gebhart/patrepeval huggingface dataset:
Floral dip: a simplified method forAgrobacterium‐mediated transformation ofArabidopsis thaliana (1998)

The Agrobacterium vacuum infiltration method has made it possible to transform Arabidopsis thaliana without plant tissue culture or regeneration. In the present study, this method was evaluated and a substantially modified transformation method was developed. The labor-intensive vacuum infiltration process was eliminated in favor of simple dipping of developing floral tissues into a solution containing Agrobacterium tumefaciens, 5% sucrose and 500 microliters per litre of surfactant Silwet L-77. Sucrose and surfactant were critical to the success of the floral dip method. Plants inoculated when numerous immature floral buds and few siliques were present produced transformed progeny at the highest rate. Plant tissue culture media, the hormone benzylamino purine and pH adjustment were unnecessary, and Agrobacterium could be applied to plants at a range of cell densities. Repeated application of Agrobacterium improved transformation rates and overall yield of transformants approximately twofold. Covering plants for 1 day to retain humidity after inoculation also raised transformation rates twofold. Multiple ecotypes were transformable by this method. The modified method should facilitate high-throughput transformation of Arabidopsis for efforts such as T-DNA gene tagging, positional cloning, or attempts at targeted gene replacement.
Feline atopic dermatitis. A model for Langerhans cell participation in disease pathogenesis. (1997)

Atopic dermatitis is a disorder characterized by cutaneous exanthemata as a consequence of exaggerated eczematous reactions to topical and systemic allergens. Langerhans cells, expressing CD1a and HLA-DR, and dermal dendritic cells, expressing HLA-DR, are known to be potent antigen-presenting cells and are thought to play an important role in the pathogenesis of atopic dermatitis. The immunophenotype of lesional skin in atopic dermatitis in humans involves increased numbers of CD1a+/MHC class II+ dendritic cells in addition to activated T cells, mast cells, and macrophages. To establish feline skin as a model for the study of human atopic dermatitis, and to elucidate the role of dendritic cells in feline atopic dermatitis, we investigated the presence of CD1a+ cells and MHC class II+ cells in the epidermis and dermis of lesional feline skin and in skin of healthy control animals. Immunohistochemistry revealed that MHC class II+ epidermal dendritic cells were CD1a+ in normal feline skin and significantly increased numbers of CD1a+ cells and MHC class II+ cells were present in the epidermis and dermis of lesional skin. These data provide the first correlative documentation of CD1a expression by feline dendritic cells containing Birbeck granules, and indicate the utility of feline skin in the study of human cutaneous atopy.
Inducible, receptor-dependent protein-DNA interactions at a dioxin-responsive transcriptional enhancer. (1988)

We have identified in mouse hepatoma cells a third cis-acting dioxin-responsive element (DRE) within the 5' flanking region of the cytochrome P1-450 gene, which is transcriptionally activated by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). The DRE can activate a heterologous promoter and functions in either orientation; therefore, it has the properties of a transcriptional enhancer. The DRE fails to activate transcription in receptor-defective cells; therefore, it requires TCDD-receptor complexes for its function. By using a gel retardation assay, we show that nuclear extracts contain a protein that binds to the DRE in TCDD-inducible, receptor-dependent, and DNA sequence-specific fashion. The protein-DNA interaction occurs within 10 min of exposure of the cell to TCDD and does not require ongoing protein synthesis. Our results imply that the TCDD-receptor complex interacts specifically with the DRE and demonstrate a relationship between protein-DNA interaction in vitro and function in vivo. Our findings also suggest that the affinity of the TCDD-receptor complex for the DRE may be relatively high in comparison to analogous protein-DNA interactions at other inducible enhancers.
N-Protected α-Aminomethylketone Analogues of C-Terminal p-Nitrobenzyl-3-Ketoesters of N-Protected Amino Acids (1989)

Abstract Hydrogenolysis of N-protected amino acid p-nitrobenzyl-3-ketoesters over palladium on charcoal in THF gave N-protected α-amino methylketones in 45-83% isolated yield.
HSET overexpression fuels tumor progression via centrosome clustering-independent mechanisms in breast cancer patients (2015)

Human breast tumors harbor supernumerary centrosomes in almost 80% of tumor cells. Although amplified centrosomes compromise cell viability via multipolar spindles resulting in death-inducing aneuploidy, cancer cells tend to cluster extra centrosomes during mitosis. As a result cancer cells display bipolar spindle phenotypes to maintain a tolerable level of aneuploidy, an edge to their survival. HSET/KifC1, a kinesin-like minus-end directed microtubule motor has recently found fame as a crucial centrosome clustering molecule. Here we show that HSET promotes tumor progression via mechanisms independent of centrosome clustering. We found that HSET is overexpressed in breast carcinomas wherein nuclear HSET accumulation correlated with histological grade and predicted poor progression-free and overall survival. In addition, deregulated HSET protein expression was associated with gene amplification and/or translocation. Our data provide compelling evidence that HSET overexpression is pro-proliferative, promotes clonogenic-survival and enhances cell-cycle kinetics through G2 and M-phases. Importantly, HSET co-immunoprecipitates with survivin, and its overexpression protects survivin from proteasome-mediated degradation, resulting in its increased steady-state levels. We provide the first evidence of centrosome clustering-independent activities of HSET that fuel tumor progression and firmly establish that HSET can serve both as a potential prognostic biomarker and as a valuable cancer-selective therapeutic target.
Chimeric human immunodeficiency virus type 1/type 2 reverse transcriptases display reversed sensitivity to nonnucleoside analog inhibitors. (1991)

Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT), an important therapeutic target in the treatment of AIDS, is effectively inhibited by a class of nonnucleoside analog compounds that includes nevirapine (BI-RG-587) and tetrahydroimidazo[4,5,1-jk]-[1,4]benzodiazepin-2(1H)-one and -thione. We show that both tyrosine residues at positions 181 and 188 flanking the putative catalytic site of HIV-1 RT are required for sensitivity of the enzyme to these compounds. HIV-2 RT, which does not have tyrosines at these positions, is resistant to these nonnucleoside analog inhibitors. Substitution of the HIV-2 RT amino acid residues at position 181 or 188 into HIV-1 RT results in an enzyme that is resistant to these compounds while retaining sensitivity to 3'-azido-2',3'-dideoxythymidine triphosphate. HIV-2 RT substituted with amino acids 176-190 from HIV-1 RT acquires sensitivity to these nonnucleoside analog inhibitors.
Characterization of AvrBs3-Like Effectors from a Brassicaceae Pathogen Reveals Virulence and Avirulence Activities and a Protein with a Novel Repeat Architecture (2005)

Xanthomonas campestris pv. armoraciae strain 5 is a Brassicaceae pathogen that expresses three members of the highly related avrBs3 gene family of type III effectors. Here, we report on the isolation and characterization of these genes, designated hax2, hax3, and hax4 (homolog of avrBs3 in Xanthomonas). All three Hax proteins are translocated from Xanthomonas spp. into the plant cell via the type III secretion system. Hax3 and Hax4 show the typical structure of AvrBs3-like effectors and contain a repetitive region in their central part consisting of 34-amino-acid (aa) repeats. By contrast, the Hax2 repeat region is composed of 35-aa repeats that are characterized by an additional proline residue. Hax2, Hax3, and Hax4 contain 21.5, 11.5, and 14.5 repeats, respectively. Genetic studies revealed an additive effect of hax2, hax3, and hax4 on disease symptom formation of X. campestris pv. armoraciae strain 5 on radish. The contribution of individual genes to the aggressiveness of strain 5 is quantitatively different, with hax2 showing the strongest effect on the development of chlorosis and necrosis. In addition, hax3 and hax4, but not hax2, have a Bs4-dependent avirulence activity in tomato and in transgenic Nicotiana benthamiana expressing the Bs4 resistance gene.
Dynamic Soil Sensing Via Horizontally-Polarized Shear Waves (2000)

This paper investigates the feasibility of site characterization via spectral analysis of horizontally-polarized shear (SH) waves as a means to filter the effects of pore water for saturated soil conditions. Using a multi-layered wave propagation model to simulate the proposed testing configuration revolving around a torsionally vibrating loading plate, it is shown that the use of generalized Love (i.e. SH body and surface) waves as a sounding tool precludes the influence of the soil's Poisson's ratio, thus reducing the number of parameters relevant for seismic data interpretation and ruling out the existence of compressional waves. Preliminary numerical simulations indicate that the dispersion curves for generalized Love waves may be sufficiently sensitive to stratigraphic variations to serve as a basis for the development of an SH alternative to the spectral analysis of surface waves commonly associated with vertically-polarized ground motion.
Colonic Eosinophilic Inflammation in Experimental Colitis Is Mediated by Ly6Chigh CCR2+ Inflammatory Monocyte/Macrophage-Derived CCL11 (2011)

Recent genome-wide association studies of pediatric inflammatory bowel disease have implicated the 17q12 loci, which contains the eosinophil-specific chemokine gene CCL11, with early-onset inflammatory bowel disease susceptibility. In the current study, we employed a murine model of experimental colitis to define the molecular pathways that regulate CCL11 expression in the chronic intestinal inflammation and pathophysiology of experimental colitis. Bone marrow chimera experiments showed that hematopoietic cell-derived CCL11 is sufficient for CCL11-mediated colonic eosinophilic inflammation. We show that dextran sodium sulfate (DSS) treatment promotes the recruitment of F4/80(+)CD11b(+)CCR2(+)Ly6C(high) inflammatory monocytes into the colon. F4/80(+)CD11b(+)CCR2(+)Ly6C(high) monocytes express CCL11, and their recruitment positively correlated with colonic eosinophilic inflammation. Phenotypic analysis of purified Ly6C(high) intestinal inflammatory macrophages revealed that these cells express both M1- and M2-associated genes, including Il6, Ccl4, Cxcl2, Arg1, Chi3l3, Ccl11, and Il10, respectively. Attenuation of DSS-induced F4/80(+)CD11b(+)CCR2(+)Ly6C(high) monocyte recruitment to the colon in CCR2(-/-) mice was associated with decreased colonic CCL11 expression, eosinophilic inflammation, and DSS-induced histopathology. These studies identify a mechanism for DSS-induced colonic eosinophilia mediated by Ly6C(high)CCR2(+) inflammatory monocyte/macrophage-derived CCL11.
Notch Promotes Radioresistance of Glioma Stem Cells (2009)

Radiotherapy represents the most effective nonsurgical treatments for gliomas. However, gliomas are highly radioresistant and recurrence is nearly universal. Results from our laboratory and other groups suggest that cancer stem cells contribute to radioresistance in gliomas and breast cancers. The Notch pathway is critically implicated in stem cell fate determination and cancer. In this study, we show that inhibition of Notch pathway with gamma-secretase inhibitors (GSIs) renders the glioma stem cells more sensitive to radiation at clinically relevant doses. GSIs enhance radiation-induced cell death and impair clonogenic survival of glioma stem cells but not non-stem glioma cells. Expression of the constitutively active intracellular domains of Notch1 or Notch2 protect glioma stem cells against radiation. Notch inhibition with GSIs does not alter the DNA damage response of glioma stem cells after radiation but rather reduces Akt activity and Mcl-1 levels. Finally, knockdown of Notch1 or Notch2 sensitizes glioma stem cells to radiation and impairs xenograft tumor formation. Taken together, our results suggest a critical role of Notch signaling to regulate radioresistance of glioma stem cells. Inhibition of Notch signaling holds promise to improve the efficiency of current radiotherapy in glioma treatment.
Radiation Enhanced Diffusion in Solids (1958)

A simple theory of radiation enhanced diffusion has been worked out which describes the dependence of this enhancement on flux and temperature under steady-state conditions. The theoretical study also shows that the measurement of enhanced diffusion as a function of temperature can indicate the mechanism by which defects are removed from the lattice. Alpha-brass was chosen for the experimental work because it is a kinetically simple system, not complicated by nucleation, in which diffusion is easily followed by measuring the electrical resistivity changes associated with changes in short-range order. The enhanced diffusion rate during irradiation in the Brookhaven reactor has been measured in this alloy at several temperatures in the range 0 to 190°C. This enhancement is independent of temperature from 0 to 150°C, in excellent agreement with the theoretical predictions for the case where the radiation induced defects finally disappear at internal surfaces. Some implications of radiation enhanced diffusion and suggestions for further study are also discussed.
Cloning of trg, a gene for a sensory transducer in Escherichia coli (1982)

Clones of trg, a gene which codes for a chemotactic transducer, were isolated linked to ColE1 and pBR322 vectors. Studies with the hybrid plasmids demonstrated unequivocally that trg is the structural gene for methyl-accepting chemotaxis protein III. The Trg protein was found to be structurally complex, electrophoresing as a series of seven bands on high-resolution sodium dodecyl sulfate-polyacrylamide gels. The multiplicity of bands is a function of the activity of cheR, which codes for a methyltransferase, and of cheB, which codes for a demethylase. It appears that Trg, a quantitatively minor transducer, resembles the two major transducer proteins, Tsr and Tar, in that all three are multiply methylated and also multiply modified in a second way which requires an active cheB gene. However, preliminary analysis of the Trg protein indicated that it is significantly less related structurally to the Tsr or Tar protein than those two transducers are to each other. This implies that the features of multiple methylation and cheB-dependent modification are likely to be critical for the common physiological functions in chemotactic excitation and adaptation performed by all three transducers.
Alkyl addition reaction of pyrimidine 2'-ketonucleosides: Synthesis of 2'-branched-chain sugar pyrimidine nucleosides. Nucleodides and nucleotides. LXXXI. (1988)

The reaction of 4-ethoxy-1-(3, 5-O-tetraisopropyldisiloxanyl-1, 3-diyl-β-D-erythro-pentofuran-2-ulosyl)-2(1H)-pyrimidinone (11) with various organometallic reagents yielded corresponding 2'-branched-chain sugar pyrimidine nucleosides. Only in the reactions with MeMgBr and EtMgBr was the more hindered β-attack observed to afford and 2'-alkyl ribofuranosides (13a, b). In the reaction of 11 with MeLi, Me3, Al, or PhMgBr, 2'-methyl or phenyl arabinosides (12a, b, c)were obtained stereoselectively. Conversion of these pyrimidine nucleosides into cytosine derivatives is also described and their antileukemic and antiviral activities are discussed.
Control of abnormal electrical cavity with applied electrical fields (1988)

Electrical fields applied to the cerebellum and the hippocampus have been shown to modulate the excitability of neurons provided that the electrical field is properly oriented with the dendritic structure. The effect of electrical fields has been tested on epileptiform electrical activity in order to determine the feasibility of blocking or reducing this type of abnormal neuronal firing. The experiments were done using the hippocampal slice in-vitro preparation, since it allows direct visual control of the position of the electrodes in order to align the electrical field with the dendrites. Epileptiform electrical activity was generated by adding 3500 units/ml of penicillin to the artificial cerebrospinal fluid solution. Low-intensity electrical fields were then applied with a monopolar or a tripolar electrode using constant current pulses. It is shown that it is possible to achieve a reduction in the amplitude of the electrical activity greater than 80%. Preliminary results have confirmed that neuronal firing is decreased by the applied fields.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Comparative inhibition of influenza and parainfluenza virus replication by ribavirin in MDCK cells (1981)

Actinomycin D inhibited the yield of influenza virus hemagglutinin from MDCK cells infected at high multiplicity, but had little effect on the yield of parainfluenza virus hemagglutinin. In similar hemagglutinin yield experiments, ribavirin was only slightly more active (threefold) against influenza virus than against parainfluenza virus replication. In plaque inhibition experiments, ribavirin depressed influenza virus plaque formation by 50% at a concentration of approximately 3 micrograms/ml, whereas the corresponding figure for parainfluenza viruses was threefold higher. The concentration of ribavirin demonstrating anti-influenza activity was indistinguishable for that inhibiting host cell growth. It is concluded that, unlike actinomycin D, ribavirin is unlikely to have a major effect on the provision of host cell 5-germinal methylated cap structures and the subsequent priming of influenza messenger ribonucleic acid synthesis.
Contrasting secretory processing of simultaneously expressed heterologous proteins in Saccharomyces cerevisiae (2005)

In this study, secretory processing of cell-surface displayed Aga2p fusions to bovine pancreatic trypsin inhibitor (BPTI) and the single chain Fv (scFv) antibody fragment D1.3 are examined. BPTI is more efficiently processed than D1.3 both when secreted and surface-displayed, and D1.3 expression imparts a greater amount of secretory stress on the cell as assayed by a reporter of the unfolded protein response (UPR). Surprisingly, simultaneous expression of the two proteins in the same cell somewhat improves BPTI surface display while decreasing D1.3 surface display with minimal effect on UPR activation. Furthermore, co-expression leads to the accumulation of punctate vacuolar aggregates of D1.3 and increased secretion of the D1.3-Aga2p fusion into the supernatant. Overexpression of the folding chaperones protein disulfide isomerase (PDI) and BiP largely mitigates the D1.3 surface expression decrease, suggesting that changes in vacuolar and cell surface targeting may be due, in part, to folding inefficiency. Titration of constitutive UPR expression across a broad range progressively decreases surface display of both proteins as UPR increases. D1.3-Aga2p traffic through the late secretory pathway appears to be strongly affected by overall secretory load as well as folding conditions in the ER.
Identifying genotype-dependent efficacy of single and combined PI3K- and MAPK-pathway inhibition in cancer (2009)

In cancer, genetically activated proto-oncogenes often induce "upstream" dependency on the activity of the mutant oncoprotein. Therapeutic inhibition of these activated oncoproteins can induce massive apoptosis of tumor cells, leading to sometimes dramatic tumor regressions in patients. The PI3K and MAPK signaling pathways are central regulators of oncogenic transformation and tumor maintenance. We hypothesized that upstream dependency engages either one of these pathways preferentially to induce "downstream" dependency. Therefore, we analyzed whether downstream pathway dependency segregates by genetic aberrations upstream in lung cancer cell lines. Here, we show by systematically linking drug response to genomic aberrations in non-small-cell lung cancer, as well as in cell lines of other tumor types and in a series of in vivo cancer models, that tumors with genetically activated receptor tyrosine kinases depend on PI3K signaling, whereas tumors with mutations in the RAS/RAF axis depend on MAPK signaling. However, efficacy of downstream pathway inhibition was limited by release of negative feedback loops on the reciprocal pathway. By contrast, combined blockade of both pathways was able to overcome the reciprocal pathway activation induced by inhibitor-mediated release of negative feedback loops and resulted in a significant increase in apoptosis and tumor shrinkage. Thus, by using a systematic chemo-genomics approach, we identify genetic lesions connected to PI3K and MAPK pathway activation and provide a rationale for combined inhibition of both pathways. Our findings may have implications for patient stratification in clinical trials.
Role of the Catalytic Serine in the Interactions of Serine Proteinases with Protein Inhibitors of the Serpin Family (1995)

The contribution of a covalent bond to the stability of complexes of serine proteinases with inhibitors of the serpin family was evaluated by comparing the affinities of beta-trypsin and the catalytic serine-modified derivative, beta-anhydrotrypsin, for several serpin and non-serpin (Kunitz) inhibitors. Kinetic analyses showed that anhydrotrypsin had little or no ability to compete with trypsin for binding to alpha 1-proteinase inhibitor (alpha 1PI), plasminogen activator inhibitor 1 (PAI-1), antithrombin (AT), or AT-heparin complex when present at up to a 100-fold molar excess over trypsin. By contrast, equimolar levels of anhydrotrypsin blocked trypsin binding to non-serpin inhibitors. Equilibrium binding studies of inhibitor-enzyme interactions monitored by inhibitor displacement of the fluorescence probe, p-aminobenzamidine, from the enzyme active site, confirmed that the binding of serpins to anhydrotrypsin was undetectable in the case of alpha 1PI or AT (KI > 10(-5) M), of low affinity in the case of AT-heparin complex (KI 7-9 x 10(-6) M), and of moderate affinity in the case of PAI-1 (KI 2 x 10(-7) M). This contrasted with the stoichiometric high affinity binding of the serpins to trypsin as well as of the non-serpin inhibitors to both trypsin and anhydrotrypsin. Maximal KI values for serpin-trypsin interactions of 1 to 8 x 10(-11) M, obtained from kinetic analyses of association and dissociation rate constants, indicated that the affinity of serpins for trypsin was minimally 4 to 6 orders of magnitude greater than that of anhydrotrypsin. Anhydrotrypsin, unlike trypsin, failed to induce the characteristic fluorescence changes in a P9 Ser-->Cys PAI-1 variant labeled with a nitrobenzofuran fluorescent probe (NBD) which were shown previously to report the serpin conformational change associated with active enzyme binding. These results demonstrate that a covalent interaction involving the proteinase catalytic serine contributes a major fraction of the binding energy to serpin-trypsin interactions and is essential for inducing the serpin conformational change involved in the trapping of enzyme in stable complexes.
Nitrogen-14 SQUID NQR of L-Ala-L-His and of Serine (1994)

Abstract 14 N nuclear quadrupole resonance spectroscopy, detected with a Superconducting Quantum Interference Device, makes possible the study of nitrogen environments in amino acids and small peptides. The present experiments characterize: 1) the effects of intermolecular interactions upon the amino nitrogen of serine upon cocrystallization of the stereoisomers in a range of concentrations; 2) the changes of the amino and imidazole nitrogen environments brought about by combining L-Alanine and L-Histidine into the dipeptide L-Ala-L-His.