gebhart/patrepeval huggingface dataset:
Microplate‐based filter paper assay to measure total cellulase activity (2004)

The standard filter paper assay (FPA) published by the International Union of Pure and Applied Chemistry (IUPAC) is widely used to determine total cellulase activity. However, the IUPAC method is not suitable for the parallel analyses of large sample numbers. We describe here a microplate-based method for assaying large sample numbers. To achieve this, we reduced the enzymatic reaction volume to 60 microl from the 1.5 ml used in the IUPAC method. The modified 60-microl format FPA can be carried out in 96-well assay plates. Statistical analyses showed that the cellulase activities of commercial cellulases from Trichoderma reesei and Aspergillus species determined with our 60-microl format FPA were not significantly different from the activities measured with the standard FPA. Our results also indicate that the 60-microl format FPA is quantitative and highly reproducible. Moreover, the addition of excess beta-glucosidase increased the sensitivity of the assay by up to 60%.
Mannose-Binding Lectin-Deficient Mice Display Defective Apoptotic Cell Clearance but No Autoimmune Phenotype (2005)

Mannose-binding lectin (MBL) is a circulating serum protein that is sequestered to sites of inflammation and infection. MBL is a member of the collectin family with structural similarities to the lung collectins and functional similarities to C1q. Both MBL and C1q activate complement; C1q activates the classical pathway and MBL the lectin pathway. Here we demonstrate that MBL binds apoptotic cells in vitro and confirm a role for MBL in clearance of apoptotic cells in vivo. Despite MBL null mice demonstrating defective apoptotic cell clearance they did not develop spontaneous autoimmunity, lymphoproliferation, or germinal center expansion although increased numbers of peritoneal B1 cells were detected. These data demonstrate an important in vivo role for MBL in clearance of dying cells and adds the MBL null animals to the few animals with demonstrable in vivo apoptotic cell clearance defects. Moreover, it demonstrates that failure of apoptotic cell clearance can be dissociated from autoimmunity.
Heritable site‐specific mutagenesis using TALENs in maize (2015)

Transcription activator-like effector nuclease (TALEN) technology has been utilized widely for targeted gene mutagenesis, especially for gene inactivation, in many organisms, including agriculturally important plants such as rice, wheat, tomato and barley. This report describes application of this technology to generate heritable genome modifications in maize. TALENs were employed to generate stable, heritable mutations at the maize glossy2 (gl2) locus. Transgenic lines containing mono- or di-allelic mutations were obtained from the maize genotype Hi-II at a frequency of about 10% (nine mutated events in 91 transgenic events). In addition, three of the novel alleles were tested for function in progeny seedlings, where they were able to confer the glossy phenotype. In a majority of the events, the integrated TALEN T-DNA segregated independently from the new loss of function alleles, producing mutated null-segregant progeny in T1 generation. Our results demonstrate that TALENs are an effective tool for genome mutagenesis in maize, empowering the discovery of gene function and the development of trait improvement.
Deletion of the TbALG3 gene demonstrates site-specific N-glycosylation and N-glycan processing in Trypanosoma brucei (2008)

We recently suggested a novel site-specific N-glycosylation mechanism in Trypanosoma brucei whereby some protein N-glycosylation sites selectively receive Man9GlcNAc2 from Man9GlcNAc2-PP-Dol while others receive Man5GlcNA(2 from Man5GlcNAc2-PP-Dol. In this paper, we test this model by creating procyclic and bloodstream form null mutants of TbALG3, the gene that encodes the alpha-mannosyltransferase that converts Man5GlcNAc2-PP-Dol to Man6GlcNAc2-PP-Dol. The procyclic and bloodstream form TbALG3 null mutants grow with normal kinetics, remain infectious to mice and tsetse flies, respectively, and have normal morphology. However, both forms display aberrant N-glycosylation of their major surface glycoproteins, procylcin, and variant surface glycoprotein, respectively. Specifically, procyclin and variant surface glycoprotein N-glycosylation sites that are modified with Man9GlcNAc2 and processed no further than Man5GlcNAc2 in the wild type are glycosylated less efficiently but processed to complex structures in the mutant. These data confirm our model and refine it by demonstrating that the biantennary glycan transferred from Man5GlcNAc2-PP-Dol is the only route to complex N-glycans in T. brucei and that Man9GlcNAc2-PP-Dol is strictly a precursor for oligomannose structures. The origins of site-specific Man5GlcNAc2 or Man9GlcNAc2 transfer are discussed and an updated model of N-glycosylation in T. brucei is presented.
High-precision spatial localization of mouse vocalizations during social interaction (2017)

Mice display a wide repertoire of vocalizations that varies with age, sex, and context. Especially during courtship, mice emit ultrasonic vocalizations (USVs) of high complexity, whose detailed structure is poorly understood. As animals of both sexes vocalize, the study of social vocalizations requires attributing single USVs to individuals. The state-of-the-art in sound localization for USVs allows spatial localization at centimeter resolution, however, animals interact at closer ranges, involving tactile, snout-snout exploration. Hence, improved algorithms are required to reliably assign USVs. We develop multiple solutions to USV localization, and derive an analytical solution for arbitrary vertical microphone positions. The algorithms are compared on wideband acoustic noise and single mouse vocalizations, and applied to social interactions with optically tracked mouse positions. A novel, (frequency) envelope weighted generalised cross-correlation outperforms classical cross-correlation techniques. It achieves a median error of ~1.4 mm for noise and ~4-8.5 mm for vocalizations. Using this algorithms in combination with a level criterion, we can improve the assignment for interacting mice. We report significant differences in mean USV properties between CBA mice of different sexes during social interaction. Hence, the improved USV attribution to individuals lays the basis for a deeper understanding of social vocalizations, in particular sequences of USVs.
N-formylmethionyl peptides as chemoattractants for leucocytes. (1975)

Leucocytes such as neutrophils are attracted by N-formylmethionine, but not by methionine. Di- and tripeptides containing formylmethionine are strong attractants for both neutrophils and macrophages, whereas the corresponding nonacylated compounds are not chemotactic. The formylated peptides may be related to an incompletely characterized chemotactic material normally produced by bacteria which attract the same animal cells.
Changes in the properties of normal human red blood cells during in vivo aging (2012)

The changes in red blood cells (RBC) as they age and the mechanisms for their eventual removal have been of interest for many years. Proposed age-related changes include dehydration with increased density and decreased size, increased membrane IgG, loss of membrane phospholipid asymmetry, and decreased activity of KCl cotransport. The biotin RBC label allows unambiguous identification of older cells and exploration of their properties as they age. Autologous normal human RBC were labeled ex vivo and, after reinfusion, compared with unlabeled RBC throughout their lifespan. RBC density increased with age, with most of the change in the first weeks. Near the end of their lifespan, RBC had increased surface IgG. However, there was no evidence for elevated external phosphatidylserine (PS) even though older RBC had significantly lower activity of aminophospholipid translocase (APLT). KCl cotransport activity persisted well past the reticulocyte stage, but eventually decreased as the RBC became older. These studies place limitations on the use of density fractionation for the study of older human RBC, and do not support loss of phospholipid asymmetry as a mechanism for human RBC senescence. However, increased levels of IgG were associated with older RBC, and may contribute to their removal from the circulation.
Effect of light on oxygen-induced retinopathy in the mouse. (1994)

In this model of oxygen-induced retinopathy, under the conditions tested, light neither exacerbated the hyperoxia-induced neovascularization nor affected normal retinal vascular development.
Protection against ischemic brain damage by GDNF affecting cell survival and death signals (2003)

Neuroprotective effects of glial cell line-derived neurotrophic factor (GDNF) on cell survival and death signals were investigated after 90 min of transient middle cerebral artery occlusion (MCAO) in rats. Immunoreactivities of phosphorylated Akt (p-Akt), cleaved caspase-9 (c-cas9), and -3 (c-cas3) increased after the reperfusion in the penumbra in vehicle group with peaks at 3 h, 8 h, and 1 day, respectively. Topical application of GDNF (6.8 micrograms/9 microliters) on brain surface potentiated and prolonged p-Akt activation, but suppressed activation of the caspases, and reduced the number of terminal deoxynucleotidyl transferase-mediated dUDP-biotin in situ nick labeling (TUNEL) positive cells. These results suggest that GDNF plays a protective role against ischemic injury by controlling the balance between Akt pathway and caspase cascades.
Exploring cell type-specific internalizing antibodies for targeted delivery of siRNA (2007)

A major challenge to the development of therapeutic small interfering RNAs (siRNAs) is specific and efficient in vivo delivery to target cells. Recent studies suggest that cell type-specific gene silencing in vivo can be achieved by combining siRNAs with cell type-specific affinity ligands such as monoclonal antibodies. The antibody-directed siRNA complex enters target cells through receptor endocytosis and is subsequently released to the cytosol to specifically silence target gene expression through biologically conserved RNA interference (RNAi) pathways. Antibody fragments fused with a small basic nucleic-acid-binding protein and antibody fragment-directed nanoimmunoliposomes are two examples of effective delivery vehicles in vivo. The demonstrated specificity of in vivo gene silencing and the lack of nonspecific immune activation and systemic toxicity encourage further development of therapies based on cell type-specific delivery of siRNA.
Thermal Cycling Enhances the Accumulation of a Temperature-Sensitive Biopolymer in Solid Tumors (2007)

The delivery of anticancer therapeutics to solid tumors remains a critical problem in the treatment of cancer. This study reports a new methodology to target a temperature-responsive macromolecular drug carrier, an elastin-like polypeptide (ELP) to solid tumors. Using a dorsal skin fold window chamber model and intravital laser scanning confocal microscopy, we show that the ELP forms micron-sized aggregates that adhere to the tumor vasculature only when tumors are heated to 41.5 degrees C. Upon return to normothermia, the vascular particles dissolve into the plasma, increasing the vascular concentration, which drives more ELPs across the tumor blood vessel and significantly increases its extravascular accumulation. These observations suggested that thermal cycling of tumors would increase the exposure of tumor cells to ELP drug carriers. We investigated this hypothesis in this study by thermally cycling an implanted tumor in nude mice from body temperature to 41.5 degrees C thrice within 1.5 h, and showed the repeated formation of adherent microparticles of ELP in the heated tumor vasculature in each thermal cycle. These results suggest that thermal cycling of tumors can be repeated multiple times to further increase the accumulation of a thermally responsive polymeric drug carrier in solid tumors over a single heat-cool cycle. More broadly, this study shows a new approach--tumor thermal cycling--to exploit stimuli-responsive polymers in vivo to target the tumor vasculature or extravascular compartment with high specificity.
3D photonic integrated circuits for WDM applications (1999)

The wafer fusion technique for realization of compact waveguide switches, filters and 3D photonic integrated circuits is investigated theoretically and experimentally. Calculations based on the beam propagation method show that very short vertical directional couplers with 40-220 &mu;m coupling lengths and high extinction ratios from 20 to 32 dB can be realized. These extinction ratios can be further improved using a slight asymmetry in waveguide structure. The optical loss at the fused interface was investigated by comparison of the transmission loss in InGaAsP-based ridge-loaded waveguide structures with and without a fused layer near the core region. This reveals an excess loss of 1.1 dB/cm at 1.55 &mu;m wavelength due to the fused interface. Fused straight vertical directional couplers have been fabricated and characterized. Waveguides separated by 0.6 &mu;m gap layer exhibit a coupling length of 62 &mu;m and a switching voltage of about 12 volts. Since GaAs and InP have different material dispersion at 1.55 &mu;m wavelength, a combination of InP and GaAs couplers is used to demonstrate an inherent polarization independent and narrowband filter.
Cloning and expression inEscherichia coli of the gene encoding β‐C‐4‐oxygenase, that converts β‐carotene to the ketocarotenoid canthaxanthin inHaematococcus pluvialis (1995)

In the green alga Haematococcus pluvialis the ketocarotenoid astaxanthin accumulates under stress conditions. Astaxanthin is a red carotenoid pigment which possess antioxidative activity. We have cloned the gene for beta-C-4 oxygenase (beta-carotene ketolase) from the green algae H. pluvialis. The cloning method took advantage of a strain of E. coli which was genetically engineered to produce beta-carotene. An expression cDNA library of H. pluvialis was transfected to cells of this strain and visually screened for brown-red pigmented colonies. One colony out of 100,000 transformants showed color change due to accumulation of canthaxanthin. The cDNA clone in this transformant colony encodes the enzyme beta-C-4 oxygenase that catalyzes the conversion of beta carotene to canthaxanthin via echinenone. This enzyme does not convert zeaxanthin to astaxanthin. It is concluded that in H. pluvialis astaxanthin is synthesized via canthaxanthin and therefore an additional enzyme is predicted, which converts canthaxanthin to astaxanthin.
CD27-CD70 Costimulation Controls T Cell Immunity during Acute and Persistent Cytomegalovirus Infection (2013)

Cytomegaloviruses (CMVs) establish lifelong infections that are controlled in part by CD4(+) and CD8(+) T cells. To promote persistence, CMVs utilize multiple strategies to evade host immunity, including modulation of costimulatory molecules on infected antigen-presenting cells. In humans, CMV-specific memory T cells are characterized by the loss of CD27 expression, which suggests a critical role of the costimulatory receptor-ligand pair CD27-CD70 for the development of CMV-specific T cell immunity. In this study, the in vivo role of CD27-CD70 costimulation during mouse CMV infection was examined. During the acute phase of infection, the magnitudes of CMV-specific CD4(+) and CD8(+) T cell responses were decreased in mice with abrogated CD27-CD70 costimulation. Moreover, the accumulation of inflationary memory T cells during the persistent phase of infection and the ability to undergo secondary expansion required CD27-CD70 interactions. The downmodulation of CD27 expression, however, which occurs gradually and exclusively on inflationary memory T cells, is ligand independent. Furthermore, the IL-2 production in both noninflationary and inflationary CMV-specific T cells was dependent on CD27-CD70 costimulation. Collectively, these results highlight the importance of the CD27-CD70 costimulation pathway for the development of CMV-specific T cell immunity during acute and persistent infection.
Architectures For Focal Plane Image Processing (1989)

Architectures for focal plane image processing are discussed. On-chip image preprocessing for solid-state imagers using analog CCD circuits is described for low, medium, and high density detector arrays. A spatially parallel architecture for low density, high throughput applications is described. For sparse illumination or event detection, a content-addressable architecture is proposed. A new pipelined vector pixel processor architecture for medium density infrared staring focal plane arrays is described. Neighborhood reconstruction during serial readout of high density TV-quality imagers for a pixel processor is considered using delay and analog frame memory techniques. The potential of on-chip read/write analog frame memory for image transformation and frame-to-frame processing is discussed.
K-ras mutations in colorectal cancer: a practice changing discovery. (2009)

Recent insights into the molecular pathogenesis of colorectal cancer have given rise to specific target-directed therapies, including monoclonal antibodies against epidermal growth factor receptor (EGFR) and vascular endothelial growth factor (VEGF). These drugs have been approved as second and third line therapies for metastatic colorectal cancer (mCRC). Activating mutations of the K-Ras family of genes are the most common genetic events in tumorigenesis and have been implicated as a predictive factor in determining response to anti-EGFR drugs in pivotal studies. Phase II and III trials, conducted for investigating the role of K-Ras status on anti-EGFR treatment, revealed that patients with wild-type K-Ras had better clinical response in terms of prolonged median progression-free survival and overall response rates when compared to mutant K-Ras. In contrast, patients with mCRC benefit from anti-VEGF treatment irrespective of K-Ras status. Interestingly, a combination of anti-EGFR and anti-VEGF demonstrates no added value in these patients. The studies concluded that pretreatment testing of K-Ras in patients with mCRC offers valuable information in deciding treatment options. There are several molecular methods for mutation detection that seem practical enough to apply in clinical practice. Further confirmatory prospective studies are needed to evaluate the role of K-Ras mutation detections in tumor metastases, early stage CRC, and method of sampling specimens.
Double-negative acoustic metamaterial (2004)

We show here the existence of acoustic metamaterial, in which both the effective density and bulk modulus are simultaneously negative, in the true and strict sense of an effective medium. Our double-negative acoustic system is an acoustic analogue of Veselago's medium in electromagnetism, and shares many unique consequences, such as negative refractive index. The double negativity in acoustics is derived from low-frequency resonances, as in the case of electromagnetism, but the negative density and modulus are derived from a single resonance structure as distinct from electromagnetism in which the negative permeability and negative permittivity originates from different resonance mechanisms.
A New ADPCM Image Compression Algorithm and the Effect of Fixed-Pattern Sensor Noise (1989)

High speed image compression algorithms that achieve visually lossless quality at low bit-rates are essential elements of many digital imaging systems. In examples such as remote sensing, there is often the additional requirement that the compression hardware be compact and consume minimal power. To meet these requirements a new adaptive differential pulse code modulation (ADPCM) algorithm was developed that significantly reduces edge errors by including quantizers that adapt to the local bias of the differential signal. In addition, to reduce the average bit-rate in certain applications a variable rate version of the algorithm called run adaptive differential coding (RADC) was developed that combines run-length and predictive coding and a variable number of levels in each quantizer to produce bit-rates comparable with adaptive discrete cosine transform (ADCT) at a visually lossless level of image quality. It will also be shown that this algorithm is relatively insensitive to fixed-pattern sensor noise and errors in sensor correction, making it possible to perform pixel correction on the decompressed image.
N-Cinnamoylated Chloroquine Analogues as Dual-Stage Antimalarial Leads (2012)

The control of malaria is challenged by drug resistance, and new antimalarial drugs are needed. New drug discovery efforts include consideration of hybrid compounds as potential multitarget antimalarials. Previous work from our group has demonstrated that hybrid structures resulting from cinnamic acid conjugation with heterocyclic moieties from well-known antimalarials present improved antimalarial activity. Now, we report the synthesis and SAR analysis of an expanded series of cinnamic acid derivatives displaying remarkably high activities against both blood- and liver-stage malaria parasites. Two compounds judged most promising, based on their in vitro activity and druglikeness according to the Lipinski rules and Veber filter, were active in vivo against blood-stage rodent malaria parasites. Therefore, the compounds reported represent a new entry as promising dual-stage antimalarial leads.
Cell-Penetrating Quantum Dots Based on Multivalent and Endosome-Disrupting Surface Coatings (2007)

We report the development of cell-penetrating quantum dots (QDs) based on the use of multivalent and endosome-disrupting (endosomolytic) surface coatings. Hyperbranched copolymer ligands such as polyethylene glycol (PEG) grafted polyethylenimine (PEI-g-PEG) are found to encapsulate and solubilize luminescent quantum dots through direct ligand-exchange reactions. Because of the positive charges and a "proton sponge effect" associated with multivalent amine groups, this class of ligand-exchanged QDs is able to penetrate cell membranes and is also able to disrupt endosomal organelles in living cells. The grafted PEG segment is essential for reducing the cytotoxicity of PEI as well as for improving the overall nanoparticle stability and biocompatibility. In comparison with previous QDs encapsulated with amphiphilic polymers, the cell-penetrating QDs are smaller in size and are considerably more stable in acidic environments. Cellular uptake and imaging studies reveal that the number of PEG grafts per PEI molecule has a pronounced effect on the intracellular pathways of internalized QDs. In particular, QDs coated with PEI-g-PEG2 are rapidly internalized by endocytosis, and are initially stored in vesicles, followed by slow endosomal escape and release into the cytoplasm. These insights are important toward the design and development of nanoparticle agents for intracellular imaging and therapeutic applications.
Mammalian Cell Culture Simplified (1991)

Research Article| May 01 1991 Mammalian Cell Culture Simplified Robert Moss, Robert Moss Search for other works by this author on: This Site PubMed Google Scholar Sondra Solomon Sondra Solomon Search for other works by this author on: This Site PubMed Google Scholar The American Biology Teacher (1991) 53 (5): 287–289. https://doi.org/10.2307/4449295 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Tools Icon Tools Get Permissions Cite Icon Cite Search Site Citation Robert Moss, Sondra Solomon; Mammalian Cell Culture Simplified. The American Biology Teacher 1 May 1991; 53 (5): 287–289. doi: https://doi.org/10.2307/4449295 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentThe American Biology Teacher Search Copyright 1990 National Association of Biology Teachers Article PDF first page preview Close Modal You do not currently have access to this content.