gebhart/patrepeval huggingface dataset:
Antigen presentation by astrocytes primes rat T lymphocytes for apoptotic cell death (1996)

In this study we have characterized apoptotic cell death of autoreactive T cells resulting from their interaction with astrocytes and the modulatory effect of steroid hormones. Time kinetics of T-cell activation by interferon (IFN)-gamma-treated astrocytes from neonatal Lewis rats and by professional antigen presenting cells (APCs) from bulk suspensions of thymus or spleen were performed. [3H]Thymidine incorporation of neuritogenic P2- and encephalitogenic myelin basic protein (MBP)-specific T-cell lines declined after 48 h in culture with astrocytes. A similar suppressive effect was observed when T cells were cocultured with thymic APCs and astrocytes. This effect disappeared when astrocytes were separated by a transwell system. After 72 h of culture with astrocytes a mean of 17.5 +/- 12.4% T cells exhibited morphological signs of apoptosis. Apoptosis was identified by light microscopy, and confirmed by electron microscopy, by in situ tailing reaction and by agarose gel electrophoresis. Glucocorticosteroids and oestrogen specifically enhanced T-cell apoptosis within 8 h (69.8 +/- 23.1% and 69 +/- 17.1%, respectively) when added after 72 h to the astrocyte system, but not at earlier time points of T-cell activation or when thymic APCs were used. Glucocorticoid-mediated T-cell apoptosis was inhibited by the steroid-receptor antagonist RU 486. Pregnenolone, lipocortin-1, indomethacin and transforming growth factor-beta did not induce apoptosis in this system. The steroid effect was not associated with CD28, IL-2 receptor, or transferrin-receptor expression, which were equally upregulated on T cells activated by astrocytes or thymic APC as shown by fluorescence activated cell sorting (FACS) analysis. We conclude that astrocytes as CNS-specific APC may render T cells susceptible for induction of apoptotic cell death. Some steroid hormones can markedly enhance this process in vitro and may augment an additional effect of a systemic corticosteroid response in vivo during recovery from autoimmune encephalomyelitis.
Role of listeriolysin-O (LLO) in the T lymphocyte response to infection with Listeria monocytogenes. Identification of T cell epitopes of LLO (1991)

Using a murine model, we investigated the role of the bacterial exotoxin listeriolysin O (LLO) in cellular immunity to Listeria monocytogenes. A correlation between LLO production by infecting bacteria and generation of protective immunity to virulent LLO-producing bacteria was noted. Using isogeneic hemolysin (Hly+ or Hly-) strains of L. monocytogenes, we demonstrated that LLO production by infecting bacteria is required to elicit T cells reactive both to bacteria-associated Ag and to the secreted LLO molecule as measured by IL-2 production in vitro. Distinct sets of T cells specific for largely nonoverlapping pools of antigenic determinants represented by LLO and cell-associated Ag (heat-killed L. monocytogenes) are generated after infection. We have used models for prediction of T cell epitopes based on primary structure of LLO, and synthetic amphipathic LLO peptides were evaluated as Ag in vitro or as immunogenes in vivo. Infection of several strains of mice (H-2k and H-2d) with LLO-producing L. monocytogenes resulted in the generation of T cells that could respond consistently to two peptides, LLO 215-234 and LLO 354-371. Mouse strains lacking expression of I-E molecules (e.g., B10.A(4R) and C57BL/6) responded to LLO but not to the peptides tested. With C3HeB/FeJ mice, antibodies to I-Ek blocked the presentation of LLO 215-234. The importance of the N-terminal portion of LLO 215-234 was evidenced by the drastic reduction in antigenic activity of truncated peptides (e.g., LLO 221-234 and LLO 224-234). LLO 215-234, the strongest and most consistent activator of T cells from L. monocytogenes-immune mice, fit well some models for antigenic peptides in several ways. It could be predicted to form an amphipathic alpha-helix, it contained multiple "Rothbard motifs" (charged residue or glycine, two or three hydrophobic amino acids and then a glycine or polar residue), it had a net charge of +2, and it contained the correct spacing of amino acids (five to six residues between a hydrophobic and basic amino acid) that is characteristic of I-Ek-binding peptides. Immunization with 8 of 10 synthetic LLO peptides generated T cells that recognized the immunizing peptide in vitro, but such T cells were only poorly reactive with LLO. Our results indicate that LLO is an important target Ag for stimulation of CD4+ L. monocytogenes-specific T cells, and that LLO 215-234 is antigenically dominant in C3HeB/FeJ mice.
The Effects of Large Blood Vessels on Temperature Distributions During Simulated Hyperthermia (1992)

Several three-dimensional vascular models have been developed to study the effects of adding equations for large blood vessels to the traditional bioheat transfer equation of Pennes when simulating tissue temperature distributions. These vascular models include "transiting" vessels, "supplying" arteries, and "draining" veins, for all of which the mean temperature of the blood in the vessels is calculated along their lengths. For the supplying arteries this spatially variable temperature is then used as the arterial temperature in the bioheat transfer equation. The different vascular models produce significantly different locations for both the maximum tumor and the maximum normal tissue temperatures for a given power deposition pattern. However, all of the vascular models predict essentially the same cold regions in the same locations in tumors: one set at the tumors' corners and another around the inlets of the large blood vessels to the tumor. Several different power deposition patterns have been simulated in an attempt to eliminate these cold regions; uniform power in the tumor, annular power in the tumor, preheating of the blood in the vessels while they are traversing the normal tissue, and an "optimal" power pattern which combines the best features of the above approaches. Although the calculations indicate that optimal power deposition patterns (which improve the temperature distributions) exist for all of the vascular models, none of the heating patterns studied eliminated all of the cold regions. Vasodilation in the normal tissue is also simulated to see its effects on the temperature fields.(ABSTRACT TRUNCATED AT 250 WORDS)
Microbial Production of Malic Acid from Biofuel-Related Coproducts and Biomass (2017)

The dicarboxylic acid malic acid synthesized as part of the tricarboxylic acid cycle can be produced in excess by certain microorganisms. Although malic acid is produced industrially to a lesser extent than citric acid, malic acid has industrial applications in foods and pharmaceuticals as an acidulant among other uses. Only recently has the production of this organic acid from coproducts of industrial bioprocessing been investigated. It has been shown that malic acid can be synthesized by microbes from coproducts generated during biofuel production. More specifically, malic acid has been shown to be synthesized by species of the fungus Aspergillus on thin stillage, a coproduct from corn-based ethanol production, and on crude glycerol, a coproduct from biodiesel production. In addition, the fungus Ustilago trichophora has also been shown to produce malic acid from crude glycerol. With respect to bacteria, a strain of the thermophilic actinobacterium Thermobifida fusca has been shown to produce malic acid from cellulose and treated lignocellulosic biomass. An alternate method of producing malic acid is to use agricultural biomass converted to syngas or biooil as a substrate for fungal bioconversion. Production of poly(β-l-malic acid) by strains of Aureobasidium pullulans from agricultural biomass has been reported where the polymalic acid is subsequently hydrolyzed to malic acid. This review examines applications of malic acid, metabolic pathways that synthesize malic acid and microbial malic acid production from biofuel-related coproducts, lignocellulosic biomass and poly(β-l-malic acid).
Has the Microbiota Played a Critical Role in the Evolution of the Adaptive Immune System? (2010)

Although microbes have been classically viewed as pathogens, it is now well established that the majority of host-bacterial interactions are symbiotic. During development and into adulthood, gut bacteria shape the tissues, cells, and molecular profile of our gastrointestinal immune system. This partnership, forged over many millennia of coevolution, is based on a molecular exchange involving bacterial signals that are recognized by host receptors to mediate beneficial outcomes for both microbes and humans. We explore how specific aspects of the adaptive immune system are influenced by intestinal commensal bacteria. Understanding the molecular mechanisms that mediate symbiosis between commensal bacteria and humans may redefine how we view the evolution of adaptive immunity and consequently how we approach the treatment of numerous immunologic disorders.
Encapsulated magnetite particles for biomedical application (2003)

The process of miniemulsification allows the generation of small, homogeneous, and stable droplets containing monomer or polymer precursors and magnetite which are then transferred by polymer reactions to the final polymer latexes, keeping their particular identity without serious exchange kinetics involved. It is shown that the miniemulsion process can excellently be used for the formulation of polymer-coated magnetic nanoparticles which can further be used for biomedical applications. The use of high shear, appropriate surfactants, and the addition of a hydrophobe in order to suppress the influence of Ostwald ripening are key factors for the formation of the small and stable droplets in miniemulsion and will be discussed. Two different approaches based on miniemulsion processes for the encapsulation of magnetite into polymer particles will be presented in detail.
Domain-specific olivocerebellar projection regulated by the EphA-ephrin-A interaction (2002)

Neural maps in the vertebrate central nervous system often show discontinuously segregated, domain-to-domain patterns. However, the molecular mechanism that establishes such maps is not well understood. Here we show that in the chicken olivocerebellar system, EphA receptors and ephrin-As are expressed with distinct levels and combinations in mapping domains. When ephrin-A2 is retrovirally overexpressed in the cerebellum, the olivocerebellar map is disrupted, excluding axons with high receptor activity from ectopic expression domains. Conversely, overexpression of a truncated EphA3 receptor in the cerebellum reduces endogenous ligand activity to undetectable levels and causes aberrant mapping, with high receptor axons invading high ligand domains. In vitro, ephrin-A2 inhibits outgrowth of inferior olive axons in a region-specific manner. These results suggest that Eph receptors and ephrins constitute domain-specific positional information, and the spatially accurate receptor-ligand interaction is essential to guide inferior olive axons to their correct target domains.
Dickkopf1 and the Spemann-Mangold head organizer (2001)

Work in amphibians indicates that inhibition of Wnt and BMP signals is essential for head development and that head induction by the Spemann-Mangold organizer may be mediated by secreted Wnt antagonists. Wnts are potent posteriorizing factors and antagonize the Spemann-Mangold organizer. Dickkopf1 (dkk1) encodes a secreted effector expressed in head organizing centers of Xenopus, mouse and zebrafish. It acts as a Wnt inhibitor and is able together with BMP inhibitors to induce the formation of ectopic embryonic heads in Xenopus. It anteriorizes both mesendoderm and neuroectoderm, promoting prechordal plate and forebrain fates. Injection of inhibitory antibodies leads to microcephaly and cyclopia. Dkk1 thus is an essential mediator of the vertebrate head organizer.
Use of laser scanning cytometry to study tumor microenvironment. (2003)

The study of phenomena occurring in the tumor microenvironment is a challenging task because of technical difficulties, particularly when dealing with hypocellular specimens. Laser scanning cytometry (LSC) is a new laboratory technology that has been recently introduced to overcome the limitations of other traditional technologies. By combining the properties and the advantages of flow cytometry (FC) and immunohistochemistry (IHC), LSC allows the investigator to obtain objective information on DNA content, protein expression and cellular localization is combination with morphological features. It has been already shown that LSC results are reliable compared to more traditional technologies, and its implementation in the clinical routine is under way. Its use in oncology, which is rapidly expanding, spans from apoptosis analysis to DNA content quantitation and tumor cell phenotyping. Here we describe the technology underlying this novel fluorescence-based device, review its use in oncology by dissecting the phenomena occurring in the tumor microenvironment and propose its application for the immunological follow-up of malignant lesions undergoing immunotherapeutic manipulation.
Real-time hidden-line elimination for a rotating polyhedral scene using the aspect representation (1990)

The three-dimensional structure of an object is easier to perceive when the object is rotating or when the viewer moves to see it from a range of viewpoints. Thus, CAD systems are usually able to display an object as it rotates. Topologists may more easily perceive the structure of a polyhedral model of a knot and biologists the structure of a molecule using such rotations. In
A point mutation at the putative ATP-binding site of protein kinase C alpha abolishes the kinase activity and renders it down-regulation-insensitive. A molecular link between autophosphorylation and down-regulation. (1990)

A protein kinase C alpha (PKC alpha) cDNA confers increased phorbol ester binding activity to intact cells when transiently expressed in COS cells or expressed stably in transfected rat 3Y1 fibroblasts. A point mutant (PKC alpha K----R) of PKC alpha, where Lys368 at the putative ATP-binding site is replaced with Arg, confers enhanced phorbol ester binding activity to both transiently and stably expressed COS and 3Y1 cells, respectively. Like endogenous and exogenously expressed wild type PKC alpha, the mutant PKC alpha K----R is translocated from the cytosol to the particulate fraction when cells are treated with a phorbol ester, 12-O-tetradecanoylphorbol-13-acetate (TPA). On the other hand, the mutant PKC alpha K----R is not degraded when cells are treated with TPA, making a clear contrast to wild type PKC alpha; i.e. the mutant is resistant to TPA-mediated down-regulation. The mutant lacks kinase activity as expected, as judged by autophosphorylation and by a kinase assay using a peptide substrate, although the phorbol ester binding activity remains intact. These results suggest a link between the kinase activity of PKC alpha and the sensitivity to TPA-mediated proteolytic degradation. We propose that autophosphorylation of PKC alpha is a prerequisite for proteolytic cleavage associated with the down-regulation of PKC alpha.
Synthetic riboswitches for external regulation of genes transferred by replication-deficient and oncolytic adenoviruses (2012)

Therapeutic gene transfer by replication-defective viral vectors or, for cancer treatment, by replication-competent oncolytic viruses shows high promise for treatment of major diseases. To ensure safety, timing or dosing in patients, external control of therapeutic gene expression is desirable or even required. In this study, we explored the potential of artificial aptazymes, ligand-dependent self-cleaving ribozymes, as an innovative tool for regulation of therapeutic gene expression. Importantly, aptazymes act on RNA intrinsically, independent of regulatory protein-nucleic acid interactions and stoichiometry, are non-immunogenic and of small size. These are key advantages compared with the widely used inducible promoters, which were also reported to lose regulation at high copy numbers, e.g. after replication of oncolytic viruses. We characterized aptazymes in therapeutic gene transfer utilizing adenovectors (AdVs), adeno-associated vectors (AAVs) and oncolytic adenoviruses (OAds), which are all in advanced clinical testing. Our results show similar aptazyme-mediated regulation of gene expression by plasmids, AdVs, AAVs and OAds. Insertion into the 5'-, 3'- or both untranslated regions of several transgenes resulted in ligand-responsive gene expression. Notably, aptazyme regulation was retained during OAd replication and spread. In conclusion, our study demonstrates the fidelity of aptazymes in viral vectors and oncolytic viruses and highlights the potency of riboswitches for medical applications.
Histone deacetylase inhibitors modulate miRNA and mRNA expression, block metaphase, and induce apoptosis in inflammatory breast cancer cells (2013)

To develop new therapies for inflammatory breast cancer (IBC) we have compared the effects of two hydroxamic acid-based histone deacetylase (HDAC) inhibitors, CG-1521 and Trichostatin A (TSA) on the biology of two IBC cell lines: SUM149PT and SUM190PT. CG-1521 and TSA induce dose (0-10 µM) and time-dependent (0-96 h) increases in the proportion of cells undergoing cell cycle arrest and apoptosis in the presence or absence of 17β-estradiol. In SUM 149PT cells, both CG-1521 and TSA increase the levels of acetylated α-tubulin; however the morphological effects are different: CG-1521 blocks mitotic spindle formation and prevents abscission during cytokinesis while TSA results in an increase in cell size. In SUM190PT cells CG-1521 does not cause an increase in acetylated-α-tubulin and even though TSA significantly increases the levels of acetylated tubulin, neither inhibitor alters the morphology of the cells. Microarray analysis demonstrates that CG-1521 modulates the expression of 876 mRNAs and 63 miRNAs in SUM149PT cells, and 1227 mRNAs and 35 miRNAs in SUM190PT cells. Only 9% of the genes are commonly modulated in both cell lines, suggesting that CG-1521 and TSA target different biological processes in the two cell lines most likely though the inhibition of different HDACs in these cell lines. Gene ontology (GO) analysis reveals that CG-1521 affects the expression of mRNAs that encode proteins associated with the spindle assembly checkpoint, chromosome segregation, and microtubule-based processes in both cell lines and has cell-type specific effects on lipid biosynthesis, response to DNA damage, and cell death.
2-(Diethylamino)thieno[1,3]oxazin-4-ones as Stable Inhibitors of Human Leukocyte Elastase (1999)

A series of 2-(diethylamino)thieno1,3ŏxazin-4-ones was synthesized and evaluated in vitro for inhibitory activity toward human leukocyte elastase (HLE). The Gewald thiophene synthesis was utilized to obtain several ethyl 2-aminothiophene-3-carboxylates. These precursors were subjected to a five-step route to obtain thieno2,3-d1,3ŏxazin-4-ones bearing various substituents at positions 5 and 6. Both thieno2,3-d and thieno3,2-d fused oxazin-4-ones possess extraordinary chemical stability, which was expressed as rate constants of the alkaline hydrolysis. The kinetic parameters of the HLE inhibition were determined. The most potent compound, 2-(diethylamino)-4H-1benzothieno2,3-d1,3ŏxazin-4-one, exhibited a K(i) value of 5.8 nM. 2-(Diethylamino)thieno1, 3ŏxazin-4-ones act as acyl-enzyme inhibitors of HLE, similar to the inhibition of serine proteases by 4H-3,1-benzoxazin-4-ones. The isosteric benzene-thiophene replacement accounts for an enhanced stability of the acyl-enzyme intermediates.
Immunocytochemical characterization of glial fibrillary tangles in Alzheimer's disease brain. (1995)

Neurofibrillary tangle is a major cytoskeletal pathology in Alzheimer's disease brains, and has been considered to develop exclusively in neuronal cells. We examined brains with Alzheimer's disease and observed argyrophilic fibrillary tangles not only in cortical neurons but also in subcortical glial cells in the frontal and temporal white matter. The tangles in glial cells were immunolabeled by antibodies against tau and ubiquitin, and double immunocytochemistry analyzed by confocal laser scanning microscopy demonstrated that the cytoplasms of tangle-bearing glia were labeled by antibodies against transferrin and 2'3'-cyclic nucleotide 3'-phosphohydrolase. Ultrastructurally, they were made up of bundles of straight filaments 16 nm in diameter and constricted filaments. These results indicate that fibrillary tangles resembling neurofibrillary tangles may develop in oligodendrocytes in brains with Alzheimer's disease and are distinguishable from glial cytoplasmic inclusions observed in multiple system atrophy brains. We referred to them as glial fibrillary tangles. Glial fibrillary tangles commonly occurred in this disease condition, and glial cells might be involved under the pathological processes similar to neuronal cells.
Reagent for introducing pyrene residues in oligonucleotides (1992)

A novel pyrenyl-containing phosphoramidite reagent, N-[4-(1-pyrenyl)butyryl]-O1-(4,4'-dimethoxytrityl)-O2- [(diisopropylamino)(2-cyanoethoxy)phosphino]-3-amino-1 ,2-propanediol (5), has been synthesized from 4-(1-pyrenyl)butanoic acid in four steps with the 52% overall yield and used to incorporate pyrene residue(s) into oligonucleotides. Oligonucleotides 6 and 7, bearing one or two pyrenes at the 5'-terminus, have been prepared by means of that reagent, characterized with fluorescence spectra, and successfully used as primers in a polymerase chain reaction.
Nanoporous Aluminum Oxide Membranes for Filtration and Biofunctionalization (2007)

Nanoporous aluminum oxide membranes with high open porosity are prepared by anodic oxidation. Conventional self-supporting as well as mechanically stabilized nanoporous membranes are produced from aluminum plates and microimprinted aluminum foils, respectively. The mechanically stabilized membranes are characterized by very thin membrane parts stabilized by surrounding thick bridges. The minimal thickness of these thin membranes with open pores on both sides is 1 microm, with a mean pore size of the parallel open pores of 185 nm. With these two kinds of membrane the flow rates for cross filtration can be tuned over a wide range. With the mechanically stabilized membranes, substantially higher flow rates are achieved and experiments that cannot be performed with thicker membranes become possible. The biofunctionalization of the pore walls with archaebacterial tetraether lipids is realized and proved using aminated semiconductor nanocrystals. The lipid layer deposited on the pore walls also changes the filtration properties.