gebhart/patrepeval huggingface dataset:
Characterization of the bipartite degron that regulates ubiquitin-independent degradation of thymidylate synthase (2012)

TS (thymidylate synthase) is a key enzyme in the de novo biosynthesis of dTMP, and is indispensable for DNA replication. Previous studies have shown that intracellular degradation of the human enzyme [hTS (human thymidylate synthase)] is mediated by the 26S proteasome, and occurs in a ubiquitin-independent manner. Degradation of hTS is governed by a degron that is located at the polypeptide's N-terminus that is capable of promoting the destabilization of heterologous proteins to which it is attached. The hTS degron is bipartite, consisting of two subdomains: an IDR (intrinsically disordered region) that is highly divergent among mammalian species, followed by a conserved amphipathic α-helix (designated hA). In the present report, we have characterized the structure and function of the hTS degron in more detail. We have conducted a bioinformatic analysis of interspecies sequence variation exhibited by the IDR, and find that its hypervariability is not due to diversifying (or positive) selection; rather, it has been subjected to purifying (or negative) selection, although the intensity of such selection is relaxed or weakened compared with that exerted on the rest of the molecule. In addition, we have verified that both subdomains of the hTS degron are required for full activity. Furthermore, their co-operation does not necessitate that they are juxtaposed, but is maintained when they are physically separated. Finally, we have identified a 'cryptic' degron at the C-terminus of hTS, which is activated by the N-terminal degron and appears to function only under certain circumstances; its role in TS metabolism is not known.
Video staging: a proxy-server-based approach to end-to-end video delivery over wide-area networks (2000)

Real-time distribution of stored video over wide-area networks (WANs) is a crucial component of many emerging distributed multimedia applications. The heterogeneity in the underlying network environments is an important factor that must be taken into consideration when designing an end-to-end video delivery system. We present a novel approach to the problem of end-to-end video delivery over WANs using proxy servers situated between local-area networks (LANs) and a backbone WAN. A major objective of our approach is to reduce the backbone WAN bandwidth requirement. Toward this end, we develop an effective video delivery technique called video staging via intelligent utilization of the disk bandwidth and storage space available at proxy servers. Using this video staging technique, only part of a video stream is retrieved directly from the central video server across the backbone WAN whereas the rest of the video stream is delivered to users locally from proxy servers attached to the LANs. In this manner, the WAN bandwidth requirement can be significantly reduced, particularly when a large number of users from the same LAN access the video data. We design several video staging methods and evaluate their effectiveness in trading the disk bandwidth of a proxy server for the backbone WAN bandwidth. We also develop two heuristic algorithms to solve the problem of designing a multiple video staging scheme for a proxy server with a given video access profile of a LAN. Our results demonstrate that the proposed proxy-server-based approach provides an effective and scalable solution to the problem of the end-to-end video delivery over WANs.
METABOLIC ENGINEERING OF SACCHAROMYCES CEREVISIAE FOR THE PRODUCTION OF BENZYLISOQUINOLINE ALKALOIDS (2009)

The completion of this thesis work was a long and arduous journey which has consumed the past five years of my life and I have many people to thank. First I would like to thank my research advisor Christina Smolke for taking me on as one of her first students. When I started in the lab, I did not even know how to use a pipette or basic principles of molecular biology. Christina gave us our first lessons in cloning but later allowed us the freedom to direct much of our own research work. I also have to thank my colleagues in the lab that have become some of my best friends. In particular, Stephanie Culler is an amazing scientist and one of the most genuine people I have ever met. Her work ethic is unparalleled and she has kept me company during many late nights and weekends. I also have to acknowledge Dr. Kevin Hoff who has always taken the time to dwell on others ’ research problems, and more often than not, come up with some valuable suggestions if not solutions. Chase Beisel is another lab member who is always willing to lend an ear, and it has been a pleasure getting to know both him and his lovely wife Amy. Finally, I have to thank Michael Siddiqui for being brave enough to take on this challenging project so that my work
Group Epitope Mapping by Saturation Transfer Difference NMR To Identify Segments of a Ligand in Direct Contact with a Protein Receptor (2001)

A protocol based on saturation transfer difference (STD) NMR spectra was developed to characterize the binding interactions at an atom level, termed group epitope mapping (GEM). As an example we chose the well-studied system of galactose binding to the 120-kDa lectin Ricinus communis agglutinin I (RCA(120)). As ligands we used methyl beta-D-galactoside and a biantennary decasaccharide. Analysis of the saturation transfer effects of methyl beta-D-galactoside showed that the H2, H3, and H4 protons are saturated to the highest degree, giving evidence of their close proximity to protons of the RCA(120) lectin. The direct interaction of the lectin with this region of the galactose is in excellent agreement with results obtained from the analysis of the binding specificities of many chemically modified galactose derivatives (Bhattacharyya, L.; Brewer, C. F. Eur. J. Biochem. 1988, 176, 207-212). This new NMR technique can identify the binding epitope of even complex ligands very quickly, which is a great improvement over time-consuming chemical modifications. Efficient GEM benefits from a relatively high off rate of the ligand and a large excess of the ligand over the receptor. Even for a ligand like the biantennary decasaccharide with micromolar binding affinity, the binding epitopes could easily be mapped to the terminal beta-D-Gal-(1-4)-beta-D-GlcNAc (beta-D-GlcNAc = N-acetyl-D-glucosamine) residues located at the nonreducing end of the two carbohydrate chains. The binding contribution of the terminal galactose residue is stronger than those of the penultimate GlcNAc residues. We could show that the GlcNAc residues bind "edge-on" with the region from H2 to H4, making contact with the protein. Analysis of STD NMR experiments performed under competitive conditions proved that the two saccharides studied bind at the same receptor site, thereby ruling out unspecific binding.
A Study to Evaluate Safety and Efficacy of Mepolizumab in Patients with Moderate Persistent Asthma (2007)

Mepolizumab treatment does not appear to add significant clinical benefit in patients with asthma with persistent symptoms despite inhaled corticosteroid therapy. Further studies are needed to investigate the effect of mepolizumab on exacerbation rates, using protocols specifically tailored to patients with asthma with persistent airway eosinophilia.
Preparation and characterization of rubber-clay nanocomposites (2000)

Rubber–clay nanocomposites were prepared by two different methods and characterized with TEM and XRD. The TEM showed clay had been dispersed to one or several layers. The XRD showed that the basal spacing in the clay was increased. It was evident that some macromolecules intercalated to the clay layer galleries. The clay layer could be uniformly dispersed in the rubber matrix on the nanometer level. The mechanical tests showed that the nanocomposites had good mechanical properties. Some properties exceeded those of rubber reinforced with carbon black, so the clay layers could be used as an important reinforcing agent as the carbon black was. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 78: 1879–1883, 2000
IRK(1–3) and GIRK(1–4) Inwardly Rectifying K+Channel mRNAs Are Differentially Expressed in the Adult Rat Brain (1996)

Molecular cloning together with functional characterization has shown that the newly identified family of inwardly rectifying K+ channels consists of several closely related members encoded by separate genes. In this report we demonstrate the differential mRNA expression and detailed cellular localization in the adult rat brain of seven members of the IRK and GIRK subfamilies. Using both radiolabeled cRNA riboprobes and specific oligonucleotide probes directed to nonconserved regions of both known and newly isolated rat brain cDNAs, in situ hybridization revealed wide distribution with partly overlapping expression of the mRNAs of IRK1-3 and GIRK1-4. Except for the low levels of GIRK4 transcripts observed, the overall distribution patterns of the other GIRK subunits were rather similar, with high levels of expression in the olfactory bulb, hippocampus, cortex, thalamus, and cerebellum. Marked differences in expression levels existed only in some thalamic, brainstem, and midbrain nuclei, e.g., the substantial nigra, superior colliculus, or inferior olive. In contrast, IRK subunits were expressed more differentially: all mRNAs were abundant in dentate gyrus, olfactory bulb, caudate putamen, and piriform cortex. IRK1 and IRK3 were restricted to these regions, but they were absent from most parts of the thalamus, cerebellum, and brainstem, where IRK2 was expressed predominantly. Because channel subunits may assemble as heteromultimers, additional functional characterization based on overlapping expression patterns may help to decipher the native K+ channels in neurons and glial cells.
Monodansylcadaverine (MDC) is a specific in vivo marker for autophagic vacuoles. (1995)

We report the use of the autofluorescent compound monodansylcadaverine (MDC) for in vivo labeling of autophagic vacuoles. When applied to various cell types (PaTu 8902, MDCK I, PC12, AR4-2J, WI-38) in culture, spherical structures were observed by fluorescence microscopy, predominantly located in the perinuclear region. Only PC12 and WI-38 cells had some of these labeled structures in their filopodiae. Dose-response experiments with PaTu 8902 showed that the optimal concentration for in vivo labeling was 0.05 to 0.1 mM, while cells detached and disintegrated, when MDC concentration exceeded 0.1 mM. After incubation with MDC and subcellular fractionations of PaTu 8902 cells on sucrose density gradients, a narrow fluorescence peak at 20 to 26% sucrose concentration equal to densities of about 1.081 to 1.108 g/cm3 was observed. Ultrastructural analysis of these fractions revealed autophagic vacuoles in different stages of their development. To investigate whether endosomal compartments were also labeled by MDC, we coincubated PaTu 8902 cells with MDC and the fluid-phase markers, RITC-dextran and ferritin, respectively. Fluorescence measurements after subcellular fractionations as well as fine structural analysis indicated that MDC-labeled autophagic vacuoles did not contain fluid-phase markers and were spatially separated from endosomal compartments. We further could demonstrate, after subcellular fractionation procedures, that MDC-labeled organelles contained the lysosomal enzymes acid phosphatase and the mature form of cathepsin D. Membrane markers of rough endoplasmic reticulum (TRAM and sec61 beta), and for smooth endoplasmic reticulum (cytochrome P450) were not detected in the same fractions. These results indicate that MDC accumulates as a selective fluorescent marker for autophagic vacuoles under in vivo conditions and is not present in the early and late endosome.
Absence of the DNA-/RNA-binding protein MSY2 results in male and female infertility (2005)

MSY2, a germ-cell-specific member of the Y-box family of DNA-/RNA-binding proteins, is proposed to function as a coactivator of transcription in the nucleus and to stabilize and store maternal and paternal mRNAs in the cytoplasm. In mice lacking Msy2, a normal Mendelian ratio is observed after matings between heterozygotes with equal numbers of phenotypically normal but sterile male and female homozygotes (Msy2-/-). Spermatogenesis is disrupted in postmeiotic null germ cells with many misshapen and multinucleated spermatids, and no spermatozoa are detected in the epididymis. Apoptosis is increased in the testes of homozygotes, and real-time RT-PCR assays reveal large reductions in the mRNA levels of postmeiotic male germ cell mRNAs and smaller reductions of meiotic germ cell transcripts. In females, there is no apparent decrease in either the number of follicles or their morphology in ovaries obtained from 2- and 8-day-old Msy2-/- mice. In contrast, follicle number and progression are reduced in 21-day-old Msy2-/- ovaries. In adult Msy2-/- females, oocyte loss increases, anovulation is observed, and multiple oocyte and follicle defects are seen. Thus, Msy2 represents one of a small number of germ-cell-specific genes whose deletion leads to the disruption of both spermatogenesis and oogenesis.
Characterization of a cell division gene from Bacillus subtilis that is required for vegetative and sporulation septum formation (1994)

We report the cloning and characterization of a cell division gene, herein designated divIC, from the gram-positive, spore-forming bacterium Bacillus subtilis. This gene was previously identified on the basis of a temperature-sensitive mutation, div-355, that blocks septum formation at restrictive temperatures. We show that the divIC gene is a 125-codon open reading frame that is capable of encoding a protein of 14.7 kDa and that div-355 is a 5-bp duplication near the 3' end of the open reading frame. We also show that divIC is an essential gene by use of an in vitro-constructed null mutation. In confirmation and extension of earlier results, we show that divIC is necessary for both vegetative and sporulation septum formation, and we demonstrate that it is required for the activation of genes expressed under the control of the sporulation transcription factors sigma F and sigma E. The divIC gene is located 1.3 kb upstream of the coding sequence for the sporulation gene spoIIE. Between divIC and spoIIE is a 128-codon open reading frame whose predicted product contains a region of similarity to the RNA-binding domains of polynucleotide phosphorylase and ribosomal protein S1 from Escherichia coli and two putative tRNA genes for methionyl-tRNA and glutamyl-tRNA, the gene order being divIC orf128 tRNA(Met) tRNA(Glu) spoIIE.
The Human myc Gene Family (1986)

The myc family of cellular oncogenes contains three well-defined members, c-myc, N-myc, and L-myc. The first-identified and most thoroughly studied member of this family, c-myc, was identified as the cellular homolog to the transforming gene of an avian retrovirus. The c-myc gene encodes a nuclear protein that appears to be involved in the growth and division of a wide variety of normal cells, and deregulated expression of the c-myc gene has been implicated as contributory to the development of numerous classes of tumors. Such deregulated expression occurs by a number of mechanisms, including viral transduction, promoter (enhancer) insertion, translocation, and gene amplification (for review, see Varmus 1984). Although the precise function of the c-myc gene has not been elucidated, it is generally thought that the c-myc protein mediates a signal associated with cell division and, thus, regulation of its expression is required for normal cell growth.
<title>End-stopped wavelets for detecting low-level features</title> (1999)

In this paper, we present two filters that simulate the behavior of biological end-stopped cells. Both are zero-mean filters, and are well located in the spatial as well as frequency domains, that is, these filters are admissible wavelets. We refer to the two filters as ES1 and ES2. The ES1 filter responds to ends of linear structures which have a specific orientation, and the ES2 filter responds to line- segments which have a specific orientation, and which have a length within a specific range. We show sample results to demonstrate the behavior of the proposed wavelets, and we also discuss the scale-space behavior of these wavelets briefly.
Sequence-Selective Recognition of DNA by Strand Displacement with a Thymine-Substituted Polyamide (1991)

A polyamide nucleic acid (PNA) was designed by detaching the deoxyribose phosphate backbone of DNA in a computer model and replacing it with an achiral polyamide backbone. On the basis of this model, oligomers consisting of thymine-linked aminoethylglycyl units were prepared. These oligomers recognize their complementary target in double-stranded DNA by strand displacement. The displacement is made possible by the extraordinarily high stability of the PNA-DNA hybrids. The results show that the backbone of DNA can be replaced by a polyamide, with the resulting oligomer retaining base-specific hybridization.
The furan counterpart of poly(ethylene terephthalate): An alternative material based on renewable resources (2008)

Polytransesterification reaction carried out to obtain a high-molecular weight poly(ethylene 2,5-furandicarboxilate) with a regular structure and high degree of crystallinity.
Immobilization of a Catalytic DNA Molecular Beacon on Au for Pb(II) Detection (2004)

A Pb(II)-specific DNAzyme fluorescent sensor has been modified with a thiol moiety in order to immobilize it on a Au surface. Self-assembly of the DNAzyme is accomplished by first adsorbing the single-thiolated enzyme strand (HS-17E-Dy) followed by adsorption of mercaptohexanol, which serves to displace any Au-N interactions and ensure that DNA is bound only through the S-headgroup. The preformed self-assembled monolayer is then hybridized with the complementary fluorophore-containing substrate strand (17DS-Fl). Upon reaction with Pb(II), the substrate strand is cleaved, releasing a fluorescent fragment for detection. Fluorescence intensity may be correlated with original Pb(II) concentration, and a linear calibration was obtained over nearly four decades: 10 microM > or = [Pb(II)] > or = 1 nM. The immobilized DNAzyme is a robust system; it may be regenerated after cleavage, allowing multiple sensing cycles. In addition, drying of fully assembled DNAzyme before reaction with Pb(II) does not significantly affect analytical performance. These results demonstrate that, in comparison with solution-based schemes, immobilization of the DNAzyme sensor onto a Au surface lowers the detection limit (from 10 to 1 nM), maintains activity and specificity, and allows sensor regeneration and long-term storage. Realization of Pb(II) detection through an immobilized DNAzyme is the first important step toward creation of a stand-alone, portable Pb(II) detection device such as those immobilizing DNAzyme recognition motifs in the nanofluidic pores of a microfluidic-nanofluidic hybrid multilayer device.
Regulation of the Human TNF Promoter by the Transcription Factor Ets (1995)

Tumor necrosis factor (TNF) affects the growth, differentiation, and function of a multitude of cell types and is viewed as a potent mediator of inflammation and cellular immune responses. In order to delineate functional domains that control TNF gene transcription, we have analyzed a 5' flanking region of the human TNF promoter spanning base pairs -115 to -98. This region contains a PEA3/Ets-1 binding motif 5' GAGGA 3' in direct juxtaposition to an AP-1/ATF-like palindromic sequence motif 5' TGAGCTCA 3'. Specific binding of Ets and Jun to their respective elements is demonstrated by competition analysis as well as by supershift assays. As shown by promoter deletion analysis, these two binding sites were essential for both basal promoter activity and responsiveness to the phorbol ester phorbol 12-myristate 13-acetate. Co-transfection of c-ets or c-jun expression plasmids along with TNF promoter-CAT reporter constructs revealed the participation of both transcription factors in the regulation of TNF gene transcription. Correspondingly, site-specific mutation of either Ets or Jun sites led to a complete loss of responsiveness to the respective transcription factor. These data suggest an essential role of Ets for the activation of TNF gene transcription.
Interference Phenomena in Waveguides with Two Corrugated Boundaries (1989)

Abstract Waveguide structures with two corrugated interfaces are considered. It is shown theoretically and experimentally that these structures can form the basis for a highly-efficient unidirectional grating coupler for slab waveguides. The anomalous light reflection from waveguides with two corrugated boundaries is also considered. The possibility of using corrugated waveguides for frequency stabilization of a semiconductor laser is demonstrated.
Preparation and properties of esters of polyorthotitanic acid (1951)

Abstract In studies of the synthesis of alkyl titanates from anhydrous butyl alcohol and titanium tetrachloride employing ammonia or an amine to neutralize the hydrogen chloride formed, Speer has reported uniformly unsuccessful results in repeating the examples of Nelles' patents on this process. Kraitzer, Winter, and others followed Nelles' process successfully employing a large excess of anhydrous butyl alcohol. Repetition of Nelles' patent examples is awkward because the ammonium chloride formed in the reaction produces a thick slurry too inconvenient to handle. However, if this slurry was diluted or extracted with an anhydrous hydrocarbon solvent, i.e., toluene, yields of 80% were achieved. Furthermore, since it is difficult to obtain rigorously anhydrous alcohols, it is more convenient to carry out the synthesis of alkyl titanates using an inert anhydrous solvent, i.e., toluene or carbon tetrachloride, as a reaction medium along with the stoichiometric quantity of alcohol instead of using a large excess of the alcohol as the reaction medium. The formation of nonvolatile residues was avoided. If the proper quantity of water dissolved in a low‐boiling alcohol is added slowly with stirring to a solution of the corresponding ester of orthotitanic acid, it is possible to obtain esters of polyorthotitanic acid of controlled average molecular weight. If less than 1 mole of water per mole of orthotitanate esters is employed, the amount of cross‐linked polymer derived is vanishingly little. When the butylorthotitanate was treated with 1.5–2.25 moles of water per mole of titanium, 1.4–1.5 moles of water were consumed per mole of titanium. Water was recovered from the system. Water in excess of 2.25‐3 moles of water per mole of titanium caused complete conversion of butylorthotitanate to titanium dioxide. The polyorthotitanates were soluble in benzene, toluene, and butyl alcohol. The uncross‐linked polymers vary in appearance from very viscous liquids to waxy solids. The polyorthotitanates enter into ester interchange reactions with alcohols in which one to all of the lower boiling alkyl groups may be replaced by the higher one. Long‐chain organic acids react with the alkyl polyorthotitanates or the alkyl titanates to replace one to all of the alkyl groups.