations, en interaction avec l’histoire des pressions de selection qu’on subies les populations par le passe. Enfin, a l’aide de simulations, j’etudie comment la variation interannuelle du systeme de reproduction peut influencer la probabilite d’adaptation de populations faisant face a un changement environnemental.
Heterogeneous localization of G protein α-subunits in rat kidney

The G s α and G i α 1-3 subunits of GTP-binding proteins were localized in sections of rat kidney using antibodies against unique synthetic decapeptides from the different Gα subunits. All of the Gα subunits were found to have a polarized distribution on renal tubule epithelial cells, and staining was typically found on either basolateral or apical membranes in a given cell type
Perfil dos participantes do núcleo UNESP-UNATI do campus de Presidente Prudente

Because of the great increase of the senior population in all world, a larger concern exists in turning the most productive and healthy old age. With this purpose, the Nucleo UNESP-UNATI of the campus of Presidente Prudente, tries to contribute offering several activities and providing an important social integration among these individuals. Like this, is necessary to characterize them and to know their interests better for refine and a planning of the activities, doing with that these assist the expectations and needs of the participant group. For the characterization data were collected on sex, education, marital status and home. It is noticed, for the results, that most of the participants lives with their relatives in detriments of the ones that live alone. In relation to the marital status the married ones prevail. In agreement with the education degree, we had a high index of participants with higher education, starting from 2002, that just in the year of 2001 it was crossed by a larger index of participants with incomplete fundamental teaching, fact that can also be explained by the type of activities that were inserted in the program. The predominant age group was of 50 and 70 years for both sexes. In agreement with the obtained results, we can notice that the senior this being moved as active agent of their own health, always looking for to improve their quality of life.
Pine sawdust as stimulator of the microbial community in post-arable afforested soil

ABSTRACT Sawdust and wood residues are considered to be stimulators of microbiological change in soil and could be used in post-arable sites designed for afforestation. In this study, we discuss changes in bacteria numbers within selected groups in relation to soil type (arable and forest) and method of sawdust application. Sawdust was spread along planting rows and mixed with the soil or put directly under roots of planted seedlings. Applying sawdust under the roots increased the number of cellulolytic bacteria in all experimental treatments. On post-arable soil, adding sawdust in rows increased the number of copiotrophic bacteria and reduced the number of fluorescent bacteria and actinomycetes (ACT). In control forest soils, the number of copiotrophic, oligotrophic and spore-forming bacteria decreased simultaneously with increased ACT in all treatments. The number of fluorescent bacteria increased when sawdust was applied on forest sites under planted trees and decreased when sawdust was spread in planting rows. Oligotrophic bacteria also decreased in the latter case. We present a list of bacteria identified by DNA – 16S rRNA gene sequences. Adding sawdust to arable soils significantly changed the quantitative and qualitative composition of microbial communities.
Effect of Feeding Graded Levels of Urea on Growing New Zealand White Rabbit Performance

2 Abstract: Forty New Zealand white rabbits of about 1340 g live weight were used to evaluate the influence of diet supplemented with urea at different levels on growth performance, blood cellular and biochemical parameters. The rabbits were assigned into four dietary treatments control, 3 urea-supplemented groups (0.5%, 1% and 1.5% urea) for two months, at the Agriculture and Veterinary Research Station, King Faisal University. Rabbits supplied with ration containing 1.5% urea had significant increase in body weight after 4 weeks than those fed 1% urea (1995±60 vs. 1829± 53 g) and 6 weeks than the 0.5% group (3175± 125 vs. 2235±50 g). Additionally, no significant trend was detected for the hemogram parameters, except for the RBC count of 0.5% urea group (6.48±0.21 x106) (P<0.05) and monocyte% for the 1% group (8.56±0.82x103) and 1.5% group (4.99±1.38x103) (P<0.05). there were significant differences (P<0.05) among treatment groups 1.5% (5.75±0.57 g/dl) and 1% (4.13±0.57 g/dl) for total protein, albumin. Serum levels of AST were significantly decreased in all experimental groups as well as control group (25.96±2088 µ/l ) except the 1.5% urea fed rabbits which showed 4 times fold the other groups (94.45±36.67 µ/l ). The blood urea increased with increase in level of urea level in diet. Serum calcium was significantly the least at 0.5% urea level (10.13±0.05 mg/dl) while the control group had the highest (16.33±0.32 mg/dl). In Conclusion, based on the results obtained, it appears that the inclusion of up to 1.5% urea in to the diets of growing rabbits has no adverse effect on growth performance, hematological parameters and serum biochemical indices.
Characterization of an aflatoxin biosynthetic gene and resistance inmaize seeds to Aspergillus flavus

HOLMES, ROBERT. Characterization of an Aflatoxin Biosynthetic Gene and Resistance in Maize Seeds to Aspergillus flavus. (Under the direction of Rebecca S. Boston and Gary A. Payne.) Crop contamination with aflatoxins produced by the fungi Aspergillus flavus and Aspergillus parasiticus is a persistent problem. I addressed aflatoxin contamination from the perspectives of resistance and biosynthesis. A review of the literature on compounds that inhibit aflatoxin biosynthesis showed that many inhibitors are plant-derived and some may be amenable to pathway engineering for defense against aflatoxin contamination. Other compounds show promise as storage protectants. Inhibitors with different modes of action could be used in transcriptional and metabolomic profiling experiments to identify regulatory networks controlling aflatoxin biosynthesis. To address host resistance in maize, I used liquid chromatography to characterize a protein fraction from kernels of the resistant maize line Tex6 that inhibits growth and aflatoxin production by A. flavus in vitro. Two proteins were associated with the inhibitory activity. Peptide sequencing identified them as chitinase A (ChitA) and zeamatin, members of the glycoside hydrolase 19 (GH19) and thaumatin-like protein (TLP) families, respectively. Removal of chitin-binding proteins from the fraction dramatically reduced its inhibitory effect. Adding the chitin-binding fraction back to the zeamatin-enriched fraction restored activity. We used bioinformatic, phylogenetic and gene expression analyses to investigate the GH19 and TLP gene families in maize. Phylogenetic analyses placed the maize GH19 genes into four major phylogenetic groups. The TLP gene family was larger and was similar to the rice TLP family. Transcripts of members of each gene family were induced during A. flavus infection of kernels. To address aflatoxin biosynthesis, I investigated an undescribed aflatoxin biosynthetic cluster gene, hypE. The predicted HypE protein contains a putative EthD domain, a domain described to date only in bacteria. A hypE mutant of A. flavus was created by gene deletion via homologous recombination with a selectable marker. The hypE mutant produced less aflatoxin B1 and B2 than control strains and accumulated a metabolite which we assigned as a tentative HypE substrate (HESUB). Aflatoxin biosynthesis could be restored in this hypE mutant by a hypE overexpression construct and this restoration was associated with loss of HESUB accumulation. Other Aspergilli and Podospora anserina have potential hypE orthologs. We identified additional hypE-like genes which were also restricted to the
Peranan Jamur Rhizoctonia SP. Asal Taman Nasional Rawa Aopa Watumohai Sulawesi Tenggara terhadap Keberhasilan Aklimatisasi dan Laju Pertumbuhan Planlet Anggrek Macan (Grammatophyllum Scriptum BL.)

The aim of this research was to know the role of Rhizoctonia sp . fungus from Taman Nasional Rawa Aopa Watumohai (TNRAW) to the successfully acclimatization and growth rate of tiger orchid planlet (Grammatophyllum scriptum Bl.) as well to know successfully infection of fungus Rhizoctonia sp. at the planlet root. The procedure of this research consists 3 main steps, they were fungus inoculation on orchid’s growing media, growth test and verification of successfully infection on planlet root. Growth test consisting of 3 treatments namely control (without nutrition and fungi) (K 0 ); Rhizoctonia sp. application (R 1 ); Rhizoctonia sp. + nutrition Potato Dextrose Borth (PDB) (R 2 ) with the repetition for 8 times, then the growth data was analysed by statistics utilizes to F-test and continue by BNT-test on 95% trusty level. The result of the research showed that R 2 treatment increase high planlet, leaf and root number. All the mean score of research indicator R 2 was highest compared R 1 and K 0 . The result of F-test showed R 1 and R 2 treatment gave significant influence toward the high planlet, leaf and root number growth. Except, fresh and dry weight planlet. Eventhough, fresh and dry weight was higher compared than K 0 acclimatization period for a month. Rhizoctonia sp. fungus infected planlet root through velamen to eksodermis and cortex by forming hifa scroll (pelotons).
The Meristem and Quiescent Centre in Cultured Root Apices of the gib-l Mutant of Tomato (Lycopersicon esculentum Mill.)

Cultured root apices of tomato bearing the gib-1 mutation, which reduces the levels of endogenous gibberellins, grew slower and were thicker than wild-type controls. This was the result of shorter and broader cells in the meristem of the mutant. Cells of both cortex and stele were affected, but this did not cause any alteration to the volume fraction occupied by these two tissues in the root meristem. Root caps were longer in the mutant and there were also more layers of rhizodermis. All these effects could be reproduced in wild-type roots by addition of 0.1 micromolar 2S,3S paclobutrazol (an inhibitor of gibberellin biosynthesis) to the culture medium and could be normalized in mutant roots by 0.1 micromolar GA3. Cell doubling times in the proximal region of the meristem were similar in mutant and wild-type roots, but were faster in both the quiescent centre (QC) and the cap meristem of the mutant. This latter feature of the mutant roots is likely to be the cause of their longer caps, while the faster rate of division in the QC accounts for the additional tiers of cells that were found to build up in the cortical portion of this zone. These additional tiers failed to form in mutant roots grown in GA3, but they could be induced in wild-type roots by 2S,3S paclobutrazol. These results suggest that endogenous gibberellins may be partly responsible for the slow rate of cell growth and proliferation in the QC.
Diagnosis of Helicobacter pylori infection in children and their mothers using some non-invasive techniques

Helicobacter pylori (H. pylori) is an important global public health concern. It infects approximately one half of the world’s population. Considering the broad spectrum of available H. pylori diagnostic methods and since a reliable diagnosis is mandatory both before and after eradication therapy; thus it is crucial to study the different methods to be able to select the highly accurate laboratory tests that could be used to efficiently diagnose H. pylori infection in clinical practice. In this descriptive-cross sectional study we aimed to evaluate some non-invasive techniques for the diagnosis of H. pylori infection in children and their mothers. Forty children and their 21 mothers who had gastrointestinal symptoms were included. Stool, serum and saliva samples were collected from each enrolled child and mother to detect H. pylori antigens (Ags) in stool using chromatographic immunoassay and IgG antibodies (Abs) in serum and saliva by enzyme linked immune sorbent assay (ELISA). Collected data were analyzed using IBM SPSS software package version. Thirty (75%) children were positive for stool Ags, 10 (25%) were positive for serum Abs and only 5.4% were positive for saliva Abs. H. pylori stool Ag test was the most reliable test in all studied individuals and testing H. pylori IgG Abs in serum was more useful in adults than in children. Key words: Helicobacter pylori, H. pylori stool antigen, H. pylori antibodies, chromatographic immunoassay, ELISA.
Updating the calculation of ammonium particle formation in the Operational Priority Substances (OPS) source-receptor model

In this report we describe the methodology for calculating a new parameterization associated with ammonium particle formation in the Operational Priority Substances (OPS) model. For this purpose, a chemical box model was employed including using the latest reaction and photochemical data applied in the CB05 chemical mechanism, with particle formation being calculated with the ISOROPPIA II module. By deriving a dependence of the hourly conversion rate of gaseous NH3 (KNH3) into NH4 particles in %/hour on the concentration ratios of SO2/NO2 and NH3/NO2 over a range of atmospheric conditions, we have derived three different parameterizations representative of the night-time, morning/early evening and day-time conversion rates. We find that the rate of particle formation has strong diurnal cycle, as seen in observations, differing by an order of magnitude between the night-time and day-time due to an associated change in the main chemical precursors. When applying the various parameterizations in OPS we find that, although the introduction of a diurnal dependency in KNH3 causes OPS to exhibit a significant low bias compared to the annually integrated measurements, adopting the new day-time KNH3 parameterization results in an improvement of the performance of OPS when compared to multi-year surface measurements.
Effect of elevated CO2 on water relation components of Brassica species under moisture stress condition

An attempt was made to study the interactive effect of elevated CO 2 and moisture stress on water relations of Brassica species grown in FACE facility. It was observed that plants respond to elevated CO 2 significantly under moisture stress condition mitigating the adverse effects on leaf relative water content and intercellular water movement. The water status of plants improved under elevated CO 2 concentration possibly by increasing water and osmotic potential due to increase in nonstructural carbohydrates, free amino acids and free fatty acids.
Time-course Changes in nutrient composition of hexaploid wheat (Triticum aestivum L.) cultivars differing in yield potential

Changes in nutrient content, nutrient uptake, and nutrient utilization efficiency at different growth stages of two spring wheat cultivars differing in yield potential were studied in a greenhouse experiment. Fresh and dry weights of shoots, leaf area per plant, and relative growth rate were higher in low yielding Barani-83 than those in high yielding Inqlab-91 at the vegetative stage. Cv. Inqlab-91 had higher amounts of N, P, K, and S in the shoots but lower uptake and utilization efficiency of essential nutrients as compared to Barani-83 at the vegetative stage. During anthesis to grain filling, fresh and dry weights of flag leaves of Inqlab-91 were lower than those of Barani-83, whereas it was not possible to discriminate between the two cultivars on the basis of biomass of older leaves. The low yielding Barani-83 maintained higher N in the first leaves and K in the second leaves as compared to Inqlab-91, thus possibly not having supplied sufficient amount of these nutrients to the developing grains. However, P was relatively high in the flag and first leaves of Inqlab-91. Total soluble sugars were higher in all the leaves of different age of Barani-83 than those in Inqlab-91 throughout the period of grain development, which reflected that most of the assimilates from the leaves of the latter cultivar were translocated to the grains. Both the cultivars were found to have used different physiological strategies for grain production. The relatively low biomass production and relative growth rate of Inqlab-91 at the vegetative stage seemed to have played a significant role towards its higher grain yield. In addition, the low fresh and dry weights of flag leaves in Inqlab-91 indicated the translocation of most of the leaf pho-toassimilates to the grains as was evident from the low accumulation of soluble sugars in the leaves. In contrast, the low grain yield of Barani-83 can be partly related to the ability of this cultivar to retain high amounts of N and K in the leaves thereby restricting the supply of these nutrients to the developing grains.
The Influence of Rapeseed Oil on Digestibility, Energy Metabolism and Tissue Fatty Acid Composition in Pigs

Abstract The influence of rapeseed oil on digestibility, energy metabolism and tissue composition in growing pigs was determined. Rapeseed oil (0, 4, 8 and 16%) was added to a soyabean meal and barley basal diet. Essential amino acids relative to net energy (NE) were kept constant by adjusting with crystalline amino acids. Rapeseed oil has a high content of the unsaturated fatty acids 18:1n-9, 18:2n-6 and 18:3n-3, and is rich in natural tocopherols, which act as antioxidants. The apparent protein digestibility was enhanced with increasing levels of rapeseed oil. Improving the ratio of essential to non-essential amino acids decreased nitrogen execretion in faeces and urine by 21% and 26%, respectively. The amount of digestible fat increased from 29 to 218 g day−1 from the control diet to the diet with 16% rapeseed oil, resulting in a fat retention of 195 to 213 g day−1. This demonstrates the ability of pig for de novo synthesis of fatty acids. The digestibility of the rapeseed oil was high (92.7), and the .