gebhart/patrepeval huggingface dataset:
Fibrino(geno)lytic Properties of Purified Hementerin, a Metalloproteinase from the Leech Haementeria depressa (1998)

The fibrino(geno)lytic protein designated hementerin contained in crude extracts of the salivary complex of Haementeria depressa leeches was purified to apparent homogeneity by gel filtration, ion exchange chromatography and preparative SDS-PAGE. It is a single-chain 80 kDa, PhMeSO2F-resistant, calcium-dependent, metalloproteinase, which specifically degrades fibrin(ogen) through a plasminogen-independent pathway. The amino terminal sequence of 8 residues shows 80% similarity with hementin, another fibrino(geno)lytic protein purified from Haementeria ghilianii leeches. However, their activities differ somewhat in terms of kinetics and with regard to the structure of the fibrin(ogen) fragments they may produce. Cleavage by hementerin of fibrinogen Aalpha, gamma and Bbeta chains, in that order, produces 270 kDa to 67 kDa fragments which differ from those produced by plasmin. Hementerin was also able to degrade cross-linked fibrin although at a lower rate as compared to fibrinogen. In conclusion, hementerin is a plasminogen-independent fibrino(geno)lytic metalloproteinase that degrades fibrinogen faster than fibrin, prevents blood coagulation and destroys fibrin clots in vitro.
Kinetics and Thermodynamics of Intermolecular Catalysis by Hairpin Ribozymes (1995)

The hairpin ribozyme, derived from the negative strand of the satellite RNA of tobacco ringspot virus, belongs to the class of small catalytic RNAs that cleave RNA to generate 2',3'-cyclic phosphate and 5'hydroxyl termini and ligate these termini in the reverse reaction to form 3',5'-phosphodiesters. Rate and equilibrium constants for binding, dissociation, cleavage, and ligation steps in the kinetic mechanism were determined using a series of hairpin ribozyme/substrate pairs that differed in the sequence and length of the intermolecular base-paired helices. All hairpin variants cleaved with rate constants of approximately 0.3 min-1 at pH 7.5 in 10 nM MgCl2 at 25 degrees C, regardless of the length or sequence of the intermolecular helices. A rate constant of approximately 3 min-1 was determined for an intermolecular ligation reaction in which both cleavage products were supplied to the ribozyme in trans. Thus, the hairpin favored ligation over cleavage by 10-fold when the ribozyme was saturated with cleavage products. Binding rate constants for cleavage substrates and products were comparable to values reported for other catalytic RNAs but were somewhat slower than binding rates typical of small RNA helices. Substrate dissociation rate constants were much slower than cleavage rate constants for all substrates. Because virtually every substrate that was bound was cleaved before it could dissociate, KMS values were not the same as KdS values. Instead, KMS reflected the ratio of cleavage and substrate binding rate constants and had the same value of approximately 30 nM for all substrates. Calculations based on empirically determined free energy parameters for simple RNA helices indicated that complexes between ribozymes and 5'-cleavage products were slightly less stable than simple helices with the same sequences. In contrast, affinities between ribozymes and cleavage substrates and between ribozymes and 3'-cleavage products were stronger than expected for simple duplexes by about -2.5 kcal/mol, evidence of stabilizing interactions in addition to those contributed by helical base pairs. This kinetic and thermodynamic study demonstrates that the kinetic mechanism of the hairpin ribozyme is distinct from the kinetic mechanisms of other well-characterized ribozymes and provides a foundation for further exploration of the hairpin structure and catalytic mechanism.
A full optically operated magnetometer array: An experimental study (2012)

We show the operation of an optically pumped magnetometer array in a 50 μT magnetic field. The various components for a fully optical and non-magnetic detector unit were constructed and evaluated, from which a prototype unit was assembled with fiber coupled electronics. In this unit the magnetometers were operated using the intensity modulated method and heated with an off-resonant laser. Calculations on the temperature distribution were used to design the magnetometer array. Different magnetometers in such a detector unit were characterized and showed identical performance. Without applying noise reduction schemes, the obtained magnetic field resolution is a factor 2.5 above the shot noise level down to frequencies of about 7 Hz.
Structural Requirements of Endotoxic Lipopolysaccharides and Bacterial Cell Walls in Induction of Interleukin-1 (1988)

A variety of compounds, synthetic, semisynthetic or bacterial, which corresponds to structural components of endotoxic lipopolysaccharides (LPS) and bacterial cell wall peptidoglycans were studied for their activity to enhance interleukin-1 (IL-1) production of murine peritoneal macrophages and the ability to activate the complement cascade in fresh adult human serum. Not only bacterial LPS and cell walls or peptidoglycans but also their structural components with appropriate size and structure induced IL-1 production by macrophages and activated the human complement cascade, which may lead to the IL-1 production by monocytes/macrophages.
Establishment of an adherent cell feeder layer from human umbilical cord blood for support of long-term hematopoietic progenitor cell growth. (1994)

Previous attempts to establish a stromal cell feeder layer from human umbilical cord blood (HUCB) have met with very limited success. It has been suggested that there is an insufficient number of stromal precursor cells in HUCB to form a hematopoietic-supporting feeder layer in primary cultures. The present study shows that HUCB does contain a significant accessory cell population that routinely develops into a confluent, adherent cell layer under defined primary culture conditions. HUCB-derived adherent layers were shown to support long-term hematopoietic activity for an average of 4 months. This was achieved by using a customized coverslip with a modified surface structure as the cell attachment substratum and using a specialized culture feeding regime. We have characterized the various cell types (including fibroblasts, macrophages, and endothelial cells) and extracellular matrix proteins (including fibronectin, collagen III, and laminin) that were present in abundance in the HUCB-derived adherent cell layer. In contrast, oil red O-staining fat cells were rarely detected. ELISA and bioassays showed that stem cell factor and interleukin 6 were produced by the HUCB stromal cell cultures, but interleukin 3 or granulocyte/macrophage colony-stimulating factor was not detected. Application of this hematopoietic culture system to transgenic and gene therapy studies of stem cells is discussed.
The C‐S lyases of higher plants. Purification and characterization of homogeneous alliin lyase of leek (Allium porrum) (1989)

The characteristic odors of freshly macerated tissue of Allium species such as garlic and onion are due to the action of the enzyme alliin lyase (EC 4.4.1.4) on endogenous S‐alkyl‐I‐cysteine sulfoxides which are present as secondary amino acids yielding volatile sulfur‐containing products. Purification and characterization of the alliin lyase of leek ( Allium porrum L.) has been carried out for comparison with the analogous enzymes previously characterized from garlic and onion. The purification involved homogenization, followed by ammonium sulfate fractionation, elution from an hydroxylapatite column, concentration of the active fractions and passage through a concanavalin A‐Sepharose 4B affinity column. The purified enzyme was found to be a glycoprotein with a pH optimum for activity of 8.0. Sodium dodecylsulfate‐urea polyacrylamide gel electrophoresis gels of the homogeneous leek enzyme showed it consisted of 1 subunit with a molecular weight of 48000. By gel filtration, 2 stable forms of the native enzyme with molecular weights of 386000 and 580000 were found.
Biosynthesis of a biologically active single peptide chain containing the human common alpha and chorionic gonadotropin beta subunits in tandem. (1995)

One of the distinguishing features of the gonadotropin and thyrotropin hormone family is their heterodimeric structure, consisting of a common alpha subunit and a hormone-specific beta subunit. Subunit assembly is vital to the function of these hormones: The conformation of the heterodimer is essential for controlling secretion, hormone-specific posttranslational modifications, and signal transduction. To address whether alpha and beta subunits can be synthesized as one chain and also maintain biological activity, a chimera composed of the human chorionic gonadotropin (hCG) beta subunit genetically fused to the alpha subunit was constructed. The resulting polypeptide hCG molecule not only was efficiently secreted but also displayed an increased biological activity in vitro and in vivo. These data show that the alpha and hCG beta subunits encoded as a single chain retain a biologically active conformation similar to that seen in the heterodimer. This approach can be used to investigate structure-function relationships of the glycoprotein hormone family that were previously not tractable because of the absolute dependence on assembly for the biological response. Moreover, other bioactive multisubunit ligands can be engineered where the combination efficiency and specificity of heterodimers and homodimers are otherwise difficult to control.
Cyanobacterial microcystin‐LR is a potent and specific inhibitor of protein phosphatases 1 and 2A from both mammals and higher plants (1990)

The cyclic heptapeptide, microcystin-LR, inhibits protein phosphatases 1 (PP1) and 2A (PP2A) with Ki values below 0.1 nM. Protein phosphatase 2B is inhibited 1000-fold less potently, while six other phosphatases and eight protein kinases tested are unaffected. These results are strikingly similar to those obtained with the tumour promoter okadaic acid. We establish that okadaic acid prevents the binding of microcystin-LR to PP2A, and that protein inhibitors 1 and 2 prevent the binding of microcystin-LR to PP1. We discuss the possibility that inhibition of PP1 and PP2A accounts for the extreme toxicity of microcystin-LR, and indicate its potential value in the detection and analysis of protein kinases and phosphatases.
OPINIONS<br>Acetyl-coenzyme A carboxylase– an attractive enzyme for biotechnology (2014)

Acetyl-CoA carboxylase catalyzes the carboxylation of acetyl-CoA to malonyl-CoA. This reaction constitutes&lt;br /&gt; the first committed step of fatty acid synthesis in most organisms, while its product also serves as a universal precursor&lt;br /&gt; for various other high-value compounds. The important regulatory and rate-limiting role of acetyl-CoA&lt;br /&gt; carboxylase makes this enzyme a powerful tool in a variety of biotechnological and medical projects. This review&lt;br /&gt; presents the current knowledge on structural and functional features of the enzyme and focuses on its divergent&lt;br /&gt; applications. Different metabolic engineering attempts that lead to the production of various compounds, such&lt;br /&gt; as fatty acids, polyketides or flavonoids, are presented and their advantages and limitations discussed. The importance&lt;br /&gt; of studies on acetyl-CoA carboxylase activity for design and development of new herbicides and antibiotics&lt;br /&gt; as well as for medical intervention is also highlighted.
CD4+CD25+ REGULATORY T CELLS IN HEALTH AND DISEASE (2006)

1. Over the past 5 years, tremendous progress has been made in understanding the suppressive mechanisms of T regulatory (Treg) cells. The Treg cells, a subpopulation of T cells, have been shown to play an important role in maintaining peripheral tolerance and the prevention of autoimmunity. 2. Various populations of Treg cells have been described, including thymically derived CD4(+)CD25(+) Treg cells. These naturally occurring Treg cells are present in the periphery and are capable of suppressing proliferation and effector T cell responses both in vitro and in vivo. 3. In addition, a second subset of Treg cells, type 1 T regulatoary (Tr1) and Th3 cells, exert their suppressive capacity via cytokines such as interleukin-10 and transforming growth factor-beta and are contact independent. 4. The present review summarizes the characteristics and molecular basis of CD4(+)CD25(+) Treg cells, as well as their therapeutic potential in modulating inflammatory diseases, such as inflammatory bowel disease and rheumatoid arthritis.
Colonization as exploitation in the Amazon rain forest, 1758-1911 (2000)

A history of 19th-century European colonization/exploitation of Amazonia through the 1911 Brazilian rubber boom. The author argues that modern-day plunder of the largest remaining rain forest in the world is yet another chapter in a long, sad story.
The kinetics of murine hematopoietic stem cells in vivo in response to prolonged increased mature blood cell production induced by granulocyte colony-stimulating factor (1995)

Because of the complexity of appropriate stem cell assays, little information on the in vivo regulation of murine stem cell biology or stemmatopoiesis is available. It is unknown whether and how in vivo the primitive hematopoietic stem cell compartment is affected during a continued increased production of mature blood cells. In this study, we present data showing that prolonged (3 weeks) administration of granulocyte colony-stimulating factor (G-CSF), which is a major regulator of mature granulocyte production, has a substantial impact on both the size and the location of various stem cell subset pools in mice. We have used the novel cobblestone area forming cell (CAFC) assay to assess the effects of G-CSF on the stem cell compartment (CAFC days 7, 14, 21, and 28). In marrow, in which normally 99% of the total number of stem cells can be found, G-CSF induced a severe depletion of particularly the most primitive stem cells to 5% to 10% of normal values. The response after 7 days of G-CSF treatment was an increased amplification between CAFC day 14 and 7. However, this response occurred at the expense of the number of CAFC day 14. It is likely that the resulting gap of CAFC day 14 cell numbers was subsequently replenished from the more primitive CAFC day 21 and 28 compartments, because these cell numbers remained low during the entire treatment period. In the spleen, the number of stem cells increased, likely caused by a migration from the marrow via the blood, leading to an accumulation in the spleen. The increased number of stem cells in the spleen overcompensated for the loss in the marrow. When total body (marrow and spleen) stem cell numbers were calculated, it appeared that a continued increased production of mature granulocytes resulted in the establishment of a higher, new steady state of the stem cell compartment; most committed stem cells (CAFC day 7) were increased threefold, CAFC day 14 were increased 2.3-fold, CAFC-day 21 were increased 1.8-fold, and the most primitive stem cells evaluated, CAFC day 28, were not different from normal, although now 95% of these cells were located in the spleen. Four weeks after discontinuation of the G-CSF treatment, the stem cell reserve in the spleen had returned to a normal level, whereas stem cell numbers in marrow had recovered to values above normal. This study shows that the primitive stem cell compartment is seriously perturbed during an increased stimulation of the production of mature blood cells.(ABSTRACT TRUNCATED AT 400 WORDS)
Adeno-associated virus type 2-mediated transduction of murine hematopoietic cells with long-term repopulating ability and sustained expression of a human globin gene in vivo (1997)

Adeno-associated virus type 2 (AAV), a nonpathogenic human parvovirus, is gaining attention as a vector for potential use in human gene therapy. We and others have described AAV-mediated beta-globin gene transfer and expression in established human and murine erythroleukemia cell lines in vitro. However, successful AAV-mediated globin gene transduction of hematopoietic stem cells and long-term expression in vivo in progeny cells have not been documented. We report here that infection of murine hematopoietic bone marrow cells ex vivo with a recombinant AAV vector containing the genomic copy of a normal human globin gene followed by transplantation of these cells into lethally irradiated congenic mice resulted in efficient gene transfer into hematopoietic cells with long-term repopulating ability as detected by the presence of the human globin gene sequences in bone marrow and spleen in primary recipient mice for at least 6 months. Long-term expression of the human globin gene was also detected in bone marrow, but not in spleen, in primary recipient mice. Furthermore, in secondary-transplant experiments, we were also able to document the presence as well as expression of the transduced human globin gene in mouse bone marrow for up to 3 months. These results provide further support for potential use of the AAV-based vector system in gene therapy of human hemoglobinopathies in general and sickle-cell anemia and beta-thalassemia in particular.
Efficient homologous recombination-mediated genome engineering in zebrafish using TALE nucleases (2014)

Custom-designed nucleases afford a powerful reverse genetic tool for direct gene disruption and genome modification in vivo. Among various applications of the nucleases, homologous recombination (HR)-mediated genome editing is particularly useful for inserting heterologous DNA fragments, such as GFP, into a specific genomic locus in a sequence-specific fashion. However, precise HR-mediated genome editing is still technically challenging in zebrafish. Here, we establish a GFP reporter system for measuring the frequency of HR events in live zebrafish embryos. By co-injecting a TALE nuclease and GFP reporter targeting constructs with homology arms of different size, we defined the length of homology arms that increases the recombination efficiency. In addition, we found that the configuration of the targeting construct can be a crucial parameter in determining the efficiency of HR-mediated genome engineering. Implementing these modifications improved the efficiency of zebrafish knock-in generation, with over 10% of the injected F0 animals transmitting gene-targeting events through their germline. We generated two HR-mediated insertion alleles of sox2 and gfap loci that express either superfolder GFP (sfGFP) or tandem dimeric Tomato (tdTomato) in a spatiotemporal pattern that mirrors the endogenous loci. This efficient strategy provides new opportunities not only to monitor expression of endogenous genes and proteins and follow specific cell types in vivo, but it also paves the way for other sophisticated genetic manipulations of the zebrafish genome.
Effect of ω-3 Polyunsaturated Fatty Acids-Derived Bioactive Lipids on Metabolic Disorders (2021)

Arachidonic acid (ARA) is an important ω-6 polyunsaturated fatty acid (PUFA), and docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA) and n-3 docosapentaenoic acid (n-3 DPA) are three well-known ω-3 PUFAs. These fatty acids can be metabolized into a number of bioactive lipids. Eicosanoids derived from ARA have drawn great attention because of their important and complex biofunctions. Although EPA, DHA and n-3 DPA have also shown powerful biofunctions, we have fewer studies of metabolites derived from them than those from ARA. Recently, growing research has focused on the bioaction of ω-3 PUFA-derived metabolites, which indicates their great potential for treating metabolic disorders. Most of the functional studies of these bioactive lipids focused on their anti-inflammatory effects. However, several studies elucidated their direct effects on pancreatic β cells, hepatocytes, adipocytes, skeletal muscle cells, and endothelial cells. These researches revealed the importance of studying the functions of metabolites derived from ω-3 polyunsaturated fatty acids other than themselves. The current review summarizes research into the effects of ω-3 PUFA-derived oxylipins on metabolic disorders, including diabetes, non-alcoholic fatty liver disease, adipose tissue dysfunction, and atherosclerosis.
Reduction of Ischemia/Reperfusion Injury With Bendavia, a Mitochondria‐Targeting Cytoprotective Peptide (2012)

Postischemic administration of Bendavia protected against reperfusion injury in several distinct models of injury. These data suggest that Bendavia is a mitochondria-targeted therapy that reduces reperfusion injury by maintaining mitochondrial energetics and suppressing cellular reactive oxygen species levels. (J Am Heart Assoc. 2012;1:e001644 doi: 10.1161/JAHA.112.001644.).
Identification of two structurally and functionally distinct sites on human platelet membrane glycoprotein IIb-IIIa using monoclonal antibodies. (1983)

Platelet membrane glycoprotein IIb-IIIa exists as a calcium-dependent complex of two large peptides (designated IIb and IIIa) in Triton X-100 solutions, but it remains unknown if these peptides are subunits of one glycoprotein or are actually two individual glycoproteins in the intact platelet membrane. We used crossed immunoelectrophoresis to define the epitopes of two monoclonal antibodies to IIb-IIIa, then used these antibodies to study the structural and functional organization of IIb and IIIa in the platelet membrane. Human platelets solubilized in Triton X-100 were electrophoresed through an intermediate gel containing 125I-monoclonal IgG, then into an upper gel containing rabbit anti-human platelet antibodies. Our previously characterized antibody. Tab, and a new monoclonal antibody, T10, both bound to the immunoprecipitate corresponding to the IIb-IIIa complex. When platelets were electrophoresed after solubilization in 5 mM EDTA, 125I-Tab bound to the dissociated IIb polypeptide, but not to IIIa. In contrast, 125-I-T10 did not react with either IIb or IIIa. Thus, Tab recognizes a determinant on IIb, while T10 recognizes a determinant created only after the association of IIb and IIIa. Gel-filtered platelets from six normal donors bound 50,600 +/- 5,600 125I-T10 molecules/platelet and 47,800 +/- 11,200 125I-Tab molecules/platelet, consistent with IIb-IIIa being a heterodimer. 125I-T10 binding was identical in unactivated platelets and platelets stimulated with 10 microM ADP. However, platelets did not aggregate or bind 125I-fibrinogen until ADP was added. T10, but not Tab or nonimmune mouse antibody, inhibited ADP-induced platelet aggregation and 125I-fibrinogen binding. Our findings suggest that IIb and IIIa exist as subunits of a single membrane glycoprotein in unstimulated platelets. Fibrinogen binding appears to require not only the interaction of IIb and IIIa, but also some additional change occurring after platelet activation.
Comparison of the properties of titanium dioxide films prepared by various techniques (1989)

Fourteen university, government, and industrial laboratories prepared a total of twenty pairs of single-layer titanium dioxide films. Several laboratories analyzed the coatings to determine their optical properties, thickness, surface roughness, absorption, wetting contact angle, and crystalline structure. Wide variations were found in the optical and physical properties of the films, even among films produced by nominally the same deposition techniques.