Biophysical Research Articles

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.

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.

Analysis on Urban Heat Island Effect of the Different Dynamics of Urban Surface Biophysical Descriptors in Shanghai City

Analysis on Urban Heat Island Effect of the Different Dynamics of Urban Surface Biophysical Descriptors in Shanghai City

Studies on the Antimutagenicity and Antioxidant Activity of the Hot Water Extract of Glechoma hederacea

Several studies have demonstrated that herbal plants contain various potential antioxidants and these antioxidant components may be potential antimutagens or anticarcinogens. Glechoma hederacea belongs to the Labiatae family. According to ancient Chinese prescriptions, G. hederacea was used for treating diuresis and stimulating blood circulation. However, there are few reports on its biophysical functions to date. The objective of this study was to evaluate the antioxidant, mutagenic and antimutagenic activities of the hot water extract of G. hederacea (HWG). G. hederacea was extracted with distilled water at 100℃ for 3h. The antioxidant activities tested included α,α-diphenyl-s-picrylhydrazyl (DPPH), 2,2'-azino-bis (3-ethylbenzthiazoline-6-sulphonic acid) and superoxide anion radical-scavenging effects, Fe^2+ -che1ating ability, reducing power and lipid peroxidation inhibition. The in vitro mutagenic and antimutagenic properties of the extracts were investigated using the Ames test. The results showed that HWG possessed antioxidant characteristics. Moreover, the antioxidant activities of HWG were significantly higher than those of Vitamin C and Trolox in terms of superoxide anion radical scavenging activity and Fe^2+ -chelating ability (p ＜ 0.05). The results of Ames test indicated that HWG had no mutagenicity toward all tester strains including Salmonella typhimurium TA97, TA98, TA100, TA102 and TA1535 with/without the metabolic activator (S9 mix). The extracts had marked inhibition effects against the mutagenicities of the diagnostic mutagens with the S9 mix System. The HWG showed antioxidant and anti-mutagenic potential. However, the active compounds of HWG need be further investigated.

A fast and accurate method for large-scale transmembrane beta barrel topology prediction

Transmembrane beta barrel proteins (TMBs) play a major role in the normal functioning of the cell and are an important constituent of the translocation machinery of the outer membrane proteins in bacteria, mitochondria and chloroplast. Currently there are only around 36 experimental 3D structures available for TMBs in PDB (at 30% sequence identity). Furthermore, with large amounts of sequence data available from high-throughput methods, it is imperative to develop accurate and fast computational methods for their identification and topology prediction. Here, we present a concept for a fast method to identify TMBs and predict their topology. The method uses sparse encoded amino acid data as input and employs a Support Vector Machine (SVM) and a Hidden Markov Model (HMM) to generate accurate topologies. The topologies in the training phase are divided into pre-barrel state, outer-loop state, inner-loop state and the transmembrane beta-strand state. In the first stage, 4 separate SVMs are used to predict the local state preference for each residue. A profile generated from the probabilities thus obtained is used as input to the HMM stage to determine the overall topology. If the number of predicted strands is between 8 and 24, then the given sequence is identified as a TMB. We see the application of our method in the proteome-wide topology prediction of TMBs, where current methods might have a limitation due to the time consuming homologous sequence search step. Funding Christoph Peters: Travel Fellowship awarded by ISCB Student Council with financial support from EMBO, 2012 J-A Ekstroms travel stipend, 2012 A fast and accurate method for large-scale transmembrane beta barrel topology prediction

Clinical use of placental hormones in pregnancy management.

Across human pregnancy, placenta represents a transit of oxygen and nutrients from the mother to the fetus and actively produces a large number of hormones that serve to regulate and balance maternal and fetal physiology. An abnormal secretion of placental hormones may be part of the pathogenesis of the main obstetric syndrome, from early to late pregnancy, in particular chromosomopathies, miscarriage, gestational trophoblastic diseases, preeclampsia, gestational diabetes, and pre-term delivery. The possibility to measure placental hormones represents an important tool not only for the diagnosis and management of gestational disorders, but it is also fundamental in the early identification of women at risk for these pregnancy complications. In the last decades, the use of ultrasound examination has provided additional biophysical markers, improving the early diagnosis of gestational diseases. In conclusion, while few placental hormones have sufficient sensitivity for clinical application, there are promising new biochemical and biophysical markers that, if used in combination, may provide a valid screening tool.

Extracellular matrix, biotensegrity and tumor microenvironment. An update and overview.

The extracellular matrix (ECM) constitutes a three-dimensional network that surrounds all cells, organs and tissues in the body. It forms a biophysical filter for protection, nutrition and cell innervation, as well as the medium for facilitating immune response, angiogenesis, fibrosis and tissue regeneration. It is the mechanism by which mechanical forces are transmitted to the basement membrane which, through the integrins, supports the tensegrity system and activates the epigenetic mechanisms of the cell. A review and update on current knowledge on this topic reveals how disturbance of the ECM leads to a loss of efficient filtering, nutrition, elimination, and cell denervation functions, in addition to loss of regeneration capacity and disorders in mechanotransduction. Furthermore, such disturbance results in a loss of substrate, and with it the ability to provide a proper immune response against tumor, toxic and infectious agents. Reciprocal communication between ECM stromal and parenchymatous cells directs gene expression. The oncogenic capacity of the stroma derives from the associated cells as well as from the tumor cells, the angiogenic microenvironment and from an alteration in tensegrity; all of which are dependent on the ECM. It has been shown that the malignant phenotype is reversible by correction of the altered cues of the ECM.

Simulation of resource-conserving technologies on productivity, income and greenhouse gas GHG emission in rice-wheat system

The Rice-wheat (RW) cropping system is one of the major agricultural production systems in four IndoGangetic Plains (IGP) countries: India, Pakistan, Bangladesh and Nepal of South Asia covering about 32% of the total rice area and 42% of the total wheat area. The excessive utilization of natural resource bases and changing climate are leading to the negative yield trend and plateauing of Rice-wheat (RW) system productivity. The conservation agriculture based efficient and environmental friendly alternative tillage and crop establishment practices have been adopted by the farmers on large scale. A few tools have been evolved to simulate the different tillage and crop establishment. In the present study, InfoRCT (Information on Use of Resource Conserving Technologies), a excel based model integrating biophysical, agronomic, and socioeconomic data to establish input-output relationships related to water, fertilizer, labor, and biocide uses; greenhouse gas (GHG) emissions; biocide residue in soil; and Nitrogen (N) fluxes in the rice-wheat system has been validated for farmer participatory practices. The assessment showed that double no-till system increased the farmer’s income, whereas raised-bed systems decreased it compared with the conventional system. The InfoRCT simulated the yield, wateruse, net income and biocide residue fairly well. The model has potential to provide assessments of various cultural practices under different scenarios of soil, climate, and crop management on a regional scale.

2PT102 蛋白質・蛋白質相互作用ネットワークにおけるドメイン及び非ドメイン間相互作用の解析(日本生物物理学会第50回年会(2012年度))

2PT102 蛋白質・蛋白質相互作用ネットワークにおけるドメイン及び非ドメイン間相互作用の解析(日本生物物理学会第50回年会(2012年度))

Development of Neutron Biophysics

Development of Neutron Biophysics

What is in Nanoscience for Biophysics?

What is in Nanoscience for Biophysics?

A Review on the Principles and Basic Methods of Remote Sensing Spectral Characteristic Parameters

The principles and methods of remote sensing spectral characteristic parameters including derivative spectrum,red edge parameter,spectrum absorption characteristics and spectrum reflectance characteristics,national and international development of hyperspectral remote sensing and its application in extracting biophysical and biochemical information of vegetation,and the feasibility of vegetation indices application are reviewed.The potentiality of further application of remote sensing technology in extracting vegetation information in order to promote remote sensing was put forward.Remote sensing spectral parameter provides a powerful tool for extracting vegetation biophysical and biochemical information.

Adoption behaviour of the farmers of Goalpara district of India towards aquaculture technology

A study was conducted during 2009 to 2010 to investigate the adoption behaviour of the fish growers towards the innovations in aquaculture technology in Goalpara district of Assam. The district produces 5,347 tonnes of fish per annum against its biophysical potential of 40,969.25 tonnes. Seven critical recommended practices of pond management were selected to study the extent of adoption and correlated with thirteen socio-economic and psychological variables of the growers. Statistical techniques and tools like frequency and percentage analysis, mean score, standard deviation (SD), Co-efficient of variance (CV) and simple correlation were used. The results revealed that the farmers of the district have not yet adopted the recommended package of practices and they lack entrepreneurial spirit in aquaculture operation. The study suggested the need of paradigm shift from the current perception on aquaculture as a poverty alleviation programme to a prestigious income generating enterprise.    Key-words: Aquaculture, adoption behaviour, pond management, scaling up.

Lipid–Drug Interaction: Biophysical Effects of Tolmetin on Membrane Mimetic Systems of Different Dimensionality

This work focuses on the application of different biophysical techniques to study the interaction of tolmetin with membrane mimetic models of different dimensionality (liposomes, monolayers, and supported lipid bilayers) composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), used as a representative phospholipid of natural membranes. Several biophysical techniques were employed: Fluorescence steady-state anisotropy to study the effects of NSAIDs on membrane microviscosity and thus to assess the main phase transition of DPPC, surface pressure-area isotherms to evaluate the adsorption and/or penetration of NSAIDs into the membrane, IRRAS to acquire structural information of the lipid membrane upon interaction with the drugs, and AFM to study the dynamic change in surface topography of the lipid bilayers caused by interaction with tolmetin. The experiments were performed taking into account the physiological conditions that tolmetin may find in the course of its in vivo therapeutic activity. Therefore, the studies covered the interactions of tolmetin with lipid membranes in both gel and liquid-crystalline phases at two pH conditions: 7.4 (plasma pH) and 5 (inflamed tissue pH). The applied models and techniques provided detailed information about different aspects of the tolmetin-membrane interaction. The studies have shown that tolmetin-membrane interaction is strongly dependent on the degree of drug ionization and of the lipid phase state, which can be related with the therapeutic action and gastro intestinal toxicity of this drug.

Biophysics and nanotechnologies: Problems and prospects

Biophysics and nanotechnologies: Problems and prospects

Research on the Reconstructing of Time-series NDVI Data

Although the Normalized Difference Vegetation Index(NDVI) time-series data derived from NOAA/AVHRR,SPOT/VEGETATION and MODIS,has been successfully used in research regarding global vegetation change,land cover classification and biophysical parameters inversion.However,due to effect of cloud and atmospheric conditions,residual noise in the NDVI time-series data will induce erroneous results in our further quantitive analysis.In this paper,some general reconstructing methods are introduced,including Maximum Value Compositing(MVC),the Best Index Slope Extraction(BISE),Media Iteration Filter(MIF),Temporal Window Operation(TWO),Fourier Transform(FT) and Savitzky-Golay Filter(S-G Filter).With the development of change detection research,it is necessary to reconstruct the NDVI time-series data sets in order to provide high-quality data for the study of vegetation response to global climate change.

Sensory input regulates spatial and subtype-specific patterns of neuronal turnover in the adult olfactory bulb glomeruli

Masato Sawada,1 Naoko Kaneko,1 Hiroyuki Inada,2 Hiroaki Wake,2,3 Yasuko Kato,1 Yuchio Yanagawa,3,4 Kazuto Kobayashi,5 Tomomi Nemoto,3,6,7 Junichi Nabekura,2,3,8 and Kazunobu Sawamoto1 1Department of Developmental and Regenerative Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan, 2Division of Homeostatic Development, Department of Developmental Physiology, National Institute for Physiological Sciences, Okazaki 444-8585, Japan, 3Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama 332-0012, Japan, 4Department of Genetic and Behavioral Neuroscience, Gunma University Graduate School of Medicine, Maebashi 371-8511, Japan, 5Department of Molecular Genetics, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan, 6Supportive Center for Brain Research, National Institute for Physiological Science, Okazaki 444-8787, Japan, 7Laboratory of Molecular and Cellular Biophysics, Research Institute for Electronic Science, Hokkaido University, Sapporo 001-0020, Japan, and 8Department of Physiological Sciences, The Graduate School for Advanced Study (Sokendai), Hayama 240-0198, Japan