gebhart/patrepeval huggingface dataset:
Transmembrane-deletion Mutants of the Membrane-type Matrix Metalloproteinase-1 Process Progelatinase A and Express Intrinsic Matrix-degrading Activity (1996)

Membrane-type matrix metalloproteinase-1 (MT-MMP-1) has been proposed to play a critical role in regulating the expression of tissue-invasive phenotypes in normal and neoplastic cells by directly or indirectly mediating the activation of progelatinase A. To begin characterizing MT-MMP-1 structure-function relationships, transmembrane-deletion mutants were constructed, and the processing of the zymogens as well as the enzymic activity of the mature proteinases was analyzed. We now demonstrate that pro-MT-MMP-1 mutants are efficiently processed to active proteinases following post-translational endoproteolysis immediately downstream of an Arg108-Arg-Lys-Arg basic motif by a proprotein convertase-dependent pathway. The secreted form of active MT-MMP-1 not only displays an N terminus identical with that described for the processed wild-type enzyme at Tyr112 (Strongin, A. Y., Collier, I., Bannikov, G., Marmer, B. L., Grants, G. A., and Goldberg, G. I. (1995) J. Biol. Chem. 270, 5331-5338), but also directly mediated progelatinase A activation via a two-step proteolytic cascade indistinguishable from that observed with intact cells. Furthermore, although the only function previously ascribed to MT-MMP-1 is its ability to act as a progelatinase A activator, purified transmembrane deletion mutants also expressed proteolytic activities against a wide range of extracellular matrix molecules. Given recent reports that MT-MMP-1 ectodomains may undergo intercellular transfer in vivo (Okada, A., Bellocq, J.-P., Rouyer, N., Chenard, M.-P., Rio, M.-C., Chambon, P., and Basset, P. (1995) Proc. Natl. Acad. Sci. U. S. A. 92, 2730-2734), our data suggest that soluble forms of the proteinase confer recipient cells with the ability to not only process progelatinase A, but also directly degrade extracellular matrix components.
T Cell Recognition of Autoantigens in Human Type 1 Diabetes: Clinical Perspectives (2011)

Type 1 diabetes (T1D) is an autoimmune disease driven by the activation of lymphocytes against pancreatic β-cells. Among β-cell autoantigens, preproinsulin has been ascribed a key role in the T1D process. The successive steps that control the activation of autoreactive lymphocytes have been extensively studied in animal models of T1D, but remains ill defined in man. In man, T lymphocytes, especially CD8(+) T cells, are predominant within insulitis. Developing T-cell assays in diabetes autoimmunity is, thus, a major challenge. It is expected to help defining autoantigens and epitopes that drive the disease process, to pinpoint key functional features of epitope-specific T lymphocytes along the natural history of diabetes and to pave the way towards therapeutic strategies to induce immune tolerance to β-cells. New T-cell technologies will allow defining autoreactive T-cell differentiation programs and characterizing autoimmune responses in comparison with physiologically appropriate immune responses. This may prove instrumental in the discovery of immune correlates of efficacy in clinical trials.
Primary Structure of the Nucleic Acid from the 1,4-α-Glucan Branching Enzyme (1979)

The primary structure of the nucleic acid from the branching enzyme 1,4-alpha-D-glucan: 1,4-alpha-D-glucan 6-alpha-(1,4-alpha-glucano)-transferase (2.5-S RNA) isolated from rabbit muscles has been elucidated. The polyribonucleotide consists of 31 nucleotides; the unique features of the polyribonucleotide are the unusually high content of modified nucleotides (32%) and guanine residues (40%). Apparently 2.5-S RNA belongs to a class of nucleic acids unknown up to now. It is the first time that the structure of a nucleic acid component from a ribonucleoenzyme has been defined. This work is a preprequisite for gaining insight into the intimate activating effect of the poly-ribonucleotide on the enzyme action.
Sarilumab, a fully human monoclonal antibody against IL-6Rα in patients with rheumatoid arthritis and an inadequate response to methotrexate: efficacy and safety results from the randomised SARIL-RA-MOBILITY Part A trial (2013)

Sarilumab improved signs and symptoms of RA over 12 weeks in patients with moderate-to-severe RA with a safety profile similar to reports with other IL-6 inhibitors. Sarilumab 150 mg and sarilumab 200 mg q2w had the most favourable efficacy, safety and dosing convenience and are being further evaluated in Phase III.
Coupled amidolytic assay for factor VII: its use with a clotting assay to determine the activity state of factor VII (1978)

A coupled amidolytic assay for factor VII (VII) has been developed that when used with a clotting assay for VII enables detection of activated VII. In the assay, VII in a test material determines generation of factor Xa in a mixture of purified factor X, tissue factor, and calcium; factor Xa is measured with a chromogenic substrate. Factor VII activity in the coupled amidolytic assay (VIIam) correlated well with VII activity in a one-stage clotting assay (VIIc) in 57 healthy subjects, 5 patients with hereditary VII deficiency, and 11 patients with liver disease. Activation of plasma VII by kaolin, clotting, or cold strikingly increased VIIc but not VIIam levels. Thus the ratio VIIc/VIIam (VII activity ratio) is a measure of VII activation. In 27 warfarin-treated patients the mean VII activity ratio was significantly decreased, reflecting a greater decline in VIIc than in VIIam. This probably stems from partially carboxylated VII being able to act during the 3-min incubation of the amidolytic assay but unable to act rapidly enough to affect the clotting assay. Measurement of VIIc/VIIam should enable evaluation of the activity state of VII in thrombotic disorders and in components for transfusion therapy.
Cloning and Characterization of α1H From Human Heart, a Member of the T-Type Ca2+Channel Gene Family (1998)

Voltage-activated Ca2+ channels exist as multigene families that share common structural features. Different Ca2+ channels are distinguished by their electrophysiology and pharmacology and can be classified as either low or high voltage-activated channels. Six alpha1 subunit genes cloned previously code for high voltage-activated Ca2+ channels; therefore, we have used a database search strategy to identify new Ca2+ channel genes, possibly including low voltage-activated (T-type) channels. A novel expressed sequence-tagged cDNA clone of alpha1G was used to screen a cDNA library, and in the present study, we report the cloning of alpha1H (or CavT.2), a low voltage-activated Ca2+ channel from human heart. Northern blots of human mRNA detected more alpha1H expression in peripheral tissues, such as kidney and heart, than in brain. We mapped the gene, CACNA1H, to human chromosome 16p13.3 and mouse chromosome 17. Expression of alpha1H in HEK-293 cells resulted in Ca2+ channel currents displaying voltage dependence, kinetics, and unitary conductance characteristic of native T-type Ca2+ channels. The alpha1H channel is sensitive to mibefradil, a nondihydropyridine Ca2+ channel blocker, with an IC50 of 1.4 micromol/L, consistent with the reported potency of mibefradil for T-type Ca2+ channels. Together with alpha1G, a rat brain T-type Ca2+ channel also cloned in our laboratory, these genes define a unique family of Ca2+ channels.
c-K-ras mutations in human carcinomas occur preferentially in codon 12. (1987)

A study was carried out to determine the frequency and distribution of mutations in the c-K-ras gene in human carcinoma tissue. The study was done on a total of 51 lung, colon and breast carcinoma tumors using a panel of oligonucleotides coding for the wild type and all possible mutations in codons 12 and 61 of c-K-ras gene. Four of 16 colon carcinomas, two of 27 lung carcinomas and one of eight breast carcinomas were found to contain mutations in codon 12. No mutations were found at position 61. Of the six possible amino acid replacements in codon 12, all but one was represented in the seven mutations identified.
A Molecular Orbital Theory of Reactivity in Aromatic Hydrocarbons (1952)

In the search for a quantitative correlation between reactivity and electronic configuration of aromatic hydrocarbons, the electron density, at each carbon atom, of the highest occupied π-orbital in the ground state of the molecule is calculated by means of the LCAO method. Comparing the result of such a calculation on fifteen condensed aromatic hydrocarbons with their chemical reactivities, we find that the position at which the electron density is largest is most readily attacked by electrophilic or oxidizing reagents. It is, therefore, concluded that distinct from other π-electrons the pair of π-electrons occupying the highest orbital, which is referred to as frontier electrons, plays a decisive role in chemical activation of these hydrocarbon molecules. The theoretical significance of this discrimination of the frontier electrons in relation to the chemical activation is discussed.
Bone Morphogenetic Protein Receptor IB Signaling Mediates Apoptosis Independently of Differentiation in Osteoblastic Cells (2004)

Bone morphogenetic protein-2 (BMP-2) is an important regulator of osteoblast differentiation. However, the regulation of osteoblast apoptosis by BMP signaling remains poorly understood. Here we examined the role of type I BMP receptor (BMP-RI) in osteoblast apoptosis promoted by BMP-2. Despite undetectable BMP-RIB expression in OHS4 cells, BMP-2 or BMP-2 overexpression increased osteoblast differentiation similarly as in SaOS2 cells which express BMP-RIB, as shown by alkaline phosphatase and CBFA1/RUNX2 expression. In contrast to SaOS2 cells, however, BMP-2 or BMP-2 overexpression did not increase caspase-9 and caspases-3, -6, and -7 activity and DNA fragmentation in OHS4 cells. Consistently, BMP-2 increased protein kinase C (PKC) activity, and PKC inhibition suppressed BMP-2-induced caspase activity in SaOS2 but not in OHS4 cells that lack BMP-RIB. A dominant negative BMP-RIB inhibited BMP-2-induced caspase activity, whereas wild-type BMP-RIB promoted caspase activity induced by BMP-2 in SaOS2 and MC3T3-E1 cells. Wild-type BMP-RIB rescued the apoptotic response to BMP-2, and a constitutively active BMP-RIB restored the apoptotic signal in OHS4 cells, supporting an essential role for BMP-RIB in osteoblast apoptosis. We also assessed whether BMP-2-induced apoptosis occurred independently of osteoblast differentiation. General inhibition of caspases did not abolish BMP-2-induced alkaline phosphatase and CBFA1/RUNX2 expression in SaOS2 cells. Furthermore, broad caspases inhibition increased matrix mineralization but did not reverse the BMP-2 effect on mineralization in MC3T3-E1 cells. These results indicate that BMP-2-induced apoptosis was mediated by BMP-RIB in osteoblasts and occurred independently of BMP-2-induced osteoblast differentiation, which provides additional insights into the dual mechanism of BMP-2 action on osteoblast fate.
Induced cell clustering enhances islet β cell formation from pancreatic ductal epithelial cells (2003)

Although islet transplantation holds great promise as a treatment for diabetes, a major limitation to its future clinical use is a shortage of donor tissue. During both fetal development and adult pancreatic regeneration, pancreatic ductal epithelial cells (PDEC) differentiate into endocrine cells. The goal of this project is to apply existing understanding of these processes to stimulate islet cell differentiation in vitro. Following 11-14 days of culturing adult human PDEC in a standard cell culture environment (tissue culture treated plastic, 10% FBS), they transdifferentiate to /spl beta/ cells at an extremely low efficiency (0.1%). /spl beta/-cell differentiation was enhanced greater than 4-fold (0.42%) when PDEC were grown on a low adhesive substrate (nontreated plastic) and in a low serum medium (5% Nu serum), conditions which are permissive to cell detachment and clustering. While the overall efficiency of transdifferentiation was still very low, the results suggest that induced cell-cell interactions and cell shape changes may be critical to stimulating /spl beta/-cell production in vitro. We are currently exploring additional factors (ECM factors, growth factors, transcription factors) that may improve the efficiency of transdifferentiation in order to optimize the creation of tissue-engineered islets.
A Structural View of Cre-loxP Site-Specific Recombination (2001)

Structural models of site-specific recombinases from the lambda integrase family of enzymes have in the last four years provided an important new perspective on the three-dimensional nature of the recombination pathway. Members of this family, which include the bacteriophage P1 Cre recombinase, bacteriophage lambda integrase, the yeast Flp recombinase, and the bacterial XerCD recombinases, exchange strands between DNA substrates in a stepwise process. One pair of strands is exchanged to form a Holliday junction intermediate, and the second pair of strands is exchanged during resolution of the junction to products. Crystal structures of reaction intermediates in the Cre-loxP site-specific recombination system, together with recent biochemical studies in the field, support a "strand swapping" model for recombination that does not require branch migration of the Holliday junction intermediate in order to test homology between recombining sites.
Generation and detection of terahertz pulses from biased semiconductor antennas (1996)

We propose a simple model based on the Drude–Lorentz theory of carrier transport to account for the details of the ultrashort terahertz pulses radiated from small photoconductive semiconductor antennas. The dynamics of the bias field under the influence of the space-charge field from the accelerated carriers is included in the model. We consider in detail the optical system used to image the terahertz radiation onto the terahertz detector, and we calculate the frequency-dependent response of the detector. The proposed model is compared with several different experiments, each focusing on different parameters of the model. Agreement between experiment and model is found in all cases, supporting the validity of this simple and appropriate model.
Expression cDNA Cloning of the KGF Receptor by Creation of a Transforming Autocrine Loop (1991)

An expression cloning strategy was devised to isolate the keratinocyte growth factor (KGF) receptor complementary DNA. NIH/3T3 fibroblasts, which secrete this epithelial cell-specific mitogen, were transfected with a keratinocyte expression complementary DNA library. Among several transformed foci identified, one demonstrated the acquisition of specific high-affinity KGF binding sites. The pattern of binding competition by related fibroblast growth factors (FGFs) indicated that this receptor had high affinity for acidic FGF as well as KGF. The rescued 4.2-kilobase complementary DNA was shown to encode a predicted membrane-spanning tyrosine kinase related to but distinct from the basic FGF receptor. This expression cloning approach may be generally applicable to the isolation of genes that constitute limiting steps in mitogenic signaling pathways.
Plant breeding in the 1990s: proceedings of the Symposium, North Carolina State University, Raleigh, North Carolina, USA, Mar 1991 (1992)

This book presents the edited papers from a major international conference on plant breeding held at Raleigh, North Carolina, in March 1991. The contents are divided into five main sections: the gene base for plant breeding; modification of plants to tolerate environmental stresses; modification of plants to tolerate stresses due to diseases and insects; contributions of biotechnology to plant improvement; strategies for utilizing unadapted germplasm. The book will therefore be of great interest to research workers throughout the world in plant breeding and allied fields such as plant biotechnology
Analysis of Japanese encephalitis (JE) virus genome and implications for recombinant JE vaccine. (1990)

From the information of nucleotide sequences and deduced amino acid sequences of flaviviruses including JEV, we can postulate processing mechanisms of a polyprotein translated from single long open reading frame of the genome and mechanisms of construction of antigenic structures of structural proteins with biologically active forms after these proteins are translated. The results of comparative analysis of amino acid sequences among flaviviruses and epitope analysis on the E proteins which are the most important antigens for protective immunity suggest that the E protein of flaviviruses may have a similar structure closely related to each other. PrM and E proteins which had predictable signal sequences upstream on the N terminals were expressed with antigenically active form and molecular size the same as the authentic ones by the recombinant viruses. However, the recombinant viruses which had no such signal sequence expressed unprocessed proteins with antigenically denatured forms. These results suggest that normal proteolytic processing is needed to construct biologically active structures of JEV structural proteins. The E proteins which were expressed by the recombinant viruses as antigenically active form could elicit nutralizing and HI antibodies in animals and protective immunity in mice. The recombinant vaccinia viruses which express the E protein could induce strong immunologic memory against the E protein in mice. These results indicate that the development of a new type of vaccine against JEV will become possible in future.
Antigenic and structural similarities between Mycobacterium tuberculosis 50- to 55-kilodalton and Mycobacterium bovis BCG 45- to 47-kilodalton antigens (1995)

The relationship between Mycobacterium tuberculosis 50- to 55-kDa protein and Mycobacterium bovis BCG 45- to 47-kDa antigen was examined by using immunological and biochemical criteria. Reciprocal cross-reactivity with a rabbit polyclonal antiserum against the M. bovis BCG protein and with a monoclonal antibody raised against the M. tuberculosis antigen was observed. The epitope recognized by this antibody was apparently present only in proteins of M. tuberculosis and M. bovis BCG among the 11 mycobacterial species tested. The amino-terminal sequences and total amino acid contents of these proteins showed strong similarities. Both antigens are glycoproteins as assessed by binding of concanavalin A, labeling of carbohydrate moieties with biotin-hydrazide, and digestion of carbohydrates with jack bean alpha-D-mannosidase, which produced a reduction of the molecular weights of the proteins and totally eliminated concanavalin A binding. Both M. tuberculosis and M. bovis BCG proteins are secreted, since they were found mainly in the culture medium. Analysis of M. tuberculosis 50- to 55-kDa antigen by two-dimensional gel electrophoresis showed at least seven different components, as previously described for the M. bovis BCG antigen. Solid-phase immunoassays showed that the purified M. tuberculosis 50- to 55-kDa protein was recognized by serum specimens from 70% of individuals with pulmonary tuberculosis from a total of 77 Mexican patients examined.
Chemotaxis and Chemokinesis in 3D Macromolecular Matrices: Relevance to Angiogenesis (2003)

Angiogenesis is a complex morphogenetic process involving the coordinate migration of several cell types, including endothelial cells (EC), pericytes, and stromal fibroblasts (1-4). Angiogenesis is regulated by interactions between cells, soluble factors, and extracellular matrix components. The extracellular matrix (EM) in contact with vascular cells changes during angiogenesis in terms of its composition and structural organization. For example, ECs lining the lumen in a "resting" vessel are attached to a 2D substratum of specialized structure and composition (i.e., the basement membrane). Following exposure to angiogenic factors, endothelial cells migrate from their 2D environment into the surrounding 3D tissue stroma. Within this 3D macromolecular environment, the endothelial cells adopt an elongated "sprouting"rdo; phenotype and synthesise new EM components. Pericytes and fibroblasts are normally resident within a 3D macromolecular matrix, as provided by the vessel basement membrane and tissue stroma, respectively. Nevertheless, pericytes also form part of the newly formed vascular sprouts and fibroblasts surround and accompany these. In addition, vascular sprouts are commonly accompanied by inflammatory cells that produce proteases and cytokines, thereby contributing to further alterations in the composition of the microenvironment. The migration of ECs, pericytes, and adjacent fibroblasts during angiogenesis is directional. As new vessels move towards the source of angiogenic stimulus, they migrate into matrices of different and variable composition (e.g., during wound healing new vessels and fibroblasts invade a fibrin clot) (1-7).
Functional antagonism of the Polycomb-Group genes eed and Bmi1 in hemopoietic cell proliferation (1999)

The murine Polycomb-Group (PcG) proteins Eed and Bmi1 govern axial patterning during embryonic development by segment-specific repression of Hox gene expression. The two proteins engage in distinct multimeric complexes that are thought to use a common molecular mechanism to render the regulatory regions of Hox and other downstream target genes inaccessible to transcriptional activators. Beyond axial patterning, Bmi1 is also involved in hemopoiesis because a loss-of-function allele causes a profound decrease in bone marrow progenitor cells. Here, evidence is presented that is consistent with an antagonistic function of eed and Bmi1 in hemopoietic cell proliferation. Heterozygosity for an eed null allele causes marked myelo- and lymphoproliferative defects, indicating that eed is involved in the negative regulation of the pool size of lymphoid and myeloid progenitor cells. This antiproliferative function of eed does not appear to be mediated by Hox genes or the tumor suppressor locus p16(INK4a)/p19(ARF) because expression of these genes was not altered in eed mutants. Intercross experiments between eed and Bmi1 mutant mice revealed that Bmi1 is epistatic to eed in the control of primitive bone marrow cell proliferation. However, the genetic interaction between the two genes is cell-type specific as the presence of one or two mutant alleles of eed trans-complements the Bmi1-deficiency in pre-B bone marrow cells. These studies thus suggest that hemopoietic cell proliferation is regulated by the relative contribution of repressive (Eed-containing) and enhancing (Bmi1-containing) PcG gene complexes.
Microtubule structure and its stabilisation (2004)

Microtubules are designed to be dynamically unstable. GTP hydrolysis converts an initially stable polymeric structure into an unstable one in which strain at the interfaces between longitudinal neighbours in the helical lattice of subunits is balanced by lateral interactions. However, stability can be modulated by a variety of factors, including associated proteins and a variety of drug molecules. Stabilising drugs such as Taxol and the assembly-promoting repeat motifs of tau protein occupy a special pocket in beta-tubulin. Microtubule destabilizing drugs such as colchicine alter the longitudinal interfaces of the subunits so that they cannot assemble into a microtubule lattice. These mechanisms are discussed in terms of the atomic structure of the protein.