Biophysical Research Articles

环形DNA分子构象统计 Conformations of DNA Loop

DNA环的形成和性质是生物物理以及软物质物理关注的基本问题。本文以蠕虫状链为模型，应用蒙特卡洛方法模拟了锚定在蛋白质上的DNA环的构象统计。给出了DNA环在不同长度序列情况下的择优构象状态，讨论了不同构象情况下DNA分子对锚定点的作用力。 The formation and property of DNA loop are the basic problems of biophysics and soft matter physics. In present work, the conformational statistics is studied by Monte Carlo method based on the wormlike chain model. The priority conformational state for the different length of DNA loop is predicted and the force acting on the grafting point is also discussed.

The development of nanobody probes for molecular imaging

The nanobody is a novel antibody fragment,which has beneficial biophysical and pharmacokinetic properties,such as the small molecular weight,high affinity and specificity for antigen.Nanobody is ideally suitable for molecular imaging as a targeting probe that could label antigen at nmol level in vitro.In animal models of xenografted tumor,atherosclerotic plaques and brain disorders,the target tissues were specifically and clearly detected and the high tumor-to-blood (T/B) ratios were obtained.Structural or chemical modified nanobodies will have higher affinity and retention to target tissues,and be convenient for the application of molecular imaging.With the development of the related research,nanobody-based molecular imaging will be gradually transformed into the clinical applications,and play an important role in early diagnosis and therapeutic assessment. Key words: Nanotechnology;  Antibodies ;  Molecular imaging ;  Trends

3P059 回転および並進運動から観たタンパク質間相互作用(01C. 蛋白質:物性,ポスター,第52回日本生物物理学会年会(2014年度))

3P059 Protein-protein interaction revealed by the rotational and translational motion (01C.

Biomarker discovery and biotherapeutics applications of photosynthetic light-harvesting and bioluminescence light-emitting chromophore-protein complexes in stem cell biology and regenerative medicine.

We have since the 1970's embarked on the development of biologically derived fluorophore-protein complexes that will find applications in the communicable and non-communicable disease etiology processes and their cures. We have since then become largely successful in these endeavors along with interspersed contributions also from investigators who have generally restricted to working in confined disciplines. Their encompassment with our works as this investigator has traversed his definitely chosen and not merely a circumstantial, coincidental, or accidental step-wise multi-disciplinary scientific path from biophysics to regenerative medicine spanning these lines of investigations for last four decades have finally yielded the much necessitated disease related applied biological interventions for human benefits. Taking a cue from our early investigations and findings on which we call attention to the identification and characterization of the use of the primary light-emitting lumazine precursor of riboflavin which is 6,7-dimethyl-8-ribityl lumazine-protein complex which we had derived from the bioluminescence bacterium (Photobacterium phosphoreum) wherein it functions as a naturally occurring fluorescence light emitter (LumP). These in vivo phenomena have been a precursor to the subsequent developments in vitro. This in vivo to in vitro investigation path of ours has been also comprised among others of binding of photosynthetic light-harvesting marine dinoflagellate algae (Glenodinium sp.) derived peridinin-chlorophyll a-protein (PerCP) complex-labeled monoclonal antibodies useful in the development of flow cytometry. These fluorescence labeled antibodies bound antigens which include those of communicable infectious diseases (HIV/AIDS - env-gp160, gag-p24), non-communicable but also potential hereditary and malignant disorders (Cancer/Tumor Markers - Melan-A/Mart-1 of melanoma), normal immune response cells (Human/Mouse/species cellular MHC/TCR/CD45/CD33/CD56/CD19/CD41), and of types of stem cells (CD34/CD38/c-Mpl/Oct4/Neuropilin-1/SOX17). Such antigens have been analyzed by us and other investigators by fluorescence-activated cell sorting (FACS - cell surface and intracellular binding), confocal fluorescence microscopy, or/and immunohistochemistry, to determine qualitative and quantitative antigen expression levels and their mechanistic implications. We have followed stem cell differentiation patterns and signaling mechanisms through marker antigen-antibody binding wherein the antibodies are labeled with covalently linked fluorophore-protein complexes or fluorescence emitting chromophores. These complexes among others also have included PerCP. We are also now in the process of developing flow cytometry applications of additional visible light emitting chromophore-protein complexes through industrial collaborations. The United States Navy has long been known for interest in the estimation of changes in illumination intensity in and under the oceans to track movements of enemy ships and other naval vessels.

2P047 大腸菌機械受容チャネルMscLの開口における脂質膜環境に影響される脂質-タンパク質間相互作用の解析(01B. 蛋白質:構造機能相関,ポスター,第52回日本生物物理学会年会(2014年度))

2P047 Analysis on Lipid-Protein Interactions Affected by Membrane Environment in Mechano-Gating of the E.coli Mechanosensitive Channel MscL (01B.

THE MATERNAL-FETAL MEDICINE: AN UPDATE

The development of Maternal-Fetal Medicine is contributing to an improvement of maternal well-being and of neonatal health, introducing a number of new and useful technologies. Advances in genomics in the field of prenatal screening and diagnosis allowed the discovery of fragments of cell-free fetal DNA in the maternal circulation and the use of chromosomal microarrays, which can test for microdeletions and microduplications in addition to aneuploidies. Color Doppler applications during pregnancy are expanding exponentially and Doppler flow velocity waveforms indices have provided important information from maternal, placental and fetal circulation with clinical implications. Ultrasound monitoring of fetal growth represents a fundamental tool to evaluate fetal wellbeing and several methods have been developed to improve fetal weight estimation accuracy. The combination of new biophysical and biochemical markers is enriching Maternal-Fetal Medicine and more research will allow to improve pregnancy outcome.

Challenges and opportunities of irrigated crop production in Gedeb river catchment: Machakel Woreda, East Gojjam Zone

This study has investigated the socioeconomic, institutional and biophysical constraints, opportunities, to what extent irrigation could improve the income of households and create employment opportunities in irrigated crop production. The river catchment has different agro-ecology and socioeconomic situations; thus, it was classified as upper, middle and lower catchments. From Laytemamagn, Yewela and Gotu irrigation areas 35, 70 and 35 households sampled randomly, and respectively. Survey, participatory rural appraisal tools and secondary sources were employed to collect primary and secondary data. For data analysis, one way ANOVA, T-test, Chi-square test, and mean were employed. The study revealed irrigated land holding size of farmers in Yewela was greater than lower and upper which cause to diversify livelihood strategy of farmers in Laytemamagn than Gotu. Crop intensity in Laytemamagn and Yewela was 200%. The extension service was inadequate and not packaged. Credit service bureaucracy like group collateral was constrained to improve irrigated crop production. Water governance was done by water users but interference by the government bodies aggravated water use conflicts. Streams drying, percolation and seepage of water determined water availability. Irrigation created employment opportunity for household members and the rural community, and also improved income. Therefore, policy makers and development practitioners should develop policies and strategies based on the agroecology and socioeconomic settings of irrigation areas to alleviate the challenges, and consolidate the opportunities.   Key words: Socioeconomic, institutional, biophysical.

The improved Riccati equation mapping method for constructing many families of exact solutions for a nonlinear partial differential equation of nanobiosciences

In this paper we apply the improved Riccati equation mapping method to construct many families of general exact solutions of a nonlinear partial differential equation involving parameters of special significant for nanobiosciences and biophysics, namely, the equation of nano-ionic currents along microtublues. Comparison between our new results and the well-known results are given. The nonlinear equation elaborated here is quite original and proposed in the context of important nanosciences problems related with cell signaling. It could be even of basic importance for explanation of congnitive processes in neurons. We can successfully recover the previously known exact solutions that have been found by other methods. The proposed method in this article can be applied to many other nonlinear partial differential equations.   Key words: Improved Riccati equation mapping method, exact traveling wave solutions, nonlinear partial differential equation of nano-ionic currents along  microtublues.

TU‐G‐108‐01: Prediction in Clinical Response to Radiation Therapy for Head and Neck Cancer

Purpose: A tumor control probability (TCP) model incorporating a generalized linear‐quadratic (gLQ) model was investigated to predict clinical outcome after radiation therapy for patients. The clinical utility of the model incorporating the following individually measured radiobiology parameters: intrinsic radiosensitivity, proliferation and number of clonogenic cells, was evaluated. The hypothesis in the study was that the incorporation of individually measured tumor parameters into the TCP model would increase its reliability in predicting treatment outcome compared with the use of average population derived data. Methods: 46 patients with head and neck tumors were included and most of them received both external beam radiotherapy and brachytherapy (as published in Acta Oncologica, 2009; 48:584–590). Primary tumor size was drawn from case records and pre‐treatment CT scans or MRI using two or three dimensional measurements to calculate tumor volume. Surviving fraction after 2 Gy (SF2), reflecting intrinsic radiosensitivity, was estimated by a soft‐agar clonogenic assay (as published in Int J Radiat Oncol Bio Phys, 2000; 46:13–19). Eighteen patients receiving external beam treatment alone were used to perform statistical analyses. Local control was determined by follow‐up records. Results: SF2 correlated significantly with tumor response (p=0.04, Mann‐Whitney test), but initial tumor volume did not (p=0.6). Eight of the 18 patients had a >95% calculated tumor control probability and none developed a local recurrence, yielding a negative predictive value of 100%, compared with 67% for population‐derived data. There was a statistically significant difference in local control levels between the patient group with >95% vs. <5% predicted probability of local control (p<0.001). Conclusion: The results suggest that incorporation of measured biological data within a TCP radiobiological model would improve its ability to predict radiation therapy outcome.

Boundary Integral Method in the Theory of Bone Porothermoelasticity

The concept of porous media is used in many areas of applied science(e.g., biology, biophysics, biomechanics) and engineering. The doubleporosity model would consider the bone fluid pressures in the vascularporosity and lacunar-canalicular porosity. A porothermoelastic approachfor double porosity materials combines the theory of heat conduction withporoelastic constitutive equations, coupling the temperature field with thestresses and the pore and fissure fluid pressures.This paper concerns with the quasi-static coupled linear theory of boneporothermoelasticity for materials with double porosity and some basic resultsof the classical theory of thermoelasticity are generalized. The systemof equations of this theory is based on the equilibrium equations, conservationof fluid mass, the effective stress concept, Darcy’s law for materialwith double porosity and Fourier law of heat conduction. The fundamentalsolution of the system of governing equations is constructed by means ofelementary functions and its basic properties are established. The Green’sformulas in the considered theory are obtained. The formulas of Somiglianatype integral representations of regular vector and regular (classical) solutionsare presented. The uniqueness theorems for classical solutions of theinternal and external boundary value problems are proved. The singlelayer,double-layer and volume potentials are constructed and their basicproperties are established. Finally, the existence theorems for classical solutionsof the boundary value problems are proved by means of the boundaryintegral method and the theory of singular integral equations.

INTERACTIVE EFFECTS OF SALINITY AND CALCIUM ON HYDRAULIC CONDUCTIVITY, OSMOTIC ADJUSTMENT, AND GROWTH IN PRIMARY ROOTS OF MAIZE SEEDLINGS

ABSTRACT Increasing the calcium ion activity in salinized root media has often been shown to ameliorate the inhibitory effect of salinity on plant growth. In order to better define the biophysical mechanisms involved in these growth responses, we investigated the interactive effects of salinity and calcium on hydraulic conductivities and osmotic potential gradients in roots of maize seedlings. The length of the primary roots was reduced by 54% after 4 days of growth in 0.1-strength Hoagland solution salinized with 100 mM NaCl and by 20% when 10 mM calcium was also added to the salinized root medium. Roots showed 69% osmotic adjustment in response to salinization, with or without extra calcium in the root medium. The mean hydraulic conductivity, L, of the apical 4 cm of maize seedling roots was determined by assaying osmotically-induced backflow. The assay was sensitive enough to detect reductions in L induced by lowering the assay temperature from 27 to 14°C. These reductions in L exceeded those caused by...

Impacts of climate change on marginal community and bio-diversity in Terai, Nepal

6Food and Agriculture Organization (FAO), Nepal. 7 Institute of Forestry (IOF), Hetauda, Nepal. 8 Netherlands Development Organisation, Nepal. Accepted 12 October, 2012 This paper aims at exploring the impacts of climate change on the marginal communities and the status of silvo-agriculture species. Mahottary district of Nepal was selected for this study in 2012. A pertinent questionnaire was used to determine the impacts of climate change. The key respondents were interviewed and workshops organized at three different levels to triangulate the information. Stratified random sampling was applied to collect the bio-physical data. The results showed a shift in flowering and ripening seasons of agriculture crops. The associate species of Shorea robusta were at threat. Those species were abundant in the past, but rarely found nowadays. The values of Shannon Weinner and Simpson indices were 2.53 and 0.86 respectively in 2005 and 2.34 and 0.85 respectively in January, 2012 showing the impacts of climate change on forest species. Bees that make hive on Bombax ceiba were not found and the marginal communities were affected. Similarly, Terai indigenous communities and Dalits were found to have been affected because of insufficient fish in the paddy fields. Frogs and storks were scarcely found in the farmlands. Extreme drought, untimely floods and mass-wasting have been damaging the wealth and health in the locality.

Moisturizing effect of cream containing Moringa oleifera (Sohajana) leaf extract by biophysical techniques: In vivo evaluation

The purpose of this present investigation is to evaluate the moisturizing effects of cosmetic creams containing extract of Moringa oleifera leaves (Sohajana) by non-invasive bioengineering techniques. The study was conducted during the winter months (October to January). A total of eleven healthy male volunteers with ages between 20 and 35 years contributed to accomplish this single blind study. The active cream and base were applied twice daily to the face (cheeks) for a period of 12 weeks. The instrumental measurements were carried out with tewameter and corneometer under a draught-free room, with controlled temperature (18.0 to 20.6°C) and relative humidity (55 to 65%). The results recommended that the assessed outcome was very well accepted, and improved skin hydration and skin barrier function by the test product. There was a significant decrease in skin transepidermal water loss (TEWL) and increase in skin hydration achieved when ANOVA and paired t-sample test were applied.   Key words: Moringa oleifera, extract, cream, corneometer, tewameter, moisturizer

Physical forces and non linear dynamics mould fractal cell shape: quantitative morphological parameters and cell phenotype.

Cell shape is mainly determined by biophysical constraints, interacting according to non-linear dynamics upon the basic units provided by the genome. In turn, the specific configuration a cell acquires plays a fundamental, permissive role in modulating gene expression and many other complex biological functions. Cell shape is tightly connected to cell activity and can be considered the most critical determinant of cell function. As a consequence, measurable parameters describing shape could be considered as 'omics' descriptors of the specific level of observation represented by the cell-stroma system. Such an approach promises to formalize some of the underlying basic mechanisms and, ultimately, provide a holistic understanding of the biological processes.

Эколого-рекреационный коридор в горном заповеднике Боготы

Bogota the capital of the Republic of Colombia is a tropical highland city located at 2650 m above sea level, the 25th largest city of the world and among the large, one of the highest. A proposal for integration of components of ecological networks in the Oriental Hills of Bogota, along a gradient from wild to built nature. Name as The Bogota Ecological and Recreational Corridor (C.E.R.) is based on three strategies: first a social being the largest border agreement with 53 km, along the entire eastern limit of the city. Second the biophysical which involves restoration of ecosystem, and third the socio-spatial which includes infrastructure for making an open air museum for integration and urban limit. The ultimate aim of the approach is to contribute as a pilot proposal in biodiversity managment and cultural transformation in ecological issues for the inhabitants.

Ecological and Recreational Corridor Bogotá Mountain Reserve

Bogota the capital of the Republic of Colombia is a tropical highland city located at 2650 m above sea level, the 25th largest city of the world and among the large, one of the highest. A proposal for integration of components of ecological networks in the Oriental Hills of Bogota, along a gradient from wild to built nature. Name as The Bogota Ecological and Recreational Corridor (C.E.R.) is based on three strategies: first a social being the largest border agreement with 53 km, along the entire eastern limit of the city. Second the biophysical which involves restoration of ecosystem, and third the socio-spatial which includes infrastructure for making an open air museum for integration and urban limit. The ultimate aim of the approach is to contribute as a pilot proposal in biodiversity managment and cultural transformation in ecological issues for the inhabitants.

Development of a scaffold displaying exoloops of RXFP1.

Relaxin family peptide receptor 1 (RXFP1), the cognate receptor for relaxin, is a G-protein coupled receptor (GPCR) possessing a unique extracellular region consisting of a domain of 10 leucine rich repeats (LRRs) linked to an N-terminal low density lipoprotein Class A module. Relaxin binds to its receptor primarily by a high affinity interaction with the LRRs. An additional low-affinity interaction has been proposed to occur between relaxin and the the exoloops (ELs) of the transmembrane domain, however the molecular detail of this interaction remains undefined. While site directed mutagenesis and subsequent functional characterisation of these mutants traditionally allows identification of residues contributing to receptor function, in this case results are complicated by the presence of the high affinity binding site in the LRRs. To create a tool to investigate the low-affinity interaction, a protein scaffold system displaying exoloops 1 and 2 from RXFP1 was designed. This was achieved by inserting RXFP1 exoloops 1 and 2 into the native loops of a thermostabilised 6 kDa GB1 protein creating EL1/EL2-GB1. This protein has been expressed and purified in milligram quantities and used in conjunction with biophysical techniques such as NMR to explore relaxin binding to the exoloops of RXFP1.

Strategy of Establishing a Rosehip Plantation Using Varieties of Rosa Canina from Spontaneous Flora of Transylvania

This study presents the methodology to achieve a plantation of wild rose, using fourvarieties of Rosa Canina from wild flora of Transylvania. Also has been considered: how to harvestthe plant material, market demand for vegetable raw material costs to establish, maintain the cultureand life of a culture. Vegetative material consists of four varieties of Rosa Canina, seen as valuable fortheir high content in vitamin C, fruit size and productivity. These varieties were selected based onmacroscopic, biophysical and biochemical studies. The results obtained can be achieved in a breedingground to be studied, characteristics of the four biotypes considered valuable. These characteristics canbe improved by scientific methods of selection and be homologated the plants which provide the bestefficiency. Planting material created and certified must then be extended by a specific technology to alarger culture.

Morphological characterization and identification of the variety and the form of eight biotypes of Rosa canina from Transylvania.

Dog Rose is a shrub species which has many varieties due to adaptation to differentenvironmental conditions. This study aims to describe the morphology of: shoots, leaves, thorns,flowers, hips (false fruits) and seeds of Rosa canina for eight biotypes of wild flora of Transylvania.Also aims to identify macroscopic features, biometric and organoleptic characteristics of rosehip fruit.Desired identifying variety and form it belongs to each of the biotypes studied. Based on theinvestigations can be selected the best genitors in the rosehip fruit size and its production. Themethodology used includes macroscopic analysis of 50 samples for each character studied of eachbiotype. There are obvious morphological differences between hips in terms of weight (1.17-3.25 g),size (1.2-4.6cm long), seeds number, fruit size and color. The explanation is that biotypes analyzed arefrom different areas with altitudes between 173-1250m. As a result studies have identified eightbiotypes of rosehip varieties and forms as belonging to the following: Var. Lutetiana f. psilogyna(Arad, GalE™a), f. flexibilis (Cluj, Feleac), f. fallens (Satu-Mare, Petea); Var. Transitoria f. ramosissima(BistriE›a-NAƒsAƒud, AgieE™el), f. montivaga (BistriE›a-NAƒsAƒud, Salva); Var. Andegavensis f. vinealis(BistriE›a-NAƒsAƒud, Beclean); Var. Assiensis (Cluj, MAƒnAƒE™tur); Var. Andegavensis f. transsilvanica(SAƒlaj, Buciumi). The results are expressed during the research that indicates the information,morphological, genetic, biological and biophysical. Analyzed biotypes can also provide solutions forquick and efficient recovery of degraded land, aspect important in the context of global warming.

Agricultural Landscapes and Biodiversity Conservation in Italy

In the last decades, agricultural areas have been acknowledged as important areas forbiodiversity conservation and provision of ecosystem services. Several international and nationalConventions have promoted the development of multifunctional agriculture and the maintenance oftraditional cultural landscapes. In this general context, this paper presents some relevant researchexperiences carried out in Italy at different spatial scales, from national to local (Province andMunicipality of Rome). The results of these studies confirm that traditional agricultural areas supportthe conservation of habitats and species of national and European interest and represent importantelements for environmental quality at the landscape scale. Moreover, they highlight the importance oftaking into account the biophysical environment, together with historical and cultural features, formapping and charactering traditional agricultural landscapes, as well as the need to focus on thedynamics of agricultural land, which is threatened by land cover change.