gebhart/patrepeval huggingface dataset:
Development and Characterization of Monoclonal Antibodies and Aptamers against Major Antigens ofMycobacterium aviumsubsp.paratuberculosis (2007)

ABSTRACT Specific antibodies, available in unlimited quantities, have not been produced against Mycobacterium avium subsp. paratuberculosis , the bacterium that causes Johne's disease (JD). To fill this gap in JD research, monoclonal antibodies (MAbs) against M. avium subsp. paratuberculosis were produced from BALB/c mice immunized with a whole-cell extract of M. avium subsp. paratuberculosis . A total of 10 hybridomas producing MAbs to proteins ranging from 25 to 85 kDa were obtained. All MAbs showed some degree of cross-reactivity when they were analyzed against a panel of whole-cell protein lysates comprising seven different mycobacterial species. The MAbs were characterized by several methods, which included isotype analysis, specificity analysis, epitope analysis, reactivity in immunoblot assays, and electron microscopy. The identities of the antigens that bound to two selected MAbs were determined by screening an M. avium subsp. paratuberculosis lambda phage expression library. This approach revealed that MAb 9G10 detects MAP1643 (isocitrate lyase) and that MAb 11G4 detects MAP3840 (a 70-kDa heat shock protein), two proteins present in high relative abundance in M. avium subsp. paratuberculosis . The epitopes for MAb 11G4 were mapped to the N-terminal half of MAP3840, whereas MAb 9G10 bound to the C-terminal half of MAP1643. Aptamers, nucleic acids that bind to specific protein sequences, against the hypothetical protein encoded by MAP0105c were also generated and tested for their binding to M. avium subsp. paratuberculosis as well as other mycobacteria. These detection reagents may be beneficial in many JD research applications.
Functional Roles of the Two Domains of Phosducin and Phosducin-like Protein (2000)

Phosducin and phosducin-like protein regulate G protein signaling pathways by binding the betagamma subunit complex (Gbetagamma) and blocking Gbetagamma association with Galpha subunits, effector enzymes, or membranes. Both proteins are composed of two structurally independent domains, each constituting approximately half of the molecule. We investigated the functional roles of the two domains of phosducin and phosducin-like protein in binding retinal G(t)betagamma. Kinetic measurements using surface plasmon resonance showed that: 1) phosducin bound G(t)betagamma with a 2. 5-fold greater affinity than phosducin-like protein; 2) phosphorylation of phosducin decreased its affinity by 3-fold, principally as a result of a decrease in k(1); and 3) most of the free energy of binding comes from the N-terminal domain with a lesser contribution from the C-terminal domain. In assays measuring the association of G(t)betagamma with G(t)alpha and light-activated rhodopsin, both N-terminal domains inhibited binding while neither of the C-terminal domains had any effect. In assays measuring membrane binding of G(t)betagamma, both the N- and C-terminal domains inhibited membrane association, but much less effectively than the full-length proteins. This inhibition could only be described by models that included a change in G(t)betagamma to a conformation that did not bind the membrane. These models yielded a free energy change of +1.5 +/- 0.25 kcal/mol for the transition from the G(t)alpha-binding to the Pd-binding conformation of G(t)betagamma.
Mitoxantrone, Vincristine, and Dexamethasone in Patients with Refractory Lymphoma (1989)

Twenty-seven patients with failed malignant lymphomas (19 with intermediate grade, 4 with low-grade, 3 with high-grade lymphomas, and 1 with Hodgkin's disease) who had failed a median of 3 prior multidrug regimens, all previously exposed to anthracyclines (median prior doxorubicin 360 mg/m2), were treated with a combination of mitoxantrone (M), vincristine (V), and dexamethasone (D) every 4 weeks. Mitoxantrone was given in a 3 times daily schedule (days 1-3), at doses between 5 and 10 mg/m2/day; vincristine, 2-mg total dose, was given on day 1 and day 8; dexamethasone, 20 mg/m2, was given on days 1-5. A total of 71 courses was administered; there were 4 complete responses (CR) and 14 partial responses (PR) (response rate 66%). At the highest doses, hematological toxicity was severe (5 patients died while pancytopenic); the nadir for WBC and platelets was on day 13, with a median hematological recovery on day 23. There were transient hepatic, renal, and oral toxicities; vincristine-related neuropathy was seen in 8 patients. All patients had normal prestudy cardiac function, as assessed by gated pool scans; follow-up scans showed a greater than 15% decrease of the left ventricular ejection fraction (LVEF) in 2 patients, without evidence of cardiac dysfunction. Although responses lasted a median of 10 weeks (range 4-37), our data indicate that mitoxantrone, at the doses and schedules used, is an effective drug in malignant, doxorubicin-resistant lymphomas. This observation warrants the use of mitoxantrone in the upfront treatment of malignant lymphoma.
Sequence Requirements in the Catalytic Core of the “10-23” DNA Enzyme (2002)

A systematic mutagenesis study of the "10-23" DNA enzyme was performed to analyze the sequence requirements of its catalytic domain. Therefore, each of the 15 core nucleotides was substituted separately by the remaining three naturally occurring nucleotides. Changes at the borders of the catalytic domain led to a dramatic loss of enzymatic activity, whereas several nucleotides in between could be exchanged without severe effects. Thymidine at position 8 had the lowest degree of conservation and its substitution by any of the other three nucleotides caused only a minor loss of activity. In addition to the standard nucleotides (adenosine, guanosine, thymidine, or cytidine) modified nucleotides were used to gain further information about the role of individual functional groups. Again, thymidine at position 8 as well as some other nucleotides could be substituted by inosine without severe effects on the catalytic activity. For two positions, additional experiments with 2-aminopurine and deoxypurine, respectively, were performed to obtain information about the specific role of functional groups. In addition to sequence-function relationships of the DNA enzyme, this study provides information about suitable sites to introduce modified nucleotides for further functional studies or for internal stabilization of the DNA enzyme against endonucleolytic attack.
Structural and functional analysis of the NF-kappa B p65 C terminus. An acidic and modular transactivation domain with the potential to adopt an alpha-helical conformation. (1994)

The p65 subunit of the NF-kappa B transcription factor contains in its C-terminal 120 amino acids at least two transcription activation domains. One domain (TA1) is contained within only the 30 C-terminal amino acids. Structural studies employing CD and NMR spectroscopy revealed that the TA1 domain is unstructured. NMR analysis of a protein corresponding to the C-terminal 123 amino acids also showed a random coil conformation. However, a portion of TA1 was found to adopt an alpha-helical conformation in the presence of hydrophobic solvents. Transcriptional analysis of point mutants revealed the functional importance of two evolutionary conserved sequence repeats, which are located in the conditionally alpha-helical region of TA1. These repeats acted synergistically in transcription activation. The inhibitory effect of some mutants indicated secondary structure constraints on TA1 in intact cells. Inverting the sequence of two acidic activation domains significantly reduced their transactivating potential, suggesting that amino acid composition is not solely essential for activity; a defined primary structure is necessary as well. Acidic sequence motifs related in primary structure and squelching activity to those of TA1 are present in the activation domains of VP16, c-Rel, and several other transcription factors. We propose a model suggesting that primarily unstructured acidic activation domains can adopt a secondary structure upon contacting their target molecules by an "induced fit" mechanism.
Sonogashira Coupling of Functionalized Trifloyl Oxazoles and Thiazoles with Terminal Alkynes:  Synthesis of Disubstituted Heterocycles (2002)

[reaction: see text] This paper describes Sonogashira cross-coupling of functionalized 2-, 4-, and 5-trifloyl oxazoles and thiazoles with terminal alkynes. This methodology has been extended to 2,4-ditrifloylthiazoles, which results in regioselective cross-coupling at the C2-position of the thiazole. The resulting 2-alkynyl-4-trifloylthiazoles are effective electrophiles in a second palladium(0)-mediated cross-coupling reaction.
Molecular Pathways: Targeting the Cyclin D–CDK4/6 Axis for Cancer Treatment (2015)

Cancer cells bypass normal controls over mitotic cell-cycle progression to achieve a deregulated state of proliferation. The retinoblastoma tumor suppressor protein (pRb) governs a key cell-cycle checkpoint that normally prevents G1-phase cells from entering S-phase in the absence of appropriate mitogenic signals. Cancer cells frequently overcome pRb-dependent growth suppression via constitutive phosphorylation and inactivation of pRb function by cyclin-dependent kinase (CDK) 4 or CDK6 partnered with D-type cyclins. Three selective CDK4/6 inhibitors, palbociclib (Ibrance; Pfizer), ribociclib (Novartis), and abemaciclib (Lilly), are in various stages of development in a variety of pRb-positive tumor types, including breast cancer, melanoma, liposarcoma, and non-small cell lung cancer. The emerging, positive clinical data obtained to date finally validate the two decades-old hypothesis that the cyclin D-CDK4/6 pathway is a rational target for cancer therapy.
Generation of Novel Epothilone Analogs with Cytotoxic Activity by Biotransformation. (2003)

The epothilones represent a new class of bacterial natural products with broad spectrum of antiproliferative activity against various types of human tumors and tumor cell lines. The attractive preclinical profile of epothilones has made them promising lead compounds for novel anticancer agents and has spurred a strong interest in obtaining different derivatives to fully evaluate their therapeutic potentials. We have generated a number of novel epothilone D and 10,11-dehydroepothilone D (Epo490) analogs via biotransformation using Amycolata autotrophica to alter the oxidation state of the parental compounds. The bioconverted compounds displayed different degrees of potency in cytotoxicity assays against a panel of human tumor cell lines, with 11-hydroxyepothilone D, 14-hydroxyepothilone D, and 21-hydroxyepothilone D showing comparable activity to that of epothilone D, and 21-hydroxy Epo490 being comparable to Epo490. The addition of hydroxyl group(s) seems to cause a decrease in cytotoxic activity against multiple drug resistant cell lines (with overexpressed P-glycoprotein). The compounds generated by biotransformation exert differential effects on tubulin polymerization, which correlate with their biological activities.
First Trimester Prenatal Treatment and Molecular Genetic Diagnosis of Congenital Adrenal Hyperplasia (21-Hydroxylase Deficiency)* (1990)

Prenatal treatment of pregnancies at risk for congenital adrenal hyperplasia due to 21-hydroxylase deficiency was carried out in conjunction with chorionic villus sampling (CVS) in the first trimester for analysis of restriction fragment length polymorphisms. Fourteen families of a total of 49 families at risk for this disease elected to undergo both prenatal treatment and diagnosis via CVS. Dexamethasone administration to the pregnant woman was initiated at a mean gestational age of 7 weeks (range, 4-10 weeks) before testing to determine whether the fetus was affected with 21-hydroxylase deficiency, and CVS was performed at a gestational age of 8-10 weeks. Two affected female fetuses were identified by molecular genetic techniques among this group; neonatal physical examination demonstrated amelioration of the degree of genital ambiguity compared with both nonprenatally treated older sisters with 21-hydroxylase deficiency. The duration of unnecessary prenatal dexamethasone treatment for unaffected or male fetuses was substantially reduced in the CVS group compared with that in a cohort of 8 prenatally treated pregnancies in which amniocentesis was performed in the early second trimester. There were no major morbidities observed in the treated pregnancies. Postnatal confirmation of CVS diagnosis was obtained in all cases in which DNA from an affected sibling was available for comparative analysis with the DNA from chorionic villus tissue. We conclude based on these data that the benefit/risk ratio is favorable for prenatal administration of dexamethasone in pregnancies at risk for 21-hydroxylase deficiency. Treatment should be initiated during the first trimester in conjunction with diagnosis by CVS/molecular genetic techniques. Long term postnatal surveillance is recommended for all offspring of dexamethasone-treated pregnancies.
Eliminating microglia in Alzheimer’s mice prevents neuronal loss without modulating amyloid-β pathology (2016)

In addition to amyloid-β plaque and tau neurofibrillary tangle deposition, neuroinflammation is considered a key feature of Alzheimer's disease pathology. Inflammation in Alzheimer's disease is characterized by the presence of reactive astrocytes and activated microglia surrounding amyloid plaques, implicating their role in disease pathogenesis. Microglia in the healthy adult mouse depend on colony-stimulating factor 1 receptor (CSF1R) signalling for survival, and pharmacological inhibition of this receptor results in rapid elimination of nearly all of the microglia in the central nervous system. In this study, we set out to determine if chronically activated microglia in the Alzheimer's disease brain are also dependent on CSF1R signalling, and if so, how these cells contribute to disease pathogenesis. Ten-month-old 5xfAD mice were treated with a selective CSF1R inhibitor for 1 month, resulting in the elimination of ∼80% of microglia. Chronic microglial elimination does not alter amyloid-β levels or plaque load; however, it does rescue dendritic spine loss and prevent neuronal loss in 5xfAD mice, as well as reduce overall neuroinflammation. Importantly, behavioural testing revealed improvements in contextual memory. Collectively, these results demonstrate that microglia contribute to neuronal loss, as well as memory impairments in 5xfAD mice, but do not mediate or protect from amyloid pathology.
Role for G protein-coupled receptor kinase in agonist-specific regulation of μ-opioid receptor responsiveness (1998)

The G protein-coupled mu-opioid receptor (mu OR) mediates the physiological effects of endogenous opioid peptides as well as the structurally distinct opioid alkaloids morphine and etorphine. An intriguing feature of mu OR signaling is the differential receptor trafficking and desensitization properties following activation by distinct agonists, which have been proposed as possible mechanisms related to opioid tolerance. Here we report that the ability of distinct opioid agonists to differentially regulate mu OR internalization and desensitization is related to their ability to promote G protein-coupled receptor kinase (GRK)-dependent phosphorylation of the mu OR. Although both etorphine and morphine effectively activate the mu OR, only etorphine elicits robust mu OR phosphorylation followed by plasma membrane translocation of beta-arrestin and dynamin-dependent receptor internalization. In contrast, corresponding to its inability to cause mu OR internalization, morphine is unable to either elicit mu OR phosphorylation or stimulate beta-arrestin translocation. However, upon the overexpression of GRK2, morphine gains the capacity to induce mu OR phosphorylation, accompanied by the rescue of beta-arrestin translocation and receptor sequestration. Moreover, overexpression of GRK2 also leads to an attenuation of morphine-mediated inhibition of adenylyl cyclase. These findings point to the existence of marked differences in the ability of different opioid agonists to promote mu OR phosphorylation by GRK. These differences may provide the molecular basis underlying the different analgesic properties of opioid agonists and contribute to the distinct ability of various opioids to induce drug tolerance.
Pupil responses to foveal exchange of monochromatic lights (1980)

Temporal exchanges of equiluminant monochromatic lights of different spectral distributions produced a momentary constriction of the pupil in man. This is not a stimulus artifact because exchanges of two lights with identical distributions in the same apparatus produced no response. Responses evoked by rod signals were successfully obviated by presenting the foveal stimulus inside a large rod saturating annulus. The amplitude of the response varied systematically with stimulus wavelength. The exchange of a standard light to either shorter or longer wavelength lights produced a momentary constriction of the pupil; the greater the wavelength difference (between them); the larger the constriction. This ability to respond to exchanges of one spectral distribution for another is not a consequence of chromatic aberration or chromatic differences in magnification. Chromatic exchanges between lights of equal chromatic aberration do not produce identical pupillary response in deuteranopes: The exchange 560 nm→650 nm produced no pupil response, while the 560 nm→498 nm exchange produced a sizable response. Exchange of equally luminant heterochromatic lights evoked a response with 50 ms longer latency than the same amplitude constriction evoked by a step increase in luminance of a homochromatic light. The homochromatic contrast needed to evoke the same constriction as a given equal luminance heterochromatic exchange closely follows the homochromatic contrast which matched the residual flicker in flicker photometry of that same wavelength pair.
Droplet Digital PCR versus qPCR for gene expression analysis with low abundant targets: from variable nonsense to publication quality data (2017)

Quantitative PCR (qPCR) has become the gold standard technique to measure cDNA and gDNA levels but the resulting data can be highly variable, artifactual and non-reproducible without appropriate verification and validation of both samples and primers. The root cause of poor quality data is typically associated with inadequate dilution of residual protein and chemical contaminants that variably inhibit Taq polymerase and primer annealing. The most susceptible, frustrating and often most interesting samples are those containing low abundant targets with small expression differences of 2-fold or lower. Here, Droplet Digital PCR (ddPCR) and qPCR platforms were directly compared for gene expression analysis using low amounts of purified, synthetic DNA in well characterized samples under identical reaction conditions. We conclude that for sample/target combinations with low levels of nucleic acids (Cq ≥ 29) and/or variable amounts of chemical and protein contaminants, ddPCR technology will produce more precise, reproducible and statistically significant results required for publication quality data. A stepwise methodology is also described to choose between these complimentary technologies to obtain the best results for any experiment.
Dynamic self-assembly and control of microfluidic particle crystals (2010)

Engineered two-phase microfluidic systems have recently shown promise for computation, encryption, and biological processing. For many of these systems, complex control of dispersed-phase frequency and switching is enabled by nonlinearities associated with interfacial stresses. Introducing nonlinearity associated with fluid inertia has recently been identified as an easy to implement strategy to control two-phase (solid-liquid) microscale flows. By taking advantage of inertial effects we demonstrate controllable self-assembling particle systems, uncover dynamics suggesting a unique mechanism of dynamic self-assembly, and establish a framework for engineering microfluidic structures with the possibility of spatial frequency filtering. Focusing on the dynamics of the particle-particle interactions reveals a mechanism for the dynamic self-assembly process; inertial lift forces and a parabolic flow field act together to stabilize interparticle spacings that otherwise would diverge to infinity due to viscous disturbance flows. The interplay of the repulsive viscous interaction and inertial lift also allow us to design and implement microfluidic structures that irreversibly change interparticle spacing, similar to a low-pass filter. Although often not considered at the microscale, nonlinearity due to inertia can provide a platform for high-throughput passive control of particle positions in all directions, which will be useful for applications in flow cytometry, tissue engineering, and metamaterial synthesis.
The design and synthesis of mimetics of peptide β‐turns (1988)

The synthesis of an 11 membered ring bis-lactam, a system which is designed as a conformationally restricted mimetic of type I and type II beta-turns is described. Computer assisted molecular modeling was used to compare the predicted low energy conformers of the turn mimetic with idealized type I and type II turn structures. Initial computational analysis indicates that the basic ring structure will provide an excellent foundation for the development of a varieity of beta-turn mimetics.
Role of oxygen vs. glucose in energy metabolism in a mammary carcinoma perfused ex vivo: direct measurement by 31P NMR. (1993)

The role of glycolysis vs. respiration in tumor energy metabolism has been studied, to date, primarily in vitro by using single cells, multicellular spheroids, or tissue slices. With the advent of in vivo NMR spectroscopy, several investigators have shown that tumor energy status depends on its blood flow. Since manipulation of blood flow alters both oxygen and glucose delivery to a solid tumor, these studies have not been able to separate the relative contribution of oxygen vs. glucose in energy metabolism in vivo. In the present study, we have overcome this problem by combining two methods: the tissue-isolated R3230AC mammary adenocarcinoma perfused ex vivo and 31P NMR spectroscopy. The isolated tumor permits one to control the perfusion pressure as well as the metabolite concentrations in the perfusate. NMR spectroscopy permits one to measure the ratio of nucleoside triphosphate to inorganic phosphate (NTP/Pi) and pH. Our results show that (i) the NTP/Pi ratio ex vivo is similar to that observed in vivo prior to surgery, (ii) the NTP/Pi ratio is insensitive to flow changes at high flow rates but is proportional to flow rate at flows comparable to those found in vivo, (iii) the NTP/Pi ratio of these tumors is resistant to hypoxia and is not maintained when glucose is removed or replaced with glutamine, and (iv) although both O2 and glucose are consumed by these tumors, the effect of perfusate flow rate appears to be mediated largely through glucose delivery. The current approach not only provides information about the role of glycolysis vs. respiration in a rodent tumor but also is general and versatile enough to provide similar data in human tumors perfused ex vivo.