Biophysical Research Articles

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.

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).

Assessing MODIS Land Cover Products over China with Probability of Interannual Change

AbstractAccurate and up-to-date land cover data are important for climate-change modeling. Quality assessment is becoming critical, as many satellite-based land cover products of differing scales have been released to meet the needs of scientific studies. In this study, the authors assessed the Moderate Resolution Imaging Spectroradiometer (MODIS) land cover products by analyzing the probability of interannual change from 2001 to 2012. The authors found that, cumulatively, 43.0% of MODIS land cover had changed over China from 2001 to 2012 at least once. Of this percentage, 12.1% was considered unreasonable change, 6.1% was considered reasonable change, and areas of confusion accounted for about 24.8%, giving rise to great uncertainty in the products. MODIS Collection 51 products clearly have less uncertainty than the Collection 5 products. Areas of reasonable change occurred in transition zones of ecological, biophysical, and climate gradients, while areas of unreasonable change appeared in heterogeneous ...

How Not to Fall Off a Cliff, or, Using Tipping Points to Improve Environmental Management

Three decades of study have revealed dozens of examples of natural systems crossing biophysical thresholds (or “tipping points”) as a result of human-induced stressors, dramatically altering ecosystem function and services. Environmental management that avoids or reverses such tipping points could prevent severe social, economic, and environmental impacts. Here, we attempt to demonstrate the desirability of, and opportunities for, environmental management using thresholds under U.S. federal law. We find that conceptually, tipping points can and do guide some regulatory decisions. However, explicitly focusing a larger set of environmental rules on avoiding

Recent doctoral theses (biochemistry, biology and biophysics) in Lithuania

Recent doctoral theses (biochemistry, biology and biophysics) in Lithuania

Hyperspectral Remote Sensing of Agriculture

Remote sensing is being increasingly used in different agricultural applications. Hyperspectral remote sensing in large continuous narrow wavebands provides significant advancement in understanding the subtle changes in biochemical and biophysical attributes of the crop plants and their different physiological processes, which otherwise are indistinct in multispectral remote sensing. This article describes spectral properties of vegetation both in the optical and thermal range of the electromagnetic spectrum as affected by its attributes. Different methods have been discussed to reduce data dimension and minimize the information redundancy. Potential applications of hyperspectral remote sensing in agriculture, i.e. spectral discrimination of crops and their genotypes, quantitative estimation of different biophysical and biochemical parameters through empirical and physical modelling, assessing abiotic and biotic stresses as developed by different researchers in India and abroad are described.

BMC Biophysics reviewer acknowledgement 2014

Contributing reviewersThe editors of BMC Biophysics would like to thank all our reviewers who have contributed to the journal in Volume 7 (2014).

W221002 マイクロ・ナノファブリケーション技術と生物物理学の融合

W221002 マイクロ・ナノファブリケーション技術と生物物理学の融合

Lipidomics study of mesenchymal stromal cells derived from human placenta

The interest for lipid metabolism in the stem cell field has increased in the last few years (1,2,3). Membrane lipidomics embraces many aspects of cell metabolism and the role of lipids is now considered more than merely inert and structural in delimitating the extra- and intra-cellular compartments (4,5). Nevertheless, we are still far from understanding the impact of membrane lipidomics in stemness maintenance and differentiation patterns. The aim of our work was to study membrane lipidomics of mesenchymal stromal cells derived from human placenta and correlate it to specific biological properties, by using chemically- defined tailored lipid supplements (Refeed®). In the experimental study, the cell membranes of freshly isolated mesenchymal stromal cells obtained from human fetal membranes (FM-MSCs) were characterized for fatty acid composition. Then, we investigated cell morphology, viability, proliferation, differentiation and immunomodulation after in-vitro exposure to Refeed® supplements. Control MSCs were cultured without lipid supplementation. Our results showed a significant reduction of membrane fluidity for in-vitro primary cells, with cell membrane fatty acid composition greatly differing from the in-vivo one. By tailoring lipid supplementation, the fatty acid composition and biophysical properties of in-vitro cell membranes resulted more similar to the in-vivo counterparts, with higher omega-6 fatty acid content and increased membrane fluidity. These modifications of membrane composition and properties had no effect on cell morphology and viability, whereas ameliorated cell proliferation rate, diffentiation ability and immunomodulatory properties. In particular, supplemented FMMSCs showed an increased expression of cell membrane molecules like Vascular Endothelial Growth Factor Receptors 1 (VEGFR-1 or Flt-1) and 2 (VEGFR-2 or KDR), that correlated with a more efficient response to angiogenic commitment. Moreover, regarding immunomodulation, supplemented FM-MSCs displayed an increased expression of the tolerogenic cell surface protein HLA-G, that positively influenced the in-vitro cell immunomodulatory ability. Finally, these data suggest that specific lipid supplementation have functional consequences on in-vitro MSC behavior and may influence cell-based therapeutic approaches.

EVALUASI LAHAN FISIK DAN EKONOMI KOMODITAS PERTANIAN UTAMA TRANSMIGRAN DI LAHAN MARJINAL KERING MASAM RANTAU PANDAN SP-4, PROVINSI JAMBI

Most of the land used for transmigration resettlement activities outside of Java Island is marginal land that requires highproduction inputs and susceptible to degradation. One of the need to be taken into consideration in the choice of location is land suitability. The objective of this study is to determine the land suitability of agricultural transmigration area with a case study of Transmigration Settlement Unit (UPT) of RantauPandan SP-4, Jambi Province, for cultivation of food crops, vegetables and perennial crops and analyse the level of biophysical and economical feasibility of several commodities. The actual land suitability assessment for the three agricultural commodities indicate the dominance land suitability classes of S3 (marginally suitable) with terrain, nutrient retention and nutrients available become dominant limiting factors. Economic land suitability analysis indicate that the biggest gross margin is rubber, while the smallest is rice. Results of analysis are used to determine the spatial land use recommendations on transmigration location. Results of analysis are not always in line with the transmigration pattern of land allocation. Nonetheless, these results suggested to be applied, for considerations of land conservation as well as farmers' welfare.Keywords: land suitability, automated land evaluation system, land quality, land characteristic

Assessment of Vulnerability to Cyclones and Floods in Odisha, India: A District-Level Analysis

Most of the districts in Odisha, India are prone to both cyclones and floods. However, the existing studies have assessed vulnerability mainly for the coastal districts, and are largely focused on the biophysical components. Therefore, a comprehensive vulnerability assessment will help unravel the scale of vulnerability across the districts of Odisha, and provide a better understanding of the adaptive capacity of households towards these extreme events. An 'integrated approach' was adopted to assess vulnerability which is viewed as a function of exposure, sensitivity and adaptive capacity. A number of proxy indicators were considered to represent these components, and a normalization procedure was adopted in order to aggregate them into a single value. Three key observations emerged. First, components like sensitivity and adaptive capacity were found to act as the major determinants of vulnerability. Secondly, eight districts were found to have a higher vulnerability score, and surprisingly, some of the districts are non-coastal. Thirdly, factors like demography, agriculture and economic capacity emerged as the major cause for increasing vulnerability. These results have policy implications in the context of prioritizing limited resources among the vulnerable districts and determinants through the disaster risk management programme at state and district levels.

Development of genodynamic metrics for exploring the biophysics of DNA polymorphisms.

Single nucleotide polymorphisms (SNPs) represent an important type of dynamic sites within the human genome. These common variants often locally correlate within more complex multi-SNP haploblocks that are maintained throughout generations in a stable population. Information encoded in the structure of SNPs and SNP haploblock variation can be characterized through a normalized information content metric. Genodynamics is being developed as the analogous "thermodynamics" characterizing the state variables for genomic populations that are stable under stochastic environmental stresses. Since living systems have not been found to develop in the absence of environmental influences, this paper describes the analogous genomic free energy metrics in a given environment. SNP haploblocks were constructed by Haploview v4.2 for five chromosomes from phase III HapMap data, and the genomic state variables for each chromosome were calculated. An in silico analysis was performed on SNP haploblocks with the lowest genomic energy measures. Highly favorable genomic energy measures were found to correlate with highly conserved SNP haploblocks. Moreover, the most conserved haploblocks were associated with an evolutionarily conserved regulatory element and domain.

Opportunities and challenges in enhancing food production and security in the context of climate change effects in sub Saharan Africa

This discussion explores the opportunities and challenges in enhancing food production and security in the context of climatic variability in Sub Saharan Africa. The promotion of sustainable use of plant and animal products with emphasis on satisfying basic human needs, improving people’s standard of living, enhancing food security and reducing poverty have taken a center stage in Sub Saharan Africa. However, the efforts in this direction are being impacted negatively by climate change, through animal and crop production which have not been spared due to the natural disasters and environmental challenges which have affected all regions of Sub Saharan Africa indiscriminately. Climate is a particularly important driver of food production systems performance at the agriculture end of the food chain. It can affect the quantities and types of food produced as well as production-related income especially for the poor resource farmers. In order to be able to adequately address food production and security in the context of climate, there is need for the region to carry out thorough climatic vulnerability and adaptation assessments. Supporting research and training of experts to carry out vulnerability and adaptation assessments on crop and livestock production is crucial in order for respective countries to develop climate change adaptation measures to meet the obligation on food production and security. Sub Saharan Africa’s agro-ecological regions are variable and need to develop specific adaptive measures to reduce vulnerability to climate change. Due to the changing climatic conditions which the continent has already witnessed many severe climatic induced vulnerability such as decline in rainfall amounts and intensity, reduced length of rain season and increasing warm and occasionally very hot conditions has affected food production and security. Crop and livestock production systems will need to adapt to higher ambient temperatures, lower nutritional value of feed resources and new diseases and parasites occurrence. It can be seen that the present crop and livestock production systems based on pastoral or rangeland grazing husbandry systems, ecological destruction through climatic variability and overgrazing due to high stocking rates in areas where feed and water has been compromised due to high temperatures caused by climate change does not augur well for future livestock productivity. The understanding of climate change variables and their impacts is the first step in climate change research and prerequisite for defining appropriate adaptive responses by local crop and livestock farmers. Sustainable crop and livestock production supporting rural development should be compatible with the goals of curbing the effects of climate change. Production priorities should be directed towards promoting local crop and livestock genetic resources by providing comprehensive research support services on the impact of climate change. Both crops and livestock play important roles in farming systems, as they offer opportunities for risk coping, farm diversification and intensification, and provide significant livelihood benefits and food security. The discussion therefore, concludes that the effectiveness of biophysical responses of crop and livestock production systems to specific environmental challenges that are anticipated as a result of climate change, and then the range of adaptive measures that might be taken by local producers to ameliorate their effects will be the prerequisite for defining appropriate societal responses and meet food security targets.

Integrating Biodiversity and Ecosystem Services in Life Cycle Assessment: Methodological Proposals for New Challenges

Life Cycle Assessment (LCA) is a method used to quantify potential environmental impacts in the entire life cycle of a product or service, starting at raw material acquisition, production, use, and eventually its disposal. It is the leading methodology for environmental metrics today – the French government recently ran a pilot for a labelling program for consumer goods where indicators displayed in labels should be calculated using LCA. The European Commission did the same for their Product Footprint Guidelines. However, LCA features many methodological shortcomings when dealing with biophysical indicators. Land use, biodiversity and ecosystem services are relevant aspects to policy-makers and consumers, but their characterization factors are not yet accurately calculated. LCA has a hard time grasping effects that are dynamic, scale-dependent, non-linear and/or hard to quantify unambiguously. In fact, out of the four conventional types of ecosystem services (provisioning services, regulating services, cultural services and supporting services) only the first and the last are partially captured in LCA results. Similarly, out of the five drivers of change to biodiversity identified by the Millennium Ecosystem Assessment (habitat change, climate change, pollution, invasive alien species and overexploitation) only the first three are included in standard LCA calculations. This review article presents a brief assessment of how biodiversity and ecosystem services are incorporated in LCA today. The standard Life Cycle Impact Assessment models are described according to the most recent developments. Ground-breaking work is undergoing, making the field very active and constantly innovating. For example, regionalized characterization factors for the impacts of biodiversity are now available using species richness as a proxy for the overall state of biodiversity. Tools for ecosystem services have also been proposed. Finally, a compilation of some challenges ahead is listed to present several ideas for the improvement of current impact assessment methods.

Breakthrough in Bio-physics: A Combination of Experiments and Theory

Breakthrough in Bio-physics: A Combination of Experiments and Theory

Current status, prospect and policy and institutional support for Conservation Agriculture in the Asia-Pacific region.

The current growing demand for Conservation Agriculture (CA) at the national level in the countries of the Asia-Pacific region presents an opportunity to promote its widespread adoption and up-scaling through national policy and institutional support that appears necessary. Despite the obvious benefits of CA, it does not spread automatically unless the constraints that hinder adoption are understood and addressed in specific situations. These can include a combination of intellectual, social, financial, biophysical, technical, infrastructure constraints, or policy related support. Knowing what the bottlenecks are is important in developing strategies to overcome them. This paper presents: (a) some of the generic policy opportunities that exist for the adoption and uptake of CA; (b) a summary proceedings and outcome of the Regional Expert Consultation Workshop held in Beijing and sponsored by FAO Regional Office for Asia-Pacific which describes the status of CA in the Asia-Pacific region; (c) the challenges to CA adoption and uptake in the Asia-Pacific region; and (d) the conditions that need to be taken into account in designing and promoting policy and institutional support strategies for up-scaling CA. Keywords: Conservation Agriculture, policy and institutional support, adoption, Asia-Pacific region, tillage, agricultural mechanization, CA alliance, institutional cooperation DOI: 10.3965/j.ijabe.20140705.001 Citation: Kassam A, Li H W, Niino Y, Friedrich T, He J, Wang X L. Current status, prospect and policy and institutional support for conservation agriculture in the Asia-Pacific region. Int J Agric & Biol Eng, 2014; 7(5): 1－13.

Green Economy: Challenges and Prospects for Improved Aquatic Agricultural System (AAS) in Niger Delta Communities

There is dire need for deliberate green action plan to solve the endemic environmental crises occasioned by unsustainable utilization of natural resources and environmental degradation in the Niger Delta; a region with its characteristic terrain and eco-fragility that is highly susceptible to adverse environmental and climate change-related disasters. But, to successfully implement a green economy plan in the Niger Delta region, there has to be a well-thought out strategy with due appraisal of baseline environmental issues and concerns. The people of the delta depend, primarily, on the exploitation of the region’s rich bio-resources with fishing and farming forming the major sources of livelihoods. Observations by independent and intergovernmental global environmental protection players indicate that, the creeks, lands, mangroves, forests, etc provide inestimable goods and ecological services to the region’s inhabitants. Yet, they have been consistently degraded over the past four decades, mainly by industrial activities. Some identified challenges in greening the region and viable alternatives for sustainable agricultural development are, also, discussed. The authors have, therefore, proposed strategies such as consideration of complex biophysical and socio-economic factors, multi-stakeholder engagement, and a paradigm shift from the contemporary fossil energy-based agriculture to the more sustainable practices of biofuels and organic agriculture. A modelled paradigm for transforming current improved aquatic agricultural systems (AAS) to become more productive while, maintaining ecosystem services is proposed. Therefore, this paper examines current environmental issues and concerns as well as efforts variously made to address them in the Niger Delta against the backdrop of existing economic activities.

Foundation of Biophysics and Establishment of Interdisciplinary Subjects in China

As a new independent subject, biophysics emerged in the early 1950's. The Institute of Biophysics, Chinese Academy of Sciences, was established in 1958. It was the milestone of the beginning of biophysics in China. This review introduces the foundation and the early development of biophysics in China, and the establishment of the interdisciplinary subjects, including radiation biology, bio-cybernetics, astrobiology, and bionics.

The Relationship between Modified Biophysical Profile, Standard Biophysical Profile, and Neonatal Outcomes of High-risk Pregnancies

Introduction: High-risk pregnancies can result in many complications for the fetus. In these pregnancies, different tests such as non-stress test (NST), biophysical profile (BPP), oxytocin contraction stress test (OCT), and Doppler sonography can be used to evaluate fetal health. As standard BBP requires more time and expertise, in this study, we evaluated the relationship between standard BPP, modified BPP, and neonatal outcomes. Therefore, in case there was a significant relationship, we could use modified BPP as a replacement for standard BPP. Methods:Overall, 106 high-risk pregnant women in their third trimester, who were admitted to the gynecology ward of Imam Reza Hospital, were included in this study. Unless the subjects had any problems leading to emergent termination of pregnancy, standard BPP and modified BPP were concurrently performed to evaluate fetal health; these tests were repeated once or twice a week. In case of delivery, the last BPP scores (both standard and modified) were compared with the neonatal outcomes. Results: In the evaluation of the last standard BPP scores, 83.1% and 16.9% of the patients obtained normal and abnormal scores, respectively; on the other hand, 73.6% and 26.4% of the patients obtained normal and abnormal scores in the last modified BPP, respectively. There was a significant relationship between neonatal outcomes and standard BPP results (P=0.05). Also, the relationship between standard BPP and modified BPP was significant (P=0.003). However, there was not a significant relationship between modified BPP and neonatal outcomes. Conclusion: As the results indicated, modified BPP score had a significant relationship with standard BPP score, and standard BPP score had a significant correlation with neonatal outcomes. Therefore, the modified test can replace the difficult and time-consuming standard method. In addition, if the modified test showed any abnormalities, standard BPP or other fetal health evaluation methods should be applied.

Synthesis and biophysics studies of threeantimicrobial peptides isolated from the scorpion pandinus imperator

UNESP Univ Estadual Paulista, Inst Chem, Dept Biochem & Chem Technol, Araraquara, S Paulo, Brazil