gebhart/patrepeval huggingface dataset:
Protein Interactions within the Set1 Complex and Their Roles in the Regulation of Histone 3 Lysine 4 Methylation (2006)

Set1 is the catalytic subunit and the central component of the evolutionarily conserved Set1 complex (Set1C) that methylates histone 3 lysine 4 (H3K4). Here we have determined protein/protein interactions within the complex and related the substructure to function. The loss of individual Set1C subunits differentially affects Set1 stability, complex integrity, global H3K4 methylation, and distribution of H3K4 methylation along active genes. The complex requires Set1, Swd1, and Swd3 for integrity, and Set1 amount is greatly reduced in the absence of the Swd1-Swd3 heterodimer. Bre2 and Sdc1 also form a heteromeric subunit, which requires the SET domain for interaction with the complex, and Sdc1 strongly interacts with itself. Inactivation of either Bre2 or Sdc1 has very similar effects. Neither is required for complex integrity, and their removal results in an increase of H3K4 mono- and dimethylation and a severe decrease of trimethylation at the 5' end of active coding regions but a decrease of H3K4 dimethylation at the 3' end of coding regions. Cells lacking Spp1 have a reduced amount of Set1 and retain a fraction of trimethylated H3K4, whereas cells lacking Shg1 show slightly elevated levels of both di- and trimethylation. Set1C associates with both serine 5- and serine 2-phosphorylated forms of polymerase II, indicating that the association persists to the 3' end of transcribed genes. Taken together, our results suggest that Set1C subunits stimulate Set1 catalytic activity all along active genes.
Structural and Genomic Correlates of Hyperthermostability (2000)

While most organisms grow at temperatures ranging between 20 and 50 degrees C, many archaea and a few bacteria have been found capable of withstanding temperatures close to 100 degrees C, or beyond, such as Pyrococcus or Aquifex. Here we report the results of two independent large scale unbiased approaches to identify global protein properties correlating with an extreme thermophile lifestyle. First, we performed a comparative proteome analyses using 30 complete genome sequences from the three kingdoms. A large difference between the proportions of charged versus polar (noncharged) amino acids was found to be a signature of all hyperthermophilic organisms. Second, we analyzed the water accessible surfaces of 189 protein structures belonging to mesophiles or hyperthermophiles. We found that the surfaces of hyperthermophilic proteins exhibited the shift already observed at the genomic level, i.e. a proportion of solvent accessible charged residues strongly increased at the expense of polar residues. The biophysical requirements for the presence of charged residues at the protein surface, allowing protein stabilization through ion bonds, is therefore clearly imprinted and detectable in all genome sequences available to date.
Induction of CD4+ T cell–dependent antitumor immunity by TAT-mediated tumor antigen delivery into dendritic cells (2002)

Dendritic cell-based (DC-based) immunotherapy represents a promising approach to the prevention and treatment of many diseases, including cancer, but current strategies have met with only limited success in clinical and preclinical studies. Previous studies have demonstrated that a TAT peptide derived from the HIV TAT protein has the ability to transduce peptides or proteins into various cells. Here, we describe the use of TAT-mediated delivery of T cell peptides into DCs to prolong antigen presentation and enhance T cell responses. While immunization of mice with DCs pulsed with an antigenic peptide derived from the human TRP2 protein generated partial protective immunity against B16 tumor, immunization with DCs loaded with a TAT-TRP2 peptide resulted in complete protective immunity, as well as significant inhibition of lung metastases in a 3-day tumor model. Although both DC/TRP2 and DC/TAT-TRP2 immunization increased the number of TRP2-specific CD8(+) T cells detected by K(b)/TRP2 tetramers, T cell activity elicited by DC/TAT-TRP2 was three- to tenfold higher than that induced by DC/TRP2. Furthermore, both CD4(+) and CD8(+) T cells were required for antitumor immunity demonstrated by experiments with antibody depletion of subsets of T cells, as well as with various knockout mice. These results suggest that a TAT-mediated antigen delivery system may have important clinical applications for cancer therapy.
Backbone-modified oligonucleotides containing a butanediol-1,3 moiety as a ‘vicarious segment’ for the deoxyribosyl moiety—synthesis and enzyme studies (1990)

Sequential single replacement of nucleosides within the decanucleotide d[GGGAATTCCC] (7) by means of a butanediol-1,3 residue allowed us to obtain a set of ten decanucleotides containing 'vicarious' (V) carbon-phosphate fragments. These analogues were further used as substrates for svPDE, nuclease PI and EcoR1 endonuclease. Interestingly, replacement of any of the nucleosides within the canonical sequence ...GAATTC... by the butanediol-1,3 'vicarious' segment discriminates such constructs 8c-h as substrates for Eco-R1 enzyme.
Enzymatic Preparation of Ginsenosides Rg2, Rh1, and F1from Protopanaxatriol-Type Ginseng Saponin Mixture (2003)

During investigations on the hydrolysis of a protopanaxatriol-type saponin mixture by various glycoside hydrolases, it was found that two minor saponins, ginsenosides Rg 2 and Rh 1, were formed in high yields by crude beta-galactosidase from Aspergillus oryzae and crude lactase from Penicillium sp., respectively. Moreover, a crude preparation of naringinase from Penicillium decumbens readily hydrolyzed a protopanaxatriol-type saponin mixture to give an intestinal bacterial metabolite, ginsenoside F 1 as the main product. A crude preparation of hesperidinase from Penicillium sp. selectively hydrolyzed ginsenoside Re into ginsenoside Rg 1. This is the first report on the enzymatic preparation of minor saponins, ginsenosides Rg 2 and Rh 1, and of an intestinal bacterial metabolite, ginsenoside F 1, with a high efficiency from a protopanaxatriol-type saponin mixture.
Methidiumpropyl-EDTA-Fe(II) and DNase I footprinting report different small molecule binding site sizes on DNA (1983)

DNase I and MPE.Fe (II) footprinting both employ partial cleavage of ligand-protected DNA restriction fragments and Maxam-Gilbert sequencing gel methods of analysis. One method utilizes the enzyme, DNase I, as the DNA cleaving agent while the other employs the synthetic molecule, methidium-propyl-EDTA (MPE). For actinomycin D, chromomycin A3 and distamycin A, DNase I footprinting reports larger binding site sizes than MPE.Fe (II). DNase I footprinting appears more sensitive for weakly bound sites. MPE.Fe (II) footprinting appears more accurate in determining the actual size and location of the binding sites for small molecules on DNA, especially in cases where several small molecules are closely spaced on the DNA. MPE.Fe (II) and DNase I report the same sequence and binding site size for lac repressor protein on operator DNA.
Rejection of skin allografts by indirect allorecognition of donor class I major histocompatibility complex peptides. (1992)

LEW (RT1l) rats were immunized with peptides corresponding to the alpha helical region of the alpha 1 domain (peptide 1), the beta sheet of the alpha 2 domain (peptide 2), and the alpha helical region of the alpha 2 domain (peptide 3) of the RT1-Aav1 classical class I molecule of the DA (RT1av1) strain. The immunizations were without carriers, and the objective was to prime to indirect allorecognition without influencing direct recognition of the RT1-Aav1 molecule. The LEW rats mounted strong primary and secondary antibody responses to peptides 1 and 3, but only weak secondary responses to peptide 2. None of the antipeptide antibodies crossreacted with intact RT1-Aav1 class I molecules. The immunization also resulted in LEW antigen-presenting cell-dependent, CD4+ T cell proliferative responses, which were very strong against peptide 1 and weakest against peptide 2. LEW rats immunized with peptides 1 or 3, but most effectively with both peptides 1 and 3 together, showed accelerated rejection of DA skin allografts. This effect was not observed in LEW rats immunized with peptide 2. In response to the DA skin allograft, the peptide-immunized LEW rats showed markedly accelerated kinetics of antibody production to the intact RT1-Aav1 molecule. These data demonstrate that indirect allorecognition can play an important role in allograft rejection and have important implications for understanding allograft rejection and its regulation.
Ubiquitin (UbC) Expression in Muscle Cells Is Increased by Glucocorticoids through a Mechanism Involving Sp1 and MEK1 (2002)

The muscle protein catabolism present in rats with insulin-dependent diabetes and other catabolic conditions is generally associated with increased glucocorticoid production and mRNAs encoding components of the ubiquitin-proteasome system. The mechanisms that increase ubiquitin (UbC) expression have not been identified. We studied the regulation of UbC expression in L6 muscle cells because dexamethasone stimulates the transcription of this gene and others encoding components of the ubiquitin-proteasome pathway. Results of in vivo genomic DNA footprinting experiments indicate that a protein(s) binds to Sp1 sites approximately 50 bp upstream from the UbC transcription start site; dexamethasone changes the methylation pattern at these sites. Sp1 binds to DNA probes corresponding to the rat or human UbC promoter, and treating cells with dexamethasone increases this binding. Deletion and mutation analyses of the rat and human UbC promoters are consistent with an important role of Sp1 in UbC induction by glucocorticoids. Dexamethasone-induced ubiquitin expression is blocked by mithramycin, an inhibitor of Sp1 binding. UO126, a pharmacologic inhibitor of MEK1, also blocks UbC transcriptional activation by dexamethasone; L6 cells transfected to express constitutively active MEK1 exhibit increased UbC promoter activity. Thus, glucocorticoids increase UbC expression in muscle cells by a novel transcriptional mechanism involving Sp1 and MEK1.
B chromosomes in plants (1995)

This review of supernumerary B chromosome systems in flowering plants deals mainly with work published in the last 15 yr, hut also includes older material which has not hitherto been presented systematically. The term B chromosome (B) is defined, and there is an introductory overview dealing with general characteristics and the significance of Bs as a widespread chromosome polymorphism. Detailed sections are then presented covering the occurrence of Bs in different taxa, their structure and molecular organization, their irregular modes of inheritance, their phenotypic effects, population dynamics and origin. Particular attention is paid to the research growth points in molecular analysis of the structure and genome organization of Bs, and to transmission genotypes in the context of their adaptive versus their selfish properties. Where appropriate, reference is also made to likely future lines of research, and also to the usefulness of B chromosomes in genetic analysis and as model systems to study general phenomena of genome organization and evolution, nuclear physiology and architecture, chromosome polymorphism and selfish DNA. CONTENTS Summary 411 I. Introduction 411 II. Occurrence 411 III. Structure and organization 415 IV. Inheritance 422 V. Phenotypic effects 426 VI. Populations 429 VII. Applications 430 VIII. Origin 430 Acknowiedgements 430 References 431.
Versatile Fluorescence Resonance Energy Transfer-Based Mesoporous Silica Nanoparticles for Real-Time Monitoring of Drug Release (2013)

We describe the development of a versatile fluorescence resonance energy transfer (FRET)-based real-time monitoring system, consisting of (a) coumarin-labeled-cysteine tethered mesoporous silica nanoparticles (MSNs) as the drug carrier, (b) a fluorescein isothiocyanate-β-cyclodextrin (FITC-β-CD) as redox-responsive molecular valve blocking the pores, and (c) a FRET donor-acceptor pair of coumarin and FITC integrated within the pore-unlocking event, thereby allowing for monitoring the release of drugs from the pores in real-time. Under nonreducing conditions, when the disulfide bond is intact, the close proximity between coumarin and FITC on the surface of MSNs results in FRET from coumarin to FITC. However, in the presence of the redox stimuli like glutathione (GSH), the disulfide bond is cleaved which leads to the removal of molecular valve (FITC-β-CD), thus triggering drug release and eliminating FRET. By engineering such a FRET-active donor-acceptor structure within the redox-responsive molecular valve, we can monitor the release of the drugs entrapped within the pores of the MSN nanocarrier, following the change in the FRET signal. We have demonstrated that, any exogenous or endogenous change in the GSH concentration will result in a change in the extent of drug release as well as a concurrent change in the FRET signal, allowing us to extend the applications of our FRET-based MSNs for monitoring the release of any type of drug molecule in real-time.
An enzyme activity from Escherichia coli that attacks single-stranded deoxyribopolymers and single-stranded DNA containing apyrimidinic sites (1982)

We have isolated an enzyme activity from extracts of Escherichia coli that catalyzes the hydrolysis of phosphodiester bonds in the single-stranded deoxyribopolymer (dU.[3H]dT)(2000) containing depyrimidinated sites created by enzymatic removal of uracil with uracil-DNA glycosylase. Nondepyrimidinated polymer is not degraded by the enzyme, nor is the depyrimidinated polymer degraded after reduction of apyrimidinic sites with sodium borohydride. The enzyme also degrades circular M13 DNA containing uracil or denatured phage PBS2 DNA (which naturally contains uracil) only after the removal of uracil from these substrates by uracil-DNA glycosylase. Undamaged or depurinated duplex PM2 or ColE1 DNA and undamaged M13 single-stranded DNA are not attacked by the enzyme. The activity sediments in glycerol gradients with a relative s value of 4.2 S and has a Stokes radius of 31 A, yielding a calculated Mr approximately 56,000. The fractional ratio (f/f0) is calculated at 1.25. The enzyme has no requirement for any known cofactors and is insensitive to inhibition by p-(chloromercuri)benzoate. Activity is inhibited in the presence of adenosine 5'0-triphosphate (ATP), tRNA or high ionic strength and is slightly stimulated by MnCl2 or CaCl2.
Basement membrane complexes with biological activity (1986)

We have studied the reconstitution of basement membrane molecules from extracts prepared from the basement membrane of the EHS tumor. Under physiological conditions and in the presence of added type IV collagen and heparan sulfate proteoglycan, gellike structures form whose ultrastructure appears as interconnected thin sheets resembling the lamina dense zone of basement membrane. The major components of the reconstituted structures include laminin, type IV collagen, heparan sulfate proteoglycan, entactin, and nidogen. These components polymerize in constant proportions on reconstitution, suggesting that they interact in defined proportions. Molecular sieve studies on the soluble extract demonstrate that laminin, entactin, and nidogen are associated in large but dissociable complexes which may be a necessary intermediate in the deposition of basement membrane. The reconstituted matrix was biologically active and stimulated the growth and differentiation of certain cells.
Differential expression and phosphorylation of Pak1 and Pak2 in ovarian cancer: effects on prognosis and cell invasion (2009)

Ovarian cancer is a gynecological malignancy with high mortality. Therefore, the identification of novel prognostic and therapeutic targets is important. p21-activated kinases (Paks) are involved in cytoskeleton reorganization. This study investigated the clinical significance of total and phosphorylated (p) Pak1 and Pak2 as well as their functional roles in ovarian cancer. Expressions of Pak1, p-Pak1 Thr(212), Pak2 and p-Pak2 Ser(20) in ovarian normal and cancerous cell lines as well as in clinical samples of ovarian tumors were evaluated. The effects of Pak1 and Pak2 on ovarian cancer cell functions were determined. Pak1, p-Pak1 and p-Pak2 were overexpressed in ovarian cancer cell lines, and clinical samples of ovarian cancers were compared with benign ovarian lesions/inclusion cysts. Similar Pak2 expression levels were observed among normal and cancerous cell lines and clinical samples. After multiple testing correction, high Pak1 and nuclear p-Pak1 expression in ovarian cancers was significantly associated with histological type and tumor grade, respectively. Pak1 and p-Pak1 expression was associated with poor overall and disease-free survival. Pak1 was an independent prognostic factor. Knockdown of Pak1 and Pak2 in ovarian cancer cell lines reduced cell migration and invasion but did not affect cell proliferation and apoptosis. Knockdown of Pak1 also reduced p38 activation and downregulated vascular endothelial growth factor. Conversely, ectopic Pak1 overexpression enhanced ovarian cancer cell migration and invasion in a kinase-dependent manner, along with increased p38 activation. Our findings suggest that Pak1, p-Pak1 and p-Pak2 play important roles in ovarian carcinogenesis. Pak1 and p-Pak1 may be potential prognostic markers and therapeutic molecular targets in ovarian cancer.
Chondrogenic Differentiation of Human Mesenchymal Stem Cells on Oriented Nanofibrous Scaffolds: Engineering the Superficial Zone of Articular Cartilage (2008)

Cell differentiation, adhesion, and orientation are known to influence the functionality of both natural and engineered tissues, such as articular cartilage. Several attempts have been devised to regulate these important cellular behaviors, including application of inexpensive but efficient electrospinning that can produce patterned extracellular matrix (ECM) features. Electrospun and oriented polycaprolactone (PCL) scaffolds (500 or 3000 nm fiber diameter) were created, and human mesenchymal stem cells (hMSCs) were cultured on these scaffolds. Cell viability, morphology, and orientation on the fibrous scaffolds were quantitatively determined as a function of time. While the fiber-guided initial cell orientation was maintained even after 5 weeks, cells cultured in the chondrogenic media proliferated and differentiated into the chondrogenic lineage, suggesting that cell orientation is controlled by the physical cues and minimally influenced by the soluble factors. Based on assessment by the chondrogenic markers, use of the nanofibrous scaffold (500 nm) appears to enhance the chondrogenic differentiation. These findings indicate that hMSCs seeded on a controllable PCL scaffold may lead to an alternate methodology to mimic the cell and ECM organization that is found, for example, in the superficial zone of articular cartilage.
Combining Immune Checkpoint Inhibitors: Established and Emerging Targets and Strategies to Improve Outcomes in Melanoma (2019)

The immune system employs several checkpoint pathways to regulate responses, maintain homeostasis and prevent self-reactivity and autoimmunity. Tumor cells can hijack these protective mechanisms to enable immune escape, cancer survival and proliferation. Blocking antibodies, designed to interfere with checkpoint molecules CTLA-4 and PD-1/PD-L1 and counteract these immune suppressive mechanisms, have shown significant success in promoting immune responses against cancer and can result in tumor regression in many patients. While inhibitors to CTLA-4 and the PD-1/PD-L1 axis are well-established for the clinical management of melanoma, many patients do not respond or develop resistance to these interventions. Concerted efforts have focused on combinations of approved therapies aiming to further augment positive outcomes and survival. While CTLA-4 and PD-1 are the most-extensively researched targets, results from pre-clinical studies and clinical trials indicate that novel agents, specific for checkpoints such as A2AR, LAG-3, IDO and others, may further contribute to the improvement of patient outcomes, most likely in combinations with anti-CTLA-4 or anti-PD-1 blockade. This review discusses the rationale for, and results to date of, the development of inhibitory immune checkpoint blockade combination therapies in melanoma. The clinical potential of new pipeline therapeutics, and possible future therapy design and directions that hold promise to significantly improve clinical prognosis compared with monotherapy, are discussed.
Quality Control Guidelines for MIC Susceptibility Testing of Omiganan Pentahydrochloride (MBI 226), a Novel Antimicrobial Peptide (2004)

Antimicrobial cationic peptides are thought to be an important self-defense mechanism against infectious agents for plants, animals, and bacterial species (2).While cationic peptides vary in their mechanisms of action, most are reactive with bacterial cytoplasmic membranes (2).Omiganan pentahydrochloride (formerly MBI 226), a novel topical mammal-derived antimicrobial peptide (sequence: ILRWPWWPWRRK-amide), acts by disrupting the cytoplasmic membranes of both grampositive and -negative bacteria, resulting in depolarization and cell death (D.
Effects of the Signal Transducer and Activator of Transcription 1 (STAT1) Gene on Milk Production Traits in Holstein Dairy Cattle (2006)

A functional candidate gene approach was used to search for genes affecting milk production traits in Holstein dairy cattle. Signal transducer and activator of transcription 1 (STAT1) was chosen because of its involvement in the development of the mammary gland. Using the pooled genomic DNA sequencing approach, we identified a single nucleotide polymorphism. Genomic DNA was extracted from 1,292 sons obtained from the Cooperative Dairy DNA Repository and from 715 blood samples of daughters of 12 bulls obtained from the University of Wisconsin resource population. Daughter yield deviation data for the sons and yield deviation for the daughters were obtained for milk production traits from the USDA Animal Improvement Programs Laboratory. For the Repository population, allele C was associated with significant increases in milk fat and protein percentages. For the University of Wisconsin population, genotypes CC and CT were associated with significant increases in milk, fat, and protein yields. Results from this study are consistent with previous studies on the role of STAT1 in regulating the transcription of genes involved in milk protein synthesis and fat metabolism.
The decarboxylation of 6-methylsalicylic acid by Valsa friesii (1973)

Valsa friesii decarboxylates 6-[ 14 C] methyl-[1,3,5- 14 C] salicylic acid to give m-cresol containing 71–81% of the original radioactivity. This indicates that 6-methylsalicylic acid can function as an efficient precursor of m-cresol.