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Effects of Papyrus Plants (Cyperus papyrus) on the Physicochemical Parameters and Nutrient Levels of Water and Sediments in Yala Swamp Wetland in Western Kenya
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作者 Violet Achieng Orodo Paul Otieno Abuom +4 位作者 Emmanuel Amukohe Shikanga Elly Tetty Osewe Douglas Nyambane Anyona Fredrick Mhina Mngube Stephen Adongo Odongo journal of biophysical chemistry 2024年第1期1-23,共24页
Yala swamp wetland is the largest fresh water wetland ecosystem in Kenya supporting a broad biodiversity. It comprises of River Yala, the Yala swamp, Lakes Kanyaboli, Namboyo and Sare, and a portion of Lake Victoria n... Yala swamp wetland is the largest fresh water wetland ecosystem in Kenya supporting a broad biodiversity. It comprises of River Yala, the Yala swamp, Lakes Kanyaboli, Namboyo and Sare, and a portion of Lake Victoria neighboring the swamp. Approximately 2300 ha of land have been reclaimed and has been used for large-scale agriculture resulting in mass destruction of papyrus to create room for framing. Papyrus are known to be important in phytoremediation but despite this role information is limited, lacks supportive evidence and the empirical aspect on the levels of these pollutants in relation to the papyrus biomass is limited. The study is aimed at determining the effects of Cyperus papyrus on the water and sediment quality in Yala Swamp wetland. Six sampling sites were purposefully selected to monitor the variations of the physicochemical parameters (temperature, dissolved oxygen: DO, pH, biological oxygen demand: BOD, total suspended solids: TSS, turbidity, electrical conductivity: EC and total dissolved solids: TSS) and the levels selected nutrients (phosphorus and nitrates) in water and sediments as River Yala flows through Dominion Farms, Lake Sare which surrounded by Cyperus papyrus and finally into Lake Victoria. The samples were collected in triplicates during the wet and dry seasons (May and September 2015 respectively). The physicochemical parameters were measured in situ using a Hydrolab muiltimeter while the nutrients were analyzed using UV/Vis spectroscopy. Statistical analysis was done using SAS V9.0 software. The mean temperature was 26.19˚C ± 0.71˚C, DO: 3.72 ± 1.02 Mg/l, BOD: 3.9 ± 0.32 Mg/l, pH: 7.52 ± 0.17, TDS: 109 ± 86.33, EC: 173.26 ± 13.8 μS/cm, TSS: 12.42 ± 18.51 Mg/l and Turbidity: 12.29 ± 10.03 NTU. The values varied significantly at P 0.05 among all the sites. The results show that papyrus is useful in maintaining the required levels of physicochemical parameters. The study will assist in conservation of the papyrus to help phytoremediate pollutants from Dominion farms and the adjacent farms in order to have ecologically sound wetland. 展开更多
关键词 Adsorbing Contaminants PHYTOREMEDIATION CONSERVATION Cyperus papyrus
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The Biochemical Impact by Covalent Shielding of the Anionic Oxygen of the Phosphate Group in DNA and RNA as Methylated Phosphotriester Linkage on the Inhibition of DNA Duplication and on HIV-1 RNA Viral Infectivity Has Been Seriously Overlooked
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作者 Henk M. Buck journal of biophysical chemistry CAS 2023年第2期59-66,共8页
With the help of model experiments, we are able to offer a detailed proposal for the inhibition of DNA duplication and no inhibition of RNA viral infectivity. As a backbone, we introduced methyl phosphotriester (MPTE)... With the help of model experiments, we are able to offer a detailed proposal for the inhibition of DNA duplication and no inhibition of RNA viral infectivity. As a backbone, we introduced methyl phosphotriester (MPTE). Duplex formation according to the traditional Watson and Crick base-pairing: [(MPTE)<sub>n−1</sub> DNA] * DNA and [(MPTE)<sub>n−1</sub> DNA] * RNA, where n = number of DNA and RNA bases. However, in the latter case, inhibition is obtained by reduction of the number of MPTE linkages, as is confirmed with model experiments and under biological conditions with micro (mi)RNA substrates. The latter results have recently been published. One or more single MPTEs are disseminated over different places of DNA without neighbour MPTEs (Prof. Wen-Yih Chen and his group, Taiwan). 展开更多
关键词 Methylated Phosphotriester (MPTE) DNA Partially MPTE DNA Model Inhibition Experiments Micro (mi)RNA HIV-1 RNA Conformational Transition
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Analysis of Vascular Endothelial Growth Factor Receptor Tyrosine Kinase Inhibitor-Induced Left Ventricular Dysfunction
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作者 Yasuhisa Hashino Kengo Umehara +3 位作者 Shinya Takada Kuninori Iwayama Koichi Ohtaki Hideki Sato journal of biophysical chemistry CAS 2023年第2期67-78,共12页
Vascular endothelial growth factor (VEGF) receptor tyrosine kinase inhibitor (VEGFR-TKI), an oral molecular targeted drug, reportedly causes serious adverse cardiovascular events such as hypertension and left ventricu... Vascular endothelial growth factor (VEGF) receptor tyrosine kinase inhibitor (VEGFR-TKI), an oral molecular targeted drug, reportedly causes serious adverse cardiovascular events such as hypertension and left ventricular failure. The association between VEGFR-TKI-induced hypertension and heart failure with preserved left ventricular ejection fraction (LVEF) (HFpEF) has been previously studied. Therefore, we investigated the relationship between hypertension onset and associated cardiac diastolic dysfunction due to VEGFR-TKI use. Patients who used VEGFR-TKIs (target drugs: sunitinib, axitinib, sorafenib, pazopanib, and cabozantinib) at the Department of Urology, Hokkaido Cancer Center were recruited between May 2009 and October 2021 and were divided into two groups based on whether their blood pressure was elevated during VEGFR-TKI use. The markers of left ventricular diastolic function (E/A, Dct (ms), mean E/e, septal e') and left ventricular systolic function (LVEF, LVDd, and LVDs) were evaluated. LVEF and mean E/e in the elevated blood pressure group (n = 41) showed significant changes before and after treatment. LVEF values (contractile function markers) in the TKI-HT (+) group significantly decreased from 70.7% ± 6.8% before treatment to 68.3% ± 7.8% after treatment (p = 0.03). Conversely, no significant difference was observed for any ventricular systolic function marker in the TKI-HT (−) group. E/e (diastolic function marker) in the TKI-HT (+) group significantly decreased from 11.9% ± 3.6% before treatment to 10.3% ± 3.0% after treatment (p = 0.02). However, no change was observed in any ventricular diastolic function marker in the TKI-HT (−) group. The results of this study suggest that cardiac function may be affected in patients using VEGFR-TKI. Furthermore, appropriate antihypertensive treatment and early monitoring with regular echocardiography, even in asymptomatic patients, may help prevent VEGFR-TKI-induced deterioration of systolic and diastolic function. 展开更多
关键词 VEGFR-TKI Left Ventricular Dysfunction Cardio-Oncology HFrEF HFpEF CTRCD
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Design of N-11-Azaartemisinins Potentially Active against Plasmodium falciparum by Combined Molecular Electrostatic Potential, Ligand-Receptor Interaction and Models Built with Supervised Machine Learning Methods
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作者 Jeferson Stiver Oliveira de Castro José Ciríaco Pinheiro +5 位作者 Sílvia Simone dos Santos de Morais Heriberto Rodrigues Bitencourt Antonio Florêncio de Figueiredo Marcos Antonio Barros dos Santos Fábio dos Santos Gil Ana Cecília Barbosa Pinheiro journal of biophysical chemistry CAS 2023年第1期1-29,共29页
N-11-azaartemisinins potentially active against Plasmodium falciparum are designed by combining molecular electrostatic potential (MEP), ligand-receptor interaction, and models built with supervised machine learning m... N-11-azaartemisinins potentially active against Plasmodium falciparum are designed by combining molecular electrostatic potential (MEP), ligand-receptor interaction, and models built with supervised machine learning methods (PCA, HCA, KNN, SIMCA, and SDA). The optimization of molecular structures was performed using the B3LYP/6-31G* approach. MEP maps and ligand-receptor interactions were used to investigate key structural features required for biological activities and likely interactions between N-11-azaartemisinins and heme, respectively. The supervised machine learning methods allowed the separation of the investigated compounds into two classes: cha and cla, with the properties ε<sub>LUMO+1</sub> (one level above lowest unoccupied molecular orbital energy), d(C<sub>6</sub>-C<sub>5</sub>) (distance between C<sub>6</sub> and C<sub>5</sub> atoms in ligands), and TSA (total surface area) responsible for the classification. The insights extracted from the investigation developed and the chemical intuition enabled the design of sixteen new N-11-azaartemisinins (prediction set), moreover, models built with supervised machine learning methods were applied to this prediction set. The result of this application showed twelve new promising N-11-azaartemisinins for synthesis and biological evaluation. 展开更多
关键词 Antimalarial Design MEP Ligand-Receptor Interaction Supervised Machine Learning Methods Models Built with Supervised Machine Learning Methods
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The Gastropod Shell Structure as a Blueprint for a Periodic System: A New Theory for Element Configurations
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作者 Nader Butto journal of biophysical chemistry CAS 2023年第2期31-58,共28页
The purpose of this article is to propose a new design for the periodic table of elements. The new design is based on a three-dimensional (3D) model of the gastropod shell structure and presents a mechanism of the for... The purpose of this article is to propose a new design for the periodic table of elements. The new design is based on a three-dimensional (3D) model of the gastropod shell structure and presents a mechanism of the formation of elements that reflects the laws of nature that guide the formation of the gastropod shell, electron orbitals, and element structure. The author also identifies challenges associated with the current standard periodic table, such as the positions of hydrogen, helium, lanthanides, and actinides. The author’s research is a response to the IUPAC’s request, dating back to 2016, to settle unresolved disputes surrounding the current standard periodic table. Hence, the author proposes the “Gastropod Shell Model”, which presents the periodic system in 2D and 3D snail shells based on a hypothesized unifying principle guiding the formation of elements: the universal unified theory that considers the spiral and vortex forms as the bridge between energy and matter. The author was able to position hydrogen, helium, lanthanides, and actinides uniquely in their proposed periodic system to solve problems associated with their positions in the standard periodic table. Readers will be interested in uncovering the “hypothesized unifying principle guiding the formation of elements”. 展开更多
关键词 3D Periodic Table Gastropod Shell Spiral Model
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“Doubling” of local photon emissions when two simultaneous, spatially-separated, chemiluminescent reactions share the same magnetic field configurations 被引量:9
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作者 Blake T. Dotta Michael A. Persinger journal of biophysical chemistry 2012年第1期72-80,共9页
The aim of the present experiments was to discern if the “entanglement”-like photon emissions from pairs of cell cultures or human brains separated by significant distances but sharing the same circling magnetic fie... The aim of the present experiments was to discern if the “entanglement”-like photon emissions from pairs of cell cultures or human brains separated by significant distances but sharing the same circling magnetic field could be demonstrated with a classic chemiluminescent reaction produced by hydrogen peroxide and hypochlorite. Simultaneous injection of the same amount of peroxide into a local dish (above a photomultiplier tube) and a dish 10 m away in a closed chamber produced a “doubling” of the durations of the photon spikes only when the two reactions were placed in the center of separate spaces around each of which magnetic fields were generated as accelerating group velocities containing decreasing phase modulations followed by decelerating group velocities embedded with increasing phase modulations. The duration of this “entanglement” was about 8 min. These results suggest that separate distances behave as if they were “the same space” if they are exposed to the same precise temporal configuration of magnetic fields with specific angular velocities. 展开更多
关键词 PHOTON Emission ENTANGLEMENT Angularly Accelerating Magnetic Fields Hydrogen Per-oxide/Hypochlorite Reaction
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Dynamic Changes in Lipid Peroxidation and Antioxidant Level in Rat’s Tissues with <i>Macrovipera</i><i>lebetina</i><i>obtusa</i>and <i>Montivipera</i><i>raddei</i>Venom Intoxication 被引量:7
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作者 N. A. Zaqaryan N. A. Ghazaryan N. M. Ayvazyan journal of biophysical chemistry 2014年第4期152-160,共9页
We investigated the balance of free radicals in different tissues (liver, heart, brain and muscle) of rats in course of in vivo and in vitro processing by Macrovipera lebetina obtusa (MLO) and Montivipera raddei (MR) ... We investigated the balance of free radicals in different tissues (liver, heart, brain and muscle) of rats in course of in vivo and in vitro processing by Macrovipera lebetina obtusa (MLO) and Montivipera raddei (MR) snake venoms. Chemiluminescence (ChL) levels were examined in tissue assays after incubation (at 37 &#176C for a period of 10 min) with venom for in vitro experiments and in tissue assays isolated of 10 min after venom injection for in vivo experiments. The TBA-test was also performed to confirm the free radical expression. The activities of antioxidant enzymes (such as superoxide dismutase and glutathione peroxidase) in isolated tissues were detected by spectro-photometry. During the in vitro processing chemiluminescence levels of tissue homogenates significantly decreased, while in course of in vivo intoxication the level of ChL was elevated in brain and liver;lipid peroxidation also increased in brain tissue, but there was no significant balance change in other tissues;the activity of superoxide dismutase mainly correlated with changes of free radical balance during intoxication. On the contrary, the activity of glutathione peroxidase showed the reverse tendencies to change. We suggest that free radicals and their oxidative stresses may play a role in the early stage of intoxication causing the so-named “spreading-effect”, which is very characteristic for the venom of vipers. 展开更多
关键词 hemiluminescence Lipid PEROXIDATION Superoxide DISMUTASE Glutathione Peroxidase Macrovipera lebetina obtusa Montivipera raddei
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Kinetic and binding equilibrium studies of dihydroflavonol 4-reductase from Vitis vinifera and its unusually strong substrate inhibition 被引量:5
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作者 Nadia Trabelsi Béatrice Langlois d'Estaintot +2 位作者 Gilles Sigaud Bernard Gallois Jean Chaudière journal of biophysical chemistry 2011年第3期332-344,共13页
Dihydroflavonol 4-reductase (DFR), a member of the short-chain dehydrogenase family, catalyzes the last common step in the biosynthesis of flavan-3-ols and condensed tannins. Initial rates of DFR were measured by moni... Dihydroflavonol 4-reductase (DFR), a member of the short-chain dehydrogenase family, catalyzes the last common step in the biosynthesis of flavan-3-ols and condensed tannins. Initial rates of DFR were measured by monitoring the 340-nm absorbance decrease resulting from the joint consumption of dihydroquercetin (DHQ) and NADPH, as a function of pH, temperature and ionic strength. At pH 6.5 and 30o C, substrate inhibition was observed above 30 μM DHQ. At lower/non-inhibitory DHQ concentrations, NADP+ behaves as a competitive inhibitor with respect to NADPH and as a mixed inhibitor with respect to DHQ, which supports a sequential ordered mechanism, with NADPH binding first and NADP+ released last. Binding-equilib-rium data obtained by means of the chromatographic method of Hummel and Dreyer at pH 7.5 and by isothermal calorimetric titration at pH 6.5 led to the conclusion that ligands of the apoenzyme included NADPH, NADP+ and DHQ. The mechanism which best accounts for substrate inhibition at pH 6.5 in the absence of product involves the formation of a binary non-productive E.DHQ complex. Thus, a productive ternary complex cannot be formed when DHQ binds first. This mechanism of inhibition may prevent the accumulation of unstable leucoanthocyanidins within cells. 展开更多
关键词 SUBSTRATE Inhibition Steady-State Kinetics HUMMEL and Dreyer Technique Isothermal TITRATION Calorimetry Non-Productive Enzyme SUBSTRATE Complex
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A spectroscopic study of the interaction of the antioxidant naringin with bovine serum albumin 被引量:5
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作者 Atanu Singha Roy Debi Ranjan Tripathy +1 位作者 Angshuman Chatterjee Swagata Dasgupta journal of biophysical chemistry 2010年第3期141-152,共12页
The interaction of naringin with bovine serum albumin has been performed using fluorescence, circular dichroism and fourier transform infrared spectroscopy in 20 mM phosphate buffer of pH 7.0 as well as molecular dock... The interaction of naringin with bovine serum albumin has been performed using fluorescence, circular dichroism and fourier transform infrared spectroscopy in 20 mM phosphate buffer of pH 7.0 as well as molecular docking studies. The changes in enthalpy (ΔH°) and entropy (ΔS°) of the interaction were found to be +18.73 kJ/mol and +143.64 J mol-1 K-1 respectively, indicating that the interaction of naringin with bovine serum albumin occurred mainly through hydrophobic interactions. Negative values of free energy change (ΔG°) at different temperatures point toward the spontaneity of the interaction. Circular dichroism studies reveal that the helical content of bovine serum albumin decreased after interaction with naringin. According to the F?rster non-radiative energy transfer theory the distance between Trp 213 residue and naringin was found to be 3.25 nm. Displacement studies suggest that naringin binds to site 1 (subdomain IIA) of bovine serum albumin (BSA) which was also substantiated by molecular docking studies. 展开更多
关键词 NARINGIN BOVINE Serum ALBUMIN Fluorescence Binding WARFARIN DOCKING
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Mode of pollen spread in clonal seed orchard of Pinus koraiensis 被引量:4
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作者 Fu-Juan Feng Xin Sui +3 位作者 Min-Min Chen Dan Zhao Hi-Jie Han Mai-He Li journal of biophysical chemistry 2010年第1期33-39,共7页
The patterns of effective pollen dispersal and the relationships between pollen dispersal and genetic composition in Pinus koraiensis are still unclear. Hence, we investigated the mode of pollen dispersal of P. koraie... The patterns of effective pollen dispersal and the relationships between pollen dispersal and genetic composition in Pinus koraiensis are still unclear. Hence, we investigated the mode of pollen dispersal of P. koraiensis in a clonal seed orchard in Lushuihe Forestry Bureau, Jilin Province, using SSR molecular markers tech-nique and the method of maximum likelihood. A total of 13 pairs of nuclear microsatellites po-lymorphic primers were used in the paternity analysis. We analyzed 100 progenies and 150 paternities. A total of 56 alleles were detected in 13 loci with 3-6 alleles (4.3 alleles in average) in a single locus. The primers of SsrPt_ctg7170 and SsrPt_ctg5333 had the maximum (6) and the minimum (3) alleles, respectively. The averaged values of observed heterozygosity, expected heterozygosity and polymorphism information content of experimental groups were 0.648, 0.601 and 0.533, respectively. The mating dis-tance of P. koraiensis followed an approximately normal distribution. The most effective pollen for the female parent came from male parent trees 15-45 m away with an average mating dis-tance of 32.60 m and the longest of 67.88 m. The pollen source of offspring was not random but greatly affected by the wind direction during the pollination season of P. koraiensis. These re-sults have important implications for seed or-chard design to improve the genetic quality of seeds and seed production. 展开更多
关键词 PINUS Koraiensis Seed ORCHARD Nuclear Microsatellites MARKERS PATERNITY Analysis POLLEN SPREAD
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Cancer chemoprevention through the induction of apoptosis by natural compounds 被引量:4
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作者 Toshiya Kuno Testuya Tsukamoto +1 位作者 Akira Hara Takuji Tanaka journal of biophysical chemistry 2012年第2期156-173,共18页
As cell and tissue homeostasis are mediated by the balance between proliferation and apoptosis, controlling this balance is important for cancer chemoprevention. Cancer chemoprevention can be achieved by the use of na... As cell and tissue homeostasis are mediated by the balance between proliferation and apoptosis, controlling this balance is important for cancer chemoprevention. Cancer chemoprevention can be achieved by the use of natural, synthetic or biologic compounds that reverse, suppress or prevent the development of epithelial malignancies. Natural compounds including flavonoids are able to reduce oxidative stress, which is the most likely mechanism mediating the protective effects against cancer development. In addition, in vitro and in vivo studies have suggested that flavonoids, such as (-)-epigallocatechin-3-gallete (EGCG), quercetin, and curcumin, act by induction of apoptosis. Several natural compounds inhibit cell proliferation and angiogenesis. Certain natural products have been shown to inhibit the activation of nuclear factor kappa B (NF-κB) and Akt signaling pathways, both of which are known to maintain a homeostatic balance between cell survival and apoptosis. Understanding the mechanism of these natural products will contribute to the development of more specific preventive strategies against cancer development. Here we focus on the ability of natural cancer chemopreventive agents to induce apoptosis, and attempt to provide evidence for the preventive and therapeutic effects of natural compounds, EGCG, quercetin, and curcumin, in a succinct manner highlightingκand Akt signaling pathways in vivo. 展开更多
关键词 CANCER CHEMOPREVENTION APOPTOSIS NATURAL COMPOUNDS
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Maintained Exposure to Spring Water but Not Double Distilled Water in Darkness and Thixotropic Conditions to Weak (~1 µT) Temporally Patterned Magnetic Fields Shift Photon Spectroscopic Wavelengths: Effects of Different Shielding Materials 被引量:2
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作者 N. J. Murugan L. M. Karbowski +1 位作者 R. M. Lafrenie M. A. Persinger journal of biophysical chemistry 2015年第1期14-28,共15页
Spring water but not double-distilled water was exposed, in darkness, to a temporally patterned weak magnetic field that has been shown to affect planarian behavior and slow the rate of cancer cell proliferation. Expo... Spring water but not double-distilled water was exposed, in darkness, to a temporally patterned weak magnetic field that has been shown to affect planarian behavior and slow the rate of cancer cell proliferation. Exposure to the magnetic field caused a reliable shift in the peak (longer) wave-length of ~10 nm for fluorescence emissions and a ~20% increase (~100 counts) in fluorescence intensity. Spectral analyses verified a shift of 5 and 10 nm, equivalent to ~1.5 × 10-20 J “periodicity” across the measured wavelengths, which could reflect a change in the an intrinsic energy as predicted by Del Giudice and Preparata and could correspond to two lengths of O-H bonds. Wrapping the water sample containers during exposure with copper foil, aluminum foil, or plastic altered these fluorescent profiles. The most conspicuous effect was the elimination of a ~280 nm peak in the UV-VIS emission spectra only for samples wrapped with copper foil but not aluminum or plastic. These results suggest that weak magnetic fields produce alterations in the water-ionic complexes sufficient to be reliably measured by spectrophotometry. Because the effect was most pronounced when the spring water was exposed in darkness and was not disturbed the role of thixotropic phenomena and Del Giudice entrapment of magnetic fields within coherent domains of Pollack virtual exclusion zones (EZ) may have set the conditions for subsequent release of the energy as photons. 展开更多
关键词 Water WEAK Magnetic Fields PHOTON Emissions DARKNESS Thixotropic Phenomena Copper Shielding Wavelength SHIFT 10-20 Joules
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A conformational B-Z DNA study monitored with phosphatemethylated DNA as a model for epigenetic dynamics focused on 5-(hydroxy)methylcytosine 被引量:2
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作者 Henk M. Buck journal of biophysical chemistry 2013年第2期37-46,共10页
This study was directed on the B- into Z-DNA isomerization with alternating CG sequences monitored with artificial DNA model-systems based on methylation of the phosphate backbone. The chemical concept for this transi... This study was directed on the B- into Z-DNA isomerization with alternating CG sequences monitored with artificial DNA model-systems based on methylation of the phosphate backbone. The chemical concept for this transition wherein shielding of the oxygen anions of the backbone phosphates plays an essential role, resulted in the preparation of the phosphatemethylated d(CpG). Even on this primitive level of only two base pair long, the B-Z conformational aspects of this self-complementary duplex could be described in solution with nuclear magnetic resonance (NMR) and circular dichroism (CD) measurements. The exclusivity of this choice became clear after synthesizing phosphatemethylated DNA with longer alternating CG fragments. It could be shown that conflicting conformational effects of the CG and GC fragments resulted in an overall B structure of the phosphatemethylated tetramer d(CPGPCPG). From our model considerations, it is clear that the internal stress introduced by the alternating CG sequences will be promoted by a complete shielding of the phosphate backbone. Elimination of this effect may be realized by a site-specific phosphate shielding. The role of the anti-syn isomerization of G in the CG fragments is clarified by methylation of the phosphate group. This anti-syn transition is absent in corresponding methylphosphonates, suggesting an exclusive role for base-backbone coordination via hydrogen bonding. In addition, we propose that the B- into Z-DNA interconversion may offer a mechanistic view for differences in dynamics between cytosine and its epigenetic derivative 5-methylcytosine. This mechanism has been extended to the demethylation of 5-methylcytosine and the exchange of information between the new epigenetic base, 5-hydroxymethylcytosine and the DNA backbone via an intramolecular phosphorylation. The role of 5-hydroxymethylcytosine in Alzheimer disease has been briefly discussed. In our opinion, this study can be considered as a new dynamic concept for epigenetics based on the dynamics of the B-Z transition in natural and phosphatemethylated DNA. 展开更多
关键词 B-Z DNA Transition Artificial DNA’s EPIGENETICS Phosphorylation-Demethylation Alzheimer
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An interactive 3D viewer of molecules compatible with the suite of ANTHEPROT programs 被引量:2
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作者 Gilbert Deléage journal of biophysical chemistry 2012年第1期35-38,共4页
In this paper, I will describe a completely new 3D module which can be called from within the well known ANTHEPROT program devoted to protein sequences analysis. This module allows fully interactive handling of high-q... In this paper, I will describe a completely new 3D module which can be called from within the well known ANTHEPROT program devoted to protein sequences analysis. This module allows fully interactive handling of high-quality 3D structures with various modes of representation (CA sticks, wireframe, ball and sticks, spacefill mod-els as well as surface, ribbons, Ramachandran plots). Alternatively, ANTHEPROT 3D can be used as an external program fully independant from the global package. It is available from the download page of the web site (http://antheprot-pbil.ibcp.fr/). More than 2800 downloads last year were recorded since the program was delivered. 展开更多
关键词 Protein SEQUENCE Analysis Structural BIOINFORMATICS Software 3D Structures
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Non-Local pH Shifts and Shared Changing Angular Velocity Magnetic Fields: Discrete Energies and the Importance of Point Durations 被引量:2
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作者 Nicolas Rouleau Trevor N. Carniello Michael A. Persinger journal of biophysical chemistry 2014年第2期44-53,共10页
Macroscopic productions of “non-locality” or “excess correlations” of dynamic changes within media between two spaces could be utilized as alternative communication systems. Previous experiments have shown that in... Macroscopic productions of “non-locality” or “excess correlations” of dynamic changes within media between two spaces could be utilized as alternative communication systems. Previous experiments have shown that injections of a weak acid within one of two volumes of spring water sharing the same patterned circular magnetic fields with changing angular accelerations separated by non-traditional (5 m) distances were associated with opposite (basic) shifts in pH within the non-injected, non-local volume. In the present experiments, employing a different technology, pairs of beakers separated by 1 m containing either 25 cc, 50 cc, or 100 cc of spring water were placed within toroids generating weak (30, 300 nT) changing acceleration magnetic fields with 1 ms, 2 ms, or 3 ms point durations or a field whose point durations changed. When a proton source (weak acid) was injected into one beaker (local) pH shifts in the other (non-local) beaker exhibit increased acidity for the 3 ms point duration but increased alkalinity for the 1 ms duration. Neither intermittent point durations nor variable point durations for the same volumes of water placed between the two magnetic field-coupled beakers exhibited significant changes from baseline. Contingent upon the point duration of the applied field, the pH shift was consistent with a fixed quantity of decreased free protons (increased pH) or increased protons (decreased pH) in the non-local beakers. The opposite directions of the pH shifts at 1 ms and 3 ms that correspond to quantitative cosmological solutions for electrons and protons suggest these results may reflect a fundamental physical process. 展开更多
关键词 EXCESS Correlations PH SHIFTS NON-LOCALITY Novel Communication Systems
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Buffer standards for the physiological pH of the zwitterionic buffer 3-[<i>N</i>-tris(hydroxymethyl)methylamino]-2-hydroxypropanesulfonic Acid (TAPSO) From (278.15 to 328.15) K 被引量:2
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作者 Lakshmi N. Roy Rabindra N. Roy +4 位作者 Blake M. Bodendorfer Zachary M. Downs Stephen D. Rocchio Jessica M. Stegner Isaac B. Henson journal of biophysical chemistry 2011年第4期414-421,共8页
The second dissociation constant, pK2, and related thermodynamic quantities for TAPSO have been previously determined and reported from the temperatures (278.15 to 328.15) K. In the current study there are five buffer... The second dissociation constant, pK2, and related thermodynamic quantities for TAPSO have been previously determined and reported from the temperatures (278.15 to 328.15) K. In the current study there are five buffer solutions without NaCl and five buffer solutions with NaCl present which yield an ionic strength (I = 0.16 mol·kg-1) similar to that of blood plasma. These buffer solutions have been evaluated in the temperature range of (278.15 to 328.15) K using the extended Debye-Hückel equation, due to the limitations of the Bates-Guggenheim convention such that it is only valid when I -1. The liquid junction potential (Ej) values between the TAPSO solution and the saturated KCl calomel electrode solution have been estimated at (298.15 and 310.15) K using a flowing junction cell measurement. The previously mentioned Ej values have been used in determining the operational pH values at (298.15 and 310.15) K. These TAPSO buffer solutions are recommended as reference solutions for pH measurements in saline media with an ionic strength of I = 0.16 mol·kg-1. 展开更多
关键词 ZWITTERIONIC BUFFER pH Liquid Junction Physiological
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Genetic diversity of color phenotypes in the koi (<i>Cyprinus carpio</i>L.) as identified by molecular markers 被引量:2
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作者 Dani Bercovich Sigal Korem +1 位作者 Lior Shauder Gad Degani journal of biophysical chemistry 2012年第3期249-255,共7页
The common carp (Cyprinus carpio) has a large variety of strains. The more popular are the koi (Japanese ornamental carp), which are still bred today to generate creative colors and patterns, giving rise to multiple p... The common carp (Cyprinus carpio) has a large variety of strains. The more popular are the koi (Japanese ornamental carp), which are still bred today to generate creative colors and patterns, giving rise to multiple phenotypes. Since koi are in great demand, there is a challenge to determine the genetics defining their quality. Two methods: 1) direct sequencing of five candidate gene regions, i.e., mitochondrial (cytochrome b, 12S gene and the D-loop) and nuclear (red sensitive opsin and Rag-1) loci, to detect single nucleotide polymorphisms (SNP)s and 2) random amplification of polymorphic DNA (RAPD), were used to differentiate among four koi strains (Kohaku, Sanke, Ghost and Ohgon) and the common carp. Novel SNPs, distinguishing between koi and the common carp, were revealed in cytochrome b, the D-loop and in the red sensitive opsin;one was a missense mutation in cytochrome b at position 15860, in which threonine in the common carp became alanine in all koi strains examined. The Kohaku strain was found to have two alleles in the mitochondrial fragments, forming two different haplotypes (subpo-pulations). These novel SNPs distinguished between koi strains and the common carp, and the RAPD method enabled further differentiation among the four koi strains. 展开更多
关键词 Koi Skin COLOR Polymorphism SNP RAPD
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Crystal structure of PqqB from <i>Pseudomonas putida</i>at 2.2 Åresolution 被引量:2
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作者 Moritz Metlitzky Sandra Puehringer Stuart J. Fisher journal of biophysical chemistry 2012年第2期206-210,共5页
Pyrroloquinoline quinone (PQQ) is an important redox-active cofactor for many bacterial dehy-drogenases. It's biosynthetic pathway involves six or seven genes, one of which is pqqB. Former studies indicated that t... Pyrroloquinoline quinone (PQQ) is an important redox-active cofactor for many bacterial dehy-drogenases. It's biosynthetic pathway involves six or seven genes, one of which is pqqB. Former studies indicated that the protein encoded by pqqB, namely PqqB, functions as a PQQ transporter. Here we report the crystal structure of PqqB from Pseudomonas putida at 2.2 ? resolution together with functional studies to verify this theory. 展开更多
关键词 PqqB PQQ Biosynthetic PATHWAY X-Ray CRYSTALLOGRAPHY
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Selection of highly efficient small interference RNA (SiRNA) targeting mammalian genes 被引量:3
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作者 Ali El-lakkani Wissam H. Abd Elgawad Eman A. Sayed journal of biophysical chemistry 2013年第2期72-79,共8页
RNAi is the method of silencing the expression of targeted genes. RNAi applications include gene function analysis and target validation. Designing highly efficient small interference RNA (siRNA) sequence with maximum... RNAi is the method of silencing the expression of targeted genes. RNAi applications include gene function analysis and target validation. Designing highly efficient small interference RNA (siRNA) sequence with maximum target specificity for mammalian RNAi is one of important topics in recent years. In this work, a statistical analysis of the information for a large number (3734) of siRNA presented in the database available on the internet is done. This is to improve the design of efficient siRNA molecules. The (3734) siRNAs are classified according to their efficiency to three groups (high efficient, moderate efficient and low efficient). Thirteen properties (positional and thermodynamics) are identified in the high efficient group in the primary statistical study. In the final statistical study, the average weight of each identified property is calculated. A very good linear correlation was found between the average percentage efficiency and the weighted score of siRNA properties. It is found that the most important feature of highly efficient siRNA is the difference in binding energy between the 5’ end and the 3’ end of the anti-sense strand. The (RISC) activation step is a critical step in RNAi process where the efficiency of this process depends on the instability of the 5’ end of the anti-sense strand. 展开更多
关键词 RNAI SIRNA SIRNA Design
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DNA Variation of <i>Capoeta</i><i>damascina</i>(Valenciennes, 1842) in Three Rivers in Northern Israel 被引量:1
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作者 Gad Degani journal of biophysical chemistry 2014年第3期107-117,共11页
The present study is in agreement with the hypothesis that the variation of ecological conditions in three rivers in northern Israel—the Dan, Hasbani and Hermon Rivers—affects the genetic variations of the species C... The present study is in agreement with the hypothesis that the variation of ecological conditions in three rivers in northern Israel—the Dan, Hasbani and Hermon Rivers—affects the genetic variations of the species Capoeta damascina. Using mitochondrial DNA (mtDNA), cytochrome b gene (Cytb), 16S and nuclear DNA (nDNA), and Random Amplified Polymorphic DNA (RAPD), four different clusters were found in the Cytb of the Hasbani and Hermon Rivers and only two in the Dan River. Moreover, the clusters in the Hasbani River differed from those found in the Hermon River. A similar result was found when an analysis was made of a different sequence from five different haplotype frequencies using the MegAlign program, the lowest being in the Dan River (only two haplotypes) and the highest in the Hasbani River (four haplotypes). The analysis of molecular variance of Cytb and 16S (AMOVA) for individuals of C. damascina from eight populations in northern Israel showed significant differences between the rivers and the populations. The analysis by mitochondrial 16S of haplotype frequencies of C. damascina populations in the rivers in northern Israel was very low compared to Ctb. Sixteen different haplotypes were found in the different rivers: eight in the Hasbani River, seven in the Dan River and only five in the Hermon River. 展开更多
关键词 16S Capoeta damascina CYTOCHROME b Gene (Cytb) Mitochondrial DNA (mtDNA) Nuclear DNA (nDNA) Random Amplified Polymorphic DNA (RAPD)
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