gebhart/patrepeval huggingface dataset:
αvβ3/αvβ5 Integrins-FAK-RhoB: A Novel Pathway for Hypoxia Regulation in Glioblastoma (2009)

The presence of hypoxic areas in glioblastoma is an important determinant in tumor response to therapy and, in particular, to radiotherapy. Here we have explored the involvement of integrins, up to now known as regulators of angiogenesis and invasion, in the regulation of tumor hypoxia driven from the tumor cell. We first show that hypoxia induces the recruitment of alpha(v)beta(3) and alpha(v)beta(5) integrins to the cellular membrane of U87 and SF763 glioblastoma cells, thereby activating the focal adhesion kinase (FAK). We then show that inhibiting alpha(v)beta(3) or alpha(v)beta(5) integrins in hypoxic cells with a specific inhibitor or with siRNA decreases the hypoxia-inducible factor 1alpha (HIF-1alpha) intracellular level. This integrin-dependent regulation of HIF-1alpha is mediated through the regulation of FAK, which in turn activates the small GTPase RhoB, leading to the inhibition of GSK3-beta. Furthermore, silencing this pathway in glioma cells of established xenografts dramatically reduces glioma hypoxia, associated with a significant decrease in vessel density. Our present results unravel a new mechanism of hypoxia regulation by establishing the existence of an alpha(v)beta(3)/alpha(v)beta(5) integrin-dependent loop of hypoxia autoregulation in glioma. Targeting this hypoxia loop may be crucial to optimizing radiotherapy efficiency.
Analysis of Human Cytomegalovirus ori Lyt Sequence Requirements in the Context of the Viral Genome (2005)

During the lytic phase of infection, replication of herpesvirus genomes initiates at the lytic origin of replication, oriLyt. Many herpesviruses harbor more than one lytic origin, but so far, only one oriLyt has been identified for human cytomegalovirus (HCMV). Evidence for the existence of additional lytic origins of HCMV has remained elusive. On the basis of transient replication assays with cloned viral fragments, HCMV oriLyt was described as a core region of 1.5 kbp (minimal oriLyt) flanked by auxiliary sequences required for maximal replication activity (complete oriLyt). It remained unclear whether minimal oriLyt alone can drive the replication of HCMV in the absence of its accessory regions. To investigate the sequence requirements of oriLyt in the context of the viral genome, mutant genomes were constructed lacking either minimal or complete oriLyt. These genomes were not infectious, suggesting that HCMV contains only one lytic origin of replication. Either minimal or complete oriLyt was then ectopically reinserted into the oriLyt-depleted genomes. Only the mutant genomes carrying complete oriLyt led to infectious progeny. Remarkably, inversion of the 1.5-kbp core origin relative to its flanking regions resulted in a replication-defective genome. Mutant genomes carrying minimal oriLyt plus the left flanking region gave rise to minifoci, but genomes harboring minimal oriLyt together with the right flanking region were noninfectious. We conclude that the previously defined minimal lytic origin is not sufficient to drive replication of the HCMV genome. Rather, our results underline the importance of the accessory regions and their correct arrangement for the function of HCMV oriLyt.
Isolation of cDNA clones encoding a human apurini/apyrimidinic endonuclease that corects DNA repair and mutagenisis defects inE.coli xth(exonuclease III) mutants (1991)

Apurinic/apyrimidinic (AP) sites in cellular DNA are considered to be both cytotoxic and mutagenic, and can arise spontaneously or following exposure to DNA damaging agents. We have isolated cDNA clones which encode an endonuclease, designated HAP1 (human AP endonuclease 1), that catalyses the initial step in AP site repair in human cells. The predicted HAP1 protein has an Mr of 35,500 and shows striking sequence similarity (93% identity) to BAP 1, a bovine AP endonuclease enzyme. Significant sequence homology to two bacterial DNA repair enzymes, E. coli exonuclease III and S. pneumoniae ExoA proteins, and to Drosophila Rrp1 protein is also apparent. We have expressed the HAP1 cDNA in E. coli mutants lacking exonuclease III (xth), endonuclease IV (nfo), or both AP endonucleases. The HAP1 protein can substitute for exonuclease III, but not for endonuclease IV, in respect of some, but not all, DNA repair and mutagenesis functions. Moreover, a dut xth (ts) double mutant, which is nonviable at 42 degrees C due to an accumulation of unrepaired AP sites following excision of uracil from DNA, was rescued by expression of the HAP1 cDNA. These results indicate that AP endonucleases show remarkable conservation of both primary sequence and function. We would predict that the HAP1 protein is important in human cells for protection against the toxic and mutagenic effects of DNA damaging agents.
Bacterial Toxins Block Endothelial Wound Repair (1997)

We investigated the effect of bacterial toxins that modify and inactivate Rho GTP-binding proteins on the migratory response of endothelial cells to wounding. C3-transferase from Clostridium botulinum, EDIN from Staphylococcus aureus, and toxin A from Clostridium difficile blocked migration of human umbilical vein endothelial cells (HUVECs) in an in vitro wound repair assay. Migrating HUVECs expressed actin microspikes (maximum at 10 minutes after wounding), ruffles (maximum at 12 hours), and fibers (maximum at 24 hours), and within these actin structures, vinculin-containing focal complexes/adhesions were formed. C3-Transferase ADP ribosylated RhoA, RhoB, and RhoC in HUVECs and abolished the formation of actin stress fibers/focal adhesions but had no effect on expression of microspikes, ruffles, or the associated vinculin-containing focal complexes. Similar results were obtained with EDIN and toxin A. These results indicate that endothelial cells migrating into a wounded area express distinct combinations of actin/vinculin structures in a spatially and temporally coordinated manner. The GTPase Rho selectively controls the formation of actin fibers/focal adhesions that occurs 2 to 24 hours after wounding. A mechanism is proposed by which Rho-specific bacterial toxins could influence vascular repair, angiogenesis, or atherosclerosis.
Osteoblast Recruitment and Bone Formation Enhanced by Cell Matrix–associated Heparin-binding Growth-associated Molecule (HB-GAM) (1998)

Bone has an enormous capacity for growth, regeneration, and remodeling. This capacity is largely due to induction of osteoblasts that are recruited to the site of bone formation. The recruitment of osteoblasts has not been fully elucidated, though the immediate environment of the cells is likely to play a role via cell- matrix interactions. We show here that heparin-binding growth-associated molecule (HB-GAM), an extracellular matrix-associated protein that enhances migratory responses in neurons, is prominently expressed in the cell matrices that act as target substrates for bone formation. Intriguingly, N-syndecan, which acts as a receptor for HB-GAM, is expressed by osteoblasts/osteoblast precursors, whose ultrastructural phenotypes suggest active cell motility. The hypothesis that HB-GAM/N-syndecan interaction mediates osteoblast recruitment, as inferred from developmental studies, was tested using osteoblast-type cells that express N-syndecan abundantly. These cells migrate rapidly to HB-GAM in a haptotactic transfilter assay and in a migration assay where HB-GAM patterns were created on culture wells. The mechanism of migration is similar to that previously described for the HB-GAM-induced migratory response of neurons. Our hypothesis that HB-GAM/N-syndecan interaction participates in regulation of osteoblast recruitment was tested using two different in vivo models: an adjuvant-induced arthritic model and a transgenic model. In the adjuvant-induced injury model, the expression of HB-GAM and of N-syndecan is strongly upregulated in the periosteum accompanying the regenerative response of bone. In the transgenic model, the HB-GAM expression is maintained in mesenchymal tissues with the highest expression in the periosteum. The HB-GAM transgenic mice develop a phenotype characterized by an increased bone thickness. HB-GAM may thus play an important role in bone formation, probably by mediating recruitment and attachment of osteoblasts/osteoblast precursors to the appropriate substrates for deposition of new bone.
Mutations in the beta-catenin gene (CTNNB1) in endometrioid ovarian carcinomas. (1998)

Mutations of the beta-catenin gene (CTNNB1) have recently been implicated in the initiation of some colon carcinomas and melanomas. In these tumors, beta-catenin abnormally accumulates in the cell nuclei. In an ongoing immunohistochemical study of the cadherin-catenin complex protein expression in ovarian carcinomas, we observed beta-catenin in tumor cell nuclei in some cases; this prompted us to study whether or not this abnormal immunostaining pattern was due to mutation in the beta-catenin gene itself. This study examines beta-catenin immunohistochemical expression in 40 stage I and II ovarian borderline tumors and carcinomas of the most common histological types. Membrane expression was heterogeneous in all 40 cases. However, the cytoplasm and nucleus of five (one borderline tumor and four carcinomas) of the six endometrioid lesions contained beta-catenin expression. PCR and sequencing analyses of a 200-bp fragment of exon 3 of the CTNNB1 gene, encompassing the sequence for glycogen synthetase kinase-3beta phosphorylation, were performed in 11 tumors. Heterozygous substitution mutations at codon 37 in two cases (S37F and S37C) and at codon 41 in one case (T41A) were found in three endometrioid lesions (one borderline tumor and two carcinomas) with abnormal beta-catenin expression. Three endometrioid carcinomas and five tumors of other histological types analyzed showed normal DNA sequences. These results implicate beta-catenin gene mutations in ovarian malignant transformation with a characteristic phenotype: endometrioid ovarian carcinoma.
Cowpea Mosaic Virus as a Scaffold for 3-D Patterning of Gold Nanoparticles (2004)

Different mutants of Cowpea Mosaic Virus (CPMV) have been used as scaffolds to bind 2 and 5 nm gold nanoparticles through gold−sulfur bond formation at specific locations on the virus to produce patterns of specific interparticle distances. TEM images confirm that the bound gold particles produce patterns of gold nanoparticles that correlate well with models built from the known locations of the inserted cysteine groups on the capsid. These results demonstrate that it is possible to use CPMV mutants as nanoscale scaffolds to place gold nanoparticles at fixed interparticle distances.
A FERM domain autoregulates Drosophila myosin 7a activity (2009)

Full-length Drosophila myosin 7a (myosin 7a-FL) has a complex tail containing a short predicted coiled coil followed by a MyTH4-FERM domain, an SH3 domain, and a C-terminal MyTH4-FERM domain. Myosin 7a-FL expressed in Sf9 cells is monomeric despite the predicted coiled coil. We showed previously that Subfragment-1 (S1) from this myosin has MgATPase of V(max) approximately 1 s(-1) and K(ATPase) approximately 1 microM actin. We find that myosin 7a-FL has V(max) similar to S1 but K(ATPase) approximately 30 microM. Thus, at low actin concentrations (5 microM), the MgATPase of S1 is fully activated, whereas that of myosin 7a-FL is low, suggesting that the tail regulates activity. Electron microscopy of myosin 7a-FL with ATP shows the tail is tightly bent back against the motor domain. Myosin 7a-FL extends at either high ionic strength or without ATP, revealing the motor domain, lever, and tail. A series of C-terminal truncations show that deletion of 99 aa (the MyTH7 subdomain of the C-terminal FERM domain) is sufficient to abolish bending, and the K(ATPase) is then similar to S1. This region is highly conserved in myosin 7a. We found that a double mutation in it, R2140A-K2143A, abolishes bending and reduces K(ATPase) to S1 levels. In addition, the expressed C-terminal FERM domain binds actin with K(d) approximately 30 microM regardless of ATP, similar to the K(ATPase) value for myosin 7a-FL. We propose that at low cellular actin concentrations, myosin 7a-FL is bent and inactive, but at high actin concentrations, it is unfolded and active because the C-terminal FERM domain binds to actin.
Paramagnetic particles and mixing in micro-scale flows (2006)

Mixing in microscale flows with rotating chains of paramagnetic particles can be enhanced by adjusting the ratio of viscous to magnetic forces so that chains dynamically break and reform. Lattice Boltzmann (LB) simulations were used to calculate the interaction between the fluid and suspended paramagnetic particles under the influence of a rotating magnetic field. Fluid velocities obtained from the LB simulations are used to solve the advection diffusion equation for massless tracer particles. At relatively high Mason numbers, small chains result in low edge velocities, and hence mixing is slower than at other Mason numbers. At low Mason numbers, long, stable chains form and produce little mixing toward the center of the chains. A peak in mixing rate is observed when chains break and reform. The uniformity of mixing is greater at higher Mason numbers because more small chains result in a larger number of small mixing areas.
Unwinding RNA Silencing (2000)

Eukaryotic cells have developed an elegant system called RNA silencing for getting rid of foreign RNAs whether they be of viral, retrotransposon, or transgene origin. In his Perspective, Baulcombe examines new findings (Wu-Scharf et al.) showing that in a green alga the gene responsible for RNA silencing encodes an RNA helicase (related to proteins in worms and other organisms) that is required for regulation of gene expression at the RNA level.
Gold-coated pacemaker implantation after allergic reactions to pacemaker compounds (2009)

An 86-year-old man underwent pacemaker implantation for symptomatic atrio-ventricular block grade 2 Mobitz II. The patient suffered repeated admissions for iterative sterile wound necrosis, leading to two generator re-implantations. No bacterial infection was detected in the microbiological screening tests. The skin patch testing to titanium was negative. Nevertheless, we decided to remove the pacemaker system and to implant a gold-plated generator with polyurethane leads. Since then, there has been no recurrence of wound complications. Gold-plated generator and polyurethane leads are effective in treating allergic reactions to pacemaker system components in selected cases. Negative skin patch testing to titanium does not exclude allergic reaction to this pacemaker component.
Identification of a New Acute Phase Protein (1995)

We have previously reported mouse SIP24 protein as a secreted inducible protein produced by quiescent Balb/c 3T3 cells. SIP24 can be produced in response to many factors, including serum, basic fibroblast growth factor, prostaglandin F2 alpha, phorbol ester, and dexamethasone. Here we present evidence to show that SIP24 is the product of mouse 24P3 mRNA. The 24P3 cDNA was originally cloned from an SV40-transformed quiescent mouse primary kidney cell culture, and it has been classified as a new member of the lipocalin protein family. We show that the SIP24/24P3 protein and mRNA increase dramatically in mouse serum and liver during the acute phase response induced by turpentine injection. Injection of mice with dexamethasone caused a modest increase of SIP24/24P3 mRNA in the liver. Tissue distribution studies revealed that SIP24/24P3 is mainly expressed in liver during the acute phase response. SIP24/24P3 was also detected in the brain and the uterus. In mouse BNL (Balb/c normal liver) cells, the production of SIP24/24P3 is stimulated by tumor necrosis factor alpha, which is a major regulator of the expression of other acute phase proteins. From its pattern of regulation, we conclude that SIP24/24P3 is a new type 1 acute phase protein.
Role of fatty acid elongases in determination of de novo synthesized monounsaturated fatty acid species (2010)

Enhanced production of monounsaturated fatty acids (FA) derived from carbohydrate-enriched diets has been implicated in the development of obesity and insulin resistance. The FA elongases Elovl-5 and Elovl-6 are regulated by nutrient and hormone status, and have been shown using intact yeast and mammalian microsome fractions to be involved in the synthesis of monounsaturated FAs (MUFA). Herein, targeted knockdown and overexpression of Elovl-5 or Elovl-6 was used to determine their roles in de novo synthesis of specific MUFA species in mammalian cells. Treatment of rat insulinoma (INS)-1 cells with elevated glucose increased de novo FA synthesis and the ratio of MUFAs to saturated FAs. Elovl-5 knockdown decreased elongation of 16:1,n-7. Elovl-5 overexpression increased synthesis of 18:1,n-7; however, this increase was dependent on stearoyl-CoA desaturase-driven 16:1,n-7 availability. Knockdown of Elovl-6 decreased elongation of 16:0 and 16:1,n-7, resulting in accumulation of 16:1,n-7. Elovl-6 overexpression preferentially drove synthesis of 16:0 elongation products 18:0 and 18:1,n-9 but not 18:1,n-7. These findings demonstrate that coordinated induction of FA elongase and desaturase activity is required for balanced synthesis of specific n-7 versus n-9 MUFA species. Given the relative abundance of 16:0 to 16:1,n-7 and the specificity of Elovl-6 for 16:0, Elovl-6 is a major elongase for 18:1,n-9 production.
Barrier and Tensile Properties of Transglutaminase Cross‐linked Gelatin Films as Affected by Relative Humidity, Temperature, and Glycerol Content (1999)

ABSTRACT Gelatin films were prepared by enzymatic cross‐linking with transglutaminase, and their mechanical and barrier properties were evaluated as functions of relative humidity (RH, 30 to 75%), temperature (15 to 35°C) and glycerol content (15 to 31%). Water and glycerol plasticized the films synergistically, resulting in greater elongation but lower tensile strength values. Films with higher glycerol contents exhibited higher moisture contents, indicating higher hydrophilicity of the films. Permeabilities of oxygen and allyl isothiocyanate (an antimicrobial vapor from Cruciferae plants) were low when the films were dry, but increased considerably when RH&gt;50%. Therefore, RH conditions during end‐use applications must be considered to optimize the performance of these films.
Interfacial Structures and Properties of Organic Materials for Biosensors: An Overview (2012)

The capabilities of biosensors for bio-environmental monitoring have profound influences on medical, pharmaceutical, and environmental applications. This paper provides an overview on the background and applications of the state-of-the-art biosensors. Different types of biosensors are summarized and sensing mechanisms are discussed. A review of organic materials used in biosensors is given. Specifically, this review focuses on self-assembled monolayers (SAM) due to their high sensitivity and high versatility. The kinetics, chemistry, and the immobilization strategies of biomolecules are discussed. Other representative organic materials, such as graphene, carbon nanotubes (CNTs), and conductive polymers are also introduced in this review.
Firefly Gene Lights Up Lab Animals From Inside Out (1997)

What better way to look inside your resident lab animal than to put a light source inside it and detect the light seeping out? A team of researchers at Stanford University has done just that by genetic engineering.
Development of a hybrid scaffold with synthetic biomaterials and hydrogel using solid freeform fabrication technology (2011)

Natural biomaterials such as hyaluronic acid, gelatin and collagen provide excellent environments for tissue regeneration. Furthermore, gel-state natural biomaterials are advantageous for encapsulating cells and growth factors. In cell printing technology, hydrogel which contains cells was printed directly to form three-dimensional (3D) structures for tissue or organ regeneration using various types of printers. However, maintaining the 3D shape of the printed structure, which is made only of the hydrogel, is very difficult due to its weak mechanical properties. In this study, we developed a hybrid scaffold consisting of synthetic biomaterials and natural hydrogel using a multi-head deposition system, which is useful in solid freeform fabrication technology. The hydrogel was intentionally infused into the space between the lines of a synthetic biomaterial-based scaffold. The cellular efficacy of the hybrid scaffold was validated using rat primary hepatocytes and a mouse pre-osteoblast MC3T3-E1 cell line. In addition, the collagen hydrogel, which encapsulates cells, was dispensed and the viability of the cells observed. We demonstrated superior effects of the hybrid scaffold on cell adhesion and proliferation and showed the high viability of dispensed cells.
Considerations on sample size and power calculations in randomized clinical trials (2003)

Many studies in orthopaedics and sports medicine have not considered sample size or statistical power as important issues in study design. This article addresses the importance of a sample size calculation in randomized clinical trials and the components of the calculations that researchers must consider in their preliminary planning of an investigation. The types of data being collected, level of significance, types I and II errors, and power are also addressed.
Human rhinovirus 2: complete nucleotide sequence and proteolytic processing signals in the capsid protein region (1985)

cDNA clones representing the entire genome of human rhinovirus 2 have been obtained and used to determine the complete nucleotide sequence. The genome consists of 7102 nucleotides and possesses a long open reading frame of 6450 nucleotides; this reading frame is initiated 611 nucleotides from the 5' end and stops 42 nucleotides from the polyA tract. The N-terminal sequences of three of the viral capsid proteins have been elucidated, thus defining the positions of three cleavage sites on the polyprotein. The extensive amino acid sequence homology with poliovirus and human rhinovirus 14 enabled the other cleavage sites to be predicted. Cleavages in the 3' half of the molecule appear to take place predominantly at Gln-Gly pairs, whereas those in the 5' half (including the capsid proteins) are more heterogeneous.
Mutations within the proteolytic cleavage site of the Rous sarcoma virus glycoprotein that block processing to gp85 and gp37 (1987)

We have investigated the specificity of the proteolytic cleavage of the Rous sarcoma virus glycoprotein precursor by introducing two mutations into the putative cleavage region (Arg-Arg-Lys-Arg). We show that neither a deletion of the cleavage sequence nor a glutamic acid for lysine substitution altered intracellular transport or surface expression of the env gene products. However, both the four-amino-acid deletion and the glutamic acid substitution block processing of the env precursor. Susceptibility of the glutamic acid-substituted env precursor to proteases indicated that tertiary protein structure was unaffected. While inhibitor experiments suggested that more than one endopeptidase might be capable of mediating the proteolytic cleavage, the results presented here point to the presence in the Golgi apparatus of a novel endopeptidase, required for retroviral glycoprotein cleavage, that has a high specificity for lysine-containing peptides.