Biophysical Research Articles

Analysis of amino acid variations of major proteins from severe acute respiratory syndrome coronavirus 2

Objective To identify key amino acid variations of major proteins from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by biophysical methods. Methods Through amino acid sequence alignment, classification of variant amino acid residues, three-dimensional structure reconstruction of proteins, and electrostatic interaction analysis of amino acid residues, the key amino acid variations of major proteins from SARS-CoV-2 was analyzed with RaTG13, the bat coronavirus with the highest homology, as the reference. Results At least ten amino acid variations that affect the possible electrostatic interactions were identified in RNA-dependent RNA polymerase (RdRp), exoribonuclease (ExoN), uridylate-specific endoribonuclease (NendoU), and spike (S) protein from SARS-CoV-2. These variations may affect the spatial conformation and biological functions of the proteins. Conclusion The key amino acid variations of the major proteins from SARS-CoV-2 have been preliminarily identified, providing clues for understanding the genetic, pathogenic and epidemiological characteristics of the virus..

What is your biophysics?

What is your biophysics?

Prof. F. Oosawa as a Best Mentor of Biophysics

Prof. F. Oosawa as a Best Mentor of Biophysics

Restoring lumbar lordosis: a systematic review of controlled trials utilizing Chiropractic Bio Physics® (CBP®) non-surgical approach to increasing lumbar lordosis in the treatment of low back disorders.

[Purpose] To systematically review controlled trial evidence for the use of lumbar extension traction by Chiropractic BioPhysics® methods for the purpose of increasing lumbar lordosis in those with hypolordosis and low back disorders. [Methods] Literature searches were performed in Pubmed, PEDro, CINAHL, Cochrane, and ICL databases. Search terms included iterations related to the lumbar spine, low back pain and extension traction rehabilitation. [Results] Four articles detailing 2 randomized and 1 non-randomized trial were located. Trials demonstrated increases in radiographic measured lordosis of 7–11°, over 10–12 weeks, after 30–36 treatment sessions. Randomized trials demonstrated traction treated groups mostly maintained lordosis correction, pain relief, and disability after 6-months follow-up. The non-randomized trial showed lordosis and pain intensity were maintained with periodic maintenance care for 1.5 years. Importantly, control/comparison groups had no increase in lumbar lordosis. Randomized trials showed comparison groups receiving physiotherapy-less the traction, had temporary pain reduction during treatment that regressed towards baseline levels as early as 3-months after treatment. [Conclusion] Limited but good quality evidence substantiates that the use of extension traction methods in rehabilitation programs definitively increases lumbar hypolordosis. Preliminarily, these studies indicate these methods provide longer-term relief to patients with low back disorders versus conventional rehabilitation approaches tested.

Local biophysical effects of land use and land cover change: towards an assessment tool for policy makers

Land use and land cover change (LULCC) affects the climate through both biogeochemical (BGC) and biophysical (BPH) mechanisms. While BGC effects are assessed at global scale and are at the heart of climate treaties such as the Paris Agreement, BPH effects are totally absent despite their increasingly recognized impact, especially at local scale. This stems from the complexity in characterizing their climate impacts both at local and global scale, which makes it impractical to offer clear advices for the development of climate policies. To overcome this barrier, we built a prototype for an assessment tool to evaluate the local BPH impact of a series of land cover transitions. It relies on a dedicated methodology, based on satellite remote sensing data, that can estimate the local change in near surface air temperature associated with BPH effects of potential LULCC. This tool follows a tiered methodological approach, using transparent methods and mirroring what is currently provided by the IPCC to estimate the BGC effects, i.e. through different levels of increasing methodological complexity, from Tier 1 (i.e. default method and factors) to Tier 2 (i.e. similar to Tier 1 but with higher level of details and complexity) and Tier 3 (i.e. tailored solution to address national circumstances). The prototype tool enables the evaluation of the local impacts of land-related BPH effects, therefore facilitating a scientifically informed and comprehensive assessment of land-based climate policies.

Docosahexaenoic acid and the brain- what is its role?

Docosahexaenoic acid (DHA) is a 22-carbon omega 3 PUFA highly enriched in the neuronal cell membranes and rod outer segment membranes. When DHA is depleted from these cell membranes it is replaced nearly quantitatively by a 22-carbon omega 6 PUFA, docosapentaenoic acid, which has similar, but less potent, biophysical and physiological properties to DHA. It is speculated that omega 6-docosapentaenoic acid is a buffer to prevent the possible catastrophic effects of DHA depletion on brain and visual function. The primary insult from the loss of DHA from cell membrane glycerophospholipids, and replacement by omega 6-docosapentaenoic acid, is on the flexibility/compression of the membrane lipids which affects the optimal function of integral membrane proteins (receptors, voltage-gated ion channels and enzymes). This leads to effects on second messenger systems, and subsequently affects neurotransmitter concentrations due to 'weakened' signals from the initiating receptors. Remembering there are more than 80 billion neurones and many times more synaptic connections between neurons, a very small loss of "efficiency" in signal due to altered properties of membrane proteins would likely result in meaningful changes in brain and visual function. Additionally, impairment of neurotransmission could be due, in part, to sub-optimal brain energy metabolism (glucose entry into the brain), which is significantly reduced in omega 3 deficiency. Many studies report that dietary omega 3 deficiency results in changes in learning, coping with stress, behavioural changes, and responses in visual function. It is thus concluded that DHA is an essential fatty acid for optimal neuronal function.

Regional Biophysics Conference: RBC2018.

Regional Biophysics Conference: RBC2018.

Modification of Crop-Soil Microclimate to Explore Different Biophysical Indicators and Yield Attributes of Barley (Hordeum vulgare L.)

An investigation was carried out involving two barley varieties V1 (DWRUB 52) and V2 (PL 807) grown on three different sowing windows viz. D1 (25th October), D2 (10th November), D3 (25th November) and three irrigation levels such as I1 (Recommended), I2 (Stress at vegetative stage) and I3 (Stress at anthesis period) to study the effect of changed microenvironment on different biophysical indicators and yield of barley during rabi 2016-17 at Ludhiana. Both leaf area index (LAI) and dry matter (DM) attained highest value under D2 (4.35 and 1640.1 g/m2); V1 recorded maximum DM of 1605.3 g/m2 than V2 (1579.6 g/m2) at harvesting and significant differences due to variation in moisture levels were observed from 45 days after sowing (DAS) and 60 DAS respectively till harvesting for LAI and DM. DWRUB 52 performed better in terms of several yield promoting factors as compared to PL 807. The 10th November crop yielded higher (45.31 q/ha) than that of 25th October (42.49 q/ha) and 25th November (37.95 q/ha) crop. Yield attributes and several biophysical indicators showed linear and positive relationship with grain yield.

Climate change impact factors in ECOWAS

Abstract Appropriate responses to climate change in the agriculture sector are dependent on knowledge of the status and trends of the factors of the climate change impact chain in the sector. The objective of the study was to broadly assess key human, environmental, and biophysical factors in the Economic Community of West African States (ECOWAS), mainly within the decade following the launching of the Comprehensive Africa Agricultural Development Programme (CAADP). This was done through a review of literature and analysis of data mainly from international databases. The status of and changes in these factors were generally unsatisfactory. Population growth rate was high. Average daily maximum temperatures were projected to rise by up to 3.5⁰C by 2050. Up to 35 % of the lands were estimated to be severely to very severely degraded. Internal renewable water resources per capita were below international requirements in many countries of ECOWAS. Renewable water resources per capita were more abundant but decreased over years. The substantial arable land and renewable water resources and carbon stored in soil (23503 Tg t) and forest biomass (6304 Tg t) are attributes of ECOWAS. Agricultural production was higher in the Gulf of Guinea zone compared to the Sudano-Sahelian zone but yields of some crops were higher in the Sudano-Sahelian zone. Food security status was unsatisfactory across ECOWAS although the production of major crops (in most cases), livestock, fisheries and aquaculture increased. The increase for aquaculture was dramatic (847%). Increase in production was mainly due to increased crop area harvested or livestock numbers. Policies should be revisited, institutions strengthened and financial investments made for ECOWAS to realize its potential to significantly contribute to food security and carbon storage.

Variación en los patrones de crecimiento previo a la muerte de individuos de Austrocedrus chilensis a lo largo de un gradiente pluviométrico en el norte de la Patagonia Andina

Fil: Vega, Leticia Maria. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Departamento de Economia, Politica y Administracion Rural.; Argentina. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Mendoza. Instituto Argentino de Nivologia, Glaciologia y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivologia, Glaciologia y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivologia, Glaciologia y Ciencias Ambientales; Argentina

Biophysical Insights into the KRAS4b-FMe-Calmodulin Interaction

Biophysical Insights into the KRAS4b-FMe-Calmodulin Interaction

The role of indigenous technical knowledge and geographical information systems (GIS) in sustainable natural resource management around the Teso Community in Kenya

There is a growing awareness on the importance of indigenous technical knowledge and the necessity of its integration into modern knowledge in order to address problems related to natural resource conservation. However, there is a lack of study that demonstrates clearly how the two types of knowledge systems could be successfully integrated together. This paper presents such a framework that has been developed through a participatory geographical information systems (GIS) approach with the Teso Community in Kenya. Data were collected using a variety of research instruments such as structured questionnaires, in-depth and face-to-face interviews, focussed group discussions, content analysis of literature, environmental check lists, and using the GIS techniques for assessing the status of the bio-physical environment. The process of developing such a framework comprises five key building blocks including stakeholder engagement, establishment of resources targeted for rehabilitation, establishment of community and scientific points of convergence and divergence, a decision on community and expert resolutions and the adoption of community-based project implementation, and monitoring and evaluation. The study recommends that the developed framework could be easily replicated with other rural communities that have similar bio-physical environmental conditions if found successful in sustainably managing natural resource management. Key words: Indigenous technical knowledge, geographical information systems (GIS), natural resource management.

Genetic and Biophysical Models Help Define Marine Conservation Focus Areas

CITATION: Mertens, L. E. A. Treml, E. A. Von Der Heyden, S. 2018. Genetic and biophysical models help define marine conservation focus areas. Frontiers in Marine Science, 5:268, doi:10.3389/fmars.2018.00268.

Technical evaluation of soil and water conservation measures in Maego Watershed, North Ethiopia

Soil and water conservation (SWC) practices have been carried out to solve land degradation problems in Ethiopia since the last 3 decades. Technical evaluation of the implemented SWC structures is essential for effectiveness and sustainability of the measures. Therefore, the objective of this study was to identify and evaluate the technical quality of constructed physical SWC structures in Maego watershed, Ethiopia. The performance of the structures was evaluated based on technical standards set by Ethiopian Ministry of Agriculture. Parallel transect walk method was used to measure the dimensions of the structures. The major types of SWC structures constructed in the study watershed are stone bund, hillside terrace, bench terrace, stone bund/hillside terrace + trench and gabion check dams. Some of the structures, especially the old ones which are found on the uncultivated land did not meet the site specific width and height standards. Furthermore, some of the spacing of SWC structures was not set depending on the desired vertical intervals/slope. With similar biophysical features of the watershed, some of the structures were narrowly spaced and some others were spaced greater than the standard. Most of the structures, especially the old ones are filled by sediment deposition. The main reasons for the failure to achieve the technical quality based on the technical standards were knowledge and skill gaps, free grazing and more attention was given to coverage areas rather than technical quality at the beginning of the watershed treatment. Furthermore, there is no maintenance of the structures on the communal lands. Therefore, awareness creation for the local community and capacity building about layout of structures for the local technical leaders should be given. Moreover, more attention should be given to technical quality rather than coverage area of SWC structures. Key words: Soil and water conservation, technical evaluation, Maego watershed.

RNA and membraneless organelles

Molecular Biology Membraneless compartments can form in cells through liquid-liquid phase separation (see the Perspective by Polymenidou). But what prevents these cellular condensates from randomly fusing together? Using the RNA-binding protein (RBP) Whi3, Langdon et al. demonstrated that the secondary structure of different RNA components determines the distinct biophysical and biological properties of the two types of condensates that Whi3 forms. Several RBPs, such as FUS and TDP43, contain prion-like domains and are linked to neurodegenerative diseases. These RBPs are usually soluble in the nucleus but can form pathological aggregates in the cytoplasm. Maharana et al. showed that local RNA concentrations determine distinct phase separation behaviors in different subcellular locations. The higher RNA concentrations in the nucleus act as a buffer to prevent phase separation of RBPs; when mislocalized to the cytoplasm, lower RNA concentrations trigger aggregation. Science , this issue p. [922][1], p. [918][2]; see also p. [859][3] [1]: /lookup/doi/10.1126/science.aar7432 [2]: /lookup/doi/10.1126/science.aar7366 [3]: /lookup/doi/10.1126/science.aat8028

Análisis de amenazas a deslizamiento de tierra e inundación y su influencia socio ambiental en la gestión de riesgo en la microcuenca El Espinal, Pueblo Nuevo, Estelí

Esta investigación se realizó en la microcuenca El Espinal afluente del rio Pueblo Nuevo, departamento de Estelí, con el fin de delimitar las áreas susceptibles a deslizamiento e inundaciones y analizar los factores de vulnerabilidad. La metodología incluyó realizar una propuesta de manejo agroecológico de carácter cualitativo tomando en cuenta los aspectos biofísicos del territorio, mapeo de las amenazas a deslizamiento e inundaciones y la participación activa de los comunitarios para la propuesta de los lineamientos en base a las situaciones problemáticas encontradas en el estudio. La microcuenca presenta una alta susceptibilidad a deslizamiento en 16.82 km2, correspondiente al 19% del área de la microcuenca, siendo la comunidad de Macuelizo la que está en estado crítico. Se delimitó 2.4 km2 en área inundable, encontrándose 128 viviendas a una distancia menor a 50 metros, siendo las comunidades de mayor riesgo La Calera, Rosario y Paso Hondo. La vulnerabilidad global resultó alta en los aspectos económicos, técnicos, ecológicos, institucionales y físicas, siendo las comunidades de San José, La Calera y el Horno las que presentaron vulnerabilidad muy alta en base a los indicadores estudiados. La propuesta de manejo agroecológico zonificó tres áreas que son: zona protectora y restauración ecológica, zona de rehabilitación y zona de desarrollo agrícola. Según los resultados y el aporte y consenso de los actores locales se definieron cinco lineamientos estratégico y acciones concertadas para la prevención y mitigación de desastres naturales.

Land suitability assessment for apple (Malus domestica) in the Republic of Korea using integrated soil and climate information, MLCM, and AHP

Apples (Malus domestica) are one of the major fruits cultivated in South Korea and worldwide. To both sustain the productivity of apple trees and preserve the land, a land suitability assessment has been conducted. Two methods were used to analyze land suitability, a Most-Limiting Characteristic Method (MLCM) and an Analytic Hierarchy Process (AHP) with integrated soil and climate information based on the FAO classification framework. The most-limiting characteristic analysis showed that almost all areas were classified as marginally suitable (S3) or not suitable (N), which together accounted for 94.54% of the land in the Republic of Korea. On the contrary, AHP showed that S1 (34.1%) and S2 (44.17%) account for the majority of the land. Keywords: land suitability evaluation, biophysical modeling, GIS, land use planning, multi-criteria analysis, Republic of Korea DOI: 10.25165/j.ijabe.20181102.2522 Citation: Kim H, Shim K. Land suitability assessment for apple (Malus domestica) in the Republic of Korea using integrated soil and climate information, MLCM, and AHP. Int J Agric & Biol Eng, 2018; 11(2): 139–144.

The role of modified biophysical profile in high risk pregnancies and fetal outcome

Objectives: In a high risk population where chances of adverse outcome are relatively high and almost all the pregnancies are under strict monitoring, biophysical profiling further helps to identify adverse outcome and thus a basis for intervention. In this study, we aim to evaluate the role of modified biophysical profile in high risk pregnancies and fetal outcome. Methods: Total 125 high risk pregnancies and were monitored for modified biophysical profiling from GA 34 weeks onwards. AFI<8 and non-reactive NST were considered as abnormal BPP. Apgar <7 at 5 min, MSL, NNU admission and neonatal death were considered as adverse fetal outcomes. Chi-square test was used to compare the data. Results: Mean age was 24.32±4.37 (range 19-35) years. Mean age at enrolment was 35.23±1.78 weeks. A total of 41 (32.8%) patients had AFI<8. Non-reactive NST was seen in 52 (41.6%) patients. Overall abnormal biophysical profile (NR-NST/AFI<8) was seen in 62 (49.6%) patients. Incidence of meconium stained liquor, Apgar<7 at 5m, NNU admission and NNU expiry was 15.2%, 20.8%, 26.4% and 4.0% respectively. NST and overall BPP showed a statistically significant association with all the outcomes however, AFI failed to show a significant association with NNU expiry. For all the outcomes NST had higher sensitivity as compared to AFI. Combined BPP showed a higher sensitivity than either of two components. Conclusion: Modified BPP was found to be useful in identification of adverse fetal outcomes, thus highlighting its role in planning interventions to avert extreme events. Keywords:

Biophysical characteristics of genipin-crosslinked amniotic membrane bio-scaffold

Objective To investigate the characteristics and feasibility of genipin-crosslinked amniotic membrane(AM) as bio-scaffold. Methods Human umbilical cord mesenchymal stem cells (hUCMSCs) were isolated from fresh umbilical cord and cultured by adherent method.The expressions of PE-CD34, PE-CD45, PE-CD90, FITC-105 and FITC-Oct-4, the markers of hUCMSCs, were detected by flow cytometry.Alizarin red and oil red O staining were performed to identify the cells after adipogenesis and osteogenesis induction on the third-generation cells.Human AMs were treated at 37 ℃ and 45 ℃ by 0.5% and 1% genipin solution for 24, 36 and 48 hours respectively, and the mechanical properties of AM in each group were measured and compared.The hUCMSCs were divided into only hUCMSCs culture group, fresh AM group, crosslinked AM group, gelatin group and crosslinked AM+ gelatin group, and the cells were cultured in the corresponding medium.The content of hydroxyproline among the groups was detected with hydroxyproline kit, and proliferation of the cells (absorbance) was assayed by MTT method to evaluate the biological compatibility of crosslinked AM. Results The maximum tensile displacement of the crosslinked-AM by 0.5% and 1% genipin was (8.31±0.43)mm and (4.49±0.37)mm respectively, and those after crosslinked with 0.5% genipin under the 37 ℃ and 45 ℃ for 24 hours was (9.89±1.09)mm and (5.39±0.59)mm, respectively, showing a significant difference between them (t=6.389, P 0.05). The loading force of the crosslinked-AM was significantly higher in the 1% genipin treated group than that in the 0.5% genipin treated group (P 0.05). Conclusions Different crosslinked temprature, crosslinking period and concentration of genipin impact the mechanical properties of AM.Crosslinked AM with genipin is feasible as a carrier scaffold of artificial cornea because of less tissue toxicity and better plasticity. Key words: Amniotic membrane; Cross-linking reagents/pharmacology; Stress, mechanical; Tensile strength; Umbilical cord mesenchymal stem cells; Biological compatibility; Genipin

Changes in the Biophysics of Lipid Memrbanes Mediated by Peptides and Drugs

Changes in the Biophysics of Lipid Memrbanes Mediated by Peptides and Drugs