gebhart/patrepeval huggingface dataset:
Preparative two‐dimensional gel electrophoresis of membrane proteins (1997)

Electrophoretic techniques, and especially two-dimensional gel electrophoresis (2-DE), have provided an indispensable set of tools for the separation of complex protein mixtures as well as for the identification of protein-protein interactions. Nevertheless, after its introduction more than twenty years ago and even with recent technical developments, the separation of integral and peripheral membrane proteins, in amounts sufficient for microsequencing, is still a difficult task. Lipids present in the membrane as well as the low solubility of hydrophobic membrane proteins result in protein aggregation both on the sample application point and on isoelectric focusing. As a consequence many proteins do not enter the first or second dimension of 2-DE. Here we describe the modification of a protocol using a combination of 3-[(3-cholamidopropyl)-dimethylammonio]-1-propane sulfonate (CHAPS), chaotropic agents (thiourea, urea), Tris base and reducing agents (1,4-dithioerythritol) to improve solubilization of integral and peripheral membrane proteins. Preparative amounts of membrane proteins (up to 2 mg) were loaded during reswelling of dry immobilized pH gradients and the resulting Coomassie staining patterns were largely superimposable with silver-stained gels obtained from identical samples (4 microg). This indicates that the recovery of proteins from the sample is not significantly compromised by the scale-up procedure. A direct application of this method for the characterization and identification of membrane proteins from cellular organelles is described in another paper in this issue (I. Fialka et al., Electrophoresis 1997, 18, 2582-2590).
Influence of Lipid-Bilayer-Associated Molecules on Lipid-Vesicle Adsorption (2009)

Supported lipid bilayers (SLBs) containing different types of bilayer-associated molecules (membrane-bound molecules) where one part of the molecule resides inside the lipid bilayer and another part of the molecule sticks out of the bilayer (e.g., membrane proteins) are important biophysical model systems. SLBs are commonly formed via lipid vesicle adsorption on certain surfaces (e.g., SiO(2)). However, vesicles doped with different types of (bio)molecules often do not form an SLB on the surface, and the reasons for this are not clear. Using a newly developed model of a lipid bilayer, simulations were performed to clarify the influence of the bilayer-associated molecules on vesicle adsorption and rupture. It is shown that by increasing the concentration of membrane-bound molecules in the vesicles the tendency for vesicle rupture decreases markedly and for a certain concentration rupture does not happen. The reason for this is that vesicles containing significant concentrations of such molecules tend to deform less on the surface (lower vesicle strain), especially for a significantly corrugated bilayer-surface potential. After vesicle rupture, membrane-bound molecules face either the surface or the solution in the resulting bilayer patch on the surface, depending on whether the molecules point outward or inward in the original vesicle, respectively. Vesicle surface diffusion is also studied for weak and strong surface corrugation, where vesicles are found to be almost immobile in the latter case.
Absorption of Flavonols Derived from Sea Buckthorn (Hippophaë rhamnoides L.) and Their Effect on Emerging Risk Factors for Cardiovascular Disease in Humans (2006)

Sea buckthorn (Hippophaë rhamnoides L.) is a rich source of flavonols, especially isorhamnetin. Most prospective cohort studies have indicated some degree of inverse association between flavonoid intake and coronary heart disease. Animal and human studies suggest that sea buckthorn flavonoids may scavenge free radicals, lower blood viscosity, and enhance cardiac function. The effects of flavonol aglycones derived from sea buckthorn on the risk factors of cardiovascular disease as well as their absorption were studied in humans. The flavonols, ingested with oatmeal porridge, did not have a significant effect on the levels of oxidized low-density lipoprotein, C-reactive protein, and homocysteine, on the plasma antioxidant potential, or on the paraoxonase activity. Flavonols at two dosages in oatmeal porridge were rapidly absorbed, and a relatively small amount of sea buckthorn oil added to the porridge seemed to have increased the bioavailability of sea buckthorn flavonols consumed at the higher dose.
An O -fucose site in the ligand binding domain inhibits Notch activation (2003)

Two glycosyltransferases that transfer sugars to EGF domains, OFUT1 and Fringe, regulate Notch signaling. However, sites of O-fucosylation on Notch that influence Notch activation have not been previously identified. Moreover, the influences of OFUT1 and Fringe on Notch activation can be positive or negative, depending on their levels of expression and on whether Delta or Serrate is signaling to Notch. Here, we describe the consequences of eliminating individual, highly conserved sites of O-fucose attachment to Notch. Our results indicate that glycosylation of an EGF domain proposed to be essential for ligand binding, EGF12, is crucial to the inhibition of Serrate-to-Notch signaling by Fringe. Expression of an EGF12 mutant of Notch (N-EGF12f) allows Notch activation by Serrate even in the presence of Fringe. By contrast, elimination of three other highly conserved sites of O-fucosylation does not have detectable effects. Binding assays with a soluble Notch extracellular domain fusion protein and ligand-expressing cells indicate that the NEGF12f mutation can influence Notch activation by preventing Fringe from blocking Notch-Serrate binding. The N-EGF12f mutant can substitute for endogenous Notch during embryonic neurogenesis, but not at the dorsoventral boundary of the wing. Thus, inhibition of Notch-Serrate binding by O-fucosylation of EGF12 might be needed in certain contexts to allow efficient Notch signaling.
Outbreak of Adenovirus 35 Pneumonia among Adult Residents and Staff of a Chronic Care Psychiatric Facility (1997)

Outbreaks of acute respiratory disease caused by adenovirus are rarely documented in civilian populations, and adenovirus 35 is an uncommon serotype best recognized as a cause of serious disease in immunocompromised patients. An outbreak of adenovirus 35 pneumonia among residents and staff of a chronic care psychiatric facility was investigated. Fourteen (26%) of 53 residents and 4 (2%) of approximately 200 staff had radiographically confirmed pneumonia. Thirteen (93%) of 14 residents with pneumonia were hospitalized, 5 (36%) required mechanical ventilation, and 1 (7%) died. One staff member was hospitalized. Adenovirus infection was diagnosed in 17 (94%) persons with pneumonia by culture or serology and was confirmed as adenovirus 35 infection in 8 persons. Residents with pneumonia had resided at the facility longer than other residents. Chronic illness was not a risk factor for severe disease. Crowding and poor hygienic behaviors probably facilitated transmission among residents.
Studies on regulatory functions of malic enzymes. VI. Purification and molecular properties of NADP-linked malic enzyme from Escherichia coli W. (1979)

NADP-linked malic enzyme [EC 1.1.1.40] was highly purified from Escherichia coli W cells. The purified enzyme was homogeneous as judged by ultracentrifugation and gel electrophoresis. The apparent molecular weights obtained by sedimentation equilibrium analysis, from diffusion and sedimentation constants, and by disc electrophoresis at various gel concentrations were 471,000, 438,000, and 495,000, respectively. The subunit molecular weights obtained by sedimentation equilibrium analysis in the presence of 6 M guanidine hydrochloride and gel electrophoresis in the presence of sodium dodecyl sulfate were 76,000 and 82,000, respectively. The sedimentation coefficient (S(0)20, W) was 13.8S, and the molecular activity was 44,700 min-1 at 30 degrees C. The amino acid composition of the enzyme was determined, and the results were compared with those of NAD-linked malic enzyme from the same organism and those of pigeon liver NADP-linked malic enzyme. The partial specific volume was calculated to be 0.738 ml/g. The Km value for L-malate was 2.3 mM at pH 7.4. Malonate, tartronate, glutarate, and DL-tartrate competitively inhibited the activity. The saturation profile for L-malate exhibited a marked cooperativity in the presence of both chloride ions and acetyl-CoA. However, acetyl-CoA alone did not show cooperativity or produce inhibition in the absence of chloride ions. Vmax and Km were determined as a function of pH. The optimum pH for the reaction was 7.8. Inspection of the Dixon plots suggested that three ionizable groups of the enzyme are essential for the enzyme activity. In addition to the oxidative decarboxylase activity, the enzyme preparation exhibited divalent metal ion-dependent oxaloacetate decarboxylase and alpha-keto acid reductase activities. Based on the above results, the molecular properties of the enzymatic reaction are discussed.
Targeted Exon Skipping in Transgenic hDMD Mice: A Model for Direct Preclinical Screening of Human-Specific Antisense Oligonucleotides (2004)

The therapeutic potential of frame-restoring exon skipping by antisense oligonucleotides (AONs) has recently been demonstrated in cultured muscle cells from a series of Duchenne muscular dystrophy (DMD) patients. To facilitate clinical application, in vivo studies in animal models are required to develop safe and efficient AON-delivery methods. However, since exon skipping is a sequence-specific therapy, it is desirable to target the human DMD gene directly. We therefore set up human sequence-specific exon skipping in transgenic mice carrying the full-size human gene (hDMD). We initially compared the efficiency and toxicity of intramuscular AON injections using different delivery reagents in wild-type mice. At a dose of 3.6 nmol AON and using polyethylenimine, the skipping levels accumulated up to 3% in the second week postinjection and lasted for 4 weeks. We observed a correlation of this long-term effect with the intramuscular persistence of the AON. In regenerating myofibers higher efficiencies (up to 9%) could be obtained. Finally, using the optimized protocols in hDMD mice, we were able to induce the specific skipping of human DMD exons without affecting the endogenous mouse gene. These data highlight the high sequence specificity of this therapy and present the hDMD mouse as a unique model to optimize human-specific exon skipping in vivo.
Quantitative tissue sodium concentration mapping of the growth of focal cerebral tumors with sodium magnetic resonance imaging (1999)

Tissue sodium concentration (TSC), as determined by in vivo 23Na magnetic resonance imaging (MRI) and the ex vivo classical 22Na radionuclide dilution assay (RDA), has been compared in a rat model of a focal glioma. The 23Na MRI method used a three-dimensional, twisted projection acquisition scheme at short echo time to minimize signal losses from relaxation of transverse magnetization. Calibration standards within the field of view allowed quantification of the sodium signal in terms of a TSC after correction for B1 nonuniformity and tissue water concentration. The 23Na MRI method measured focally increased TSC values in tumors that were equivalent statistically to the destructive 22Na RDA method. The noninvasive 23Na MRI method provided a quantitative means with which to monitor focal brain tumor growth.
Photoelectrochemical Properties of Nanostructured Tungsten Trioxide Films (2001)

The photoelectrochemical characteristics of highly transparent nanoporous WO3 films are described. The photocurrent versus excitation wavelength spectra of these photoelectrodes exhibit a maximum close to 400 nm and a significant photoresponse to the blue part of the visible spectrum. The observed conversion efficiencies attain 75% for the photogeneration of oxygen from 1 M aq HClO4 and reach 190% in the presence of methanol in the solution, denoting in the latter case the occurrence of a perfect photocurrent doubling. Experiments conducted under simulated solar AM 1.5 illumination resulted in steady-state anodic photocurrents of the order of several mA/cm2.
The wavelength dependence of pulse oximetry (1996)

Although the `AC/DC' ratios (except in transmission below 600nm) have the same basic form as the HbO, spectra (as would be expected from pulse oximeter theory since the arterial blood in a healthy subject is mainly HbO,) the quantitative agreement, using simple models, is very poor. In addition, although the graphs above 600 nm in reflection and transmission modes are similar they are clearly not the same, demonstrating that there is indeed a difference between the 2 modes of operation. It is interesting to note that the ratios of the `AC/DC' ratios at 660 nm and 940 nm (at which many commercial devices operate) are very similar (approximately 0.5) in both reflection and transmission modes. This means that using the same pulse oximeter with either reflection or transmission probes will produce reliable results. However, if wavelengths other than 660 and 940 nm were employed the authors' figure suggests that this would not longer be so. A further finding of significance to the operation of commercial pulse oximeters was that the `AC' signal in reflection mode was at its lowest, and prone to noise, at 660 nm. Consequently, the worst `red' wavelength to use in a reflection pulse oximeter would be 660 nm. Finally, these results demonstrate that it is possible to produce `AC/DC' ratios below 600 nm, that is in the visible part of the spectrum which has been largely ignored for pulse oximetry. Although the high absorption of light by blood in this part of the spectrum may cause some problems it is clear that pulse oximeters operating in the visible could be constructed. Potential advantages are that: the actual `AC/DC' ratios are larger; there is more `structure' to the absorption spectra of HbO, which could be used for verification of data; and that other haemoglobin compounds also possess distinctive spectra in this region which should allow their presence to be monitored. (3 pages)
Comparison of Adeno-Associated Viral Vector Serotypes for Spinal Cord and Motor Neuron Gene Delivery (2011)

Gene therapy for motor neuron diseases requires efficient gene delivery to motor neurons (MNs) throughout the spinal cord and brainstem. The present study compared adeno-associated viral (AAV) vector serotypes 1, 6, 8, and 9 for spinal cord delivery in adult mice, by the intraparenchymal or intrathecal route of administration. Whereas intraparenchymal injections resulted in local transduction of the lumbar segment of the spinal cord, intrathecal injections led to a broader distribution, transducing cells along the sacral, lumbar, and lower thoracic spinal cord. Overall, AAV6 and AAV9 performed better than the other serotypes. Dramatic differences in cell-specific expression patterns could be observed when constructs bearing the chicken β-actin (Cba) versus cytomegalovirus (CMV) promoter were compared. In summary, intrathecal delivery of AAV6 or AAV9 vectors containing the CMV promoter yielded the strongest levels of biodistribution and MN transduction in the spinal cord.
A genetic locus of enterocyte effacement conserved among diverse enterobacterial pathogens. (1995)

Enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli O157:H7 are intestinal pathogens that profoundly damage the microvilli and subapical cytoskeleton of epithelial cells. Here we report finding in EPEC a 35-kbp locus containing several regions implicated in formation of these lesions. DNA probes throughout this locus hybridize to E. coli O157:H7 and other pathogens of three genera that cause similar lesions but do not hybridize to avirulent members of the same species. The EPEC locus and a different virulence locus of uropathogenic E. coli insert into the E. coli chromosome at the identical site and share highly similar sequences near the point of insertion.
Two-Photon Imaging of Lymphocyte Motility and Antigen Response in Intact Lymph Node (2002)

Lymphocyte motility is vital for trafficking within lymphoid organs and for initiating contact with antigen-presenting cells. Visualization of these processes has previously been limited to in vitro systems. We describe the use of two-photon laser microscopy to image the dynamic behavior of individual living lymphocytes deep within intact lymph nodes. In their native environment, T cells achieved peak velocities of more than 25 micrometers per minute, displaying a motility coefficient that is five to six times that of B cells. Antigenic challenge changed T cell trajectories from random walks to "swarms" and stable clusters. Real-time two-photon imaging reveals lymphocyte behaviors that are fundamental to the initiation of the immune response.
Alipogene tiparvovec, an adeno-associated virus encoding the Ser(447)X variant of the human lipoprotein lipase gene for the treatment of patients with lipoprotein lipase deficiency. (2009)

Amsterdam Molecular Therapeutics BV is developing alipogene tiparvovec (Glybera, AMT-011, AAV1-LPLS447X), a Ser(447)X variant of the human lipoprotein lipase (LPL) gene (LPLSer(447)X) in an adeno-associated virus vector, as a potential intramuscular gene therapy for the treatment of LPL deficiency. Familial LPL deficiency is a rare, autosomal-recessive disorder of lipoprotein metabolism that is characterized by severe hypertriglyceridemia with episodes of abdominal pain, acute pancreatitis and eruptive cutaneous xanthomatosis. The lack of functional LPL in patients with LPL deficiency causes an accumulation of triglyceride (TG)-rich lipoproteins in the plasma. The LPLSer(447)X variant is associated with decreased levels of plasma TGs and increased HDL cholesterol concentrations compared with wild-type LPL. Preclinical studies evaluating alipogene tiparvovec in a mouse model of LPL deficiency demonstrated a long-term, dose-dependent correction of the lipid abnormalities. The first clinical trials in patients with LPL deficiency appear promising, with a significant decrease in the levels of plasma TGs observed in the first 3 months following the administration of alipogene tiparvovec, and an increase in local LPL activity and protein levels observed after 6 months. In addition, a decrease in pancreatitis frequency was observed during a 3-year follow-up period. At the time of publication, a phase II/III trial in patients with LPL deficiency, being conducted to further support the submission of an MAA to the EMEA for alipogene tiparvovec, was ongoing. The compound is also under investigation for the treatment of type V hyperlipoproteinemia, Syndrome X and non-alcoholic steatohepatitis.
Laser-Induced Shape Changes of Colloidal Gold Nanorods Using Femtosecond and Nanosecond Laser Pulses (2000)

Gold nanorods have been found to change their shape after excitation with intense pulsed laser irradiation. The final irradiation products strongly depend on the energy of the laser pulse as well as on its width. We performed a series of measurements in which the excitation power was varied over the range of the output power of an amplified femtosecond laser system producing pulses of 100 fs duration and a nanosecond optical parametric oscillator (OPO) laser system having a pulse width of 7 ns. The shape transformations of the gold nanorods are followed by two techniques: (1) visible absorption spectroscopy by monitoring the changes in the plasmon absorption bands characteristic for gold nanoparticles; (2) transmission electron microscopy (TEM) in order to analyze the final shape and size distribution. While at high laser fluences (∼1 J cm-2) the gold nanoparticles fragment, a melting of the nanorods into spherical nanoparticles (nanodots) is observed when the laser energy is lowered. Upon decreasing the energy of the excitation pulse, only partial melting of the nanorods takes place. Shorter but wider nanorods are observed in the final distribution as well as a higher abundance of particles having odd shapes (bent, twisted, φ-shaped, etc.). The threshold for complete melting of the nanorods with femtosecond laser pulses is about 0.01 J cm-2. Comparing the results obtained using the two different types of excitation sources (femtosecond vs nanosecond laser), it is found that the energy threshold for a complete melting of the nanorods into nanodots is about 2 orders of magnitude higher when using nanosecond laser pulses than with femtosecond laser pulses. This is explained in terms of the successful competitive cooling process of the nanorods when the nanosecond laser pulses are used. For nanosecond pulse excitation, the absorption of the nanorods decreases during the laser pulse because of the bleaching of the longitudinal plasmon band. In addition, the cooling of the lattice occurring on the 100 ps time scale can effectively compete with the rate of absorption in the case of the nanosecond pulse excitation but not for the femtosecond pulse excitation. When the excitation source is a femtosecond laser pulse, the involved processes (absorption of the photons by the electrons (100 fs), heat transfer between the hot electrons and the lattice (<10 ps), melting (30 ps), and heat loss to the surrounding solvent (>100 ps) are clearly separated in time.
SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state (2009)

Transcription factors that play key roles in regulating embryonic stem (ES) cell state have been identified, but the chromatin regulators that help maintain ES cells are less well understood. A high-throughput shRNA screen was used to identify novel chromatin regulators that influence ES cell state. Loss of histone H3 Lys 9 (H3K9) methyltransferases, particularly SetDB1, had the most profound effects on ES cells. Chromatin immunoprecipitation (ChIP) coupled with massively parallel DNA sequencing (ChIP-Seq) and functional analysis revealed that SetDB1 and histone H3K9-methylated nucleosomes occupy and repress genes encoding developmental regulators. These SetDB1-occupied genes are a subset of the "bivalent" genes, which contain nucleosomes with H3K4me3 (H3K4 trimethylation) and H3K27me3 modifications catalyzed by Trithorax and Polycomb group proteins, respectively. These genes are subjected to repression by both Polycomb group proteins and SetDB1, and loss of either regulator can destabilize ES cell state.
Effect of short-term culture on functional and stress-related parameters in isolated human islets (2008)

The Edmonton protocol for islet transplantation utilizes fresh islet grafts but other protocols increasingly transplant short-term cultured grafts mainly for practical reasons. To improve our understanding of the impact of culture pretreatment of human islets, we assessed post-transplant function by nude mouse bioassay, islet ATP, activity of stress-activated MAP kinases, and expression of stress-related genes by focused cDNA array in freshly isolated and cultured islets. Mean blood glucose levels over 4 weeks after transplantation (2000 IE) of (i) freshly isolated, (ii) cultured and preculture counted (recovery rate; 78 +/- 6%), and (iii) cultured and postculture counted islets in diabetic mice were 330 +/- 40, 277 +/- 65, and 256 +/- 52 mg/dl (i versus ii, P = 0.004; i versus iii, P = 0.002). During culture, islet ATP/DNA and ATP/ADP increased; JNK and p38 MAPK activities decreased. Among 96 genes studied, mRNA expression of heat shock protein 70 genes decreased >twofold during culture in all four pairs; expression of cyclooxygenase-2, superoxide dismutase-2, interleukin-6 and cytochromes P450 1A1 genes increased. Our results show that culturing human islets before transplantation is not disadvantageous in regard of functional recovery from changes induced by nonphysiologic stimuli during islet isolation. The increase in expression of several stress-related genes during culture also shows that improving culture conditions may further enhance post-transplant islet function.