gebhart/patrepeval huggingface dataset:
Deletions in the C-terminal coding region of the v-sis gene: dimerization is required for transformation. (1986)

The v-sis gene encodes chain B of platelet-derived growth factor. However, this gene codes for additional amino acids at both the N terminus and the C terminus of its gene product which are not present in the amino acid sequence of platelet-derived growth factor. We constructed a series of deletion mutants with deletions in the v-sis gene in order to define the C-terminal limit of the v-sis gene product which is required for transformation. Deletion mutants of the v-sis gene which encoded truncated gene products up to 57 residues shorter than the v-siswt gene product were still able to transform cells. The minimal transforming region of the v-sis gene product contained six residues fewer than were present in chain B of platelet-derived growth factor. Only 10 residues, including the sequence Cys-Lys-Cys, separated the smallest transforming gene product from the largest nontransforming gene product. These cysteine residues were also important for dimerization of the v-sis gene product, since all of the nontransforming v-sis deletions were unable to form dimers when they were analyzed under nonreducing conditions. Our results suggest that there is a strong connection between transformation and dimerization.
Phorbol ester effect on differentiation of human myeloid leukemia cell lines blocked at different stages of maturation. (1981)

The control of differentiation by tumor-promoting phorbol diesters including 12-O-tetradecanoylphorbol-13-acetate (TPA) was investigated using cells from human myeloid leukemia lines and sublines that were blocked at different stages of maturation. The myeloid leukemia cells that were blocked at the myeloblast-promyelocyte stage of maturation (KG-1, HL-60, and ML-3) had a prominent response when cultured with TPA. The cells became adherent, developed pseudopodia, displayed macrophage characteristics by light microscopy, developed nonspecific acid esterase activity, phagocytized yeast, slightly reduced nitro blue tetrazolium, displayed Fc-immunoglobulin G receptors, and killed bacteria. Lysozyme secretion and enzyme activity for beta-glucuronidase and acid phosphatase increased 2- to 20-fold concomitant with macrophage differentiation. The myeloid leukemia cells that were blocked at the undifferentiated myeloid blast stage of maturation (KG-1a and K562) were completely resistant to TPA-induced macrophage differentiation. We examined ten macrophage functions in the myeloid cell lines and sublines after exposure to phorbol diesters. The leukemic lines blocked at the myeloblast-promyelocyte stage of maturation expressed almost all the macrophage-specific functions. Phorbol diesters probably induced differentiation through a common cellular mechanism because the macrophage-differentiated events could not be dissociated. In sharp contrast, the early myeloid blast cells (KG-1a and K562) were incapable of acquiring any of the macrophage-specific functions after exposure to phorbol diesters. The KG-1a variant, in particular, should provide a good model to help elucidate the regulatory mechanism controlling the expression of macrophage functions during exposure to phorbol diesters.
Thrombolytic properties of Desmodus rotundus (vampire bat) salivary plasminogen activator in experimental pulmonary embolism in rats (1992)

Abstract rDSPA alpha 1 (recombinant Desmodus salivary plasminogen activator alpha 1) is a recombinant protein corresponding to a natural plasminogen activator from the vampire bat Desmodus rotundus. The thrombolytic properties of rDSPA alpha 1 and tissue-type plasminogen activator (t-PA) were compared in a rat model of pulmonary embolism. Whole blood clots, produced in vitro and labeled with 125I-fibrinogen, were embolized into the lungs of anesthetized rats. Thrombolysis was calculated from the difference between initial clot radioactivity and that remaining in the lungs at 60 minutes. Blood was sampled for gamma counting, measurement of hemostatic factors, and plasminogen activator antigen levels. Thrombolysis at 3, 10, 30, and 100 nmol/kg intravenously (10% bolus, 90% over 60 minutes) amounted to 30% +/- 2%, 51% +/- 4%, 85% +/- 4%, 98% +/- 0% for rDSPA alpha 1 and 30% +/- 3%, 41% +/- 3%, 57% +/- 6%, 93% +/- 2% for t-PA (controls: 29% +/- 2%; mean +/- SEM, n greater than or equal to 6). t-PA at 100 nmol/kg significantly decreased fibrinogen, plasminogen, and alpha 2- antiplasmin levels by 33% +/- 7%, 38% +/- 8%, and 61% +/- 9%, whereas rDSPA alpha 1 at 100 nmol/kg only lowered alpha 2-antiplasmin significantly (by 29% +/- 6%). Compared with t-PA, rDSPA alpha 1 is the more potent and more clot selective (fibrin specific) thrombolytic agent. These results suggest that rDSPA alpha 1 may be safer and more efficacious than currently used thrombolytics.
GDF-3 and GDF-9: two new members of the transforming growth factor-beta superfamily containing a novel pattern of cysteines. (1993)

Two new mammalian members (growth/differentiation factor 3 (GDF-3) and GDF-9) of the transforming growth factor-beta superfamily were identified using degenerate oligonucleotides corresponding to conserved regions among known family members. By Northern analysis, GDF-3 transcripts were detected primarily in adult bone marrow, spleen, thymus, and adipose tissue. In contrast, GDF-9 transcripts were detected only in the ovary. Based on their cDNA sequences, the predicted GDF-3 and GDF-9 polypeptides each contain a potential signal sequence for secretion, a putative tetrabasic proteolytic processing site, and a COOH-terminal region that shows significant homology to the known members of the transforming growth factor-beta superfamily. In the COOH-terminal region, GDF-3 and GDF-9 are most homologous to Xenopus Vg-1 (57%) and human bone morphogenetic protein 4 (34%), respectively. Unlike all previously described members of this superfamily, both GDF-3 and GDF-9 lack the conserved cysteine residue that is believed to form the sole disulfide linkage between subunits in other family members. These findings raise new possibilities regarding subunit interactions among members of this superfamily.
ERK and p38 MAPK Activities Determine Sensitivity to PI3K/mTOR Inhibition via Regulation of MYC and YAP (2016)

Aberrant activation of the PI3K/mTOR pathway is a common feature of many cancers and an attractive target for therapy, but resistance inevitably evolves as is the case for any cancer cell-targeted therapy. In animal tumor models, chronic inhibition of PI3K/mTOR initially inhibits tumor growth, but over time, tumor cells escape inhibition. In this study, we identified a context-dependent mechanism of escape whereby tumor cells upregulated the proto-oncogene transcriptional regulators c-MYC and YAP1. This mechanism was dependent on both constitutive ERK activity as well as inhibition of the stress kinase p38. Inhibition of p38 relieved proliferation arrest and allowed upregulation of MYC and YAP through stabilization of CREB. These data provide new insights into cellular signaling mechanisms that influence resistance to PI3K/mTOR inhibitors. Furthermore, they suggest that therapies that inactivate YAP or MYC or augment p38 activity could enhance the efficacy of PI3K/mTOR inhibitors. Cancer Res; 76(24); 7168-80. ©2016 AACR.
Synthesis and Evaluation of Novel Substrates and Inhibitors of N-Succinyl-ll-diaminopimelate Aminotransferase (DAP-AT) from Escherichia coli (1996)

N-Succinyl-ll-diaminopimelate aminotransferase (DAP-AT) (EC 2.6.1.17), a key enzyme in the bacterial pathway to l-lysine, was purified to near homogeneity (1500-fold) in five steps from wild type Escherichia coli ATCC 9637. This pyridoxal phosphate (PLP) dependent enzyme has a molecular weight of 39.9 kDa, appears to form an active homodimer, and uses l-glutamate as the amino group donor for its substrate, N-succinyl-α-amino-ε-ketopimelic acid (1a) (Km = 0.18 ± 0.04 mM, kcat = 86 ± 5 s-1). Progress of the reaction is monitored by spectrophotometric observation of decrease in NADPH concentration at 340 nm in a coupled enzyme assay with l-glutamate dehydrogenase (EC 1.4.1.4). Stereochemically pure 1a was synthesized as its trilithium salt by ene reaction of methyl glyoxylate with methyl N-succinyl-l-allylglycinate (4a) followed by hydrogenation of the double bond, Dess−Martin oxidation of the alcohol, and careful lithium hydroxide hydrolysis. Similar approaches allowed synthesis of a series of substrate analogues 1b−g having different N-acyl substituents, as well as derivatives missing the carboxyl group or the amide functionality (13 and 17, respectively). Compounds lacking the keto functionality (18a, 18c, and 19) were also prepared. Assay of DAP-AT shows that the enzyme has quite strict requirements for substrate recognition, but it will accept compounds with an aromatic ring in place of the terminal succinyl carboxyl group in 1a (e.g. N-Cbz-α-amino-ε-ketopimelic acid (1c)). Reaction of substrates 1a,c with hydrazine hydrate followed by NaCNBH3 reduction gives 2-(N-(succinylamino))- (20a) and 2-(N-Cbz-amino)-6-hydrazinoheptane-1,7-dioic acids (20c), respectively. These are the most potent slow-binding inhibitors of any DAP-metabolyzing enzyme reported so far (Ki* for DAP-AT: 20a is 22 ± 4 nM; 20c is 54 ± 9 nM).
Isolation of two populations of myoblasts from porcine skeletal muscle (1999)

Studies on the effects of time and passage on porcine primary muscle cell cultures and methods to purify myoblasts were conducted using flow cytometry and fluorescence-activated cell sorting (FACS). Primary muscle cells cultured on single plates revealed a small cell (<10 mm diameter) population consisting of 90% desmin-positive myoblasts and a large cell (> or = 10 mm diameter) population containing desmin-positive myoblasts and nonmyoblasts. The small myoblasts were detectable up to 28 days but after cell sorting and passage, they became indistinguishable from the large myoblast population. This indicates that pig muscle contains small self-renewing myoblasts similar to humans, that become larger when induced to proliferate. A human myoblast-specific monoclonal antibody allows FACS of both large and small myoblasts from primary cells within 2 days of culture and independent of passage. These characteristics of porcine myoblasts indicate that the pig may be a suitable large animal model for myoblast-mediated gene transfer.
Low density lipoprotein receptor internalizes low density and very low density lipoproteins that are bound to heparan sulfate proteoglycans via lipoprotein lipase (1993)

It has previously been shown that lipoprotein lipase (LPL) enhances the binding of low density lipoproteins (LDL) and very low density lipoproteins (VLDL) to HepG2 cells and fibroblasts, up to 80-fold. This increase in binding is LDL receptor-independent and is due to a bridging of LPL between extracellular heparan sulfate proteoglycans (HSPG) and the lipoproteins. In the present paper, we show that preincubation of the cells with LPL, followed by washing prior to the binding experiment, increased binding to the same extent as occurs when the binding is performed in the presence of LPL. This indicates that the formation of a complex of LPL with the lipoproteins is not a prerequisite of binding. Binding curves and Scatchard analyses reveal that both the number of binding sites and the affinity of the binding are increased 20-30-fold by the addition of 3.4 micrograms/ml LPL. The addition of LPL also resulted in an enhanced uptake and subsequent lysosomal degradation of both LDL and VLDL when compared with binding, although to a lesser extent (up to 25-fold when measured after 5 h at 37 degrees C). Strikingly, enhanced uptake did not occur in LDL receptor-negative fibroblasts. In addition, down-regulation of the LDL receptor activity by preincubation of the cells for 48 h with either LDL or beta-VLDL resulted in a parallel decrease in the uptake of LPL-mediated HSPG-bound LDL, whereas the LPL-mediated binding itself was not diminished. These observations indicate that the uptake of LPL-mediated HSPG-bound LDL and VLDL mainly proceeds via the LDL receptor. Binding of labeled LDL to the cells at 4 degrees C for 2 h followed by a chase period at 37 degrees C revealed that in absolute terms, the initial rate of internalization of HSPG-bound LDL is comparable with that of LDL receptor-bound LDL (0.58 and 0.44 ng/min/mg of cell protein, respectively). We conclude that in LDL receptor-positive cells, the LPL-mediated binding of LDL and VLDL to HSPG is followed by internalization of the lipoproteins mainly through the rapid process of the classical LDL receptor recycling system, whereas only a minor portion is internalized via the much slower process of HSPG uptake.
Clustering of cytokine genes on mouse chromosome 11. (1990)

The presence of positionally conserved amino acid residues suggests that the mouse proteins TCA3, P500, MIP1-alpha, MIP1-beta, and JE are members of a single gene family. These proteins are activation specific and can be expressed by both myeloid and lymphoid cells. MIP1-alpha/MIP1-beta and MCAF (the putative human homologue of JE) act as chemotactic and activating agents for neutrophils and macrophages, respectively. The functions of TCA3 and P500 are unknown. We have used interspecies somatic cell hybrids and recombinant inbred mouse strains to show that the genes encoding TCA3, MIP1-alpha, MIP1-beta, and JE (provisionally termed Tca3, Mip-1a, Mip-1b, and Sigje, respectively) map as a cluster on the distal portion of mouse chromosome 11 near the Hox-2 gene complex. DNA sequence analysis indicates that the P500 and TCA3 proteins are encoded by alternative splicing products of one genomic gene. Additionally, the genes encoding TCA3 and JE are found to be strikingly similar with respect to the positions of intron-exon boundaries. Together, these data support the model that the cytokines TCA3, P500, MIP1-alpha, MIP1-beta, and JE are encoded by a single cluster of related genes. The gene encoding IL-5 (Il-5), which acts as a T cell-replacing factor, a B cell growth factor, and an eosinophil differentiation factor, is also mapped to mouse chromosome 11.Il-5 maps approximately 25 cM proximal to the Tca-3 gene and appears tightly linked to a previously described gene cluster that includes Il-3, Il-4, and Csfgm. We discuss the potential relevance of the two cytokine gene clusters described here with particular attention to specific human hematologic malignancies associated with chromosomal aberrations at corresponding locations on human chromosomes 5 and 17.
Polymer Scaffolds as Synthetic Microenvironments for Extrahepatic Islet Transplantation (2006)

These findings indicate that a synthetic polymer scaffold can serve as a platform for islet transplantation and improves the function of extrahepatically transplanted islets compared to islets transplanted without a scaffold. The scaffold may also be useful to deliver bioactive molecules to modify the microenvironment surrounding the transplanted islets and, thus, enhance islet survival and function.
Evaluation of a tetrazolium-based semiautomated colorimetric assay: assessment of chemosensitivity testing. (1987)

Drug sensitivity assays were performed using a variation of a colorimetric [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)] assay on V79, CHO-AuxB1, CHRC5, NCI-H460, and NCI-H249 cell lines following optimization of experimental conditions for each cell line. Results from this assay were compared with data assimilated simultaneously by clonogenic assay and by dye exclusion assay. Good correlation was observed using the CHO-AuxB1 cell line and the pleiotropic drug-resistant mutant CHRC5, with similar degrees of relative resistance observed with both the MTT and clonogenic assays. Good correlation was observed between the clonogenic and MTT assays for 1-h drug exposures, although the MTT assay was more sensitive to vinblastine. In general, the clonogenic assay was more sensitive when continuous drug exposures were utilized, although this was primarily related to the increased drug exposure time. While the use of the MTT assay in drug sensitivity testing of primary tumor samples is limited, since contaminating normal cells may also reduce the tetrazolium, the MTT assay can be semiautomated, and therefore it offers a valid, simple method of assessing chemosensitivity in established cell lines.
Targeting of Glyoxysomal Proteins to Peroxisomes in Leaves and Roots of a Higher Plant (1993)

Laura J. Olsen, William F. Ettinger, Barbara Damsz, Kelly Matsudaira, Mary Alice Webb, John J. Harada, Targeting of Glyoxysomal Proteins to Peroxisomes in Leaves and Roots of a Higher Plant, The Plant Cell, Vol. 5, No. 8 (Aug., 1993), pp. 941-952
Fabrication of glassy carbon microstructures by pyrolysis of microfabricated polymeric precursors (1997)

High‐carbin mcirostructures as components in microelectromechanical structures and microreactors are of particular interest because their mechanical, electrical, and chemical properties can be controlled by the temperature of preparation. The range of electrical properties is especially impressive. A method of fabricating microstructures of glassy carbon and other high‐carbon solids is presented, based on micromolding of polymers to form precursors to these structures and pyrolysis to yield the carbon solids. The advantages of the technique are discussed.
Activation of HIF1α ubiquitination by a reconstituted von Hippel-Lindau (VHL) tumor suppressor complex (2000)

Mutations in the VHL tumor suppressor gene result in constitutive expression of many hypoxia-inducible genes, at least in part because of increases in the cellular level of hypoxia-inducible transcription factor HIF1alpha, which in normal cells is rapidly ubiquitinated and degraded by the proteasome under normoxic conditions. The recent observation that the VHL protein is a subunit of an Skp1-Cul1/Cdc53-F-box (SCF)-like E3 ubiquitin ligase raised the possibility that VHL may be directly responsible for regulating cellular levels of HIF1alpha by targeting it for ubiquitination and proteolysis. In this report, we test this hypothesis directly. We report development of methods for production of the purified recombinant VHL complex and present direct biochemical evidence that it can function with an E1 ubiquitin-activating enzyme and E2 ubiquitin-conjugating enzyme to activate HIF1alpha ubiquitination in vitro. Our findings provide new insight into the function of the VHL tumor suppressor protein, and they provide a foundation for future investigations of the mechanisms underlying VHL regulation of oxygen-dependent gene expression.
Monoclonal Antibodies for the Identification and Purification of vNAR Domains and IgNAR Immunoglobulins from the Horn Shark Heterodontus francisci (2011)

In addition to conventional antibodies, cartilaginous fish have evolved a distinctive type of immunoglobulin, designated as IgNAR, which lacks the light polypeptide chains and is composed entirely by heavy chains. IgNAR molecules can be manipulated by molecular engineering to produce the variable domain of a single heavy chain polypeptide (vNARs). These, together with the VHH camel domains, constitute the smallest naturally occurring domains able to recognize an antigen. Their special features, such as small size, long extended finger-like CDR3, and thermal and chemical stability, make them suitable candidates for biotechnological purposes. Here we describe the generation of two mouse monoclonal antibodies (MAbs), MAb 370-12 and MAb 533-10, that both specifically react with vNAR domains of the horn shark Heterodontus francisci. While the former recognizes a broad spectrum of recombinant vNAR proteins, the latter is more restricted. MAb 370-12 precipitated a single band from whole shark serum, which was identified as IgNAR by mass spectrometry. Additionally, we used MAb 370-12 to follow the IgNAR-mediated immune response of sharks during immunization protocols with two different antigens (complete cells and a synthethic peptide), thus corroborating that MAb 370-12 recognizes both isolated vNAR domains and whole IgNAR molecules. Both MAbs represent an affordable molecular, biochemical, and biotechnological tool in the field of shark single-domain antibodies.
Advanced power system protection and incipient fault detection and protection of spaceborne power systems (1989)

This research concentrated on the application of advanced signal processing, expert system, and digital technologies for the detection and control of low grade, incipient faults on spaceborne power systems. The researchers have considerable experience in the application of advanced digital technologies and the protection of terrestrial power systems. This experience was used in the current contracts to develop new approaches for protecting the electrical distribution system in spaceborne applications. The project was divided into three distinct areas: (1) investigate the applicability of fault detection algorithms developed for terrestrial power systems to the detection of faults in spaceborne systems; (2) investigate the digital hardware and architectures required to monitor and control spaceborne power systems with full capability to implement new detection and diagnostic algorithms; and (3) develop a real-time expert operating system for implementing diagnostic and protection algorithms. Significant progress has been made in each of the above areas. Several terrestrial fault detection algorithms were modified to better adapt to spaceborne power system environments. Several digital architectures were developed and evaluated in light of the fault detection algorithms.
Semiconductor lasers without population inversion (1994)

We propose a new scheme for lasing without population inversion that utilizes interferences in double-quantum-well intersubband transitions. In contrast to the previous inversionless laser schemes based on atomic systems, the new proposal permits us to use band-gap engineering to choose the subband energies, coupling strengths, and decay rates, as desired, and permits us to create a laser system that does not require population inversion. We present detailed calculations on a specific scheme and discuss possible extensions.
Isolation and Characterization of a Vibrio vulnificus Mutant Deficient in Both Extracellular Metalloprotease and Cytolysin (2001)

We isolated a Vibrio vulnificus mutant that was deficient in both metalloprotease and cytolysin by allelic exchange. The virulence of this mutant in mice and its cytotoxicity for HEp-2 cells were comparable to those of the wild-type strain, indicating that neither factor was essential for these properties. The cytolysin, but not the protease, seemed to be important for causing damage in the alimentary tract of the mice.
BCL-2 inhibition in AML: an unexpected bonus? (2018)

B-cell lymphoma 2 (BCL-2) was discovered at the breakpoint of the t(14;18) in follicular lymphoma >30 years ago. Although inhibition of BCL-2 first proved valuable in lymphoid malignancies, clinical progress in myeloid malignancies lagged. Here, we summarize the basic biology and preclinical results that spurred clinical BCL-2 inhibition in acute myeloid leukemia (AML). Response rates and toxicity for venetoclax in combination with standard AML agents, such as azacitidine, decitabine, and low-dose cytarabine, compare favorably with conventional induction chemotherapy. Durability of response requires further study.