Biophysical Research Articles

Introduction to Biophysics Week: What is Biophysics?

DNA-binding regulation of tumor suppressor p53 revealed by biophysical approach

The biophysics, biochemistry and physiology of CFTR

OP12.07: Prediction of pre‐eclampsia by maternal characteristic and biophysical markers during the first trimester of pregnancy

P16.04: Hemodynamic, biophysical and biochemical assessment in the first trimester as early screening for patients at risk of pre‐eclampsia

An Individual Tree-Based Automated Registration of Aerial Images to Lidar Data in a Forested Area

Abstract In this paper, we demonstrate an approach to align aerial images to airborne lidar data by using common object features (tree tops) from both data sets under the condition that conventional correlation-based approaches are challenging due to the fact that the spatial pattern of pixel gray-scale values in aerial images hardly exist in lidar data. We extracted tree tops by using an image processing technique called extended-maxima transformation from both aerial images and lidar data. Our approach was tested at the Angelo Coast Range Reserve on the South Fork Eel River forests in Mendocino County, California. Although the aerial images were acquired simultaneously with the lidar data, the images had only approximate exposure point locations and average flight elevation information, which mimicked the condition of limited information availability about the aerial images. Our results showed that this approach enabled us to align aerial images to airborne lidar data at the single-tree level with reasonable accuracy. With a local transformation model (piecewise linear model), the rmse and the median absolute deviation ( mad ) of the registration were 9.2 pixels (2.3 meters) and 6.8 pixels (1.41 meters), respectively. We expect our approach to be applicable to fine scale change detection for forest ecosystems and may serve to extract detailed forest biophysical parameters.

Comparison of Landsat 8 OLI and Landsat 7 ETM+ for estimating grassland LAI using model inversion and spectral indices

The leaf area index LAI is the key biophysical indicator used to assess the condition of rangeland. In this study, we investigated the implications of narrow spectral response, high radiometric res...

Research properties of the environment on basis of vegetable components from extract soy at the cryopreservation of sperm of bulls

By cryobiological, immunological and biophysical methods it is established that in the mechanism of temperature shock of cell the leading role is assigned to osmosis, and instant movement of water through it at the expense of an equilibration of osmotic pressure that is the reason of destruction of a cell membrane deprives a cytoplasmic membrane of properties of semipermeability. It was studied the fortification mechanism sperm when cooling and it is established that the fortificant accumulates on surfaces of a cell and creates a hydrophobic phase that slows down the osmotic action connected with an balancing  of concentration gradients in ''cell-wednesday'' system. It is established, also, that the protective layer is created on a cytoplasmatic membrane on an extent of 2-5 minutes from the moment of its contact with an anti-shock component – fortificanty and then strongly is kept on it even at reusable washing of cells by isotonic environments. These theoretical research were taken as a basis of a technique of determination of anti-shock properties of cryoresistance various the bioactive substances and biochemical connections by search, development and improvement of environments for a cryopreservation of sperm of different types of animals. When freezing sperm in nitrogen, an obligatory component of the cryoprotective environment is the native yolk of eggs containing many phospholipids and lipoproteins which at interaction with plasma membranes sperm modify them by increase of resistant and stability. Being adsorbed by lipophilic and hydrophilic sites of plasma membranes lipid complexes almost by 2-3 times thickencell membrane that gives stability to sperm to extreme temperature, osmotic, immunological, physical and chemical and mechanical to damages.

[Study on the Prediction of Cotton Yield within Field Scale with Time Series Hyperspectral Imagery].

Pixel-based processing method mainly extracts spectral information from hyperspectral remote sensing images, but site specific management zone (SSMZ) delineation and crop yield estimation with images need to take spatiotemporal heterogeneity into account. As the spatial resolution of remote sensing data increases, the so-called “salt-and-pepper” problem of pixel-based classification becomes more serious. The spatiotemporal heterogeneity of soil properties and crop biophysical parameters are mainly delineated with grid sampling and geostatistics interpolation, but the widely used method has some problems: time consuming and high cost. Satellite imageries are introduced to delineate SSMZ, but there are also problems needed to be resolved: (1) single date imagery is used to map SSMZ which is difficult to determine the optimal date for SSMZ delineation; (2) only few SSMZs were mapped, which limited application of site specific fertilizing and management; (3) pixel-based method for SSMZ delineation didn’t concern the spatial relationship between pixels and site specific management does not implement at pixel level, but at SSMZ level. To improve the accuracy of crop yield estimation, a time-series of hyperspectral airborne images with high spatial resolution (1 m) of a cotton field, which is located in San Joaquin Valley, California US, were acquired and classified by using object-oriented segmentation, then yield predicting models were built, and the accuracy and stability of yield models were validated with determining coefficients R2 and the root mean square error (RMSE). Results are as follows: (1) object-oriented SSMZ delineating method combines spectral, spatial and temporal information, reduces noises in images and yield data, improves the accuracy of yield prediction; (2) for same SSMZ number, first derivative predicting model is more accurate; (3) for same spectral input, models with fewer SSMZs show higher accuracy, which is due to spatial errors of airborne images and yield data. The results will improve monitoring methods for crop growth and yield while accelerate the application of UAV remote sensing in precision agriculture.

Science Writing Workshop

The Current Science Association has introduced Science Writing Workshops for the benefit of students, teachers and researchers to improve their science writing skills. The first such workshop was held in Bengaluru. Inaugurating the workshop, P. Balaram (Molecular Biophysics Unit, IISc and former Editor of Current Science ) gave a brief history of Current Science . The journal, founded in 1932 has completed 84 years. He mentioned that punctuality in publication has been a remarkable feature of the journal.

On the molecular mechanism that links glycation with aggregation: the case of lysozyme glycated with ribose

Protein glycation (PG) usually induces the loss of protein function and consequently, the development of diabetes-related diseases1. It has been assumed that this process occurs as a result of a structural modification induced by PG, which is also able to trigger protein aggregation. Therefore, neurodegenerative disorders such as Parkinson or Alzheimer diseases increase their prevalence under diabetes mellitus. Trying to describe in detail the molecular mechanism that links PG with protein aggregation we have studied the glycation of lysozyme (HEWL) with ribose2. HEWL has been used as a model since it holds a reduced aggregation tendency under its native state and possesses putative glycation targets (lysine and arginine)3. On the other hand, ribose induces protein aggregation4 and it physiological concentration rapidly rises in diabetic patients5. Through the combination of different biophysical techniques (NMR, CD, SAXS, etc.), we have proved that HEWL glycation mediated by ribose mainly occurs on lysine without altering the protein structure. However, glycation induces a change on the overall protein charge generating different hydrophobic patches which are responsible for the native aggregation of glycated HEWL. This aggregation process initiates with the formation of soluble oligomers which finally assemble to form insoluble aggregates.

Значение симпатовагального баланса как биофизического маркера преэклампсии

Преэклампсия (ПЭ) является одним из серьезных осложнений беременности, которое приводит к синдрому полиорганной недостаточности. Целью исследования было изучение взаимосвязи симпатовагального баланса и типа центральной материнской гемодинамики у беременных с ПЭ. Материалы и методы. Было проведено изучение типа центральной материнской гемодинамики и вариабельности сердечного ритма у 102 пациенток в 32–37 недель беременности. 30 из них были с физиологическим течением процесса гестации и составили группу I (контроля). Во II группе под наблюдением находилось 40 беременных с ПЭ легкой и средней степени. К III группе были отнесены 32 пациентки с ПЭ тяжелой степени. Результаты. Показатели вариабельности сердечного ритма матери отражали гиперсимпатикотонию на фоне ПЭ. Полученные данные подтверждали известную гипердинамическую модель легкой и среднетяжелой ПЭ. Сохранность гестационной гиперволемии на фоне повышенного периферического сопротивления сосудов приводила к увеличению сердечного выброса. Переход к гиповолемии и низкому сердечному выбросу отражал гиподинамическую гемоциркуляцию на фоне тяжелой ПЭ. Повышение симпатовагального баланса было признаком вазоконстрикции и гипоперфузии. Это было подтверждено наличием сильной корреляции между симпатовагальным балансом и общим периферическим сопротивлением сосудов (R = 0,70; р < 0,05), симпатовагальным балансом и сердечным индексом (R = –0,63; р < 0,05 ). Вывод. Повышение симпатовагального баланса более 2,0 было биофизическим маркером ПЭ.

Biophysics to bedside — the transition

Building biophysics in China

Principles and Methods for the Retrieval of Biophysical Variables in Mountainous Areas

Relationships between normal or borderline blood pressure and some neural, endocrine, metabolic and biophysic parameters in women and men

Vovchyna Yuliya V., Voronych Nataliya M., Zukow W alery, Popovych Igor L. Relationships between normal or borderline blood pressure and some neural, endocrine, metabolic and biophysic parameters in women and men. Journal of Education, Health and Sport. 2016;6(2):163-182. eISSN 2391-8306. DOI http://dx.doi.org/10.6084/m9.figshare.2525023 http://ojs.ukw.edu.pl/index.php/johs/article/view/3396 https://pbn.nauka.gov.pl/works/715715 The journal has had 7 points in Ministry of Science and Higher Education parametric evaluation. Part B item 755 (23.12.2015). 755 Journal of Education, Health and Sport eISSN 2391-8306 7 © The Author (s) 2016; This article is published with open access at Licensee Open Journal Systems of Kazimierz Wielki University in Bydgoszcz, Poland Open Access. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. This is an open access article licensed under the terms of the Creative Commons Attribution Non Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted, non commercial use, distribution and reproduction in any medium, provided the work is properly cited. This is an open access article licensed under the terms of the Creative Commons Attribution Non Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted, non commercial use, distribution and reproduction in any medium, provided the work is properly cited. The authors declare that there is no conflict of interests regarding the publication of this paper. Received: 05.01.2016. Revised 12.02.2016. Accepted: 21.02.2016. RELATIONSHIPS BETWEEN NORMAL OR BORDERLINE BLOOD PRESSURE AND SOME NEURAL, ENDOCRINE, METABOLIC AND BIOPHYSIC PARAMETERS IN WOMEN AND MEN Yuliya V. Vovchyna 1,2 , Nataliya M. Voronych 2 , W alery Zukow 3 , Igor L. Popovych 4 1 Sanatorium “Kryshtalevyǐ Palats” SAD , Truskavets’, Ukraine yulija_if@mail.ru 2 Department of Normal Physiology, National Medical University, Ivano-Frankivs’k, Ukraine 3 Faculty of Physical Education, Health and Tourism, Kazimierz Wielki University, Bydgoszcz, Poland w.zukow@ukw.edu.pl 4 Laboratory of Experimental Balneology, OO Bohomolets’ Institute of Physiology NAS, Truskavets’-Kyiv , Ukraine i.popovych@biph.kiev.ua Abstracts Background. We conduct a systematic study of the effect of balneotherapy spa Truskavets (Ukraine) on blood pressure. The aim of this study is to elucidate the links between normal and marginal blood pressure, on the one hand, and some neural, endocrine, metabolic and biophysical factors on the other. Material and research methods. We recorded twice at ten women and ten men aged 33-76 years without clinical diagnose Blood Pressure, Heart Rate, heart rate variability (HRV), electroencephalogram (EEG), electro-skin conductance acupuncture points (ESCAP) Pg(ND), TR(X) and MC(AVL), determined the rate of electronegative nuclei of buccal epithelium (named as Electrokinetic Index) as well as plasma levels of Calcitonin, Testosterone, Cortisol, Triiod-thyronin, Cholesterol, Uric Acid, Chloride, Phosphate, Sodium, Potassium, Calcium and Magnesium. Results. Observed contingent characterized generally normal for a particular age or borderline high blood pressure, predominantly diastolic. In the final regression model were included 4 metabolic parameters (Cholesterol, Uric Acid, Phosphate and Calcium), 3 neural (α-rhythm Index as well as RMSSD and Triangulary Index as markers of Vagal tone) and ESCAP  TR(X) Right as marker activity of endocrine system, which taken together determines Systolic Blood Pressure on 77%. Diastolic Blood Pressure determined on 74% by 7 neural parameters (4 HRV markers of Vagal and Sympathetic tone as well as α-rhythm Amplitude and Deviation and θ-rhythm Frequency), 2 biophysic parameters (ESCAP  TR(X) Right and Electrokinetic Index as marker of biological age) as well as Chloride and Hender. Conclusion. Normal and marginal blood pressure determined by some neural, biophysical and metabolic factorss well as Hender. Keywords: blood pressure, HRV, EEG, hormones, electrolytes, relationships.

The Perfect Enzyme : Revisiting the Modelling of Initial Proton Transfer in Triosephosphate Isomerase.

The understanding of the factors governing the enzyme catalysis is one of the most important goals of biochemistry and biophysics. In this context the contribution of theoretical research might be of high relevance. However, despite the huge amount of proposed approaches, the modelling of enzyme reactions still represents a very difficult task and a definitive and conclusive theoretical-computational strategy is still far from being available. In this study, after a presentation of the main difficulties associated to a coherent and possibly rigorous modelling of these processes, we present a computational theoretical method specifically designed for addressing complex molecular systems eventually applied to a benchmark reaction: the initial proton transfer in Triosephosphate Isomerase. This latter species, termed as the 'perfect enzyme' because of its exceptional ability as catalyst, provides an excellent test for evaluating the different environmental and intrinsic determinants at the basis of enzyme activity.

Involvement of Notch signaling in the osteogenic differentiation of human mesenchymal stem cells stimulated by pulsed electromagnetic fields

Biophysical stimulation with pulsed electromagnetic fields (PEMFs), used in clinics to promote bone repair, favour osteogenic differentiation in human mesenchymal stem cells (hMSCs), however their molecular mechanisms are not clarified. Notch is a pathway regulating cell fate decisions which play a role in skeletal development. Notch signaling is initiated by binding a Notch ligand to a cell surface Notch receptor, resulting in a cleavage of receptor and releasing Notch intracellular domain which translocates to the nucleus and activates transcription of nuclear Notch target genes, such as the Hes/Hey family.The aim of this study is to establish if the known PEMF-induced osteogenic effects may occur through the modulation of Notch pathway. Bone marrow hMSCs cultured in basal condition (control) and in osteoinductive medium (OM) for 28 days were unexposed or continuously exposed to PEMFs (75 Hz, 1.5 mT) (Igea, Carpi, Italy). To block Notch pathway, the Notch inhibitor DAPT was used to treat a series of hMSCs cultured in OM. At different time points (day 1,3,7,14,21,28), osteogenic markers (alkaline phosphatase activity, osteocalcin and matrix mineralization), mRNA expression of osteogenic transcription factors (Runx2, Dlx5, Osterix) as well as of Notch receptors (Notch1-4), their ligands (Jagged1, Dll1 and Dll4) and nuclear target genes (Hey1, Hey2, Hes1, Hes5) were analysed.Our results showed that osteogenic markers and transcription factors increased in OM compared to control and they were further stimulated by PEMFs. Notably, PEMFs significantly increased the expression of Notch4, Dll4, Hey1, Hes1 and Hes5 in the middle phase of differentiation in OM compared to control. In the presence of DAPT, osteogenic markers as well Hes1 and Hes5 expression were significantly inhibited, in unexposed and PEMF-exposed hMSCs. Hey1 was not inhibited by DAPT suggesting a possible regulation by other signaling pathway.These new findings show that PEMFs favor osteogenic differentiation acting through Notch pathway, adding important knowledge concerning the molecular mechanisms by which PEMFs can modulate osteogenesis. This work was supported by grants from IGEA, Carpi, Italy.

Body structure of the macedonian population

Establishing the structural components of the body: bone, muscle and fat is of great significance in sport orientation and selection as in entire biophysical development in young people. Nowdays, when there is hypokinetics in the modern world, there is a greater disbalance between active (muscle) and inactive (fat) components, which enlarge the value of “ballast” tissue. The material comprised personal files of 200 Macedonian examinees 14 years old,100 females and 100 males. On the basis of manifested anthropometrical variables, structural components of the body are established, in Macedonian children at age 14 who live in Skopje area, living in approximately equal socio-economic conditions. For quantitative determination of the absolute values of the bone (0 kg), muscle (M kg) and fat tissue (D kg), the dynamic anthropometric method by J. Meteigka was applied. At the age of 14 years, the absolute values of the bone mass (0 kg) was 9.91 (17,04%) in the males and in the females it was 7,83 (14,63%). The muscle mass (M kg) was 31.52 (52,04%) in the males and 27.89 (51.49%) in the females. The fat structural component (D kg) was 7.18 (11.14 %) in males and 7.02 (12.32 %) in females. The difference among sexes in the Macedonian population at the age of 14 years is very significant for the bone mass. At this age in male examinees bone mass is in high correlation with the diameter of the knee joint and in females with the diameter of the elbow, so they can serve as most valid sign in maintaining the bone mass. Muscle mass at 14 year age is in correlation with the circumference of the upper arm in males and with total muscle mass in females. Fat structural component at this age is higher in females then in male examinees, and is in high correlation with the body mass.

BMC Biophysics reviewer acknowledgement 2015

Contributing reviewersThe editors of BMC Biophysics would like to thank all our reviewers who have contributed to the journal in Volume 8 (2015).