Ultraviolet germicidal irradiation and its effects on elemental distributions in mouse embryonic fibroblast cells in x-ray fluorescence microanalysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Qiaoling; Vogt, Stefan; Lai, Barry

Rapidly-frozen hydrated (cryopreserved) specimens combined with cryo-scanning x-ray fluorescence microscopy provide an ideal approach for investigating elemental distributions in biological cells and tissues. However, because cryopreservation does not deactivate potentially infectious agents associated with Risk Group 2 biological materials, one must be concerned with contamination of expensive and complicated cryogenic x-ray microscopes when working with such materials. We employed ultraviolet germicidal irradiation to decontaminate previously cryopreserved cells under liquid nitrogen, and then investigated its effects on elemental distributions under both frozen hydrated and freeze dried states with x-ray fluorescence microscopy. We show that the contents and distributions of most biologicallymore » important elements remain nearly unchanged when compared with non-ultraviolet-irradiated counterparts, even after multiple cycles of ultraviolet germicidal irradiation and cryogenic x-ray imaging. This provides a potential pathway for rendering Risk Group 2 biological materials safe for handling in multiuser cryogenic x-ray microscopes without affecting the fidelity of the results.« less

Ultraviolet germicidal irradiation and its effects on elemental distributions in mouse embryonic fibroblast cells in x-ray fluorescence microanalysis

DOE PAGES

Jin, Qiaoling; Vogt, Stefan; Lai, Barry; ...

2015-02-23

Rapidly-frozen hydrated (cryopreserved) specimens combined with cryo-scanning x-ray fluorescence microscopy provide an ideal approach for investigating elemental distributions in biological cells and tissues. However, because cryopreservation does not deactivate potentially infectious agents associated with Risk Group 2 biological materials, one must be concerned with contamination of expensive and complicated cryogenic x-ray microscopes when working with such materials. We employed ultraviolet germicidal irradiation to decontaminate previously cryopreserved cells under liquid nitrogen, and then investigated its effects on elemental distributions under both frozen hydrated and freeze dried states with x-ray fluorescence microscopy. We show that the contents and distributions of most biologicallymore » important elements remain nearly unchanged when compared with non-ultraviolet-irradiated counterparts, even after multiple cycles of ultraviolet germicidal irradiation and cryogenic x-ray imaging. This provides a potential pathway for rendering Risk Group 2 biological materials safe for handling in multiuser cryogenic x-ray microscopes without affecting the fidelity of the results.« less

Towards molecular medicine: a case for a biological periodic table.

PubMed

Gawad, Charles

2005-01-01

The recently amplified pace of development in the technologies to study both normal and aberrant cellular physiology has allowed for a transition from the traditional reductionist approaches to global interrogations of human biology. This transformation has created the anticipation that we will soon more effectively treat or contain most types of diseases through a 'systems-based' approach to understanding and correcting the underlying etiology of these processes. However, to accomplish these goals, we must first have a more comprehensive understanding of all the elements involved in human cellular physiology, as well as why and how they interact. With the vast number of biological components that have and are being discovered, creating methods with modern computational techniques to better organize biological elements is the next requisite step in this process. This article aims to articulate the importance of the organization of chemical elements into a periodic table had on the conversion of chemistry into a quantitative, translatable science, as well as how we can apply the lessons learned in that transition to the current transformation taking place in biology.

Classifying Life, Reconstructing History and Teaching Diversity: Philosophical Issues in the Teaching of Biological Systematics and Biodiversity

NASA Astrophysics Data System (ADS)

Reydon, Thomas A. C.

2013-02-01

Classification is a central endeavor in every scientific field of work. Classification in biology, however, is distinct from classification in other fields of science in a number of ways. Thus, understanding how biological classification works is an important element in understanding the nature of biological science. In the present paper, I discuss a number of philosophical issues that are characteristic for classification in biological science, paying special attention to questions related to science education. My aims are (1) to provide science educators and others concerned with the teaching of biology with an accessible overview of the philosophy of biological classification and (2) to show how knowledge of the philosophy of classification can play an important role in science teaching.

50 CFR 223.203 - Anadromous fish.

Code of Federal Regulations, 2013 CFR

2013-10-01

... maximize consideration of the important biological diversity contained within the listed ESU, respond to... education. Coordination among involved jurisdictions is an important element in ensuring regulatory... impacts. (E) Provide for effective monitoring and adaptive management. (F) Use the best available science...

50 CFR 223.203 - Anadromous fish.

Code of Federal Regulations, 2014 CFR

2014-10-01

... defined, given biological and life history traits, so as to maximize consideration of the important... jurisdictions is an important element in ensuring regulatory effectiveness and coverage. (H) Include... effective monitoring and adaptive management. (F) Use the best available science and technology, including...

Biological monitoring of welders' exposure to chromium, molybdenum, tungsten and vanadium.

PubMed

Ellingsen, Dag G; Chashchin, Maxim; Berlinger, Balazs; Fedorov, Vladimir; Chashchin, Valery; Thomassen, Yngvar

2017-05-01

Welders are exposed to a number of metallic elements during work. Bioaccessability, that is important for element uptake, has been little studied. This study addresses bioaccessability and uptake of chromium (Cr), molybdenum (Mo), tungsten (W) and vanadium (V) among welders. Bioaccessability of Cr, Mo, V and W was studied in airborne particulate matter collected by personal sampling of the workroom air among shipyard welders by using the lung lining fluid simulant Hatch solution. Associations between concentrations of Hatch soluble and non-soluble elements (Hatch sol and Hatch non-sol ) and concentrations of the four elements in whole blood, serum, blood cells and urine were studied. Air concentrations of the four elements were low. Only a small fraction of Cr, V and W was Hatch sol , while similar amounts of Mo were Hatch sol and Hatch non-sol . Welders (N=70) had statistically significantly higher concentrations of all four elements in urine and serum when compared to referents (N=74). Highly statistically significant associations were observed between urinary W and Hatch sol W (p<0.001) and serum V and Hatch sol V (p<0.001), in particular when air samples collected the day before collection of biological samples were considered. Associations between Hatch sol elements in air and their biological concentrations were higher than when Hatch non-sol concentrations were considered. Associations were generally higher when air samples collected the day before biological sampling were considered as compared to air samples collected two days before. Copyright © 2017 Elsevier GmbH. All rights reserved.

Man in the Living Environment. A Report on Global Ecological Problems.

ERIC Educational Resources Information Center

Inger, Robert F.; And Others

The findings of four groups of ecologists are synthesized in chapter I of this report on global ecological problems prepared as a data base for the United Nations Conference on the Human Environment. The other chapters contain the reports of each group. In "Cycles of Elements" the biologically important elements, phosphorus, sulfur, and nitrogen,…

Geological and Chemical Factors that Impacted the Biological Utilization of Cobalt in the Archean Eon

NASA Astrophysics Data System (ADS)

Moore, Eli K.; Hao, Jihua; Prabhu, Anirudh; Zhong, Hao; Jelen, Ben I.; Meyer, Mike; Hazen, Robert M.; Falkowski, Paul G.

2018-03-01

The geosphere and biosphere coevolved and influenced Earth's biological and mineralogical diversity. Changing redox conditions influenced the availability of different transition metals, which are essential components in the active sites of oxidoreductases, proteins that catalyze electron transfer reactions across the tree of life. Despite its relatively low abundance in the environment, cobalt (Co) is a unique metal in biology due to its importance to a wide range of organisms as the metal center of vitamin B12 (aka cobalamin, Cbl). Cbl is vital to multiple methyltransferase enzymes involved in energetically favorable metabolic pathways. It is unclear how Co availability is linked to mineral evolution and weathering processes. Here we examine important biological functions of Co, as well as chemical and geological factors that may have influenced the utilization of Co early in the evolution of life. Only 66 natural minerals are known to contain Co as an essential element. However, Co is incorporated as a minor element in abundant rock-forming minerals, potentially representing a reliable source of Co as a trace element in marine systems due to weathering processes. We developed a mineral weathering model that indicates that dissolved Co was potentially more bioavailable in the Archean ocean under low S conditions than it is today. Mineral weathering, redox chemistry, Co complexation with nitrogen-containing organics, and hydrothermal environments were crucial in the incorporation of Co in primitive metabolic pathways. These chemical and geological characteristics of Co can inform the biological utilization of other trace metals in early forms of life.

A biological compression model and its applications.

PubMed

Cao, Minh Duc; Dix, Trevor I; Allison, Lloyd

2011-01-01

A biological compression model, expert model, is presented which is superior to existing compression algorithms in both compression performance and speed. The model is able to compress whole eukaryotic genomes. Most importantly, the model provides a framework for knowledge discovery from biological data. It can be used for repeat element discovery, sequence alignment and phylogenetic analysis. We demonstrate that the model can handle statistically biased sequences and distantly related sequences where conventional knowledge discovery tools often fail.

Mind the gap; seven reasons to close fragmented genome assemblies.

PubMed

Thomma, Bart P H J; Seidl, Michael F; Shi-Kunne, Xiaoqian; Cook, David E; Bolton, Melvin D; van Kan, Jan A L; Faino, Luigi

2016-05-01

Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including those that study non-model organisms. Thus, hundreds of fungal genomes have been sequenced and are publically available today, although these initiatives have typically yielded considerably fragmented genome assemblies that often lack large contiguous genomic regions. Many important genomic features are contained in intergenic DNA that is often missing in current genome assemblies, and recent studies underscore the significance of non-coding regions and repetitive elements for the life style, adaptability and evolution of many organisms. The study of particular types of genetic elements, such as telomeres, centromeres, repetitive elements, effectors, and clusters of co-regulated genes, but also of phenomena such as structural rearrangements, genome compartmentalization and epigenetics, greatly benefits from having a contiguous and high-quality, preferably even complete and gapless, genome assembly. Here we discuss a number of important reasons to produce gapless, finished, genome assemblies to help answer important biological questions. Copyright © 2015 Elsevier Inc. All rights reserved.

Mass fractionation processes of transition metal isotopes

NASA Astrophysics Data System (ADS)

Zhu, X. K.; Guo, Y.; Williams, R. J. P.; O'Nions, R. K.; Matthews, A.; Belshaw, N. S.; Canters, G. W.; de Waal, E. C.; Weser, U.; Burgess, B. K.; Salvato, B.

2002-06-01

Recent advances in mass spectrometry make it possible to utilise isotope variations of transition metals to address some important issues in solar system and biological sciences. Realisation of the potential offered by these new isotope systems however requires an adequate understanding of the factors controlling their isotope fractionation. Here we show the results of a broadly based study on copper and iron isotope fractionation during various inorganic and biological processes. These results demonstrate that: (1) naturally occurring inorganic processes can fractionate Fe isotope to a detectable level even at temperature ˜1000°C, which challenges the previous view that Fe isotope variations in natural system are unique biosignatures; (2) multiple-step equilibrium processes at low temperatures may cause large mass fractionation of transition metal isotopes even when the fractionation per single step is small; (3) oxidation-reduction is an importation controlling factor of isotope fractionation of transition metal elements with multiple valences, which opens a wide range of applications of these new isotope systems, ranging from metal-silicate fractionation in the solar system to uptake pathways of these elements in biological systems; (4) organisms incorporate lighter isotopes of transition metals preferentially, and transition metal isotope fractionation occurs stepwise along their pathways within biological systems during their uptake.

Biogeochemical Cycles of Carbon and Sulfur on Early Earth (and on Mars?)

NASA Technical Reports Server (NTRS)

DesMarais, D. J.

2004-01-01

The physical and chemical interactions between the atmosphere, hydrosphere, geosphere and biosphere can be examined for elements such as carbon (C) and sulfur (S) that have played central roles for both life and the environment. The compounds of C are highly important, not only as organic matter, but also as atmospheric greenhouse gases, pH buffers in seawater, oxidation-reduction buffers virtually everywhere, and key magmatic constituents affecting plutonism and volcanism. S assumes important roles as an oxidation-reduction partner with C and Fe in biological systems, as a key constituent in magmas and volcanic gases, and as a major influence upon pH in certain environments. These multiple roles of C and S interact across a network of elemental reservoirs interconnected by physical, chemical and biological processes. These networks are termed biogeochemical C and S cycles.

Trace element and isotope deposition across the air–sea interface: progress and research needs

PubMed Central

Landing, W. M.; Bucciarelli, E.; Cheize, M.; Fietz, S.; Hayes, C. T.; Kadko, D.; Morton, P. L.; Rogan, N.; Sarthou, G.; Shelley, R. U.; Shi, Z.; Shiller, A.; van Hulten, M. M. P.

2016-01-01

The importance of the atmospheric deposition of biologically essential trace elements, especially iron, is widely recognized, as are the difficulties of accurately quantifying the rates of trace element wet and dry deposition and their fractional solubility. This paper summarizes some of the recent progress in this field, particularly that driven by the GEOTRACES, and other, international research programmes. The utility and limitations of models used to estimate atmospheric deposition flux, for example, from the surface ocean distribution of tracers such as dissolved aluminium, are discussed and a relatively new technique for quantifying atmospheric deposition using the short-lived radionuclide beryllium-7 is highlighted. It is proposed that this field will advance more rapidly by using a multi-tracer approach, and that aerosol deposition models should be ground-truthed against observed aerosol concentration data. It is also important to improve our understanding of the mechanisms and rates that control the fractional solubility of these tracers. Aerosol provenance and chemistry (humidity, acidity and organic ligand characteristics) play important roles in governing tracer solubility. Many of these factors are likely to be influenced by changes in atmospheric composition in the future. Intercalibration exercises for aerosol chemistry and fractional solubility are an essential component of the GEOTRACES programme. This article is part of the themed issue ‘Biological and climatic impacts of ocean trace element chemistry’. PMID:29035268

Trace element and isotope deposition across the air-sea interface: progress and research needs

NASA Astrophysics Data System (ADS)

Baker, A. R.; Landing, W. M.; Bucciarelli, E.; Cheize, M.; Fietz, S.; Hayes, C. T.; Kadko, D.; Morton, P. L.; Rogan, N.; Sarthou, G.; Shelley, R. U.; Shi, Z.; Shiller, A.; van Hulten, M. M. P.

2016-11-01

The importance of the atmospheric deposition of biologically essential trace elements, especially iron, is widely recognized, as are the difficulties of accurately quantifying the rates of trace element wet and dry deposition and their fractional solubility. This paper summarizes some of the recent progress in this field, particularly that driven by the GEOTRACES, and other, international research programmes. The utility and limitations of models used to estimate atmospheric deposition flux, for example, from the surface ocean distribution of tracers such as dissolved aluminium, are discussed and a relatively new technique for quantifying atmospheric deposition using the short-lived radionuclide beryllium-7 is highlighted. It is proposed that this field will advance more rapidly by using a multi-tracer approach, and that aerosol deposition models should be ground-truthed against observed aerosol concentration data. It is also important to improve our understanding of the mechanisms and rates that control the fractional solubility of these tracers. Aerosol provenance and chemistry (humidity, acidity and organic ligand characteristics) play important roles in governing tracer solubility. Many of these factors are likely to be influenced by changes in atmospheric composition in the future. Intercalibration exercises for aerosol chemistry and fractional solubility are an essential component of the GEOTRACES programme. This article is part of the themed issue 'Biological and climatic impacts of ocean trace element chemistry'.

Trace element and isotope deposition across the air-sea interface: progress and research needs.

PubMed

Baker, A R; Landing, W M; Bucciarelli, E; Cheize, M; Fietz, S; Hayes, C T; Kadko, D; Morton, P L; Rogan, N; Sarthou, G; Shelley, R U; Shi, Z; Shiller, A; van Hulten, M M P

2016-11-28

The importance of the atmospheric deposition of biologically essential trace elements, especially iron, is widely recognized, as are the difficulties of accurately quantifying the rates of trace element wet and dry deposition and their fractional solubility. This paper summarizes some of the recent progress in this field, particularly that driven by the GEOTRACES, and other, international research programmes. The utility and limitations of models used to estimate atmospheric deposition flux, for example, from the surface ocean distribution of tracers such as dissolved aluminium, are discussed and a relatively new technique for quantifying atmospheric deposition using the short-lived radionuclide beryllium-7 is highlighted. It is proposed that this field will advance more rapidly by using a multi-tracer approach, and that aerosol deposition models should be ground-truthed against observed aerosol concentration data. It is also important to improve our understanding of the mechanisms and rates that control the fractional solubility of these tracers. Aerosol provenance and chemistry (humidity, acidity and organic ligand characteristics) play important roles in governing tracer solubility. Many of these factors are likely to be influenced by changes in atmospheric composition in the future. Intercalibration exercises for aerosol chemistry and fractional solubility are an essential component of the GEOTRACES programme.This article is part of the themed issue 'Biological and climatic impacts of ocean trace element chemistry'. © 2015 The Authors.

An experimental and finite element poroelastic creep response analysis of an intervertebral hydrogel disc model in axial compression.

PubMed

Silva, P; Crozier, S; Veidt, M; Pearcy, M J

2005-07-01

A hydrogel intervertebral disc (IVD) model consisting of an inner nucleus core and an outer anulus ring was manufactured from 30 and 35% by weight Poly(vinyl alcohol) hydrogel (PVA-H) concentrations and subjected to axial compression in between saturated porous endplates at 200 N for 11 h, 30 min. Repeat experiments (n=4) on different samples (N=2) show good reproducibility of fluid loss and axial deformation. An axisymmetric nonlinear poroelastic finite element model with variable permeability was developed using commercial finite element software to compare axial deformation and predicted fluid loss with experimental data. The FE predictions indicate differential fluid loss similar to that of biological IVDs, with the nucleus losing more water than the anulus, and there is overall good agreement between experimental and finite element predicted fluid loss. The stress distribution pattern indicates important similarities with the biological IVD that includes stress transference from the nucleus to the anulus upon sustained loading and renders it suitable as a model that can be used in future studies to better understand the role of fluid and stress in biological IVDs.

Attraction Basins as Gauges of Robustness against Boundary Conditions in Biological Complex Systems

PubMed Central

Demongeot, Jacques; Goles, Eric; Morvan, Michel; Noual, Mathilde; Sené, Sylvain

2010-01-01

One fundamental concept in the context of biological systems on which researches have flourished in the past decade is that of the apparent robustness of these systems, i.e., their ability to resist to perturbations or constraints induced by external or boundary elements such as electromagnetic fields acting on neural networks, micro-RNAs acting on genetic networks and even hormone flows acting both on neural and genetic networks. Recent studies have shown the importance of addressing the question of the environmental robustness of biological networks such as neural and genetic networks. In some cases, external regulatory elements can be given a relevant formal representation by assimilating them to or modeling them by boundary conditions. This article presents a generic mathematical approach to understand the influence of boundary elements on the dynamics of regulation networks, considering their attraction basins as gauges of their robustness. The application of this method on a real genetic regulation network will point out a mathematical explanation of a biological phenomenon which has only been observed experimentally until now, namely the necessity of the presence of gibberellin for the flower of the plant Arabidopsis thaliana to develop normally. PMID:20700525

[Study of biological performance of Chinese materia medica with either a cold or hot property based on the three-element mathematical analysis model].

PubMed

Jin, Rui; Zhang, Bing; Liu, Xiao-Qing; Liu, Sen-Mao; Liu, Xin; Li, Lian-Zhen; Zhang, Qian; Xue, Chun-Miao

2011-07-01

The properties of Chinese materia medica are believed to be the summarization of the effects of biological performance on the various body states. Systemic discussion of chemical-factor elements, body-condition elements, biological-performance elements and their interrelationships is needed for research into the properties of Chinese materia medica. Following the practical characteristics of Chinese medicine, the three-element mathematical model was formed by introducing some mathematical concepts and methods and was used to study the cold or hot property of Chinese medicine, and to investigate the difference in biological performances of the two properties. By using the concept of different functionality of Chinese medicine on abnormal states and the idea of interaction in mathematics, the effects of chemical-factor elements and body-condition elements were normalized to the amount of biological performance which was represented by some important indicators. The three-element mathematical model was formed with scatter plots through four steps, including effect separation, intensity calculation, frequency statistics and relevance analysis. A comparison pharmacology experiment of administration of hot property medicines, Fuzi (Radix Aconiti Lateralis Preparata) and Rougui (Cortex Cinnamomi), and cold property medicines, Huangbai (Cortex Phellodendri) and Zhizi (Fructus Gardeniae) on normal and glucocorticoid-induced yang-deficiency and yin-deficiency states was designed. The results were analyzed by the mathematical model. The scatter plots were the main output of model analysis. The expression of cold property and hot property was able to be quantified by frequency distribution of biological indexes of administrations on yang-deficiency and yin-deficiency states in the "efficacy zone" and "toxicity zone" of the plots and by the relevance analysis. The ratios of biological indicator frequency in the "efficacy zone" of administrations on yang-deficiency state and yin-deficiency state were 7:3 for Fuzi, 3:3 for Rougui, 4:4 for Huangbai and 1:5 for Zhizi. The sums of the biological indicator frequency in the "toxicity zone" of administration on the two states were 4 for Fuzi, 0 for Rougui, 2 for Huangbai and 4 for Zhizi. The relevance analysis showed that the order from Fuzi, Rougui, Huangbai to Zhizi was proportional to the change from "be true of yang-deficiency state" to "be true of yin-deficiency state". The extent of the hot property decreased while that of the cold property increased in the order of Fuzi, Rougui, Huangbai and Zhizi. The stronger the efficacy of above medicines is, the more obvious the toxicity displayed. The three-element mathematical model employed in this study is effectively capable of explaining the different biological expressions between hot property medicines and cold property medicines. This suggests that it may provide a mathematical tool and theoretical basis for the modern interpretation of cold property and hot property of Chinese medicine, and provide new ideas for further studing into the essence of Chinese medicine property theory.

Biological data warehousing system for identifying transcriptional regulatory sites from gene expressions of microarray data.

PubMed

Tsou, Ann-Ping; Sun, Yi-Ming; Liu, Chia-Lin; Huang, Hsien-Da; Horng, Jorng-Tzong; Tsai, Meng-Feng; Liu, Baw-Juine

2006-07-01

Identification of transcriptional regulatory sites plays an important role in the investigation of gene regulation. For this propose, we designed and implemented a data warehouse to integrate multiple heterogeneous biological data sources with data types such as text-file, XML, image, MySQL database model, and Oracle database model. The utility of the biological data warehouse in predicting transcriptional regulatory sites of coregulated genes was explored using a synexpression group derived from a microarray study. Both of the binding sites of known transcription factors and predicted over-represented (OR) oligonucleotides were demonstrated for the gene group. The potential biological roles of both known nucleotides and one OR nucleotide were demonstrated using bioassays. Therefore, the results from the wet-lab experiments reinforce the power and utility of the data warehouse as an approach to the genome-wide search for important transcription regulatory elements that are the key to many complex biological systems.

Novel green tissue-specific synthetic promoters and cis-regulatory elements in rice.

PubMed

Wang, Rui; Zhu, Menglin; Ye, Rongjian; Liu, Zuoxiong; Zhou, Fei; Chen, Hao; Lin, Yongjun

2015-12-11

As an important part of synthetic biology, synthetic promoter has gradually become a hotspot in current biology. The purposes of the present study were to synthesize green tissue-specific promoters and to discover green tissue-specific cis-elements. We first assembled several regulatory sequences related to tissue-specific expression in different combinations, aiming to obtain novel green tissue-specific synthetic promoters. GUS assays of the transgenic plants indicated 5 synthetic promoters showed green tissue-specific expression patterns and different expression efficiencies in various tissues. Subsequently, we scanned and counted the cis-elements in different tissue-specific promoters based on the plant cis-elements database PLACE and the rice cDNA microarray database CREP for green tissue-specific cis-element discovery, resulting in 10 potential cis-elements. The flanking sequence of one potential core element (GEAT) was predicted by bioinformatics. Then, the combination of GEAT and its flanking sequence was functionally identified with synthetic promoter. GUS assays of the transgenic plants proved its green tissue-specificity. Furthermore, the function of GEAT flanking sequence was analyzed in detail with site-directed mutagenesis. Our study provides an example for the synthesis of rice tissue-specific promoters and develops a feasible method for screening and functional identification of tissue-specific cis-elements with their flanking sequences at the genome-wide level in rice.

Mechanisms of extracellular signal-regulated kinase/cAMP response element-binding protein/brain-derived neurotrophic factor signal transduction pathway in depressive disorder☆

PubMed Central

Wang, Hongyan; Zhang, Yingquan; Qiao, Mingqi

2013-01-01

The extracellular signal-regulated kinase/cAMP response element-binding protein/brain-derived neurotrophic factor signal transduction pathway plays an important role in the mechanism of action of antidepressant drugs and has dominated recent studies on the pathogenesis of depression. In the present review we summarize the known roles of extracellular signal-regulated kinase, cAMP response element-binding protein and brain-derived neurotrophic factor in the pathogenesis of depression and in the mechanism of action of antidepressant medicines. The extracellular signal-regulated kinase/cAMP response element-binding protein/brain-derived neurotrophic factor pathway has potential to be used as a biological index to help diagnose depression, and as such it is considered as an important new target in the treatment of depression. PMID:25206732

Vital effects in coral skeletal composition display strict three-dimensional control

USGS Publications Warehouse

Meibom, A.; Yurimoto, H.; Cuif, J.-P.; Domart-Coulon, I.; Houlbreque, F.; Constantz, B.; Dauphin, Y.; Tambutte, E.; Tambutte, S.; Allemand, D.; Wooden, J.; Dunbar, R.

2006-01-01

Biological control over coral skeletal composition is poorly understood but critically important to paleoenvironmental reconstructions. We present microanalytical measurements of trace-element abundances as well as oxygen and carbon isotopic compositions of individual skeletal components in the zooxanthellate coral Colpophyllia sp. Our data show that centers of calcification (COC) have higher trace element concentrations and distinctly lighter isotopic compositions than the fibrous components of the skeleton. These observations necessitate that COC and the fibrous skeleton are precipitated by different mechanisms, which are controlled by specialized domains of the calicoblastic cell-layer. Biological processes control the composition of the skeleton even at the ultra-structure level. Copyright 2006 by the American Geophysical Union.

Abundance and Distribution of Geographically Isolated Wetlands across the Conterminous United States

EPA Science Inventory

Geographically isolated wetlands (GIWS) are important landscape elements involved in hydrologic, biogeochemical, and biological functioning. Their influence, under certain circumstances, can significantly affect other waters of the Unites States. However, there have been no data-...

Cross Section Calculations and Comparison to Experiment

NASA Technical Reports Server (NTRS)

Townsend, L. W.; Ford, W. P.; Dewet, W. C.; Werneth, C. M.

2016-01-01

Understanding fragmentation of galactic cosmic ray nuclei in collisions within spacecraft structures and human tissues is an important element in assessing biological risk to crew members from this radiation source. Over the past four decades, various models have been developed to describe these important processes. Some models invoke semi-classical concepts based upon geometric descriptions of collisions between spherical nuclei.

Ultra-Sensitive Elemental Analysis Using Plasmas 7.Application to Criminal Investigation

NASA Astrophysics Data System (ADS)

Suzuki, Yasuhiro

This paper describes the application of trace elemental analysis using ICP-AES and ICP-MS to criminal investigation. The comparison of trace elements, such as Rb, Sr, Zr, and so on, is effective for the forensic discrimination of glass fragments, which can be important physical evidence for connecting a suspect to a crime scene or to a victim. This procedure can be applied also to lead shotgun pellets by the removal of matrix lead as the sulfate precipitate after the dissolution of a pellet sample. The determination of a toxic element in bio-logical samples is required to prove that a victim ingested this element. Arsenous acids produced in Japan, China, Germany and Switzerland show characteristic patterns of trace elements characteristic to each country.

Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters.

PubMed

Yamaguchi-Shinozaki, Kazuko; Shinozaki, Kazuo

2005-02-01

cis-Acting regulatory elements are important molecular switches involved in the transcriptional regulation of a dynamic network of gene activities controlling various biological processes, including abiotic stress responses, hormone responses and developmental processes. In particular, understanding regulatory gene networks in stress response cascades depends on successful functional analyses of cis-acting elements. The ever-improving accuracy of transcriptome expression profiling has led to the identification of various combinations of cis-acting elements in the promoter regions of stress-inducible genes involved in stress and hormone responses. Here we discuss major cis-acting elements, such as the ABA-responsive element (ABRE) and the dehydration-responsive element/C-repeat (DRE/CRT), that are a vital part of ABA-dependent and ABA-independent gene expression in osmotic and cold stress responses.

The Metals in the Biological Periodic System of the Elements: Concepts and Conjectures

PubMed Central

Maret, Wolfgang

2016-01-01

A significant number of chemical elements are either essential for life with known functions, or present in organisms with poorly defined functional outcomes. We do not know all the essential elements with certainty and we know even less about the functions of apparently non-essential elements. In this article, I discuss a basis for a biological periodic system of the elements and that biochemistry should include the elements that are traditionally part of inorganic chemistry and not only those that are in the purview of organic chemistry. A biological periodic system of the elements needs to specify what “essential” means and to which biological species it refers. It represents a snapshot of our present knowledge and is expected to undergo further modifications in the future. An integrated approach of biometal sciences called metallomics is required to understand the interactions of metal ions, the biological functions that their chemical structures acquire in the biological system, and how their usage is fine-tuned in biological species and in populations of species with genetic variations (the variome). PMID:26742035

The cost of copy number in a selfish genetic element: the 2-μm plasmid of Saccharomyces cerevisiae.

PubMed

Harrison, Ellie; Koufopanou, V; Burt, A; MacLean, R C

2012-11-01

Many autonomously replicating genetic elements exist as multiple copies within the cell. The copy number of these elements is often assumed to have important fitness consequences for both element and host, yet the forces shaping its evolution are not well understood. The 2 μm is a multicopy plasmid of Saccharomyces yeasts, encoding just four genes that are solely involved in plasmid replication. One simple model for the fitness relationship between yeasts and 2 μm is that plasmid copy number evolves as a trade-off between selection for increased vertical transmission, favouring high copy number, and selection for decreased virulence, favouring low copy number. To test this model, we experimentally manipulated the copy number of the plasmid and directly measured the fitness cost, in terms of growth rate reduction, associated with high plasmid copy number. We find that the fitness burden imposed by the 2 μm increases with plasmid copy number, such that each copy imposes a fitness burden of 0.17% (± 0.008%), greatly exceeding the cost expected for it to be stably maintained in yeast populations. Our results demonstrate the crucial importance of copy number in the evolution of yeast per 2 μm associations and pave the way for future studies examining how selection can shape the cost of multicopy elements. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Is lithium biologically an important or toxic element to living organisms? An overview.

PubMed

Shahzad, Babar; Mughal, Mudassar Niaz; Tanveer, Mohsin; Gupta, Dorin; Abbas, Ghazanfar

2017-01-01

Industrialized world is exposing living organisms to different chemicals and metals such as lithium (Li). Due to their use in common household items to industrial applications, it is imperative to examine their bioavailability. Lithium belongs to the group IA and also has wider uses such as in batteries, air conditioners to atomic reactors. Lithium occurs naturally in soil and water, mostly at low concentrations, and enters the food chain. It is not one of the essential minerals though various studies indicate that low levels of Li have beneficial effects on living organisms, whereas high levels expose them to toxicity and related detrimental effects. This review suggests that Li could be biologically important to living organism depending upon its concentration/exposure. Little is known about its biological importance and molecular understanding of its accumulation and mode of action, which might have future implications for Li's long-term effects on living organisms.

Ratios of Biogenic Elements for Distinguishing Recent from Fossil Microorganisms

NASA Technical Reports Server (NTRS)

Hoover, Richard B.

2007-01-01

The ability to distinguish possible microfossils from recent biological contaminants is of great importance to Astrobiology. In this paper we discuss the application of the ratios of life critical biogenic elements (C/O; C/N; and C/S) as determined by Energy Dispersive X-ray Spectroscopy (EDS) to this problem. Biogenic element ratios will be provided for a wide variety of living cyanobacteria and other microbial extremophiles, preserved herbarium materials, and ancient biota from the Antarctic Ice Cores and Siberian and Alaskan Permafrost for comparison with megafossils and microfossils in ancient terrestrial rocks and carbonaceous meteorites.

Stable isotopes of transition and post-transition metals as tracers in environmental studies

USGS Publications Warehouse

Bullen, Thomas D.; Baskaran, Mark

2011-01-01

The transition and post-transition metals, which include the elements in Groups 3–12 of the Periodic Table, have a broad range of geological and biological roles as well as industrial applications and thus are widespread in the environment. Interdisciplinary research over the past decade has resulted in a broad understanding of the isotope systematics of this important group of elements and revealed largely unexpected variability in isotope composition for natural materials. Significant kinetic and equilibrium isotope fractionation has been observed for redox sensitive metals such as iron, chromium, copper, molybdenum and mercury, and for metals that are not redox sensitive in nature such as cadmium and zinc. In the environmental sciences, the isotopes are increasingly being used to understand important issues such as tracing of metal contaminant sources and fates, unraveling metal redox cycles, deciphering metal nutrient pathways and cycles, and developing isotope biosignatures that can indicate the role of biological activity in ancient and modern planetary systems.

A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion

PubMed Central

Sommer, Morten OA; Church, George M; Dantas, Gautam

2010-01-01

Sustainable biofuel alternatives to fossil fuel energy are hampered by recalcitrance and toxicity of biomass substrates to microbial biocatalysts. To address this issue, we present a culture-independent functional metagenomic platform for mining Nature's vast enzymatic reservoir and show its relevance to biomass conversion. We performed functional selections on 4.7 Gb of metagenomic fosmid libraries and show that genetic elements conferring tolerance toward seven important biomass inhibitors can be identified. We select two metagenomic fosmids that improve the growth of Escherichia coli by 5.7- and 6.9-fold in the presence of inhibitory concentrations of syringaldehyde and 2-furoic acid, respectively, and identify the individual genes responsible for these tolerance phenotypes. Finally, we combine the individual genes to create a three-gene construct that confers tolerance to mixtures of these important biomass inhibitors. This platform presents a route for expanding the repertoire of genetic elements available to synthetic biology and provides a starting point for efforts to engineer robust strains for biofuel generation. PMID:20393580

Nestedness across biological scales

PubMed Central

Marquitti, Flavia M. D.; Raimundo, Rafael L. G.; Sebastián-González, Esther; Coltri, Patricia P.; Perez, S. Ivan; Brandt, Débora Y. C.; Nunes, Kelly; Daura-Jorge, Fábio G.; Floeter, Sergio R.; Guimarães, Paulo R.

2017-01-01

Biological networks pervade nature. They describe systems throughout all levels of biological organization, from molecules regulating metabolism to species interactions that shape ecosystem dynamics. The network thinking revealed recurrent organizational patterns in complex biological systems, such as the formation of semi-independent groups of connected elements (modularity) and non-random distributions of interactions among elements. Other structural patterns, such as nestedness, have been primarily assessed in ecological networks formed by two non-overlapping sets of elements; information on its occurrence on other levels of organization is lacking. Nestedness occurs when interactions of less connected elements form proper subsets of the interactions of more connected elements. Only recently these properties began to be appreciated in one-mode networks (where all elements can interact) which describe a much wider variety of biological phenomena. Here, we compute nestedness in a diverse collection of one-mode networked systems from six different levels of biological organization depicting gene and protein interactions, complex phenotypes, animal societies, metapopulations, food webs and vertebrate metacommunities. Our findings suggest that nestedness emerge independently of interaction type or biological scale and reveal that disparate systems can share nested organization features characterized by inclusive subsets of interacting elements with decreasing connectedness. We primarily explore the implications of a nested structure for each of these studied systems, then theorize on how nested networks are assembled. We hypothesize that nestedness emerges across scales due to processes that, although system-dependent, may share a general compromise between two features: specificity (the number of interactions the elements of the system can have) and affinity (how these elements can be connected to each other). Our findings suggesting occurrence of nestedness throughout biological scales can stimulate the debate on how pervasive nestedness may be in nature, while the theoretical emergent principles can aid further research on commonalities of biological networks. PMID:28166284

Review of S100A9 Biology and its Role in Cancer

PubMed Central

Markowitz, Joseph; Carson, William E.

2013-01-01

S100A9 is a calcium binding protein with multiple ligands and post-translation modifications that is involved in inflammatory events and the initial development of the cancer cell through to the development of metastatic disease. This review has a threefold purpose: 1) describe S100A9 structural elements important for its biological activity, 2) describe S100A9 biology in the context of the immune system, and 3) illustrate the role of S100A9 in the development of malignancy via interactions with the immune system and other cellular processes. PMID:23123827

Nonlinear dynamics based digital logic and circuits.

PubMed

Kia, Behnam; Lindner, John F; Ditto, William L

2015-01-01

We discuss the role and importance of dynamics in the brain and biological neural networks and argue that dynamics is one of the main missing elements in conventional Boolean logic and circuits. We summarize a simple dynamics based computing method, and categorize different techniques that we have introduced to realize logic, functionality, and programmability. We discuss the role and importance of coupled dynamics in networks of biological excitable cells, and then review our simple coupled dynamics based method for computing. In this paper, for the first time, we show how dynamics can be used and programmed to implement computation in any given base, including but not limited to base two.

High Throughput Analyses of Budding Yeast ARSs Reveal New DNA Elements Capable of Conferring Centromere-Independent Plasmid Propagation

PubMed Central

Hoggard, Timothy; Liachko, Ivan; Burt, Cassaundra; Meikle, Troy; Jiang, Katherine; Craciun, Gheorghe; Dunham, Maitreya J.; Fox, Catherine A.

2016-01-01

The ability of plasmids to propagate in Saccharomyces cerevisiae has been instrumental in defining eukaryotic chromosomal control elements. Stable propagation demands both plasmid replication, which requires a chromosomal replication origin (i.e., an ARS), and plasmid distribution to dividing cells, which requires either a chromosomal centromere for segregation or a plasmid-partitioning element. While our knowledge of yeast ARSs and centromeres is relatively advanced, we know less about chromosomal regions that can function as plasmid partitioning elements. The Rap1 protein-binding site (RAP1) present in transcriptional silencers and telomeres of budding yeast is a known plasmid-partitioning element that functions to anchor a plasmid to the inner nuclear membrane (INM), which in turn facilitates plasmid distribution to daughter cells. This Rap1-dependent INM-anchoring also has an important chromosomal role in higher-order chromosomal structures that enhance transcriptional silencing and telomere stability. Thus, plasmid partitioning can reflect fundamental features of chromosome structure and biology, yet a systematic screen for plasmid partitioning elements has not been reported. Here, we couple deep sequencing with competitive growth experiments of a plasmid library containing thousands of short ARS fragments to identify new plasmid partitioning elements. Competitive growth experiments were performed with libraries that differed only in terms of the presence or absence of a centromere. Comparisons of the behavior of ARS fragments in the two experiments allowed us to identify sequences that were likely to drive plasmid partitioning. In addition to the silencer RAP1 site, we identified 74 new putative plasmid-partitioning motifs predicted to act as binding sites for DNA binding proteins enriched for roles in negative regulation of gene expression and G2/M-phase associated biology. These data expand our knowledge of chromosomal elements that may function in plasmid partitioning and suggest underlying biological roles shared by such elements. PMID:26865697

Br-rich tips of calcified crab claws are less hard but more fracture resistant: a comparison of mineralized and heavy-element biological materials.

PubMed

Schofield, Robert M S; Niedbala, Jack C; Nesson, Michael H; Tao, Ye; Shokes, Jacob E; Scott, Robert A; Latimer, Matthew J

2009-06-01

We find that the spoon-like tips of the chelipeds (large claws) of the crab Pachygrapsus crassipes differ from the rest of the claw in that they are not calcified, but instead contain about 1% bromine--thus they represent a new example of a class of structural biological materials that contain heavy elements such as Zn, Mn, Fe, Cu, and Br bound in an organic matrix. X-ray absorption spectroscopy data suggest that the bromine is bound to phenyl rings, possibly in tyrosine. We measure a broad array of mechanical properties of a heavy-element biological material for the first time (abrasion resistance, coefficient of kinetic friction, energy of fracture, hardness, modulus of elasticity and dynamic mechanical properties), and we make a direct comparison with a mineralized tissue. Our results suggest that the greatest advantage of bromine-rich cuticle over calcified cuticle is resistance to fracture (the energy of fracture is about an order of magnitude greater than for calcified cuticle). The greatest advantage relative to unenriched cuticle, represented by ant mandible cuticle, is a factor of about 1.5 greater hardness and modulus of elasticity.The spoon-like tips gain additional fracture resistance from the orientation of the constituent laminae and from the viscoelasticity of the material. We suggest that fracture resistance is of greater importance in smaller organisms, and we speculate that one function of heavy elements in structural biological materials is to reduce molecular resonant frequencies and thereby increase absorption of energy from impacts.

Attraction of posture and motion-trajectory elements of conspecific biological motion in medaka fish.

PubMed

Shibai, Atsushi; Arimoto, Tsunehiro; Yoshinaga, Tsukasa; Tsuchizawa, Yuta; Khureltulga, Dashdavaa; Brown, Zuben P; Kakizuka, Taishi; Hosoda, Kazufumi

2018-06-05

Visual recognition of conspecifics is necessary for a wide range of social behaviours in many animals. Medaka (Japanese rice fish), a commonly used model organism, are known to be attracted by the biological motion of conspecifics. However, biological motion is a composite of both body-shape motion and entire-field motion trajectory (i.e., posture or motion-trajectory elements, respectively), and it has not been revealed which element mediates the attractiveness. Here, we show that either posture or motion-trajectory elements alone can attract medaka. We decomposed biological motion of the medaka into the two elements and synthesized visual stimuli that contain both, either, or none of the two elements. We found that medaka were attracted by visual stimuli that contain at least one of the two elements. In the context of other known static visual information regarding the medaka, the potential multiplicity of information regarding conspecific recognition has further accumulated. Our strategy of decomposing biological motion into these partial elements is applicable to other animals, and further studies using this technique will enhance the basic understanding of visual recognition of conspecifics.

Biological accumulation of tellurium nanorod structures via reduction of tellurite by Shewanella oneidensis MR-1.

PubMed

Kim, Dong-Hun; Kanaly, Robert A; Hur, Hor-Gil

2012-12-01

The dissimilatory metal-reducing bacterium, Shewanella oneidensis MR-1, reduced tellurite (Te(IV), TeO(3)(2-)) to elemental tellurium under anaerobic conditions resulting in the intracellular accumulation of needle shaped crystalline Te(0) nanorods. Fatty acid analyses showed that toxic Te(IV) increased the unsaturated fatty acid composition of the lipid components of the cell membrane, implying a deconstruction of the integrity of the cellular membrane structure. The current results suggest that dissimilatory metal reducing bacteria such as S. oneidensis MR-1 may play an important role in recycling toxic tellurium elements, and may be applied as a novel selective biological filter via the accumulation of industry-applicable rare materials, Te(0) nanorods, in the cell. Copyright © 2012 Elsevier Ltd. All rights reserved.

Subcellular trace element distribution in Geosiphon pyriforme

NASA Astrophysics Data System (ADS)

Maetz, Mischa; Schüßler, Arthur; Wallianos, Alexandros; Traxel, Kurt

1999-04-01

Geosiphon pyriforme is a unique endosymbiotic consortium consisting of a soil dwelling fungus and the cyanobacterium Nostoc punctiforme. At present this symbiosis becomes very interesting because of its phylogenetic relationship to the arbuscular mycorrhizal (AM) fungi. Geosiphon pyriforme could be an important model system for these obligate symbiotic fungi, which supply 80-90% of all land plant species with nutrients, in particular phosphorous and trace elements. Combined PIXE and STIM analyses of the various compartments of Geosiphon give hints for the matter exchange between the symbiotic partners and their environment and the kind of nutrient storage and acquisition, in particular related to nitrogen fixation and metabolism. To determine the quality of our PIXE results we analysed several geological and biological standards over a time period of three years. This led to an overall precision of about 6% and an accuracy of 5-10% for nearly all detectable elements. In combination with the correction model for the occurring mass loss during the analyses this holds true even for biological targets.

[Mathematical exploration of essence of herbal properties based on "Three-Elements" theory].

PubMed

Jin, Rui; Zhao, Qian; Zhang, Bing

2014-10-01

Herbal property theory of traditional Chinese medicines is the theoretical guidance on authentication of medicinal plants, herborization, preparation of herbal medicines for decoction and clinical application, with important theoretical value and prac- tical significance. Our research team proposed the "three-element" theory for herbal properties for the first time, conducted a study by using combined methods of philology, chemistry, pharmacology and mathematics, and then drew the research conclusion that herbal properties are defined as the chemical compositions-based comprehensive expression with complex and multi-level (positive/negative) biological effects in specific organism state. In this paper, researchers made a systematic mathematical analysis in four aspects--the correlation between herbal properties and chemical component factors, the correlation between herbal properties and organism state fac- tor, the correlation between herbal properties and biological effect factor and the integration study of the three elements, proposed future outlook, and provided reference to mathematical studies and mathematical analysis of herbal properties.

Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements

NASA Astrophysics Data System (ADS)

Fernandez-Chamorro, Javier; Lozano, Gloria; Garcia-Martin, Juan Antonio; Ramajo, Jorge; Dotu, Ivan; Clote, Peter; Martinez-Salas, Encarnacion

2016-04-01

The function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor conserved RNA motifs critical for internal initiation of translation. A conserved motif is the pyrimidine-tract located upstream of the functional initiation codon in type I and II picornavirus IRES. By computationally designing synthetic RNAs to fold into a structure that sequesters the polypyrimidine tract in a hairpin, we establish a correlation between predicted inaccessibility of the pyrimidine tract and IRES activity, as determined in both in vitro and in vivo systems. Our data supports the hypothesis that structural sequestration of the pyrimidine-tract within a stable hairpin inactivates IRES activity, since the stronger the stability of the hairpin the higher the inhibition of protein synthesis. Destabilization of the stem-loop immediately upstream of the pyrimidine-tract also decreases IRES activity. Our work introduces a hybrid computational/experimental method to determine the importance of structural motifs for biological function. Specifically, we show the feasibility of using the software RNAiFold to design synthetic RNAs with particular sequence and structural motifs that permit subsequent experimental determination of the importance of such motifs for biological function.

Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses.

PubMed

Muhire, Brejnev Muhizi; Golden, Michael; Murrell, Ben; Lefeuvre, Pierre; Lett, Jean-Michel; Gray, Alistair; Poon, Art Y F; Ngandu, Nobubelo Kwanele; Semegni, Yves; Tanov, Emil Pavlov; Monjane, Adérito Luis; Harkins, Gordon William; Varsani, Arvind; Shepherd, Dionne Natalie; Martin, Darren Patrick

2014-02-01

Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here.

Evidence of Pervasive Biologically Functional Secondary Structures within the Genomes of Eukaryotic Single-Stranded DNA Viruses

PubMed Central

Muhire, Brejnev Muhizi; Golden, Michael; Murrell, Ben; Lefeuvre, Pierre; Lett, Jean-Michel; Gray, Alistair; Poon, Art Y. F.; Ngandu, Nobubelo Kwanele; Semegni, Yves; Tanov, Emil Pavlov; Monjane, Adérito Luis; Harkins, Gordon William; Varsani, Arvind; Shepherd, Dionne Natalie

2014-01-01

Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here. PMID:24284329

INAA Application for Trace Element Determination in Biological Reference Material

NASA Astrophysics Data System (ADS)

Atmodjo, D. P. D.; Kurniawati, S.; Lestiani, D. D.; Adventini, N.

2017-06-01

Trace element determination in biological samples is often used in the study of health and toxicology. Determination change to its essentiality and toxicity of trace element require an accurate determination method, which implies that a good Quality Control (QC) procedure should be performed. In this study, QC for trace element determination in biological samples was applied by analyzing the Standard Reference Material (SRM) Bovine muscle 8414 NIST using Instrumental Neutron Activation Analysis (INAA). Three selected trace element such as Fe, Zn, and Se were determined. Accuracy of the elements showed as %recovery and precision as %coefficient of variance (%CV). The result showed that %recovery of Fe, Zn, and Se were in the range between 99.4-107%, 92.7-103%, and 91.9-112%, respectively, whereas %CV were 2.92, 3.70, and 5.37%, respectively. These results showed that INAA method is precise and accurate for trace element determination in biological matrices.

Selfish genetic elements, genetic conflict, and evolutionary innovation.

PubMed

Werren, John H

2011-06-28

Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual's genome but are neutral or harmful to the individual as a whole. As a result, genetic conflict occurs between SGEs and other genetic elements in the genome. There is growing evidence that SGEs, and the resulting genetic conflict, are an important motor for evolutionary change and innovation. In this review, the kinds of SGEs and their evolutionary consequences are described, including how these elements shape basic biological features, such as genome structure and gene regulation, evolution of new genes, origin of new species, and mechanisms of sex determination and development. The dynamics of SGEs are also considered, including possible "evolutionary functions" of SGEs.

Selfish genetic elements, genetic conflict, and evolutionary innovation

PubMed Central

Werren, John H.

2011-01-01

Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual's genome but are neutral or harmful to the individual as a whole. As a result, genetic conflict occurs between SGEs and other genetic elements in the genome. There is growing evidence that SGEs, and the resulting genetic conflict, are an important motor for evolutionary change and innovation. In this review, the kinds of SGEs and their evolutionary consequences are described, including how these elements shape basic biological features, such as genome structure and gene regulation, evolution of new genes, origin of new species, and mechanisms of sex determination and development. The dynamics of SGEs are also considered, including possible “evolutionary functions” of SGEs. PMID:21690392

Metal biogeochemistry in surface-water systems; a review of principles and concepts

USGS Publications Warehouse

Elder, John F.

1988-01-01

Metals are ubiquitous in natural surface-water systems, both as dissolved constituents and as particulate constituents. Although concentrations of many metals are generally very low (hence the common term 'trace metals'), their effects on the water quality and the biota of surfacewater systems are likely to be substantial. Biogeochemical partitioning of metals results in a diversity of forms, including hydrated or 'free' ions, colloids, precipitates, adsorbed phases, and various coordination complexes with dissolved organic and inorganic ligands. Much research has been dedicated to answering questions about the complexities of metal behavior and effects in aquatic systems. Voluminous literature on the subject has been produced. This paper synthesizes the findings of aquatic metal studies and describes some general concepts that emerge from such a synthesis. Emphasis is on sources, occurrence, partitioning, transport, and biological interactions of metals in freshwater systems of North America. Biological interactions, in this case, refer to bioavailability, effects of metals on ecological characteristics and functions of aquatic systems, and roles of biota in controlling metal partitioning. This discussion is devoted primarily to the elements aluminum, arsenic, cadmium, chromium, copper, iron, lead, manganese, mercury, nickel, and zinc and secondarily to cobalt, molybdenum, selenium, silver, and vanadium. Sources of these elements are both natural and anthropogenic. Significant anthropogenic sources are atmospheric deposition, discharges of municipal and industrial wastes, mine drainage, and urban and agricultural runoff. Biogeochemical partitioning of metals is controlled by various characteristics of the water and sediments in which the metals are found. Among the most important controlling factors are pH, oxidation-reduction potential, hydrologic features, sediment grain size, and the existence and nature of clay minerals, organic matter, and hydrous oxides of manganese and iron. Partitioning is also controlled by biological processes that provide mechanisms for detoxification of metals and for enhanced uptake of nutritive metals. Partitioning is important largely because availability to biota is highly variable among different phases. Hence, accumulation in biological tissues and toxicity of an element are dependent not only on total concentration of the element but also on the factors that control partitioning.

Endotoxin contamination: a key element in the interpretation of nanosafety studies.

PubMed

Li, Yang; Boraschi, Diana

2016-02-01

The study of toxicity and potential risks of engineered nanoparticles is of particular importance in nanomedicine. Endotoxin, a common contaminant of bacterial origin, has biological effects that can mask the true biological effects of nanoparticles, if its presence is overlooked. In this review, we report the features of nanoparticle contamination by endotoxin, and the different biological effects of endotoxin-contaminated nanoparticles. We will describe different methods for endotoxin detection applied to nanoparticles, and discuss their pros and cons. Eventually, we describe various methods for eliminating endotoxin contamination in nanoparticles. Although there is no universal technique for efficiently removing endotoxin from nanoparticles, specific solutions can be found case by case, which can allow us to perform nanosafety studies in biologically relevant conditions.

Determination of trace elements in the reproduction systems of some rare animals using pixe

NASA Astrophysics Data System (ADS)

Suqing, Chen; Nengming, Wang; Jianxuan, Chen; Dazhong, Zhang

In order to search for the significance of artificial feeding, reproduction and heredity, trace elements in the reproductive systems of some rare animals, including giant panda, lesser panda, marmot and river deer, have been determined. Typcial X-ray spectra of various samples are given. The elemental contents in ovary and testis of the giant panda and the lesser panda are calculated by means of yttrium as an internal standard. Elemental relative concentrations are calculated from peak areas in the spectra for thick samples. It is found that for the concentration of the elements Cr, Mn, Fe, Ni, Cu, As in the ovary there exist no significant different between the giant panda and the lesser panda. The concentration of Zn, however, shows a remakable difference. The importance of zinc in biological processes is discussed.

Epigenomics and the concept of degeneracy in biological systems

PubMed Central

Mason, Paul H.; Barron, Andrew B.

2014-01-01

Researchers in the field of epigenomics are developing more nuanced understandings of biological complexity, and exploring the multiple pathways that lead to phenotypic expression. The concept of degeneracy—referring to the multiple pathways that a system recruits to achieve functional plasticity—is an important conceptual accompaniment to the growing body of knowledge in epigenomics. Distinct from degradation, redundancy and dilapidation; degeneracy refers to the plasticity of traits whose function overlaps in some environments, but diverges in others. While a redundant system is composed of repeated identical elements performing the same function, a degenerate system is composed of different elements performing similar or overlapping functions. Here, we describe the degenerate structure of gene regulatory systems from the basic genetic code to flexible epigenomic modifications, and discuss how these structural features have contributed to organism complexity, robustness, plasticity and evolvability. PMID:24335757

Nitrogen input inventory in the Nooksack-Abbotsford-Sumas Transboundary Region: Key component of an international nitrogen management study

EPA Science Inventory

Nitrogen (N) is an essential biological element, so optimizing N use for food production while minimizing the release of N and co-pollutants to the environment is an important challenge. The Nooksack-Abbotsford-Sumas Transboundary (NAS) Region, spanning a portion of the western...

Nitrogen input inventory in the Nooksack-Abbotsford-Sumas Transboundary Region: Key component of an international nitrogen management study.

EPA Science Inventory

Background/Question/Methods: Nitrogen (N) is an essential biological element, so optimizing N use for food production while minimizing the release of N and co-pollutants to the environment is an important challenge. The Nooksack-lower Fraser Valley, spanning a portion of the w...

COMMON ISSUES IN HUMAN AND ECOSYSTEM EXPOSURE ASSESSMENT: THE SIGNIFICANCE OF PARTITIONING, KINETICS, AND UPTAKE AT BIOLOGICAL EXCHANGE SURFACES

EPA Science Inventory

Exogenous chemicals enter organisms through critical surfaces in the lung, gills, gut, and skin. Transfer across these boundaries is the first step in characterizing the ratio of tissue dose to external exposure. Surface processes and fugacity are important elements of both human...

Demographic and habitat requirements for conservation of bull trout

Treesearch

Bruce E. Rieman; John D. Mclntyre

1993-01-01

Elements in bull trout biology, population dynamics, habitat, and biotic interactions important to conservation of the species are identified. Bull trout appear to have more specific habitat requirements than other salmonids, but no critical thresholds of acceptable habitat condition were found. Size, temporal variation, and spatial distribution are likely to influence...

Aligning Biochemistry to the Interests of Biology Students Using Haloperoxidase to Illustrate Reactions of Environmental and Biomedical Importance

ERIC Educational Resources Information Center

Jervis, Les; Jervis, Loretta M.; Giovannelli, Donato

2005-01-01

Undergraduate degree programs in the biosciences almost always include elements of biochemistry. In the United Kingdom, biosciences programs often have optional pathways to accommodate students of diverse interests. These programs rarely require students to demonstrate any school-level chemistry knowledge, and many students find biochemistry…

Cre/lox-recombinase-mediated cassette exchange for reversible site-specific genomic targeting of the disease vector, Aedes aegypti

USDA-ARS?s Scientific Manuscript database

Site-specific genome modification is an important tool for mosquito functional genomics studies that help to uncover gene functions, identify gene regulatory elements, and perform comparative gene expression studies, all of which contribute to a better understanding of mosquito biology and are thus ...

Lineage-specific genomics: Frequent birth and death in the human genome: The human genome contains many lineage-specific elements created by both sequence and functional turnover.

PubMed

Young, Robert S

2016-07-01

Frequent evolutionary birth and death events have created a large quantity of biologically important, lineage-specific DNA within mammalian genomes. The birth and death of DNA sequences is so frequent that the total number of these insertions and deletions in the human population remains unknown, although there are differences between these groups, e.g. transposable elements contribute predominantly to sequence insertion. Functional turnover - where the activity of a locus is specific to one lineage, but the underlying DNA remains conserved - can also drive birth and death. However, this does not appear to be a major driver of divergent transcriptional regulation. Both sequence and functional turnover have contributed to the birth and death of thousands of functional promoters in the human and mouse genomes. These findings reveal the pervasive nature of evolutionary birth and death and suggest that lineage-specific regions may play an important but previously underappreciated role in human biology and disease. © 2016 The Authors BioEssays Published by WILEY Periodicals, Inc.

Optical Sensors for Biomolecules Using Nanoporous Sol-Gel Materials

NASA Technical Reports Server (NTRS)

Fang, Jonathan; Zhou, Jing C.; Lan, Esther H.; Dunn, Bruce; Gillman, Patricia L.; Smith, Scott M.

2004-01-01

An important consideration for space missions to Mars is the ability to detect biosignatures. Solid-state sensing elements for optical detection of biological entities are possible using sol-gel based biologically active materials. We have used these materials as optical sensing elements in a variety of bioassays, including immunoassays and enzyme assays. By immobilizing an appropriate biomolecule in the sol-gel sensing element, we have successfully detected analytes such as amino acids and hormones. In the case of the amino acid glutamate, the enzyme glutamate dehydrogenase was the immobilized molecule, whereas in the case of the hormone cortisol, an anti-cortisol antibody was immobilized in the sensing element. In this previous work with immobilized enzymes and antibodies, excellent sensitivity and specificity were demonstrated in a variety of formats including bulk materials, thin films and fibers. We believe that the sol-gel approach is an attractive platform for bioastronautics sensing applications because of the ability to detect a wide range of entities such as amino acids, fatty acids, hopanes, porphyrins, etc. The sol-gel approach produces an optically transparent 3D silica matrix that forms around the biomolecule of interest, thus stabilizing its structure and functionality while allowing for optical detection. This encapsulation process protects the biomolecule and leads to a more "rugged" sensor. The nanoporous structure of the sol-gel matrix allows diffusion of small target molecules but keeps larger, biomolecules immobilized in the pores. We are currently developing these biologically active sol-gel materials into small portable devices for on-orbit cortisol detection

Environmental mineralogy - Understanding element behavior in ecosystems

NASA Astrophysics Data System (ADS)

Brown, Gordon E., Jr.; Calas, Georges

2011-02-01

Environmental Mineralogy has developed over the past decade in response to the recognition that minerals are linked in many important ways with the global ecosystem. Minerals are the main repositories of the chemical elements in Earth's crust and thus are the main sources of elements needed for the development of civilization, contaminant and pollutant elements that impact global and local ecosystems, and elements that are essential plant nutrients. These elements are released from minerals through natural processes, such as chemical weathering, and anthropogenic activities, such as mining and energy production, agriculture and industrial activities, and careless waste disposal. Minerals also play key roles in the biogeochemical cycling of the elements, sequestering elements and releasing them as the primary minerals in crustal rocks undergo various structural and compositional transformations in response to physical, chemical, and biological processes that produce secondary minerals and soils. These processes have resulted in the release of toxic elements such as arsenic in groundwater aquifers, which is having a major impact on the health of millions of people in South and Southeast Asia. The interfaces between mineral surfaces and aqueous solutions are the locations of most chemical reactions that control the composition of the natural environment, including the composition of natural waters. The nuclear fuel cycle, from uranium mining to the disposition of high-level nuclear waste, is also intimately related to minerals. A fundamental understanding of these processes requires molecular-scale information about minerals, their bulk structures and properties such as solubility, their surfaces, and their interactions with aqueous solutions, atmospheric and soil gases, natural organic matter, and biological organisms. Gaining this understanding is further complicated by the presence of natural, incidental, and manufactured nanoparticles in the environment, which are becoming increasingly important due to the rapidly developing field of nanotechnology. As a result of this complexity, Environmental Mineralogy requires the use of the most modern molecular-scale analytical and theoretical methods and overlaps substantially with closely related fields such as Environmental Sciences, low-temperature Geochemistry, and Geomicrobiology. This paper provides brief overviews of the above topics and discusses the complexity of minerals, natural vs. anthropogenic inputs of elements and pollutants into the biosphere, the role of minerals in the biogeochemical cycling of elements, natural nanoparticles, and the Environmental Mineralogy of three major potential pollutant elements (Hg, As and U).

Integrating data from biological experiments into metabolic networks with the DBE information system.

PubMed

Borisjuk, Ljudmilla; Hajirezaei, Mohammad-Reza; Klukas, Christian; Rolletschek, Hardy; Schreiber, Falk

2005-01-01

Modern 'omics'-technologies result in huge amounts of data about life processes. For analysis and data mining purposes this data has to be considered in the context of the underlying biological networks. This work presents an approach for integrating data from biological experiments into metabolic networks by mapping the data onto network elements and visualising the data enriched networks automatically. This methodology is implemented in DBE, an information system that supports the analysis and visualisation of experimental data in the context of metabolic networks. It consists of five parts: (1) the DBE-Database for consistent data storage, (2) the Excel-Importer application for the data import, (3) the DBE-Website as the interface for the system, (4) the DBE-Pictures application for the up- and download of binary (e. g. image) files, and (5) DBE-Gravisto, a network analysis and graph visualisation system. The usability of this approach is demonstrated in two examples.

Soundscapes from a Tropical Eastern Pacific reef and a Caribbean Sea reef

NASA Astrophysics Data System (ADS)

Staaterman, E.; Rice, A. N.; Mann, D. A.; Paris, C. B.

2013-06-01

Underwater soundscapes vary due to the abiotic and biological components of the habitat. We quantitatively characterized the acoustic environments of two coral reef habitats, one in the Tropical Eastern Pacific (Panama) and one in the Caribbean (Florida Keys), over 2-day recording durations in July 2011. We examined the frequency distribution, temporal variability, and biological patterns of sound production and found clear differences. The Pacific reef exhibited clear biological patterns and high temporal variability, such as the onset of snapping shrimp noise at night, as well as a 400-Hz daytime band likely produced by damselfish. In contrast, the Caribbean reef had high sound levels in the lowest frequencies, but lacked clear temporal patterns. We suggest that acoustic measures are an important element to include in reef monitoring programs, as the acoustic environment plays an important role in the ecology of reef organisms at multiple life-history stages.

A comparison of sample preparation strategies for biological tissues and subsequent trace element analysis using LA-ICP-MS.

PubMed

Bonta, Maximilian; Török, Szilvia; Hegedus, Balazs; Döme, Balazs; Limbeck, Andreas

2017-03-01

Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) is one of the most commonly applied methods for lateral trace element distribution analysis in medical studies. Many improvements of the technique regarding quantification and achievable lateral resolution have been achieved in the last years. Nevertheless, sample preparation is also of major importance and the optimal sample preparation strategy still has not been defined. While conventional histology knows a number of sample pre-treatment strategies, little is known about the effect of these approaches on the lateral distributions of elements and/or their quantities in tissues. The technique of formalin fixation and paraffin embedding (FFPE) has emerged as the gold standard in tissue preparation. However, the potential use for elemental distribution studies is questionable due to a large number of sample preparation steps. In this work, LA-ICP-MS was used to examine the applicability of the FFPE sample preparation approach for elemental distribution studies. Qualitative elemental distributions as well as quantitative concentrations in cryo-cut tissues as well as FFPE samples were compared. Results showed that some metals (especially Na and K) are severely affected by the FFPE process, whereas others (e.g., Mn, Ni) are less influenced. Based on these results, a general recommendation can be given: FFPE samples are completely unsuitable for the analysis of alkaline metals. When analyzing transition metals, FFPE samples can give comparable results to snap-frozen tissues. Graphical abstract Sample preparation strategies for biological tissues are compared with regard to the elemental distributions and average trace element concentrations.

Imaging mass spectrometer with mass tags

DOEpatents

Felton, James S.; Wu, Kuang Jen; Knize, Mark G.; Kulp, Kristen S.; Gray, Joe W.

2010-06-01

A method of analyzing biological material by exposing the biological material to a recognition element, that is coupled to a mass tag element, directing an ion beam of a mass spectrometer to the biological material, interrogating at least one region of interest area from the biological material and producing data, and distributing the data in plots.

Characterization of noncoding regulatory DNA in the human genome.

PubMed

Elkon, Ran; Agami, Reuven

2017-08-08

Genetic variants associated with common diseases are usually located in noncoding parts of the human genome. Delineation of the full repertoire of functional noncoding elements, together with efficient methods for probing their biological roles, is therefore of crucial importance. Over the past decade, DNA accessibility and various epigenetic modifications have been associated with regulatory functions. Mapping these features across the genome has enabled researchers to begin to document the full complement of putative regulatory elements. High-throughput reporter assays to probe the functions of regulatory regions have also been developed but these methods separate putative regulatory elements from the chromosome so that any effects of chromatin context and long-range regulatory interactions are lost. Definitive assignment of function(s) to putative cis-regulatory elements requires perturbation of these elements. Genome-editing technologies are now transforming our ability to perturb regulatory elements across entire genomes. Interpretation of high-throughput genetic screens that incorporate genome editors might enable the construction of an unbiased map of functional noncoding elements in the human genome.

Reaction-based small-molecule fluorescent probes for chemoselective bioimaging

PubMed Central

Chan, Jefferson; Dodani, Sheel C.; Chang, Christopher J.

2014-01-01

The dynamic chemical diversity of elements, ions and molecules that form the basis of life offers both a challenge and an opportunity for study. Small-molecule fluorescent probes can make use of selective, bioorthogonal chemistries to report on specific analytes in cells and in more complex biological specimens. These probes offer powerful reagents to interrogate the physiology and pathology of reactive chemical species in their native environments with minimal perturbation to living systems. This Review presents a survey of tools and tactics for using such probes to detect biologically important chemical analytes. We highlight design criteria for effective chemical tools for use in biological applications as well as gaps for future exploration. PMID:23174976

Trace Element Analysis of Biological Samples.

ERIC Educational Resources Information Center

Veillon, Claude

1986-01-01

Reviews background of atomic absorption spectrometry techniques. Discusses problems encountered and precautions to be taken in determining trace elements in the parts-per-billion concentration range and below. Concentrates on determining chromium in biological samples by graphite furnace atomic absorption. Considers other elements, matrices, and…

Selfish DNA: a pharmaceutical perspective.

PubMed

Winckler, T

2013-07-01

Almost 25 years ago, Theo Dingermann published the discovery of a new mobile genetic element in the unicellular microbe Dictyostelium discoideum in the journal Science. An interesting property of this new molecular parasite, the Dictyostelium Repetitive Element (DRE), was that all integrations were found approximately 50 base pairs (bp) upstream of transfer RNA (tRNA) genes in the D. discoideum genome, thus implying an active targeting mechanism to avoid the disruption of host cell genes by the retrotransposition process. Since then, the facultative multicellular "social amoeba" D. discoideum has become a popular model for analyzing complex cellular functions such as cell movement, chemotaxis, phagocytosis, and cell differentiation, important areas of biomedical research that are often hard to investigate in cells from "higher organisms" including humans. Therefore, progress in the development of methods to study Dictyostelium biology has also provoked research on transposable elements in this organism. Early work on the DRE element suggested that studying its molecular mechanism of site-specific integration might promote human gene therapy technology through the design of integrating gene transfer vectors with low intrinsic genotoxic potential. In this review article, I will briefly review the original research performed on the DRE transposable element in the Dingermann lab and report on how the emergence of genomics technologies and the development of tools to analyze de novo retrotransposition events in D. discoideum cells will expand our knowledge of DRE biology in the future.

NMR spectroscopy of Group 13 metal ions: biologically relevant aspects.

PubMed

André, J P; Mäcke, H R

2003-12-01

In spite of the fact that Group 13 metal ions (Al(3+), Ga(3+), In(3+) and Tl(+/3+)) show no main biological role, they are NMR-active nuclides which can be used in magnetic resonance spectroscopy of biologically relevant systems. The fact that these metal ions are quadrupolar (with the exception of thallium) means that they are particularly sensitive to ligand type and coordination geometry. The line width of the NMR signals of their complexes shows a strong dependence on the symmetry of coordination, which constitutes an effective tool in the elucidation of structures. Here we report published NMR studies of this family of elements, applied to systems of biological importance. Special emphasis is given to binding studies of these cations to biological molecules, such as proteins, and to chelating agents of radiopharmaceutical interest. The possibility of in vivo NMR studies is also stressed, with extension to (27)Al-based MRI (magnetic resonance imaging) experiments.

The role of biological uptake in iron and manganese cycling in Lake Baikal

USGS Publications Warehouse

Granina, L.Z.; Callender, E.

2006-01-01

The role of biological uptake in the internal cycling of Fe and Mn in Lake Baikal was quantified. Biological uptake, sedimentation consisting of the biogenic and lithogenic fluxes, and remineralization have been evaluated. The results of calculations show that about 5-10% of Fe and Mn accumulated in the lake are annually taken up by biota. More than 80% of this amount is again recycled after remineralization of biological material. At this, the biogenic fluxes of Fe and Mn are 2-4 times less compared to lithogenic ones. Thus not only is oxidation of Fe and Mn within the water column highly enriched in the oxygen that results in settling of Fe and Mn oxides, but also intensive biological uptake of these elements contributes to their fast removal from internal cycling. However, essential remineralization makes this process of minor importance to Fe and Mn cycling in Lake Baikal. ?? Springer 2006.

Endowing carbon nanotubes with biological and biomedical properties by chemical modifications.

PubMed

Battigelli, Alessia; Ménard-Moyon, Cécilia; Da Ros, Tatiana; Prato, Maurizio; Bianco, Alberto

2013-12-01

The scope of nanotechnology is gaining importance in biology and medicine. Carbon nanotubes (CNTs) have emerged as a promising tool due to their unique properties, high specific surface area, and capacity to cross biological barriers. These properties offer a variety of opportunities for applications in nanomedicine, such as diagnosis, disease treatment, imaging, and tissue engineering. Nevertheless, pristine CNTs are insoluble in water and in most organic solvents; thereby functionalization of their surface is necessary to increase biocompatibility. Derivatization of CNTs also gives the possibility to conjugate different biological and bioactive molecules including drugs, proteins, and targeting ligands. This review focuses on the chemical modifications of CNTs that have been developed to impart specific properties for biological and medical purposes. Biomolecules can be covalently grafted or non-covalently adsorbed on the nanotube surface. In addition, the inner core of CNTs can be exploited to encapsulate drugs, nanoparticles, or radioactive elements. © 2013.

Bioseguridad in Mexico: Pursuing Security between Local and Global Biologies.

PubMed

Wanderer, Emily Mannix

2017-09-01

In the aftermath of the 2009 outbreak of H1N1 influenza, scientists in Mexico sought to develop bioseguridad, that is, to protect biological life in Mexico by safely conducting research on infectious disease. Drawing on ethnographic research in laboratories and with scientists in Mexico, I look at how scientists make claims about local differences in regulations, infrastructure, bodies, and culture. The scientists working with infectious microbes sought to establish how different microbial ecologies, human immune systems, and political and regulatory systems made the risks of research different in Mexico from other countries. In developing bioseguridad, the idea of globalized biology that animates many public health projects was undermined as scientists attended to the elements of place that affected human health and safety. Scientists argued for the importance of local biologies, generating tension with global public health projects and regulations premised on the universality of biology. © 2016 by the American Anthropological Association.

Repeatability and reproducibility of intracellular molar concentration assessed by synchrotron-based x-ray fluorescence microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Merolle, L., E-mail: lucia.merolle@elettra.eu; Gianoncelli, A.; Malucelli, E., E-mail: emil.malucelli@unibo.it

2016-01-28

Elemental analysis of biological sample can give information about content and distribution of elements essential for human life or trace elements whose absence is the cause of abnormal biological function or development. However, biological systems contain an ensemble of cells with heterogeneous chemistry and elemental content; therefore, accurate characterization of samples with high cellular heterogeneity may only be achieved by analyzing single cells. Powerful methods in molecular biology are abundant, among them X-Ray microscopy based on synchrotron light source has gaining increasing attention thanks to its extremely sensitivity. However, reproducibility and repeatability of these measurements is one of the majormore » obstacles in achieving a statistical significance in single cells population analysis. In this study, we compared the elemental content of human colon adenocarcinoma cells obtained by three distinct accesses to synchrotron radiation light.« less

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease.

PubMed

Torres, Matthew P; Dewhurst, Henry; Sundararaman, Niveda

2016-11-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable body of potential regulatory elements that impact hundreds of different biological processes important in eukaryotic biology and human health. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Emergy Evaluations of the Global Biogeochemical Cycles of Six Biologically Active Elements and Two Compounds

EPA Science Inventory

Estimates of the emergy carried by the flows of biologically active elements (BAE) and compounds are needed to accurately evaluate the near and far field effects of anthropogenic wastes. The transformities and specific emergies of these elements and of their different chemical sp...

Biologically Inspired Technology Using Electroactive Polymers (EAP)

NASA Technical Reports Server (NTRS)

Bar-Cohen, Yoseph

2006-01-01

Evolution allowed nature to introduce highly effective biological mechanisms that are incredible inspiration for innovation. Humans have always made efforts to imitate nature's inventions and we are increasingly making advances that it becomes significantly easier to imitate, copy, and adapt biological methods, processes and systems. This brought us to the ability to create technology that is far beyond the simple mimicking of nature. Having better tools to understand and to implement nature's principles we are now equipped like never before to be inspired by nature and to employ our tools in far superior ways. Effectively, by bio-inspiration we can have a better view and value of nature capability while studying its models to learn what can be extracted, copied or adapted. Using electroactive polymers (EAP) as artificial muscles is adding an important element to the development of biologically inspired technologies.

Modularization of genetic elements promotes synthetic metabolic engineering.

PubMed

Qi, Hao; Li, Bing-Zhi; Zhang, Wen-Qian; Liu, Duo; Yuan, Ying-Jin

2015-11-15

In the context of emerging synthetic biology, metabolic engineering is moving to the next stage powered by new technologies. Systematical modularization of genetic elements makes it more convenient to engineer biological systems for chemical production or other desired purposes. In the past few years, progresses were made in engineering metabolic pathway using synthetic biology tools. Here, we spotlighted the topic of implementation of modularized genetic elements in metabolic engineering. First, we overviewed the principle developed for modularizing genetic elements and then discussed how the genetic modules advanced metabolic engineering studies. Next, we picked up some milestones of engineered metabolic pathway achieved in the past few years. Last, we discussed the rapid raised synthetic biology field of "building a genome" and the potential in metabolic engineering. Copyright © 2015 Elsevier Inc. All rights reserved.

Analytical electron microscopy in the study of biological systems.

PubMed

Johnson, D E

1986-01-01

The AEM is a powerful tool in biological research, capable of providing information simply not available by other means. The use of a field emission STEM for this application can lead to a significant improvement in spatial resolution in most cases now allowed by the quality of the specimen preparation but perhaps ultimately limited by the effects of radiation damage. Increased elemental sensitivity is at least possible in selected cases with electron energy-loss spectrometry, but fundamental aspects of ELS will probably confine its role to that of a limited complement to EDS. The considerable margin for improvement in sensitivity of the basic analytical technique means that the search for technological improvement will continue. Fortunately, however, current technology can also continue to answer important biological questions.

A Guide to the Elements, Rev. Edition (by Albert Stwertka)

NASA Astrophysics Data System (ADS)

Berger, Reviewed By Daniel

1999-12-01

This edition is identical in format and content to the 1996 edition, now sold as the "library edition", except that the names and information for elements 104-109 have been updated. My earlier review still applies; a page-by-page comparison found this edition identical to the first except as noted in the previous sentence. The major revision has been in size and price. The 50% price reduction is welcome, but the format was not changed when the size was reduced, and the resulting 9-point font puts readers at risk of eyestrain. I would like to correct one of the criticisms in my earlier review There is excellent discussion of the industrial uses of each element, as well as its most common source minerals. The more economically important elements are given extensive discussions, detailing industrial uses of the element and its compounds. However, biological activity is given spotty coverage. There is no mention - under "iron" or elsewhere - of the central biological role of iron in oxygen transport or of magnesium in photosynthesis. When coverage appears it is not bad: the roles of calcium in vertebrate and invertebrate skeletons, of fluorine in reducing tooth decay by changing hydroxyapatite to fluorapatite, and of cobalt in vitamin B12 are discussed. While information on transuranium elements has been updated, there has been no attempt to correct several minor errors in spelling, placement, or even information. On page 14 the 1s subshell appears as part of the L (n = 2) shell, and upon the electrolysis of molten sodium chloride on page 54, "sodium collects atthe cathode, and chloride [sic] at...the anode." On page 73 the etymology of "potash" is still given as "potassium-rich ash" rather than "ash burned down in pots", though it is obvious that the latter is intended. On page 74, a picture caption claims that black powder ("potassium nitrate, wood charcoal, and sulfur") is used in modern, high-powered rifle cartridges. In spite of the mistakes, which are relatively few, there is much good information in this book. The essential chemical properties of each element are detailed so that periodic trends may be easily seen; important industrial uses are presented in some detail; transuranium elements and radioisotopes are given careful coverage; and biological activity is (occasionally) discussed. The presentation is interesting and eye-catching, designed to hold the interest of a student who knows little about chemistry. And now, the price has been made more reasonable. While the hardcover edition remains $35.00, the paperback edition, at half price, should bring this useful book into wider use.

A Miniaturized On-Chip Colorimeter for Detecting NPK Elements

PubMed Central

Liu, Rui-Tao; Tao, Lu-Qi; Liu, Bo; Tian, Xiang-Guang; Mohammad, Mohammad Ali; Yang, Yi; Ren, Tian-Ling

2016-01-01

Recently, precision agriculture has become a globally attractive topic. As one of the most important factors, the soil nutrients play an important role in estimating the development of precision agriculture. Detecting the content of nitrogen, phosphorus and potassium (NPK) elements more efficiently is one of the key issues. In this paper, a novel chip-level colorimeter was fabricated to detect the NPK elements for the first time. A light source–microchannel photodetector in a sandwich structure was designed to realize on-chip detection. Compared with a commercial colorimeter, all key parts are based on MEMS (Micro-Electro-Mechanical System) technology so that the volume of this on-chip colorimeter can be minimized. Besides, less error and high precision are achieved. The cost of this colorimeter is two orders of magnitude less than that of a commercial one. All these advantages enable a low-cost and high-precision sensing operation in a monitoring network. The colorimeter developed herein has bright prospects for environmental and biological applications. PMID:27527177

A Miniaturized On-Chip Colorimeter for Detecting NPK Elements.

PubMed

Liu, Rui-Tao; Tao, Lu-Qi; Liu, Bo; Tian, Xiang-Guang; Mohammad, Mohammad Ali; Yang, Yi; Ren, Tian-Ling

2016-08-04

Recently, precision agriculture has become a globally attractive topic. As one of the most important factors, the soil nutrients play an important role in estimating the development of precision agriculture. Detecting the content of nitrogen, phosphorus and potassium (NPK) elements more efficiently is one of the key issues. In this paper, a novel chip-level colorimeter was fabricated to detect the NPK elements for the first time. A light source-microchannel photodetector in a sandwich structure was designed to realize on-chip detection. Compared with a commercial colorimeter, all key parts are based on MEMS (Micro-Electro-Mechanical System) technology so that the volume of this on-chip colorimeter can be minimized. Besides, less error and high precision are achieved. The cost of this colorimeter is two orders of magnitude less than that of a commercial one. All these advantages enable a low-cost and high-precision sensing operation in a monitoring network. The colorimeter developed herein has bright prospects for environmental and biological applications.

Biological forcing controls the chemistry of reef-building coral skeleton

NASA Astrophysics Data System (ADS)

Meibom, Anders; Mostefaoui, Smail; Cuif, Jean-Pierre; Dauphin, Yannicke; Houlbreque, Fanny; Dunbar, Robert; Constantz, Brent

2007-01-01

We present analyses of major elements C and Ca and trace elements N, S, Mg and Sr in a Porites sp. exoskeleton with a spatial resolution better than ˜150 nm. Trace element variations are evaluated directly against the ultra-structure of the skeleton and are ascribed to dynamic biological forcing. Individual growth layers in the bulk fibrous aragonite skeleton form on sub-daily timescales. Magnesium concentration variations are dramatically correlated with the growth layers, but are uncorrelated with Sr concentration variations. Observed (sub)seasonal relationships between water temperature and skeletal trace-element chemistry are secondary, mediated by sensitive biological processes to which classical thermodynamic formalism does not apply.

Biological toxicity of lanthanide elements on algae.

PubMed

Tai, Peidong; Zhao, Qing; Su, Dan; Li, Peijun; Stagnitti, Frank

2010-08-01

The biological toxicity of lanthanides on marine monocellular algae was investigated. The specific objective of this research was to establish the relationship between the abundance in the seawater of lanthanides and their biological toxicities on marine monocellular algae. The results showed that all single lanthanides had similar toxic effects on Skeletonema costatum. High concentrations of lanthanides (29.04+/-0.61 micromol L(-1)) resulted in 50% reduction in growth of algae compared to the controls (0 micromol L(-1)) after 96 h (96 h-EC50). The biological toxicity of 13 lanthanides on marine monocellular algae was unrelated with the abundance of different lanthanide elements in nature, and the "Harkins rule" was not appropriate for the lanthanides. A mixed solution that contained equivalent concentrations of each lanthanide element had the same inhibition effect on algae cells as each individual lanthanide element at the same total concentration. This phenomenon is unique compared to the groups of other elements in the periodic table. Hence, we speculate that the monocellular organisms might not be able to sufficiently differentiate between the almost chemically identical lanthanide elements. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Preserving elemental content in adherent mammalian cells for analysis by synchrotron-based x-ray fluorescence microscopy

DOE PAGES

Jin, Qiaoling; Paunesku, Tatjana; Lai, Barry; ...

2016-08-31

Trace metals play important roles in biological function, and x-ray fluorescence microscopy (XFM) provides a way to quantitatively image their distribution within cells. The faithfulness of these measurements is dependent on proper sample preparation. Using mouse embryonic fibroblast NIH/3T3 cells as an example, we compare various approaches to the preparation of adherent mammalian cells for XFM imaging under ambient temperature. Direct side-by-side comparison shows that plunge-freezing-based cryoimmobilization provides more faithful preservation than conventional chemical fixation for most biologically important elements including P, S, Cl, K, Fe, Cu, Zn and possibly Ca in adherent mammalian cells. Although cells rinsed with freshmore » media had a great deal of extracellular background signal for Cl and Ca, this approach maintained cells at the best possible physiological status before rapid freezing and it does not interfere with XFM analysis of other elements. If chemical fixation has to be chosen, the combination of 3% paraformaldehyde and 1.5 % glutaraldehyde preserves S, Fe, Cu and Zn better than either fixative alone. Lastly, when chemically fixed cells were subjected to a variety of dehydration processes, air drying was proved to be more suitable than other drying methods such as graded ethanol dehydration and freeze drying. This first detailed comparison for x-ray fluorescence microscopy shows how detailed quantitative conclusions can be affected by the choice of cell preparation method.« less

Preserving elemental content in adherent mammalian cells for analysis by synchrotron-based x-ray fluorescence microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Qiaoling; Paunesku, Tatjana; Lai, Barry

Trace metals play important roles in biological function, and x-ray fluorescence microscopy (XFM) provides a way to quantitatively image their distribution within cells. The faithfulness of these measurements is dependent on proper sample preparation. Using mouse embryonic fibroblast NIH/3T3 cells as an example, we compare various approaches to the preparation of adherent mammalian cells for XFM imaging under ambient temperature. Direct side-by-side comparison shows that plunge-freezing-based cryoimmobilization provides more faithful preservation than conventional chemical fixation for most biologically important elements including P, S, Cl, K, Fe, Cu, Zn and possibly Ca in adherent mammalian cells. Although cells rinsed with freshmore » media had a great deal of extracellular background signal for Cl and Ca, this approach maintained cells at the best possible physiological status before rapid freezing and it does not interfere with XFM analysis of other elements. If chemical fixation has to be chosen, the combination of 3% paraformaldehyde and 1.5 % glutaraldehyde preserves S, Fe, Cu and Zn better than either fixative alone. Lastly, when chemically fixed cells were subjected to a variety of dehydration processes, air drying was proved to be more suitable than other drying methods such as graded ethanol dehydration and freeze drying. This first detailed comparison for x-ray fluorescence microscopy shows how detailed quantitative conclusions can be affected by the choice of cell preparation method.« less

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease*

PubMed Central

Dewhurst, Henry; Sundararaman, Niveda

2016-01-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable body of potential regulatory elements that impact hundreds of different biological processes important in eukaryotic biology and human health. PMID:27697855

Marine Biogeochemistry of Particulate Trace Elements in the Exclusive Economic Zone (eez) of the State of Qatar

NASA Astrophysics Data System (ADS)

Yigiterhan, O.; Al-Ansari, I. S.; Abdel-Moati, M.; Murray, J. W.; Al-Ansi, M.

2016-02-01

We focus on the trace element geochemistry of particulate matter in the Exclusive Economic Zone (EEZ) of Qatar. A main goal of this research was to analyze a complete suite of trace elements on particulate matter samples from the water column from different oceanographic biogeochemical zones of the EEZ around Qatar. The sample set also includes plankton samples which are the main source of biogenic particles, dust samples which are a source of abiological particles to surface seawater and surface sediments which can be a source of resuspended particles and a sink for settling particles. The 15 metals and 2 non-metals analyzed in this study will be Al, Ti, V, Cd, Co, Cu, Fe, Mn, Ni, Pb, Zn, Mo, Ag, Ba, U and P, N. Many factors control the composition of trace elements in marine particles. Most of these are important in the EEZ of Qatar, including:1. Natural sources: These are rivers, atmospheric dust, sediment resuspension and leaks from oil beds. However, due to very limited rainfall rivers play no major role in Qatar but resuspension of shallow carbonate rich sediments and input of atmospheric dust are important due to strong currents and surrounding deserts.2. Adsorption/desorption: These chemical processes occur everywhere in the ocean and transfer metals between particles and the solution phase.3. Biological uptake: This process is likewise a universal ocean process and results in transport of metals from the solution phase to biological particles.4. Redox conditions: These are important chemical reactions in the oxic, suboxic and anoxic zones. This can be the dominant controlling mechanism in the northeastern hypoxic deeper waters of the Qatar EEZ.5. Anthropogenic sources: The eastern part of the Qatar contains numerous industrial sites, petroleum/gas platforms and refineries. There are numerous industrial sources but the main hot spots are the port of Doha and the industrial cities of Mesaieed, Khor Al-Odaid, and Ras Laffan. We aimed to determine the influence of the different current systems, water masses, and terrestrial inputs on the distribution, fractionation, and fate of trace metal contaminants and elemental pollutants. We have also observed the level of anthropogenic enrichments for some of the elements which have not been previously documented. This research should be viewed as the first stage of a complete study.

The genomic view of genes responsive to the antagonistic phytohormones, abscisic acid, and gibberellin.

PubMed

Yazaki, Junshi; Kikuchi, Shoshi

2005-01-01

We now have the various genomics tools for monocot (Oryza sativa) and a dicot (Arabidopsis thaliana) plant. Plant is not only a very important agricultural resource but also a model organism for biological research. It is important that the interaction between ABA and GA is investigated for controlling the transition from embryogenesis to germination in seeds using genomics tools. These studies have investigated the relationship between dormancy and germination using genomics tools. Genomics tools identified genes that had never before been annotated as ABA- or GA-responsive genes in plant, detected new interactions between genes responsive to the two hormones, comprehensively characterized cis-elements of hormone-responsive genes, and characterized cis-elements of rice and Arabidopsis. In these research, ABA- and GA-regulated genes have been classified as functional proteins (proteins that probably function in stress or PR tolerance) and regulatory proteins (protein factors involved in further regulation of signal transduction). Comparison between ABA and/or GA-responsive genes in rice and those in Arabidopsis has shown that the cis-element has specificity in each species. cis-Elements for the dehydration-stress response have been specified in Arabidopsis but not in rice. cis-Elements for protein storage are remarkably richer in the upstream regions of the rice gene than in those of Arabidopsis.

Extrachromosomal genetic elements in Micrococcus.

PubMed

Dib, Julián Rafael; Liebl, Wolfgang; Wagenknecht, Martin; Farías, María Eugenia; Meinhardt, Friedhelm

2013-01-01

Micrococci are Gram-positive G + C-rich, nonmotile, nonspore-forming actinomycetous bacteria. Micrococcus comprises ten members, with Micrococcus luteus being the type species. Representatives of the genus play important roles in the biodegradation of xenobiotics, bioremediation processes, production of biotechnologically important enzymes or bioactive compounds, as test strains in biological assays for lysozyme and antibiotics, and as infective agents in immunocompromised humans. The first description of plasmids dates back approximately 28 years, when several extrachromosomal elements ranging in size from 1.5 to 30.2 kb were found in Micrococcus luteus. Up to the present, a number of circular plasmids conferring antibiotic resistance, the ability to degrade aromatic compounds, and osmotolerance are known, as well as cryptic elements with unidentified functions. Here, we review the Micrococcus extrachromosomal traits reported thus far including phages and the only quite recently described large linear extrachromosomal genetic elements, termed linear plasmids, which range in size from 75 kb (pJD12) to 110 kb (pLMA1) and which confer putative advantageous capabilities, such as antibiotic or heavy metal resistances (inferred from sequence analyses and curing experiments). The role of the extrachromosomal elements for the frequently proven ecological and biotechnological versatility of the genus will be addressed as well as their potential for the development and use as genetic tools.

Imaging and elemental mapping of biological specimens with a dual-EDS dedicated scanning transmission electron microscope

PubMed Central

Wu, J.S.; Kim, A. M.; Bleher, R.; Myers, B.D.; Marvin, R. G.; Inada, H.; Nakamura, K.; Zhang, X.F.; Roth, E.; Li, S.Y.; Woodruff, T. K.; O'Halloran, T. V.; Dravid, Vinayak P.

2013-01-01

A dedicated analytical scanning transmission electron microscope (STEM) with dual energy dispersive spectroscopy (EDS) detectors has been designed for complementary high performance imaging as well as high sensitivity elemental analysis and mapping of biological structures. The performance of this new design, based on a Hitachi HD-2300A model, was evaluated using a variety of biological specimens. With three imaging detectors, both the surface and internal structure of cells can be examined simultaneously. The whole-cell elemental mapping, especially of heavier metal species that have low cross-section for electron energy loss spectroscopy (EELS), can be faithfully obtained. Optimization of STEM imaging conditions is applied to thick sections as well as thin sections of biological cells under low-dose conditions at room- and cryogenic temperatures. Such multimodal capabilities applied to soft/biological structures usher a new era for analytical studies in biological systems. PMID:23500508

Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deng, Junjing; Vine, David J.; Chen, Si

Trace metals play important roles in normal and in disease-causing biological functions. X-ray fluorescence microscopy reveals trace elements with no dependence on binding affinities (unlike with visible light fluorophores) and with improved sensitivity relative to electron probes. However, X-ray fluorescence is not very sensitive for showing the light elements that comprise the majority of cellular material. Here we show that X-ray ptychography can be combined with fluorescence to image both cellular structure and trace element distribution in frozen-hydrated cells at cryogenic temperatures, with high structural and chemical fidelity. Ptychographic reconstruction algorithms deliver phase and absorption contrast images at a resolutionmore » beyond that of the illuminating lens or beam size. Using 5.2-keV X-rays, we have obtained sub-30-nm resolution structural images and ~90-nm-resolution fluorescence images of several elements in frozen-hydrated green algae. Finally, this combined approach offers a way to study the role of trace elements in their structural context.« less

Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae

DOE PAGES

Deng, Junjing; Vine, David J.; Chen, Si; ...

2015-02-24

Trace metals play important roles in normal and in disease-causing biological functions. X-ray fluorescence microscopy reveals trace elements with no dependence on binding affinities (unlike with visible light fluorophores) and with improved sensitivity relative to electron probes. However, X-ray fluorescence is not very sensitive for showing the light elements that comprise the majority of cellular material. Here we show that X-ray ptychography can be combined with fluorescence to image both cellular structure and trace element distribution in frozen-hydrated cells at cryogenic temperatures, with high structural and chemical fidelity. Ptychographic reconstruction algorithms deliver phase and absorption contrast images at a resolutionmore » beyond that of the illuminating lens or beam size. Using 5.2-keV X-rays, we have obtained sub-30-nm resolution structural images and ~90-nm-resolution fluorescence images of several elements in frozen-hydrated green algae. Finally, this combined approach offers a way to study the role of trace elements in their structural context.« less

Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deng, Junjing; Vine, David J.; Chen, Si

Trace metals play important roles in normal and in disease-causing biological functions. X-ray fluorescence microscopy reveals trace elements with no dependence on binding affinities (unlike with visible light fluorophores) and with improved sensitivity relative to electron probes. However, X-ray fluorescence is not very sensitive for showing the light elements that comprise the majority of cellular material. Here we show that X-ray ptychography can be combined with fluorescence to image both cellular structure and trace element distribution in frozen-hydrated cells at cryogenic temperatures, with high structural and chemical fidelity. Ptychographic reconstruction algorithms deliver phase and absorption contrast images at a resolutionmore » beyond that of the illuminating lens or beam size. Using 5.2-keV X-rays, we have obtained sub-30-nm resolution structural images and similar to 90-nm-resolution fluorescence images of several elements in frozen-hydrated green algae. This combined approach offers a way to study the role of trace elements in their structural context.« less

Design of an elemental analysis system for CELSS research

NASA Technical Reports Server (NTRS)

Schwartzkopf, Steven H.

1987-01-01

The results of experiments conducted with higher plants in tightly sealed growth chambers provide definite evidence that the physical closure of a chamber has significant effects on many aspects of a plant's biology. One of these effects is seen in the change in rates of uptake, distribution, and re-release or nutrient elements by the plant (mass balance). Experimental data indicates that these rates are different from those recorded for plants grown in open field agriculture, or in open growth chambers. Since higher plants are a crucial component of a controlled ecological life support system (CELSS), it is important that the consequences of these rate differences be understood with regard to the growth and yield of the plants. A description of a system for elemental analysis which can be used to monitor the mass balance of nutrient elements in CELSS experiments is given. Additionally, data on the uptake of nutrient elements by higher plants grown in a growth chamber is presented.

Design methodology and results evaluation of a heating functionality in modular lab-on-chip systems

NASA Astrophysics Data System (ADS)

Streit, Petra; Nestler, Joerg; Shaporin, Alexey; Graunitz, Jenny; Otto, Thomas

2018-06-01

Lab-on-a-chip (LoC) systems offer the opportunity of fast and customized biological analyses executed at the ‘point-of-need’ without expensive lab equipment. Some biological processes need a temperature treatment. Therefore, it is important to ensure a defined and stable temperature distribution in the biosensor area. An integrated heating functionality is realized with discrete resistive heating elements including temperature measurement. The focus of this contribution is a design methodology and evaluation technique of the temperature distribution in the biosensor area with regard to the thermal-electrical behaviour of the heat sources. Furthermore, a sophisticated control of the biosensor temperature is proposed. A finite element (FE) model with one and more integrated heat sources in a polymer-based LoC system is used to investigate the impact of the number and arrangement of heating elements on the temperature distribution around the heating elements and in the biosensor area. Based on this model, various LOC systems are designed and fabricated. Electrical characterization of the heat sources and independent temperature measurements with infrared technique are performed to verify the model parameters and prove the simulation approach. The FE model and the proposed methodology is the foundation for optimization and evaluation of new designs with regard to temperature requirements of the biosensor. Furthermore, a linear dependency of the heater temperature on the electric current is demonstrated in the targeted temperature range of 20 °C to 70 °C enabling the usage of the heating functionality for biological reactions requiring a steady-state temperature up to 70 °C. The correlation between heater and biosensor area temperature is derived for a direct control through the heating current.

Beyond dichotomies-(m)others' structuring and the development of toddlers' prosocial behavior across cultures.

PubMed

Kärtner, Joscha

2018-04-01

Basic elements of prosociality-(pro)social cognition, motivation, and prosocial behavior-emerge during the first and second year of life. These elements are rooted in biological predispositions and the developmental system is complemented by caregivers' structuring. By structuring, (m)others integrate toddlers' unrefined (pro)social sentiments and behavioral inclinations into coherent patterns and align toddlers' experience and behavior with the population's cultural model. These cultural models specify target states for appropriate affective, motivational and behavioral responses regarding toddlers' prosociality and these target states, in turn, inform (m)others' appraisal and guide their structuring. The experiences that toddlers make in these social interactions have important implications for how the basic elements of prosociality are refined and further develop. Copyright © 2017 Elsevier Ltd. All rights reserved.

Trace element doping in calcium phosphate ceramics to Understand osteogenesis and angiogenesis

PubMed Central

Bose, Susmita; Fielding, Gary; Tarafder, Solaiman; Bandyopadhyay, Amit

2013-01-01

The general trends in synthetic bone grafting materials are shifting towards approaches that can illicit osteoinductive properties. Pharmacologics and biologics have been used in combination with calcium phosphate (CaP) ceramics, however, recently have become the target of scrutiny over the safety. The importance of trace elements in natural bone health is well documented. Ions, e.g. lithium, zinc, magnesium, manganese, silicon, strontium etc. have shown to increase osteogenesis and neovascularization. Incorporation of dopants into CaPs can provide a platform for safe and efficient delivery in clinical applications where increased bone healing is favorable. This review highlights use of trace elements in CaP biomaterials, and offers an insight into the mechanisms of how metal ions can enhance both osteogenesis and angiogenesis. PMID:24012308

Project Based Learning on Students' Performance in the Concept of Classification of Organisms among Secondary Schools in Kenya

ERIC Educational Resources Information Center

Wekesa, Noah Wafula; Ongunya, Raphael Odhiambo

2016-01-01

The concept of classification of organisms in Biology seems to pose a problem to Secondary School students in Kenya. Though, the topic is important for understanding of the basic elements of the subject. The Examinations Council in Kenya has identified teacher centred pedagogical techniques as one of the main causes for this. Project based…

Cognitive Processes in Folk Ornithology: The Identification of Gulls. Working Papers of the Language Behavior Research Laboratory, No. 42.

ERIC Educational Resources Information Center

Hunn, Eugene

Recent studies of folk biology clearly reveal the detailed empirical knowledge of living things which is an important and characteristic element of pre-scientific cultures. This paper attempts a contribution to the study of such systems of knowledge by analyzing the comparable skills of a few American birdwatchers. The process of identification of…

Multiscale structural gradients enhance the biomechanical functionality of the spider fang

PubMed Central

Bar-On, Benny; Barth, Friedrich G.; Fratzl, Peter; Politi, Yael

2014-01-01

The spider fang is a natural injection needle, hierarchically built from a complex composite material comprising multiscale architectural gradients. Considering its biomechanical function, the spider fang has to sustain significant mechanical loads. Here we apply experiment-based structural modelling of the fang, followed by analytical mechanical description and Finite-Element simulations, the results of which indicate that the naturally evolved fang architecture results in highly adapted effective structural stiffness and damage resilience. The analysis methods and physical insights of this work are potentially important for investigating and understanding the architecture and structural motifs of sharp-edge biological elements such as stingers, teeth, claws and more. PMID:24866935

Trace Elements Speciation of Submicron Particulate Matter (PM1) Collected in the Surroundings of Power Plants.

PubMed

Zajusz-Zubek, Elwira; Kaczmarek, Konrad; Mainka, Anna

2015-10-16

This study reports the concentrations of PM1 trace elements (As, Cd, Co, Cr, Hg, Mn, Ni, Pb, Sb and Se) content in highly mobile (F1), mobile (F2), less mobile (F3) and not mobile (F4) fractions in samples that were collected in the surroundings of power plants in southern Poland. It also reports source identification by enrichment factors (EF) and a principal component analysis (PCA). There is limited availability of scientific data concerning the chemical composition of dust, including fractionation analyses of trace elements, in the surroundings of power plants. The present study offers important results in order to fill this data gap. The data collected in this study can be utilized to validate air quality models in this rapidly developing area. They are also crucial for comparisons with datasets from similar areas all over the world. Moreover, the identification of the bioavailability of selected carcinogenic and toxic elements in the future might be used as output data for potential biological and population research on risk assessment. This is important in the context of air pollution being hazardous to human health.

Current strategies for mobilome research.

PubMed

Jørgensen, Tue S; Kiil, Anne S; Hansen, Martin A; Sørensen, Søren J; Hansen, Lars H

2014-01-01

Mobile genetic elements (MGEs) are pivotal for bacterial evolution and adaptation, allowing shuffling of genes even between distantly related bacterial species. The study of these elements is biologically interesting as the mode of genetic propagation is kaleidoscopic and important, as MGEs are the main vehicles of the increasing bacterial antibiotic resistance that causes thousands of human deaths each year. The study of MGEs has previously focused on plasmids from individual isolates, but the revolution in sequencing technology has allowed the study of mobile genomic elements of entire communities using metagenomic approaches. The problem in using metagenomic sequencing for the study of MGEs is that plasmids and other mobile elements only comprise a small fraction of the total genetic content that are difficult to separate from chromosomal DNA based on sequence alone. The distinction between plasmid and chromosome is important as the mobility and regulation of genes largely depend on their genetic context. Several different approaches have been proposed that specifically enrich plasmid DNA from community samples. Here, we review recent approaches used to study entire plasmid pools from complex environments, and point out possible future developments for and pitfalls of these approaches. Further, we discuss the use of the PacBio long-read sequencing technology for MGE discovery.

Non-native, N-terminal Hsp70 Molecular Motor Recognition Elements in Transit Peptides Support Plastid Protein Translocation*

PubMed Central

Chotewutmontri, Prakitchai; Bruce, Barry D.

2015-01-01

Previously, we identified the N-terminal domain of transit peptides (TPs) as a major determinant for the translocation step in plastid protein import. Analysis of Arabidopsis TP dataset revealed that this domain has two overlapping characteristics, highly uncharged and Hsp70-interacting. To investigate these two properties, we replaced the N-terminal domains of the TP of the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase and its reverse peptide with a series of unrelated peptides whose affinities to the chloroplast stromal Hsp70 have been determined. Bioinformatic analysis indicated that eight out of nine peptides in this series are not similar to the TP N terminus. Using in vivo and in vitro protein import assays, the majority of the precursors containing Hsp70-binding elements were targeted to plastids, whereas none of the chimeric precursors lacking an N-terminal Hsp70-binding element were targeted to the plastids. Moreover, a pulse-chase assay showed that two chimeric precursors with the most uncharged peptides failed to translocate into the stroma. The ability of multiple unrelated Hsp70-binding elements to support protein import verified that the majority of TPs utilize an N-terminal Hsp70-binding domain during translocation and expand the mechanistic view of the import process. This work also indicates that synthetic biology may be utilized to create de novo TPs that exceed the targeting activity of naturally occurring sequences. PMID:25645915

Mineral Nutrition of Plants. Chapter 9

NASA Technical Reports Server (NTRS)

Wignarajah, Kanapathipillai

1995-01-01

The ultimate source of nutrients for all living organisms consists of the inanimate nutrient reserves found on earth. Of the elements known to exist, seven are considered essential to plants in large amounts (macronutrients), and many others are required in smaller quantities (micronutrients). Essentiality of a nutrient is defined according to the following concepts: (a) A deficiency of the element makes it impossible for the plant to complete the vegetative or reproductive stage of its cycle; (b) such deficiency is specific to the element in question and can be prevented or corrected only by supplying this element; (c) the element is directly involved in the nutrition of the plant quite apart from its possible effects in correcting some unfavorable microbiological or chemical condition of the soil or other culture medium. From that standpoint a favorable response from adding a given element to the culture medium does not constitute conclusive evidence of its indispensability in plant nutrition. All the elements occurring in the outer part of the earth are in constant turnover among the different components of earth. This overall migration is referred to as geochemical cycling. When cycling includes a role for biological organisms, it is referred to as "biogeochemical cycling." Like most cyclical processes in nature, the biogeochemical cycling of elements is not continuous, nor does it proceed in a well-defined direction. At stages, it may be halted or short-circuited, or it may change. Any changes will eventually impact the survival, evolution, and development of biological species in the system. The relationship of the various systems is represented in a schematic manner. To assess the efficiency of operation of the biogeochemical cycles, it is important to include both natural and human activities. Often reliable values on use by man are difficult to obtain for a number of reasons, such as lack of international cooperation, and lack of proper bookkeeping and auditing by individual nations. However, a general estimate of the annual world consumption of elements and their compounds is presented.

Feedback Interactions between Trace Metal Nutrients and Phytoplankton in the Ocean

PubMed Central

Sunda, William G.

2012-01-01

In addition to control by major nutrient elements (nitrogen, phosphorus, and silicon) the productivity and species composition of marine phytoplankton communities are also regulated by a number of trace metal nutrients (iron, zinc, cobalt, manganese, copper, and cadmium). Of these, iron is most limiting to phytoplankton growth and has the greatest effect on algal species diversity. It also plays an important role in limiting di-nitrogen (N2) fixation rates, and thus is important in controlling ocean inventories of fixed nitrogen. Because of these effects, iron is thought to play a key role in regulating biological cycles of carbon and nitrogen in the ocean, including the biological transfer of carbon to the deep sea, the so-called biological CO2 pump, which helps regulate atmospheric CO2 and CO2-linked global warming. Other trace metal nutrients (zinc, cobalt, copper, and manganese) have lesser effects on productivity; but may exert an important influence on the species composition of algal communities because of large differences in metal requirements among species. The interactions between trace metals and ocean plankton are reciprocal: not only do the metals control the plankton, but the plankton regulate the distributions, chemical speciation, and cycling of these metals through cellular uptake and recycling processes, downward flux of biogenic particles, biological release of organic chelators, and mediation of redox reactions. This two way interaction has influenced not only the biology and chemistry of the modern ocean, but has had a profound influence on biogeochemistry of the ocean and earth system as a whole, and on the evolution of marine and terrestrial biology over geologic history. PMID:22701115

Distinguishing friends, foes, and freeloaders in giant genomes.

PubMed

Bennetzen, Jeffrey L; Park, Minkyu

2018-04-01

Most annotations of large eukaryotic genomes initially find transposable elements (TEs) and other repeats, then mask them so that subsequent efforts can be concentrated on the annotation and study of non-TE genes. However, TEs often contribute to host biology, and their community biologies are of intrinsic interest. This review discusses the challenges, rationale and technologies for comprehensive TE annotation in the commonly giant genomes of animals and plants. Complete discovery of the TEs in a fully sequenced genome is laborious, but feasible, with current strategies in the hands of a careful researcher. These deep TE studies have begun to provide important perspectives on how genomes evolve and the degree to which genome changes do and do not affect eukaryotic biology. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

The Kuwait Oil Fire Health Risk Assessment Biological Surveillance Initiative.

PubMed

Deeter, David P

2011-07-01

An important environmental concern during the first Gulf War (Operation Desert Storm) was assessing exposures and potential health effects in U.S. forces exposed to the Kuwait oil fires. With only 3 weeks for planning, a Biological Surveillance Initiative (BSI) was developed and implemented for a U.S. Army unit. The BSI included blood and urine collections, questionnaire administration, and other elements during the predeployment, deployment, and post-deployment phases. Many BSI objectives were accomplished. Difficulties encountered included planning failures, loss of data and information, and difficulty in interpreting laboratory results. In order for biological surveillance initiatives to provide useful information for future deployments where environmental exposures may be a concern, meaningful, detailed, and realistic planning and preparation must occur long before the deployment is initiated.

Impact of hydrothermalism on the ocean iron cycle

PubMed Central

Resing, Joseph

2016-01-01

As the iron supplied from hydrothermalism is ultimately ventilated in the iron-limited Southern Ocean, it plays an important role in the ocean biological carbon pump. We deploy a set of focused sensitivity experiments with a state of the art global model of the ocean to examine the processes that regulate the lifetime of hydrothermal iron and the role of different ridge systems in governing the hydrothermal impact on the Southern Ocean biological carbon pump. Using GEOTRACES section data, we find that stabilization of hydrothermal iron is important in some, but not all regions. The impact on the Southern Ocean biological carbon pump is dominated by poorly explored southern ridge systems, highlighting the need for future exploration in this region. We find inter-basin differences in the isopycnal layer onto which hydrothermal Fe is supplied between the Atlantic and Pacific basins, which when combined with the inter-basin contrasts in oxidation kinetics suggests a muted influence of Atlantic ridges on the Southern Ocean biological carbon pump. Ultimately, we present a range of processes, operating at distinct scales, that must be better constrained to improve our understanding of how hydrothermalism affects the ocean cycling of iron and carbon. This article is part of the themed issue ‘Biological and climatic impacts of ocean trace element chemistry’. PMID:29035256

Impact of hydrothermalism on the ocean iron cycle.

PubMed

Tagliabue, Alessandro; Resing, Joseph

2016-11-28

As the iron supplied from hydrothermalism is ultimately ventilated in the iron-limited Southern Ocean, it plays an important role in the ocean biological carbon pump. We deploy a set of focused sensitivity experiments with a state of the art global model of the ocean to examine the processes that regulate the lifetime of hydrothermal iron and the role of different ridge systems in governing the hydrothermal impact on the Southern Ocean biological carbon pump. Using GEOTRACES section data, we find that stabilization of hydrothermal iron is important in some, but not all regions. The impact on the Southern Ocean biological carbon pump is dominated by poorly explored southern ridge systems, highlighting the need for future exploration in this region. We find inter-basin differences in the isopycnal layer onto which hydrothermal Fe is supplied between the Atlantic and Pacific basins, which when combined with the inter-basin contrasts in oxidation kinetics suggests a muted influence of Atlantic ridges on the Southern Ocean biological carbon pump. Ultimately, we present a range of processes, operating at distinct scales, that must be better constrained to improve our understanding of how hydrothermalism affects the ocean cycling of iron and carbon.This article is part of the themed issue 'Biological and climatic impacts of ocean trace element chemistry'. © 2016 The Author(s).

Simulation of temperature distribution in tumor Photothermal treatment

NASA Astrophysics Data System (ADS)

Zhang, Xiyang; Qiu, Shaoping; Wu, Shulian; Li, Zhifang; Li, Hui

2018-02-01

The light transmission in biological tissue and the optical properties of biological tissue are important research contents of biomedical photonics. It is of great theoretical and practical significance in medical diagnosis and light therapy of disease. In this paper, the temperature feedback-controller was presented for monitoring photothermal treatment in realtime. Two-dimensional Monte Carlo (MC) and diffuse approximation were compared and analyzed. The results demonstrated that diffuse approximation using extrapolated boundary conditions by finite element method is a good approximation to MC simulation. Then in order to minimize thermal damage, real-time temperature monitoring was appraised by proportional-integral-differential (PID) controller in the process of photothermal treatment.

Catfish Biology and Farming.

PubMed

Dunham, Rex A; Elaswad, Ahmed

2018-02-15

This article summarizes the biology and culture of ictalurid catfish, an important commercial, aquaculture, and sport fish family in the United States. The history of the propagation as well as spawning of common catfish species in this family is reviewed, with special emphasis on channel catfish and its hybridization with blue catfish. The importance of the channel catfish female×blue catfish male hybrid, including current and future methods of hybrid catfish production, and the potential role it plays in the recovery of the US catfish industry are discussed. Recent advances in catfish culture elements, including environment, management, nutrition, feeding, disease control, culture systems, genetic improvement programs, transgenics, and the application of genome-based approaches in catfish production and welfare, are reviewed. The current status, needs, and future projections are discussed, as well as genetically modified organism developments that are changing the future.

The Review of Nuclear Microscopy Techniques: An Approach for Nondestructive Trace Elemental Analysis and Mapping of Biological Materials.

PubMed

Mulware, Stephen Juma

2015-01-01

The properties of many biological materials often depend on the spatial distribution and concentration of the trace elements present in a matrix. Scientists have over the years tried various techniques including classical physical and chemical analyzing techniques each with relative level of accuracy. However, with the development of spatially sensitive submicron beams, the nuclear microprobe techniques using focused proton beams for the elemental analysis of biological materials have yielded significant success. In this paper, the basic principles of the commonly used microprobe techniques of STIM, RBS, and PIXE for trace elemental analysis are discussed. The details for sample preparation, the detection, and data collection and analysis are discussed. Finally, an application of the techniques to analysis of corn roots for elemental distribution and concentration is presented.

Inhibition of nitrogenase by oxygen in marine cyanobacteria controls the global nitrogen and oxygen cycles

NASA Astrophysics Data System (ADS)

Berman-Frank, I.; Chen, Y.-B.; Gerchman, Y.; Dismukes, G. C.; Falkowski, P. G.

2005-03-01

Cyanobacterial N2-fixation supplies the vast majority of biologically accessible inorganic nitrogen to nutrient-poor aquatic ecosystems. The process, catalyzed by the heterodimeric protein complex, nitrogenase, is thought to predate that of oxygenic photosynthesis. Remarkably, while the enzyme plays such a critical role in Earth's biogeochemical cycles, the activity of nitrogenase in cyanobacteria is markedly inhibited in vivo at a post-translational level by the concentration of O2 in the contemporary atmosphere leading to metabolic and biogeochemical inefficiency in N2 fixation. We illustrate this crippling effect with data from Trichodesmium spp. an important contributor of "new nitrogen" to the world's subtropical and tropical oceans. The enzymatic inefficiency of nitrogenase imposes a major elemental taxation on diazotrophic cyanobacteria both in the costs of protein synthesis and for scarce trace elements, such as iron. This restriction has, in turn, led to a global limitation of fixed nitrogen in the contemporary oceans and provides a strong biological control on the upper bound of oxygen concentration in Earth's atmosphere.

Cognitive impairment, genomic instability and trace elements.

PubMed

Meramat, A; Rajab, N F; Shahar, S; Sharif, R

2015-01-01

Cognitive impairments are often related to aging and micronutrient deficiencies. Various essential micronutrients in the diet are involved in age-altered biological functions such as, zinc, copper, iron, and selenium that play pivotal roles either in maintaining and reinforcing the antioxidant performances or in affecting the complex network of genes (nutrigenomic approach) involved in encoding proteins for biological functions. Genomic stability is one of the leading causes of cognitive decline and deficiencies or excess in trace elements are two of the factors relating to it. In this review, we report and discuss the role of micronutrients in cognitive impairment in relation to genomic stability in an aging population. Telomere integrity will also be discussed in relation to aging and cognitive impairment, as well as, the micronutrients related to these events. This review will provide an understanding on how these three aspects can relate with each other and why it is important to keep a homeostasis of micronutrients in relation to healthy aging. Micronutrient deficiencies and aging process can lead to genomic instability.

Differential Nutrient Limitation of Soil Microbial Biomass and Metabolic Quotients (qCO2): Is There a Biological Stoichiometry of Soil Microbes?

PubMed Central

Hartman, Wyatt H.; Richardson, Curtis J.

2013-01-01

Background Variation in microbial metabolism poses one of the greatest current uncertainties in models of global carbon cycling, and is particularly poorly understood in soils. Biological Stoichiometry theory describes biochemical mechanisms linking metabolic rates with variation in the elemental composition of cells and organisms, and has been widely observed in animals, plants, and plankton. However, this theory has not been widely tested in microbes, which are considered to have fixed ratios of major elements in soils. Methodology/Principal Findings To determine whether Biological Stoichiometry underlies patterns of soil microbial metabolism, we compiled published data on microbial biomass carbon (C), nitrogen (N), and phosphorus (P) pools in soils spanning the global range of climate, vegetation, and land use types. We compared element ratios in microbial biomass pools to the metabolic quotient qCO2 (respiration per unit biomass), where soil C mineralization was simultaneously measured in controlled incubations. Although microbial C, N, and P stoichiometry appeared to follow somewhat constrained allometric relationships at the global scale, we found significant variation in the C∶N∶P ratios of soil microbes across land use and habitat types, and size-dependent scaling of microbial C∶N and C∶P (but not N∶P) ratios. Microbial stoichiometry and metabolic quotients were also weakly correlated as suggested by Biological Stoichiometry theory. Importantly, we found that while soil microbial biomass appeared constrained by soil N availability, microbial metabolic rates (qCO2) were most strongly associated with inorganic P availability. Conclusions/Significance Our findings appear consistent with the model of cellular metabolism described by Biological Stoichiometry theory, where biomass is limited by N needed to build proteins, but rates of protein synthesis are limited by the high P demands of ribosomes. Incorporation of these physiological processes may improve models of carbon cycling and understanding of the effects of nutrient availability on soil C turnover across terrestrial and wetland habitats. PMID:23526933

Social relationships and social support among post-war youth in Northern Uganda.

PubMed

De Nutte, Leen; Okello, James; Derluyn, Ilse

2017-08-01

Although social relationships and social support are salient factors for post-war adolescents' psychosocial coping and adjustment, there is only limited information regarding war-affected adolescents' views on social support and the relationships within which social support is provided. This study therefore explored both elements among a clinical sample of 20 adolescents living in post-war Northern Uganda. Following Braun and Clarke's thematic analysis, we found a prominent role of the biological mother and other primary biological family members in the upbringing of our participants. Spiritual and material support were perceived to be the most important type of support, respectively, while the adolescents were growing up and in their current lives. These findings provide support for the perception that caregiving systems are adaptable to particular sociocultural contexts. Further, the importance of particular functions of social support could signify a potentially selective buffering effect of these functions in adverse contexts. Because of the importance of the primary biological family and the salient role of parent-child relationships in the face of adversity, future research needs to focus on this particular kind of social relationship in contexts of prolonged collective violence. © 2015 International Union of Psychological Science.

Trace elements at the intersection of marine biological and geochemical evolution

USGS Publications Warehouse

Robbins, Leslie J.; Lalonde, Stefan V.; Planavsky, Noah J.; Partin, Camille A.; Reinhard, Christopher T.; Kendall, Brian; Scott, Clinton T.; Hardisty, Dalton S.; Gill, Benjamin C.; Alessi, Daniel S.; Dupont, Christopher L.; Saito, Mak A.; Crowe, Sean A.; Poulton, Simon W.; Bekker, Andrey; Lyons, Timothy W.; Konhauser, Kurt O.

2016-01-01

Life requires a wide variety of bioessential trace elements to act as structural components and reactive centers in metalloenzymes. These requirements differ between organisms and have evolved over geological time, likely guided in some part by environmental conditions. Until recently, most of what was understood regarding trace element concentrations in the Precambrian oceans was inferred by extrapolation, geochemical modeling, and/or genomic studies. However, in the past decade, the increasing availability of trace element and isotopic data for sedimentary rocks of all ages has yielded new, and potentially more direct, insights into secular changes in seawater composition – and ultimately the evolution of the marine biosphere. Compiled records of many bioessential trace elements (including Ni, Mo, P, Zn, Co, Cr, Se, and I) provide new insight into how trace element abundance in Earth's ancient oceans may have been linked to biological evolution. Several of these trace elements display redox-sensitive behavior, while others are redox-sensitive but not bioessential (e.g., Cr, U). Their temporal trends in sedimentary archives provide useful constraints on changes in atmosphere-ocean redox conditions that are linked to biological evolution, for example, the activity of oxygen-producing, photosynthetic cyanobacteria. In this review, we summarize available Precambrian trace element proxy data, and discuss how temporal trends in the seawater concentrations of specific trace elements may be linked to the evolution of both simple and complex life. We also examine several biologically relevant and/or redox-sensitive trace elements that have yet to be fully examined in the sedimentary rock record (e.g., Cu, Cd, W) and suggest several directions for future studies.

Mobile element biology – new possibilities with high-throughput sequencing

PubMed Central

Xing, Jinchuan; Witherspoon, David J.; Jorde, Lynn B.

2014-01-01

Mobile elements compose more than half of the human genome, but until recently their large-scale detection was time-consuming and challenging. With the development of new high-throughput sequencing technologies, the complete spectrum of mobile element variation in humans can now be identified and analyzed. Thousands of new mobile element insertions have been discovered, yielding new insights into mobile element biology, evolution, and genomic variation. We review several high-throughput methods, with an emphasis on techniques that specifically target mobile element insertions in humans, and we highlight recent applications of these methods in evolutionary studies and in the analysis of somatic alterations in human cancers. PMID:23312846

Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions.

PubMed

Jiang, Tingting; Raviram, Ramya; Snetkova, Valentina; Rocha, Pedro P; Proudhon, Charlotte; Badri, Sana; Bonneau, Richard; Skok, Jane A; Kluger, Yuval

2016-10-14

Use of low resolution single cell DNA FISH and population based high resolution chromosome conformation capture techniques have highlighted the importance of pairwise chromatin interactions in gene regulation. However, it is unlikely that associations involving regulatory elements act in isolation of other interacting partners that also influence their impact. Indeed, the influence of multi-loci interactions remains something of an enigma as beyond low-resolution DNA FISH we do not have the appropriate tools to analyze these. Here we present a method that uses standard 4C-seq data to identify multi-loci interactions from the same cell. We demonstrate the feasibility of our method using 4C-seq data sets that identify known pairwise and novel tri-loci interactions involving the Tcrb and Igk antigen receptor enhancers. We further show that the three Igk enhancers, MiEκ, 3'Eκ and Edκ, interact simultaneously in this super-enhancer cluster, which add to our previous findings showing that loss of one element decreases interactions between all three elements as well as reducing their transcriptional output. These findings underscore the functional importance of simultaneous interactions and provide new insight into the relationship between enhancer elements. Our method opens the door for studying multi-loci interactions and their impact on gene regulation in other biological settings. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions

PubMed Central

Jiang, Tingting; Raviram, Ramya; Snetkova, Valentina; Rocha, Pedro P.; Proudhon, Charlotte; Badri, Sana; Bonneau, Richard; Skok, Jane A.; Kluger, Yuval

2016-01-01

Use of low resolution single cell DNA FISH and population based high resolution chromosome conformation capture techniques have highlighted the importance of pairwise chromatin interactions in gene regulation. However, it is unlikely that associations involving regulatory elements act in isolation of other interacting partners that also influence their impact. Indeed, the influence of multi-loci interactions remains something of an enigma as beyond low-resolution DNA FISH we do not have the appropriate tools to analyze these. Here we present a method that uses standard 4C-seq data to identify multi-loci interactions from the same cell. We demonstrate the feasibility of our method using 4C-seq data sets that identify known pairwise and novel tri-loci interactions involving the Tcrb and Igk antigen receptor enhancers. We further show that the three Igk enhancers, MiEκ, 3′Eκ and Edκ, interact simultaneously in this super-enhancer cluster, which add to our previous findings showing that loss of one element decreases interactions between all three elements as well as reducing their transcriptional output. These findings underscore the functional importance of simultaneous interactions and provide new insight into the relationship between enhancer elements. Our method opens the door for studying multi-loci interactions and their impact on gene regulation in other biological settings. PMID:27439714

Quantification of 2D elemental distribution maps of intermediate-thick biological sections by low energy synchrotron μ-X-ray fluorescence spectrometry

NASA Astrophysics Data System (ADS)

Kump, P.; Vogel-Mikuš, K.

2018-05-01

Two fundamental-parameter (FP) based models for quantification of 2D elemental distribution maps of intermediate-thick biological samples by synchrotron low energy μ-X-ray fluorescence spectrometry (SR-μ-XRF) are presented and applied to the elemental analysis in experiments with monochromatic focused photon beam excitation at two low energy X-ray fluorescence beamlines—TwinMic, Elettra Sincrotrone Trieste, Italy, and ID21, ESRF, Grenoble, France. The models assume intermediate-thick biological samples composed of measured elements, the sources of the measurable spectral lines, and by the residual matrix, which affects the measured intensities through absorption. In the first model a fixed residual matrix of the sample is assumed, while in the second model the residual matrix is obtained by the iteration refinement of elemental concentrations and an adjusted residual matrix. The absorption of the incident focused beam in the biological sample at each scanned pixel position, determined from the output of a photodiode or a CCD camera, is applied as a control in the iteration procedure of quantification.

Patient care in a biological safety level-4 (BSL-4) environment.

PubMed

Marklund, LeRoy A

2003-06-01

The greatest threats to America's public health include accidental importation of deadly diseases by international travelers and the release of biologic weapons by our adversaries. The greatest failure is unpreparedness because international travel and dispersion of biologic agents by our enemies are inevitable. An effective medical defense program is the recommended deterrent against these threats. The United States has a federal response plan in place that includes patient care and patient transport by using the highest level of biologic containment: BSL-4. The DoD has the capability to provide intensive care for victims infected with highly infectious yet unknown biologic agents in an environment that protects the caregiver while allowing scientists to study the characteristics of these new agents and assess the effectiveness of treatment. Army critical care nurses are vital in the biologic medical defense against unidentified infectious diseases, accidental occupational exposures, or intentional dispersion of weaponized biologic agents. Research that carefully advances healthcare using BSL-4 technology addresses the challenges of the human element of BSL-4 containment patient care, and BSL-4 patient transport enhances our nation's ability to address the emerging biologic threats we confront in the future.

Monitoring of human populations for early markers of cadmium toxicity: A review

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fowler, Bruce A.

2009-08-01

Exposure of human populations to cadmium (Cd) from air, food and water may produce effects in organs such as the kidneys, liver, lungs, cardiovascular, immune and reproductive systems. Since Cd has been identified as a human carcinogen, biomarkers for early detection of susceptibility to cancer are of an importance to public health. The ability to document Cd exposure and uptake of this element through biological monitoring is a first step towards understanding its health effects. Interpretation and application of biological monitoring data for predicting human health outcomes require correlation with biological measures of organ system responses to the documented exposure.more » Essential to this understanding is the detection and linkage of early biological responses toxic effects in target cell populations. Fortunately, advances in cell biology have resulted in the development of pre-clinical biological markers (biomarkers) that demonstrate measurable and characteristic molecular changes in organ systems following chemical exposures that occur prior to the onset of overt clinical disease or development of cancer. Technical advances have rendered a number of these biomarkers practical for monitoring Cd-exposed human populations. Biomarkers will be increasingly important in relation to monitoring effects from the exposure to new Cd-based high technology materials. For example, cadmium-selenium (CdSe), nano-materials made from combinations of these elements have greatly altered cellular uptake characteristics due to particle size. These differences may greatly alter effects at the target cell level and hence risks for organ toxicities from such exposures. The value of validated biomarkers for early detection of systemic Cd-induced effects in humans cannot be underestimated due to the rapid expansion of nano-material technologies. This review will attempt to briefly summarize the applications, to date, of biomarker endpoints for assessing target organ system effects in humans and experimental systems from Cd exposure. Further, it will attempt to provide a prospective look at the possible future of biomarkers. The emphasis will be on the detection of early toxic effects from exposure to Cd in new products such as nano-materials and identification of populations at special risk for Cd toxicity.« less

Monitoring of human populations for early markers of cadmium toxicity: a review.

PubMed

Fowler, Bruce A

2009-08-01

Exposure of human populations to cadmium (Cd) from air, food and water may produce effects in organs such as the kidneys, liver, lungs, cardiovascular, immune and reproductive systems. Since Cd has been identified as a human carcinogen, biomarkers for early detection of susceptibility to cancer are of an importance to public health. The ability to document Cd exposure and uptake of this element through biological monitoring is a first step towards understanding its health effects. Interpretation and application of biological monitoring data for predicting human health outcomes require correlation with biological measures of organ system responses to the documented exposure. Essential to this understanding is the detection and linkage of early biological responses toxic effects in target cell populations. Fortunately, advances in cell biology have resulted in the development of pre-clinical biological markers (biomarkers) that demonstrate measurable and characteristic molecular changes in organ systems following chemical exposures that occur prior to the onset of overt clinical disease or development of cancer. Technical advances have rendered a number of these biomarkers practical for monitoring Cd-exposed human populations. Biomarkers will be increasingly important in relation to monitoring effects from the exposure to new Cd-based high technology materials. For example, cadmium-selenium (CdSe), nano-materials made from combinations of these elements have greatly altered cellular uptake characteristics due to particle size. These differences may greatly alter effects at the target cell level and hence risks for organ toxicities from such exposures. The value of validated biomarkers for early detection of systemic Cd-induced effects in humans cannot be underestimated due to the rapid expansion of nano-material technologies. This review will attempt to briefly summarize the applications, to date, of biomarker endpoints for assessing target organ system effects in humans and experimental systems from Cd exposure. Further, it will attempt to provide a prospective look at the possible future of biomarkers. The emphasis will be on the detection of early toxic effects from exposure to Cd in new products such as nano-materials and identification of populations at special risk for Cd toxicity.

Biologically Self-Assembled Memristive Circuit Elements

DTIC Science & Technology

2010-01-01

hydrothermal approach, TiO2 nanoparticles were synthesized by slowly stirring a 1:3 volumetric ratio mixture of titanium isopropoxide (TTIP) and isopropyl...Synthesis of TiO2 nanoparticles by hydrolysis and peptization of titanium isopropoxide solution. Journal of Materials Processing Technology 2007, 189...important role interfacing with group IV metal oxides such as hafnium, providing a stable linkage to the surface [3]. Titanium dioxide (TiO2), which is

Trace Elements in Ovaries: Measurement and Physiology.

PubMed

Ceko, Melanie J; O'Leary, Sean; Harris, Hugh H; Hummitzsch, Katja; Rodgers, Raymond J

2016-04-01

Traditionally, research in the field of trace element biology and human and animal health has largely depended on epidemiological methods to demonstrate involvement in biological processes. These studies were typically followed by trace element supplementation trials or attempts at identification of the biochemical pathways involved. With the discovery of biological molecules that contain the trace elements, such as matrix metalloproteinases containing zinc (Zn), cytochrome P450 enzymes containing iron (Fe), and selenoproteins containing selenium (Se), much of the current research focuses on these molecules, and, hence, only indirectly on trace elements themselves. This review focuses largely on two synchrotron-based x-ray techniques: X-ray absorption spectroscopy and x-ray fluorescence imaging that can be used to identify the in situ speciation and distribution of trace elements in tissues, using our recent studies of bovine ovaries, where the distribution of Fe, Se, Zn, and bromine were determined. It also discusses the value of other techniques, such as inductively coupled plasma mass spectrometry, used to garner information about the concentrations and elemental state of the trace elements. These applications to measure trace elemental distributions in bovine ovaries at high resolutions provide new insights into possible roles for trace elements in the ovary. © 2016 by the Society for the Study of Reproduction, Inc.

Imaging and elemental mapping of biological specimens with a dual-EDS dedicated scanning transmission electron microscope.

PubMed

Wu, J S; Kim, A M; Bleher, R; Myers, B D; Marvin, R G; Inada, H; Nakamura, K; Zhang, X F; Roth, E; Li, S Y; Woodruff, T K; O'Halloran, T V; Dravid, Vinayak P

2013-05-01

A dedicated analytical scanning transmission electron microscope (STEM) with dual energy dispersive spectroscopy (EDS) detectors has been designed for complementary high performance imaging as well as high sensitivity elemental analysis and mapping of biological structures. The performance of this new design, based on a Hitachi HD-2300A model, was evaluated using a variety of biological specimens. With three imaging detectors, both the surface and internal structure of cells can be examined simultaneously. The whole-cell elemental mapping, especially of heavier metal species that have low cross-section for electron energy loss spectroscopy (EELS), can be faithfully obtained. Optimization of STEM imaging conditions is applied to thick sections as well as thin sections of biological cells under low-dose conditions at room and cryogenic temperatures. Such multimodal capabilities applied to soft/biological structures usher a new era for analytical studies in biological systems. Copyright © 2013 Elsevier B.V. All rights reserved.

Insights into Structural and Mechanistic Features of Viral IRES Elements

PubMed Central

Martinez-Salas, Encarnacion; Francisco-Velilla, Rosario; Fernandez-Chamorro, Javier; Embarek, Azman M.

2018-01-01

Internal ribosome entry site (IRES) elements are cis-acting RNA regions that promote internal initiation of protein synthesis using cap-independent mechanisms. However, distinct types of IRES elements present in the genome of various RNA viruses perform the same function despite lacking conservation of sequence and secondary RNA structure. Likewise, IRES elements differ in host factor requirement to recruit the ribosomal subunits. In spite of this diversity, evolutionarily conserved motifs in each family of RNA viruses preserve sequences impacting on RNA structure and RNA–protein interactions important for IRES activity. Indeed, IRES elements adopting remarkable different structural organizations contain RNA structural motifs that play an essential role in recruiting ribosomes, initiation factors and/or RNA-binding proteins using different mechanisms. Therefore, given that a universal IRES motif remains elusive, it is critical to understand how diverse structural motifs deliver functions relevant for IRES activity. This will be useful for understanding the molecular mechanisms beyond cap-independent translation, as well as the evolutionary history of these regulatory elements. Moreover, it could improve the accuracy to predict IRES-like motifs hidden in genome sequences. This review summarizes recent advances on the diversity and biological relevance of RNA structural motifs for viral IRES elements. PMID:29354113

Laser ablation for mineral analysis in the human body: integration of LIFS with LIBS

NASA Astrophysics Data System (ADS)

Samek, Ota; Liska, Miroslav; Kaiser, Josef; Krzyzanek, Vladislav; Beddows, David C.; Belenkevitch, Alexander; Morris, Gavin W.; Telle, Helmut H.

1999-01-01

Trace mineral analysis of the body is invaluable in biology, medicine and dentistry when considering the role of mineral nutrition and metabolism in the context of maintaining human health. The presence of key elements in the body, such as boron, calcium, chromium, copper, iron, silicon and zinc are known to be of vital importance, but are often found to be present in inadequate quantity. In sharp contrast, the accumulation of other elements, such as aluminum, cadmium, lead and mercury is less favorable, since frequently these metals are already toxic at extremely low concentration levels, interfering with essential chemical processing of vitamins and minerals. Here we report on the application of laser-induced breakdown spectroscopy and laser-induced fluorescence spectroscopy to the analysis of important minerals and toxic elements within the body. Samples from different parts of the body have been studied, including specimens of skin tissue, finger nails and teeth. It is particularly noteworthy that specific sample preparation was not needed for any of these laser spectroscopic measurements, but that specimens could be used as taken from the source.

Marine Bioinorganic Chemistry: The Role of Trace Metals in the Oceanic Cycles of Major Nutrients

NASA Astrophysics Data System (ADS)

Morel, F. M. M.; Milligan, A. J.; Saito, M. A.

2003-12-01

The bulk of living biomass is chiefly made up of only a dozen "major" elements - carbon, hydrogen, oxygen, nitrogen, phosphorus, sodium, potassium, chlorine, calcium, magnesium, sulfur (and silicon in diatoms) - whose proportions vary within a relatively narrow range in most organisms. A number of trace elements, particularly first row transition metals - manganese, iron, nickel, cobalt, copper, and zinc - are also "essential" for the growth of organisms. At the molecular level, the chemical mechanisms by which such elements function as active centers or structural factors in enzymes and by which they are accumulated and stored by organisms is the central topic of bioinorganic chemistry. At the scale of ocean basins, the interplay of physical, chemical, and biological processes that govern the cycling of biologically essential elements in seawater is the subject of marine biogeochemistry. For those interested in the growth of marine organisms, particularly in the one-half of the Earth's primary production contributed by marine phytoplankton, bioinorganic chemistry and marine biogeochemistry are critically linked by the extraordinary paucity of essential trace elements in surface seawater, which results from their biological utilization and incorporation in sinking organic matter. How marine organisms acquire elements that are present at nano- or picomolar concentrations in surface seawater; how they perform critical enzymatic functions when necessary metal cofactors are almost unavailable are the central topics of "marine bioinorganic chemistry." The central aim of this field is to elucidate at the molecular level the metal-dependent biological processes involved in the major biogeochemical cycles.By examining the solutions that emerged from the problems posed by the scarcity of essential trace elements, marine bioinorganic chemists bring to light hitherto unknown ways to take up or utilize trace elements, new molecules, and newer "essential" elements. Focusing on molecular mechanisms involved in such processes as inorganic carbon fixation, organic carbon respiration, or nitrogen transformation, they explain how the cycles of trace elements are critically linked to those of major nutrients such as carbon or nitrogen. But we have relatively little understanding of the binding molecules and the enzymes that mediate the biochemical role of trace metals in the marine environment. In this sense, this chapter is more a "preview" than a review of the field of marine bioinorganic chemistry. To exemplify the concepts and methods of this field, we have chosen to focus on one of its most important topics: the potentially limiting role of trace elements in primary marine production. As a result we center our discussion on particular subsets of organisms, biogeochemical cycles, and trace elements. Our chief actors are marine phytoplankton, particularly eukaryotes, while heterotrophic bacteria make only cameo appearances. The biogeochemical cycles that will serve as our plot are those of the elements involved in phytoplankton growth, the major algal nutrients - carbon, nitrogen, phosphorus, and silicon - leaving aside, e.g., the interesting topic of the marine sulfur cycle. Seven trace metals provide the intrigue: manganese, iron, nickel, cobalt, copper, zinc, and cadmium. But several other trace elements such as selenium, vanadium, molybdenum, and tungsten (and, probably, others not yet identified) will assuredly add further twists in future episodes.We begin this chapter by discussing what we know of the concentrations of trace elements in marine microorganisms and of the relevant mechanisms and kinetics of trace-metal uptake. We then review the biochemical role of trace elements in the marine cycles of carbon, nitrogen, phosphorus, and silicon. Using this information, we examine the evidence, emanating from both laboratory cultures and field measurements, relevant to the mechanisms and the extent of control by trace metals of marine biogeochemical cycles. Before concluding with a wistful glimpse of the future of marine bioinorganic chemistry we discuss briefly some paleoceanographic aspects of this new field: how the chemistry of the planet "Earth" - particularly the concentrations of trace elements in the oceans - has evolved since its origin, chiefly as a result of biological processes and how the evolution of life has, in turn, been affected by the availability of essential trace elements.

An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures

PubMed Central

Zandi, Kasra; Butler, Gregory; Kharma, Nawwaf

2016-01-01

Computational design of RNA sequences that fold into targeted secondary structures has many applications in biomedicine, nanotechnology and synthetic biology. An RNA molecule is made of different types of secondary structure elements and an important RNA element named pseudoknot plays a key role in stabilizing the functional form of the molecule. However, due to the computational complexities associated with characterizing pseudoknotted RNA structures, most of the existing RNA sequence designer algorithms generally ignore this important structural element and therefore limit their applications. In this paper we present a new algorithm to design RNA sequences for pseudoknotted secondary structures. We use NUPACK as the folding algorithm to compute the equilibrium characteristics of the pseudoknotted RNAs, and describe a new adaptive defect weighted sampling algorithm named Enzymer to design low ensemble defect RNA sequences for targeted secondary structures including pseudoknots. We used a biological data set of 201 pseudoknotted structures from the Pseudobase library to benchmark the performance of our algorithm. We compared the quality characteristics of the RNA sequences we designed by Enzymer with the results obtained from the state of the art MODENA and antaRNA. Our results show our method succeeds more frequently than MODENA and antaRNA do, and generates sequences that have lower ensemble defect, lower probability defect and higher thermostability. Finally by using Enzymer and by constraining the design to a naturally occurring and highly conserved Hammerhead motif, we designed 8 sequences for a pseudoknotted cis-acting Hammerhead ribozyme. Enzymer is available for download at https://bitbucket.org/casraz/enzymer. PMID:27499762

Milk as a medium for pediatric formulations: Experimental findings and regulatory aspects.

PubMed

Soulele, Konstantina; Macheras, Panos

2015-08-15

In the case of pediatric medicinal products the selection of an appropriate and palatable liquid dosage form can make the difference between treatment success and failure. Since the recent adoption of Pediatric Regulations in the U.S. and E.U., there is a greater demand for age-appropriate medicines for children. Extended research on the use of milk on drug administration in pediatric population has shown the multiple benefits of its use. Milk exhibits great solubilizing, gastroprotective and taste masking properties, which are very important characteristics in the case of insoluble, irritating and bitter-tasting active compounds. Milk-based formulations rely on a novel, simple and user-friendly approach for the delivery of ionized and unionized lipophilic drugs. In parallel they can provide critical nutritive elements and a wide range of biologically active peptides, very important elements especially for pediatric patients. Copyright © 2015. Published by Elsevier B.V.

'Treat to Target' - Lessons Learnt.

PubMed

Kurti, Zsuzsanna; Vegh, Zsuzsanna; Golovics, Petra Anna; Lakatos, Peter Laszlo

2016-01-01

Therapeutic management in inflammatory bowel diseases (IBD) has significantly changed in the last decades with the advent of biological therapy resulting in new treatment targets other than clinical symptoms. Patient stratification in the early stage of the disease is an important step to identify patients with poor prognosis, who might benefit from early aggressive treatment to avoid complications in the later disease course. Recent randomized and hypothesis driven (e.g., Randomized Evaluation of an Algorithm for Crohn's Treatment, Post-Operative Crohn's Endoscopic Recurrence) clinical trials conducted in the biological era underscore the need of objective disease monitoring including assessment of biomarkers (e.g., C-reactive protein and calprotectin), mucosal healing and, for biologically treated patients, therapeutic drug monitoring beside clinical symptom assessment in both Crohn's disease and ulcerative colitis. Assessing the treatment efficacy objectively has become an important element of patient monitoring besides clinical symptom assessment. Further clinical studies are needed to assess whether implementation of new therapeutic algorithms based on these targets and tight monitoring in clinical practice have the potential to further improve long-term disease outcomes in IBD. © 2016 S. Karger AG, Basel.

Coastal Research Imaging Spectrometer

NASA Technical Reports Server (NTRS)

Lucey, Paul G.; Williams, Timothy; Horton, Keith A.

2002-01-01

The Coastal Research Imaging Spectrometer (CRIS) is an airborne remote-sensing system designed specifically for research on the physical, chemical, and biological characteristics of coastal waters. The CRIS includes a visible-light hyperspectral imaging subsystem for measuring the color of water, which contains information on the biota, sediment, and nutrient contents of the water. The CRIS also includes an infrared imaging subsystem, which provides information on the temperature of the water. The combination of measurements enables investigation of biological effects of both natural and artificial flows of water from land into the ocean, including diffuse and point-source flows that may contain biological and/or chemical pollutants. Temperature is an important element of such measurements because temperature contrasts can often be used to distinguish among flows from different sources: for example, a sewage outflow could manifest itself in spectral images as a local high-temperature anomaly.

A program in global biology. [biota-environment interaction important to life

NASA Technical Reports Server (NTRS)

Mooneyhan, D. W.

1983-01-01

NASA's Global Biology Research Program and its goals for greater understanding of planetary biological processes are discussed. Consideration is given to assessing major pathways and rates of exchange of elements such as carbon and nitrogen, extrapolating local rates of anaerobic activities, determining exchange rates of ocean nutrients, and developing models for the global cycles of carbon, nitrogen, sulfur, and phosphorus. Satellites and sensors operating today are covered: the Nimbus, NOAA, and Landsat series. Block diagrams of the software and hardware for a typical ground data processing and analysis system are provided. Samples of the surface cover data achieved with the Advanced Very High Resolution Radiometer, the Multispectral Scanner, and the Thematic Mapper are presented, as well as a productive capacity model for coastal wetlands. Finally, attention is given to future goals, their engineering requirements, and the necessary data analysis system.

Methods for improving simulations of biological systems: systemic computation and fractal proteins

PubMed Central

Bentley, Peter J.

2009-01-01

Modelling and simulation are becoming essential for new fields such as synthetic biology. Perhaps the most important aspect of modelling is to follow a clear design methodology that will help to highlight unwanted deficiencies. The use of tools designed to aid the modelling process can be of benefit in many situations. In this paper, the modelling approach called systemic computation (SC) is introduced. SC is an interaction-based language, which enables individual-based expression and modelling of biological systems, and the interactions between them. SC permits a precise description of a hypothetical mechanism to be written using an intuitive graph-based or a calculus-based notation. The same description can then be directly run as a simulation, merging the hypothetical mechanism and the simulation into the same entity. However, even when using well-designed modelling tools to produce good models, the best model is not always the most accurate one. Frequently, computational constraints or lack of data make it infeasible to model an aspect of biology. Simplification may provide one way forward, but with inevitable consequences of decreased accuracy. Instead of attempting to replace an element with a simpler approximation, it is sometimes possible to substitute the element with a different but functionally similar component. In the second part of this paper, this modelling approach is described and its advantages are summarized using an exemplar: the fractal protein model. Finally, the paper ends with a discussion of good biological modelling practice by presenting lessons learned from the use of SC and the fractal protein model. PMID:19324681

The Distribution of Dissolved Iron in the West Atlantic Ocean

PubMed Central

Rijkenberg, Micha J. A.; Middag, Rob; Laan, Patrick; Gerringa, Loes J. A.; van Aken, Hendrik M.; Schoemann, Véronique; de Jong, Jeroen T. M.; de Baar, Hein J. W.

2014-01-01

Iron (Fe) is an essential trace element for marine life. Extremely low Fe concentrations limit primary production and nitrogen fixation in large parts of the oceans and consequently influence ocean ecosystem functioning. The importance of Fe for ocean ecosystems makes Fe one of the core chemical trace elements in the international GEOTRACES program. Despite the recognized importance of Fe, our present knowledge of its supply and biogeochemical cycle has been limited by mostly fragmentary datasets. Here, we present highly accurate dissolved Fe (DFe) values measured at an unprecedented high intensity (1407 samples) along the longest full ocean depth transect (17500 kilometers) covering the entire western Atlantic Ocean. DFe measurements along this transect unveiled details about the supply and cycling of Fe. External sources of Fe identified included off-shelf and river supply, hydrothermal vents and aeolian dust. Nevertheless, vertical processes such as the recycling of Fe resulting from the remineralization of sinking organic matter and the removal of Fe by scavenging still dominated the distribution of DFe. In the northern West Atlantic Ocean, Fe recycling and lateral transport from the eastern tropical North Atlantic Oxygen Minimum Zone (OMZ) dominated the DFe-distribution. Finally, our measurements showed that the North Atlantic Deep Water (NADW), the major driver of the so-called ocean conveyor belt, contains excess DFe relative to phosphate after full biological utilization and is therefore an important source of Fe for biological production in the global ocean. PMID:24978190

Trace element distribution in the rat cerebellum

NASA Astrophysics Data System (ADS)

Kwiatek, W. M.; Long, G. J.; Pounds, J. G.; Reuhl, K. R.; Hanson, A. L.; Jones, K. W.

1990-04-01

Spatial distributions and concentrations of trace elements (TE) in the brain are important because TE perform catalytic and structural functions in enzymes which regulate brain function and development. We have investigated the distributions of TE in rat cerebellum. Structures were sectioned and analyzed by the Synchrotron Radiation Induced X-ray Emission (SRIXE) method using the NSLS X-26 white-light microprobe facility. Advantages important for TE analysis of biological specimens with X-ray microscopy include short time of measurement, high brightness and flux, good spatial resolution, multielemental detection, good sensitivity, and nondestructive irradiation. Trace elements were measured in thin rat brain sections of 20 μm thickness. The analyses were performed on sample volumes as small as 0.2 nl with Minimum Detectable Limits (MDL) of 50 ppb wet weight for Fe, 100 ppb wet weight for Cu, and Zn, and 1 ppm wet weight for Pb. The distribution of TE in the molecular cell layer, granule cell layer and fiber tract of rat cerebella was investigated. Both point analyses and two-dimensional semiquantitative mapping of the TE distribution in a section were used. All analyzed elements were observed in each structure of the cerebellum except mercury which was not observed in granule cell layer or fiber tract. This approach permits an exacting correlation of the TE distribution in complex structure with the diet, toxic elements, and functional status of the animal.

Tuning the properties of conjugated polyelectrolytes and application in a biosensor platform

DOEpatents

Chen, Liaohai

2004-05-18

The present invention provides a method of detecting a biological agent including contacting a sample with a sensor including a polymer system capable of having an alterable measurable property from the group of luminescence, anisotropy, redox potential and uv/vis absorption, the polymer system including an ionic conjugated polymer and an electronically inert polyelectrolyte having a biological agent recognition element bound thereto, the electronically inert polyelectrolyte adapted for undergoing a conformational structural change upon exposure to a biological agent having affinity for binding to the recognition element bound to the electronically inert polyelectrolyte, and, detecting the detectable change in the alterable measurable property. A chemical moiety being the reaction product of (i) a polyelectrolyte monomer and (ii) a biological agent recognition element-substituted polyelectrolyte monomer is also provided.

Elemental mapping of biological samples using a scanning proton microprobe

NASA Astrophysics Data System (ADS)

Watt, F.; Grime, G. W.

1988-03-01

Elemental mapping using a scanning proton microprobe (SPM) can be a powerful technique for probing trace elements in biology, allowing complex interfaces to be studied in detail, identifying contamination and artefacts present in the specimen, and in certain circumstances obtaining indirect chemical information. Examples used to illustrate the advantages of the technique include the elemental mapping of growing pollen tubes, honey bee brain section, a mouse macrophage cell, human liver section exhibiting primary biliary cirrhosis, and the attack by a mildew fungus on a pea leaf.

Why is migraine so common?

PubMed

Edmeads, J

1998-08-01

Migraine is clearly a very common biological disorder, but this knowledge has not been sufficient as yet to ensure completely effective treatment strategies. There appears to be discrepancy between what migraine patients desire as the outcome of consultations and what doctors think patients want. Patients seem, from Packard's selective study (11), to want explanation and reassurance before they get pain relief, whereas doctors view pain relief as the most important aim of management. It is possible that doctors still have underlying assumptions about psychological elements of migraine which color their perceptions of their patients. Communicating the relevance of scientific progress in migraine to neurologists and PCPs is an important challenge, as is calling attention to the patient's expectations from treatment. To be effective in improving education in this area, perhaps we should first ascertain the level of knowledge about the biology and treatment of headache among general neurologists.

Effective Educational Videos: Principles and Guidelines for Maximizing Student Learning from Video Content.

PubMed

Brame, Cynthia J

Educational videos have become an important part of higher education, providing an important content-delivery tool in many flipped, blended, and online classes. Effective use of video as an educational tool is enhanced when instructors consider three elements: how to manage cognitive load of the video; how to maximize student engagement with the video; and how to promote active learning from the video. This essay reviews literature relevant to each of these principles and suggests practical ways instructors can use these principles when using video as an educational tool. © 2016 C. J. Brame. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Prediction of interface residue based on the features of residue interaction network.

PubMed

Jiao, Xiong; Ranganathan, Shoba

2017-11-07

Protein-protein interaction plays a crucial role in the cellular biological processes. Interface prediction can improve our understanding of the molecular mechanisms of the related processes and functions. In this work, we propose a classification method to recognize the interface residue based on the features of a weighted residue interaction network. The random forest algorithm is used for the prediction and 16 network parameters and the B-factor are acting as the element of the input feature vector. Compared with other similar work, the method is feasible and effective. The relative importance of these features also be analyzed to identify the key feature for the prediction. Some biological meaning of the important feature is explained. The results of this work can be used for the related work about the structure-function relationship analysis via a residue interaction network model. Copyright © 2017 Elsevier Ltd. All rights reserved.

Fish gelatin thin film standards for biological application of PIXE

NASA Astrophysics Data System (ADS)

Manuel, Jack E.; Rout, Bibhudutta; Szilasi, Szabolcs Z.; Bohara, Gyanendra; Deaton, James; Luyombya, Henry; Briski, Karen P.; Glass, Gary A.

2014-08-01

There exists a critical need to understand the flow and accumulation of metallic ions, both naturally occurring and those introduced to biological systems. In this paper the results of fabricating thin film elemental biological standards containing nearly any combination of trace elements in a protein matrix are presented. Because it is capable of high elemental sensitivity, particle induced X-ray emission spectrometry (PIXE) is an excellent candidate for in situ analysis of biological tissues. Additionally, the utilization of microbeam PIXE allows the determination of elemental concentrations in and around biological cells. However, obtaining elemental reference standards with the same matrix constituents as brain tissue is difficult. An excellent choice for simulating brain-like tissue is Norland® photoengraving glue which is derived from fish skin. Fish glue is water soluble, liquid at room temperature, and resistant to dilute acid. It can also be formed into a thin membrane which dries into a durable, self-supporting film. Elements of interest are introduced to the fish glue in precise volumetric additions of well quantified atomic absorption standard solutions. In this study GeoPIXE analysis package is used to quantify elements intrinsic to the fish glue as well as trace amounts of manganese added to the sample. Elastic (non-Rutherford) backscattered spectroscopy (EBS) and the 1.734 MeV proton-on-carbon 12C(p,p)12C resonance is used for a normalization scheme of the PIXE spectra to account for any discrepancies in X-ray production arising from thickness variation of the prepared standards. It is demonstrated that greater additions of the atomic absorption standard cause a viscosity reduction of the liquid fish glue resulting in thinner films but the film thickness can be monitored by using simultaneous PIXE and EBS proton data acquisition.

A model for genesis of transcription systems.

PubMed

Burton, Zachary F; Opron, Kristopher; Wei, Guowei; Geiger, James H

2016-01-01

Repeating sequences generated from RNA gene fusions/ligations dominate ancient life, indicating central importance of building structural complexity in evolving biological systems. A simple and coherent story of life on earth is told from tracking repeating motifs that generate α/β proteins, 2-double-Ψ-β-barrel (DPBB) type RNA polymerases (RNAPs), general transcription factors (GTFs), and promoters. A general rule that emerges is that biological complexity that arises through generation of repeats is often bounded by solubility and closure (i.e., to form a pseudo-dimer or a barrel). Because the first DNA genomes were replicated by DNA template-dependent RNA synthesis followed by RNA template-dependent DNA synthesis via reverse transcriptase, the first DNA replication origins were initially 2-DPBB type RNAP promoters. A simplifying model for evolution of promoters/replication origins via repetition of core promoter elements is proposed. The model can explain why Pribnow boxes in bacterial transcription (i.e., (-12)TATAATG(-6)) so closely resemble TATA boxes (i.e., (-31)TATAAAAG(-24)) in archaeal/eukaryotic transcription. The evolution of anchor DNA sequences in bacterial (i.e., (-35)TTGACA(-30)) and archaeal (BRE(up); BRE for TFB recognition element) promoters is potentially explained. The evolution of BRE(down) elements of archaeal promoters is potentially explained.

The biology and evolution of transposable elements in parasites.

PubMed

Thomas, M Carmen; Macias, Francisco; Alonso, Carlos; López, Manuel C

2010-07-01

Transposable elements (TEs) are dynamic elements that can reshape host genomes by generating rearrangements with the potential to create or disrupt genes, to shuffle existing genes, and to modulate their patterns of expression. In the genomes of parasites that infect mammals several TEs have been identified that probably have been maintained throughout evolution due to their contribution to gene function and regulation of gene expression. This review addresses how TEs are organized, how they colonize the genomes of mammalian parasites, the functional role these elements play in parasite biology, and the interactions between these elements and the parasite genome. Copyright 2010 Elsevier Ltd. All rights reserved.

ElemeNT: a computational tool for detecting core promoter elements.

PubMed

Sloutskin, Anna; Danino, Yehuda M; Orenstein, Yaron; Zehavi, Yonathan; Doniger, Tirza; Shamir, Ron; Juven-Gershon, Tamar

2015-01-01

Core promoter elements play a pivotal role in the transcriptional output, yet they are often detected manually within sequences of interest. Here, we present 2 contributions to the detection and curation of core promoter elements within given sequences. First, the Elements Navigation Tool (ElemeNT) is a user-friendly web-based, interactive tool for prediction and display of putative core promoter elements and their biologically-relevant combinations. Second, the CORE database summarizes ElemeNT-predicted core promoter elements near CAGE and RNA-seq-defined Drosophila melanogaster transcription start sites (TSSs). ElemeNT's predictions are based on biologically-functional core promoter elements, and can be used to infer core promoter compositions. ElemeNT does not assume prior knowledge of the actual TSS position, and can therefore assist in annotation of any given sequence. These resources, freely accessible at http://lifefaculty.biu.ac.il/gershon-tamar/index.php/resources, facilitate the identification of core promoter elements as active contributors to gene expression.

The impact of horizontal gene transfer on the biology of Clostridium difficile.

PubMed

Roberts, Adam P; Allan, Elaine; Mullany, Peter

2014-01-01

Clostridium difficile infection (CDI) is now recognised as the main cause of healthcare associated diarrhoea. Over the recent years there has been a change in the epidemiology of CDI with certain related strains dominating infection. These strains have been termed hyper-virulent and have successfully spread across the globe. Many C. difficile strains have had their genomes completely sequenced allowing researchers to build up a very detailed picture of the contribution of horizontal gene transfer to the adaptive potential, through the acquisition of mobile DNA, of this organism. Here, we review and discuss the contribution of mobile genetic elements to the biology of this clinically important pathogen. © 2014 Elsevier Ltd All rights reserved.

Carbon and nitrogen biogeochemistry in the ocean: A study using stable isotope natural abundance

NASA Technical Reports Server (NTRS)

Rau, G. H.; Desmarais, David J.

1985-01-01

Determining the biogeochemical pathways traveled by carbon and nitrogen in the ocean is fundamental to the understanding of how the ocean participates in the cycling of these elements within the biosphere. Because biological production, metabolism, and respiration can significantly alter the natural abundance of C-13 and N-15, these abundances can provide important information about the nature of these biological processes and their variability in the marine environment. The research initially seeks to characterize the spatial and temporal patterns of stable isotope abundances in organic matter, and to relate these abundances to C and N biogeochemical processes within selected areas of the northeastern Pacific Ocean.

Inter-individual variation in expression: a missing link in biomarker biology?

PubMed

Little, Peter F R; Williams, Rohan B H; Wilkins, Marc R

2009-01-01

The past decade has seen an explosion of variation data demonstrating that diversity of both protein-coding sequences and of regulatory elements of protein-coding genes is common and of functional importance. In this article, we argue that genetic diversity can no longer be ignored in studies of human biology, even research projects without explicit genetic experimental design, and that this knowledge can, and must, inform research. By way of illustration, we focus on the potential role of genetic data in case-control studies to identify and validate cancer protein biomarkers. We argue that a consideration of genetics, in conjunction with proteomic biomarker discovery projects, should improve the proportion of biomarkers that can accurately classify patients.

Differential Multiphoton Laser Scanning Microscopy

PubMed Central

Field, Jeffrey J.; Sheetz, Kraig E.; Chandler, Eric V.; Hoover, Erich E.; Young, Michael D.; Ding, Shi-you; Sylvester, Anne W.; Kleinfeld, David; Squier, Jeff A.

2016-01-01

Multifocal multiphoton microscopy (MMM) in the biological and medical sciences has become an important tool for obtaining high resolution images at video rates. While current implementations of MMM achieve very high frame rates, they are limited in their applicability to essentially those biological samples that exhibit little or no scattering. In this paper, we report on a method for MMM in which imaging detection is not necessary (single element point detection is implemented), and is therefore fully compatible for use in imaging through scattering media. Further, we demonstrate that this method leads to a new type of MMM wherein it is possible to simultaneously obtain multiple images and view differences in excitation parameters in a single shot. PMID:27390511

New Tools & Techniques for the Metallomics Revolution

NASA Astrophysics Data System (ADS)

Koppenaal, D. W.; Hieftje, G. M.

2004-12-01

The metallome has been defined as the complete complement of metals and metal moieties in a biological cell, tissue, or system. This definition is akin to that of the genome (genes), proteome (proteins), and metabolome (metabolites). Metallomics accordingly is the study of metals and metal species, and their interactions, transformations, and functions in biological systems. While traditional bioinorganic chemistry has focused on the role and interactions of a single (or few) metals in a protein or enzyme system, metallomics purports to study global, multi-element interactions and relationships. The metallomics challenges for analytical chemistry and biochemical characterization are significant. This paper will discuss these challenges and the emergent techniques and tools that are being developed to address them. Mass spectrometry will play an important and pivotal role. Two approaches are currently being developed in the authors' laboratories. At Pacific Northwest National Laboratory, an extremely high-resolution approach using Fourier Transform Ion Cyclotron Resonance mass spectrometry (FT-ICRMS) is under development. At Indiana University, a rapid, dual-reflectron Time-of-Flight mass spectrometry (TOFMS) technique is being developed. Both approaches rely on dual inductively coupled plasma (ICP) and electrospray ionization (ESI) sources for elemental and biomolecular ion generation. The initial development of these techniques, and their potential application to systems biology and environmental characterization, will be discussed.

Life on rock. Scaling down biological weathering in a new experimental design at Biosphere-2

NASA Astrophysics Data System (ADS)

Zaharescu, D. G.; Dontsova, K.; Burghelea, C. I.; Chorover, J.; Maier, R.; Perdrial, J. N.

2012-12-01

Biological colonization and weathering of bedrock on Earth is a major driver of landscape and ecosystem development, its effects reaching out into other major systems such climate and geochemical cycles of elements. In order to understand how microbe-plant-mycorrhizae communities interact with bedrock in the first phases of mineral weathering we developed a novel experimental design in the Desert Biome at Biosphere-2, University of Arizona (U.S.A). This presentation will focus on the development of the experimental setup. Briefly, six enclosed modules were designed to hold 288 experimental columns that will accommodate 4 rock types and 6 biological treatments. Each module is developed on 3 levels. A lower volume, able to withstand the weight of both, rock material and the rest of the structure, accommodates the sampling elements. A middle volume, houses the experimental columns in a dark chamber. A clear, upper section forms the habitat exposed to sunlight. This volume is completely sealed form exterior and it allows a complete control of its air and water parameters. All modules are connected in parallel with a double air purification system that delivers a permanent air flow. This setup is expected to provide a model experiment, able to test important processes in the interaction rock-life at grain-to- molecular scale.

Alu Elements as Novel Regulators of Gene Expression in Type 1 Diabetes Susceptibility Genes?

PubMed

Kaur, Simranjeet; Pociot, Flemming

2015-07-13

Despite numerous studies implicating Alu repeat elements in various diseases, there is sparse information available with respect to the potential functional and biological roles of the repeat elements in Type 1 diabetes (T1D). Therefore, we performed a genome-wide sequence analysis of T1D candidate genes to identify embedded Alu elements within these genes. We observed significant enrichment of Alu elements within the T1D genes (p-value < 10e-16), which highlights their importance in T1D. Functional annotation of T1D genes harboring Alus revealed significant enrichment for immune-mediated processes (p-value < 10e-6). We also identified eight T1D genes harboring inverted Alus (IRAlus) within their 3' untranslated regions (UTRs) that are known to regulate the expression of host mRNAs by generating double stranded RNA duplexes. Our in silico analysis predicted the formation of duplex structures by IRAlus within the 3'UTRs of T1D genes. We propose that IRAlus might be involved in regulating the expression levels of the host T1D genes.

A parameterization scheme for the x-ray linear attenuation coefficient and energy absorption coefficient.

PubMed

Midgley, S M

2004-01-21

A novel parameterization of x-ray interaction cross-sections is developed, and employed to describe the x-ray linear attenuation coefficient and mass energy absorption coefficient for both elements and mixtures. The new parameterization scheme addresses the Z-dependence of elemental cross-sections (per electron) using a simple function of atomic number, Z. This obviates the need for a complicated mathematical formalism. Energy dependent coefficients describe the Z-direction curvature of the cross-sections. The composition dependent quantities are the electron density and statistical moments describing the elemental distribution. We show that it is possible to describe elemental cross-sections for the entire periodic table and at energies above the K-edge (from 6 keV to 125 MeV), with an accuracy of better than 2% using a parameterization containing not more than five coefficients. For the biologically important elements 1 < or = Z < or = 20, and the energy range 30-150 keV, the parameterization utilizes four coefficients. At higher energies, the parameterization uses fewer coefficients with only two coefficients needed at megavoltage energies.

Large Deformation Dynamic Three-Dimensional Coupled Finite Element Analysis of Soft Biological Tissues Treated as Biphasic Porous Media

DTIC Science & Technology

2014-11-01

response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and...over time , when a bipha- sic soft tissue is subjected to dynamic loading. Also, after the initial transient, the variation of solid skeleton stresses...will be naturally calculated as the fluid phase pressure dissipates over time . This is important for developing physiologically- relevant degradation

The effects of morphological irregularity on the mechanical behavior of interdigitated biological sutures under tension.

PubMed

Liu, Lei; Jiang, Yunyao; Boyce, Mary; Ortiz, Christine; Baur, Jeffery; Song, Juha; Li, Yaning

2017-06-14

Irregular interdigitated morphology is prevalent in biological sutures in nature. Suture complexity index has long been recognized as the most important morphological parameter to govern the mechanical properties of biological sutures. However, the suture complexity index alone does not reflect all aspects of suture morphology. The goal of this investigation was to determine that besides suture complexity index, whether the degree of morphological irregularity of biological sutures has influences on the mechanical properties, and if there is any, how to quantify these influences. To explore these issues, theoretical and finite element (FE) suture models with the same suture complexity index but different levels of morphological irregularity were developed. The quasi-static stiffness, strength for damage initiation and post-failure process of irregular sutures were studied. It was shown that for the same suture complexity index, when the level of morphological irregularity increases, the overall strain to failure will increase while tensile stiffness is retained; also, the total energy to fracture increases with a sacrifice in strength to damage initiation. These results reveal that morphological irregularity is another important independent parameter to govern and balance the mechanical properties of biological sutures. Therefore, from the mechanics point of view, the prevalence of irregular suture morphology in nature is a merit, not a defect. Copyright © 2017 Elsevier Ltd. All rights reserved.

Systems biology approaches for identifying adverse drug reactions and elucidating their underlying biological mechanisms.

PubMed

Boland, Mary Regina; Jacunski, Alexandra; Lorberbaum, Tal; Romano, Joseph D; Moskovitch, Robert; Tatonetti, Nicholas P

2016-01-01

Small molecules are indispensable to modern medical therapy. However, their use may lead to unintended, negative medical outcomes commonly referred to as adverse drug reactions (ADRs). These effects vary widely in mechanism, severity, and populations affected, making ADR prediction and identification important public health concerns. Current methods rely on clinical trials and postmarket surveillance programs to find novel ADRs; however, clinical trials are limited by small sample size, whereas postmarket surveillance methods may be biased and inherently leave patients at risk until sufficient clinical evidence has been gathered. Systems pharmacology, an emerging interdisciplinary field combining network and chemical biology, provides important tools to uncover and understand ADRs and may mitigate the drawbacks of traditional methods. In particular, network analysis allows researchers to integrate heterogeneous data sources and quantify the interactions between biological and chemical entities. Recent work in this area has combined chemical, biological, and large-scale observational health data to predict ADRs in both individual patients and global populations. In this review, we explore the rapid expansion of systems pharmacology in the study of ADRs. We enumerate the existing methods and strategies and illustrate progress in the field with a model framework that incorporates crucial data elements, such as diet and comorbidities, known to modulate ADR risk. Using this framework, we highlight avenues of research that may currently be underexplored, representing opportunities for future work. © 2015 Wiley Periodicals, Inc.

Biological role in the transformation of platinum-group mineral grains

NASA Astrophysics Data System (ADS)

Reith, Frank; Zammit, Carla M.; Shar, Sahar S.; Etschmann, Barbara; Bottrill, Ralph; Southam, Gordon; Ta, Christine; Kilburn, Matthew; Oberthür, Thomas; Ball, Andrew S.; Brugger, Joël

2016-04-01

Platinum-group elements are strategically important metals. Finding new deposits is becoming increasingly difficult owing to our limited understanding of the processes that affect their mobility in surface environments. Microorganisms have been shown to promote the mobility of metals around ore deposits. Here we show that microorganisms influence the mobility of platinum-group elements in mineral grains collected from Brazil, Australia and Colombia. Scanning electron microscopy showed biofilms covering the platinum-group mineral grains. The biofilms contained abundant platinum-group element nanoparticles and microcrystalline aggregates, and were dominated by Proteobacteria, many of which were closely related to known metal-resistant species. Some platinum-group mineral grains contained carbon, nitrogen, sulfur, selenium and iodine, suggesting the grains may be biogenic in origin. Molecular analyses show that Brazilian platinum-palladium grains hosted specific bacterial communities, which were different in composition from communities associated with gold grains, or communities in surrounding soils and sediments. Nano-phase metallic platinum accumulated when a metallophillic bacterium was incubated with a percolating platinum-containing medium, suggesting that biofilms can cause the precipitation of mobile platinum complexes. We conclude that biofilms are capable of forming or transforming platinum-group mineral grains, and may play an important role for platinum-group element dispersion and re-concentration in surface environments.

Current strategies for mobilome research

PubMed Central

Jørgensen, Tue S.; Kiil, Anne S.; Hansen, Martin A.; Sørensen, Søren J.; Hansen, Lars H.

2015-01-01

Mobile genetic elements (MGEs) are pivotal for bacterial evolution and adaptation, allowing shuffling of genes even between distantly related bacterial species. The study of these elements is biologically interesting as the mode of genetic propagation is kaleidoscopic and important, as MGEs are the main vehicles of the increasing bacterial antibiotic resistance that causes thousands of human deaths each year. The study of MGEs has previously focused on plasmids from individual isolates, but the revolution in sequencing technology has allowed the study of mobile genomic elements of entire communities using metagenomic approaches. The problem in using metagenomic sequencing for the study of MGEs is that plasmids and other mobile elements only comprise a small fraction of the total genetic content that are difficult to separate from chromosomal DNA based on sequence alone. The distinction between plasmid and chromosome is important as the mobility and regulation of genes largely depend on their genetic context. Several different approaches have been proposed that specifically enrich plasmid DNA from community samples. Here, we review recent approaches used to study entire plasmid pools from complex environments, and point out possible future developments for and pitfalls of these approaches. Further, we discuss the use of the PacBio long-read sequencing technology for MGE discovery. PMID:25657641

In vitro element release and biological aspects of base–metal alloys for metal-ceramic applications

PubMed Central

Holm, Charlotta; Morisbak, Else; Kalfoss, Torill; Dahl, Jon E.

2015-01-01

Abstract Objective: The aims of this study were to investigate the release of element from, and the biological response in vitro to, cobalt–chromium alloys and other base–metal alloys used for the fabrication of metal-ceramic restorations. Material and methods: Eighteen different alloys were investigated. Nine cobalt–chromium alloys, three nickel–chromium alloys, two cobalt–chromium–iron alloys, one palladium–silver alloy, one high-noble gold alloy, titanium grade II and one type III copper–aluminium alloy. Pure copper served as positive control. The specimens were prepared according to the ISO standards for biological and corrosion testing. Passive leaching of elements was measured by using Inductively Coupled Plasma – Mass Spectrometry (ICP-MS) after incubation in cell culture media, MEM, for 3 days. Corrosion testing was carried out in 0.9% sodium chloride (NaCl) and 1% lactic acid for 7 days, and the element release was measured by Inductively Coupled Plasma – Optical Emission Spectroscopy (ICP-OES). The biological response from the extract solutions was measured though MTT cytotoxicity testing and the Hen's egg test-chorio-allantoic membrane (HET-CAM) technique for irritationt. Results: The corrosion test showed similar element release from base-metal alloys compared to noble alloys such as gold. Apart from the high-copper alloy, all alloys expressed low element release in the immersion test, no cytotoxic effect in the MTT test, and were rated non-irritant in the HET-CAM test. Conclusions: Minimal biological response was observed for all the alloys tested, with the exception of the high-copper alloy. PMID:28642904

The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.

PubMed

Hogan, William R; Wagner, Michael M; Brochhausen, Mathias; Levander, John; Brown, Shawn T; Millett, Nicholas; DePasse, Jay; Hanna, Josh

2016-08-18

We developed the Apollo Structured Vocabulary (Apollo-SV)-an OWL2 ontology of phenomena in infectious disease epidemiology and population biology-as part of a project whose goal is to increase the use of epidemic simulators in public health practice. Apollo-SV defines a terminology for use in simulator configuration. Apollo-SV is the product of an ontological analysis of the domain of infectious disease epidemiology, with particular attention to the inputs and outputs of nine simulators. Apollo-SV contains 802 classes for representing the inputs and outputs of simulators, of which approximately half are new and half are imported from existing ontologies. The most important Apollo-SV class for users of simulators is infectious disease scenario, which is a representation of an ecosystem at simulator time zero that has at least one infection process (a class) affecting at least one population (also a class). Other important classes represent ecosystem elements (e.g., households), ecosystem processes (e.g., infection acquisition and infectious disease), censuses of ecosystem elements (e.g., censuses of populations), and infectious disease control measures. In the larger project, which created an end-user application that can send the same infectious disease scenario to multiple simulators, Apollo-SV serves as the controlled terminology and strongly influences the design of the message syntax used to represent an infectious disease scenario. As we added simulators for different pathogens (e.g., malaria and dengue), the core classes of Apollo-SV have remained stable, suggesting that our conceptualization of the information required by simulators is sound. Despite adhering to the OBO Foundry principle of orthogonality, we could not reuse Infectious Disease Ontology classes as the basis for infectious disease scenarios. We thus defined new classes in Apollo-SV for host, pathogen, infection, infectious disease, colonization, and infection acquisition. Unlike IDO, our ontological analysis extended to existing mathematical models of key biological phenomena studied by infectious disease epidemiology and population biology. Our ontological analysis as expressed in Apollo-SV was instrumental in developing a simulator-independent representation of infectious disease scenarios that can be run on multiple epidemic simulators. Our experience suggests the importance of extending ontological analysis of a domain to include existing mathematical models of the phenomena studied by the domain. Apollo-SV is freely available at: http://purl.obolibrary.org/obo/apollo_sv.owl .

A glimpse on biological activities of tellurium compounds.

PubMed

Cunha, Rodrigo L O R; Gouvea, Iuri E; Juliano, Luiz

2009-09-01

Tellurium is a rare element which has been regarded as a toxic, non-essential trace element and its biological role is not clearly established to date. Besides of that, the biological effects of elemental tellurium and some of its inorganic and organic derivatives have been studied, leading to a set of interesting and promising applications. As an example, it can be highlighted the uses of alkali-metal tellurites and tellurates in microbiology, the antioxidant effects of organotellurides and diorganoditellurides and the immunomodulatory effects of the non-toxic inorganic tellurane, named AS-101, and the plethora of its uses. Inasmuch, the nascent applications of organic telluranes (organotelluranes) as protease inhibitors and its applications in disease models are the most recent contribution to the scenario of the biological effects and applications of tellurium and its compounds discussed in this manuscript.

Mechano-biological Coupling of Cellular Responses to Microgravity

NASA Astrophysics Data System (ADS)

Long, Mian; Wang, Yuren; Zheng, Huiqiong; Shang, Peng; Duan, Enkui; Lü, Dongyuan

2015-11-01

Cellular response to microgravity is a basic issue in space biological sciences as well as space physiology and medicine. It is crucial to elucidate the mechano-biological coupling mechanisms of various biological organisms, since, from the principle of adaptability, all species evolved on the earth must possess the structure and function that adapts their living environment. As a basic element of an organism, a cell usually undergoes mechanical and chemical remodeling to sense, transmit, transduce, and respond to the alteration of gravitational signals. In the past decades, new computational platforms and experimental methods/techniques/devices are developed to mimic the biological effects of microgravity environment from the viewpoint of biomechanical approaches. Mechanobiology of plant gravisensing in the responses of statolith movements along the gravity vector and the relevant signal transduction and molecular regulatory mechanisms are investigated at gene, transcription, and protein levels. Mechanotransduction of bone or immune cell responses and stem cell development and tissue histogenesis are elucidated under microgravity. In this review, several important issues are briefly discussed. Future issues on gravisensing and mechanotransducing mechanisms are also proposed for ground-based studies as well as space missions.

Imaging of Vanadium in Microfossils: A New Potential Biosignature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marshall, Craig P.; Marshall, Alison Olcott; Aitken, Jade B.

Being able to distinguish unambiguously the biogenicity of microfossil-like structures in the ancient rock record is a fundamental predicament facing Archean paleobiologists and astrobiologists. Therefore, novel methods for discriminating biological from non-biological chemistries of microfossil-like structures are of the utmost importance in the search for evidence of early life on Earth. This too, is important for the search for life on Mars; either by in situ analyses via rovers, or sample return missions for future analysis here on Earth. Here, we report the application of synchrotron X-ray fluorescence imaging of vanadium, within thermally altered organic-walled microfossils of bona fide biologicalmore » origin. From our data, we demonstrate that vanadium is present within microfossils of undisputable biological origin. It is well known in the organic geochemistry literature, that elements such as vanadium are enriched and contained within crude oils, asphalts, and black shales that have been formed by diagensis of biological organic material. It has been demonstrated that the origin of vanadium is due to the diagenetic alteration of precursor chlorophyll and heme porphyrin pigment compounds from living organisms. Here, we propose that taken together, microfossil-like morphology, carbonaceous composition, and the presence of vanadium could be used in tandem as a biosignature to ascertain the biogenecity of putative microfossil-like structures.« less

Imaging of Vanadium in Microfossils: A New Potential Biosignature

DOE PAGES

Marshall, Craig P.; Marshall, Alison Olcott; Aitken, Jade B.; ...

2017-11-01

Being able to distinguish unambiguously the biogenicity of microfossil-like structures in the ancient rock record is a fundamental predicament facing Archean paleobiologists and astrobiologists. Therefore, novel methods for discriminating biological from non-biological chemistries of microfossil-like structures are of the utmost importance in the search for evidence of early life on Earth. This too, is important for the search for life on Mars; either by in situ analyses via rovers, or sample return missions for future analysis here on Earth. Here, we report the application of synchrotron X-ray fluorescence imaging of vanadium, within thermally altered organic-walled microfossils of bona fide biologicalmore » origin. From our data, we demonstrate that vanadium is present within microfossils of undisputable biological origin. It is well known in the organic geochemistry literature, that elements such as vanadium are enriched and contained within crude oils, asphalts, and black shales that have been formed by diagensis of biological organic material. It has been demonstrated that the origin of vanadium is due to the diagenetic alteration of precursor chlorophyll and heme porphyrin pigment compounds from living organisms. Here, we propose that taken together, microfossil-like morphology, carbonaceous composition, and the presence of vanadium could be used in tandem as a biosignature to ascertain the biogenecity of putative microfossil-like structures.« less

Imaging of Vanadium in Microfossils: A New Potential Biosignature

NASA Astrophysics Data System (ADS)

Marshall, Craig P.; Marshall, Alison Olcott; Aitken, Jade B.; Lai, Barry; Vogt, Stefan; Breuer, Pierre; Steemans, Philippe; Lay, Peter A.

2017-11-01

The inability to unambiguously distinguish the biogenicity of microfossil-like structures in the ancient rock record is a fundamental predicament facing Archean paleobiologists and astrobiologists. Therefore, novel methods for discriminating biological from nonbiological chemistries of microfossil-like structures are of the utmost importance in the search for evidence of early life on Earth. This, too, is important for the search for life on Mars by in situ analyses via rovers or sample return missions for future analysis here on Earth. Here, we report the application of synchrotron X-ray fluorescence imaging of vanadium, within thermally altered organic-walled microfossils of bona fide biological origin. From our data, we demonstrate that vanadium is present within microfossils of undisputable biological origin. It is well known in the organic geochemistry literature that elements such as vanadium are enriched and contained within crude oils, asphalts, and black shales that have been formed by diagenesis of biological organic material. It has been demonstrated that the origin of vanadium is due to the diagenetic alteration of precursor chlorophyll and heme porphyrin pigment compounds from living organisms. We propose that, taken together, microfossil-like morphology, carbonaceous composition, and the presence of vanadium could be used in tandem as a biosignature to ascertain the biogenicity of putative microfossil-like structures.

Nuclear microscopy in trace-element biology — from cellular studies to the clinic

NASA Astrophysics Data System (ADS)

Lindh, Ulf

1993-05-01

The concentration and distribution of trace and major elements in cells are of great interest in cell biology. PIXE can provide elemental concentrations in the bulk of cells or organelles as other bulk techniques such as atomic absorption spectrophotometry and nuclear activation analysis. Supplementary information, perhaps more exciting, on the intracellular distributions of trace elements can be provided using nuclear microscopy. Intracellular distributions of trace elements in normal and malignant cells are presented. The toxicity of mercury and cadmium can be prevented by supplementation of the essential trace element selenium. Some results from an experimental animal model are discussed. The intercellular distribution of major and trace elements in isolated blood cells, as revealed by nuclear microscopy, provides useful clinical information. Examples are given concerning inflammatory connective-tissue diseases and the chronic fatigue syndrome.

Geosphere-biosphere circulation of chemical elements in soil and plant systems from a 100 km transect from southern central Norway.

PubMed

Reimann, Clemens; Fabian, Karl; Flem, Belinda; Andersson, Malin; Filzmoser, Peter; Englmaier, Peter

2018-05-17

Geochemical element separation is studied in 14 different sample media collected at 41 sites along an approximately 100-km long transect north of Oslo. At each site, soil C and O horizons and 12 plant materials (birch/spruce/cowberry/blueberry leaves/needles and twigs, horsetail, braken fern, pine bark and terrestrial moss) were sampled. The observed concentrations of 29 elements (K, Ca, P, Mg, Mn, S, Fe, Zn, Na, B, Cu, Mo, Co, Al, Ba, Rb, Sr, Ti, Ni, Pb, Cs, Cd, Ce, Sn, La, Tl, Y, Hg, Ag) were used to investigate soil-plant relations, and to evaluate the element differentiation between different plants, or between foliage and twigs of the same plant. In relation to the soil C horizon, the O horizon is strongly enriched (O/C ratio > 5) in Ag, Hg, Cd, Sn, S and Pb. Other elements (B, K, Ca, P, S, Mn) show higher concentrations in the plants than in the substrate represented by the C horizon, and often even higher concentrations than in the soil O horizon. Elements like B, K, Ca, S, Mg, P, Ba, and Cu are well tuned to certain concentration levels in most of the plants. This is demonstrated by their lower interquartile variability in the plants than in the soil. Cross-plots of element concentration, variance, and ratios, supported by linear discrimination analysis, establish that different plants are marked by their individual element composition, which is separable from, and largely independent of the natural substrate variability across the Gjøvik transect. Element allocation to foliage or twigs of the same plants can also be separated and thus dominantly depend on metabolism, physiology, and structure linked to biological functions, and only to a lesser degree on the substrate and environmental background. The results underline the importance of understanding the biological mechanisms of plant-soil interaction in order to correctly quantify anthropogenic impact on soil and plant geochemistry. Copyright © 2018 Elsevier B.V. All rights reserved.

A finite element simulation of biological conversion processes in landfills.

PubMed

Robeck, M; Ricken, T; Widmann, R

2011-04-01

Landfills are the most common way of waste disposal worldwide. Biological processes convert the organic material into an environmentally harmful landfill gas, which has an impact on the greenhouse effect. After the depositing of waste has been stopped, current conversion processes continue and emissions last for several decades and even up to 100years and longer. A good prediction of these processes is of high importance for landfill operators as well as for authorities, but suitable models for a realistic description of landfill processes are rather poor. In order to take the strong coupled conversion processes into account, a constitutive three-dimensional model based on the multiphase Theory of Porous Media (TPM) has been developed at the University of Duisburg-Essen. The theoretical formulations are implemented in the finite element code FEAP. With the presented calculation concept we are able to simulate the coupled processes that occur in an actual landfill. The model's theoretical background and the results of the simulations as well as the meantime successfully performed simulation of a real landfill body will be shown in the following. Copyright © 2010 Elsevier Ltd. All rights reserved.

Biosensor Recognition Elements

DTIC Science & Technology

2008-01-01

Systematics, bioinformatics, systems biology, regulation, genetics, genomics, metabolism, ecology, development . Epstein - Barr Virus Latency and...and C, Simian immunodeficiency, Ebola, Rabies, Epstein – Barr , and Measles viruses as well as biological agents such as botulinum neurotoxin A/B...time metabolic vigilance via sensor based ligand specific biorecognition elements is immense. Virus -based nanoparticles have been developed for

Biological aspects of tissue-engineered cartilage.

PubMed

Hoshi, Kazuto; Fujihara, Yuko; Yamawaki, Takanori; Harai, Motohiro; Asawa, Yukiyo; Hikita, Atsuhiko

2018-04-01

Cartilage regenerative medicine has been progressed well, and it reaches the stage of clinical application. Among various techniques, tissue engineering, which incorporates elements of materials science, is investigated earnestly, driven by high clinical needs. The cartilage tissue engineering using a poly lactide scaffold has been exploratorily used in the treatment of cleft lip-nose patients, disclosing good clinical results during 3-year observation. However, to increase the reliability of this treatment, not only accumulation of clinical evidence on safety and usefulness of the tissue-engineered products, but also establishment of scientific background on biological mechanisms, are regarded essential. In this paper, we reviewed recent trends of cartilage tissue engineering in clinical practice, summarized experimental findings on cellular and matrix changes during the cartilage regeneration, and discussed the importance of further studies on biological aspects of tissue-engineered cartilage, especially by the histological and the morphological methods.

Interrogating the variation of element masses and distribution patterns in single cells using ICP-MS with a high efficiency cell introduction system.

PubMed

Wang, Hailong; Wang, Meng; Wang, Bing; Zheng, Lingna; Chen, Hanqing; Chai, Zhifang; Feng, Weiyue

2017-02-01

Cellular heterogeneity is an inherent condition of cell populations, which results from stochastic expression of genes, proteins, and metabolites. The heterogeneity of individual cells can dramatically influence cellular decision-making and cell fate. So far, our knowledge about how the variation of endogenous metals and non-metals in individual eukaryotic cells is limited. In this study, ICP-MS equipped with a high efficiency cell introduction system (HECIS) was developed as a method of single-cell ICP-MS (SC-ICP-MS). The method was applied to the single-cell analysis of Mn, Fe, Co, Cu, Zn, P, and S in human cancer cell lines (HeLa and A549) and normal human bronchial epithelial cell line (16HBE). The analysis showed obvious variation of the masses of Cu, Fe, Zn, and P in individual HeLa cells, and variation of Fe, Zn, and P in individual A549 cells. On the basis of the single-cell data, a multimodal distribution of the elements in the cell population was fitted, which showed marked differences among the various cell lines. Importantly, subpopulations of the elements were found in the cell populations, especially in the HeLa cancer cells. This study demonstrates that SC-ICP-MS is able to unravel the extent of variation of endogenous elements in individual cells, which will help to improve our fundamental understanding of cellular biology and reveal novel insights into human biology and medicine. Graphical abstract The variations of masses and distribution patterns of elements Mn, Fe, Co, Cu, Zn, P, and S in single cells were successfully detected by ICP-MS coupled with a high efficiency cell introduction system (HECIS).

Monte Carlo Simulation to Determine Geometry Effects on Quantitative X-ray Microanalysis in Plant Cell Walls Using Gelatin Standards

NASA Astrophysics Data System (ADS)

Tylko, Grzegorz; Dubchak, Sergyi; Banach, Zuzanna; Turnau, Katarzyna

2010-04-01

Monte Carlo simulations of gelatin matrices with known elemental concentrations confirmed the suitability of protein standards to quantify elements of cellulose material in x-ray microanalysis. However, gelatin standards and cellulose plant cell walls differ in structure, what influences x-ray generation and emission in both specimens. The goal of the project was to establish the influence of gelatin structure on x-ray generation and its usefulness to calculate elemental concentrations in plant cell walls of different width. Roots of Medicago truncatula as well as gelatin standards with known elemental composition were prepared according to freeze-drying protocols. The thermanox polymer was chosen to establish background formation for flat and compact organic materials. All analyses were performed with the scanning electron microscope operated at 10 keV and probe current of 350 pA. The Monte Carlo code Casino was applied to calculate the intensities of the generated and the emitted x-rays from biological matrix of different width. No topography effects of gelatin structure were visible when the raster mode of electron impact was applied to the specimen. Monte Carlo simulations of gelatin of different width revealed that a significant decrease of the generated x-ray intensity appears at the width of the specimen around 3.5 μm. However, an increase of emission of low energy x-ray intensities (Na, Mg) was noted at 3.5 μm size with constant emission of higher energy x-rays (Cl, K) down to 2.5 μm width. It determines the minimal size of plant specimen useful for comparison to bulk gelatin standard when quantitative analysis is performed for biologically important elements.

Discovering functional DNA elements using population genomic information: a proof of concept using human mtDNA.

PubMed

Schrider, Daniel R; Kern, Andrew D

2014-06-09

Identifying the complete set of functional elements within the human genome would be a windfall for multiple areas of biological research including medicine, molecular biology, and evolution. Complete knowledge of function would aid in the prioritization of loci when searching for the genetic bases of disease or adaptive phenotypes. Because mutations that disrupt function are disfavored by natural selection, purifying selection leaves a detectable signature within functional elements; accordingly, this signal has been exploited for over a decade through the use of genomic comparisons of distantly related species. While this is so, the functional complement of the genome changes extensively across time and between lineages; therefore, evidence of the current action of purifying selection in humans is essential. Because the removal of deleterious mutations by natural selection also reduces within-species genetic diversity within functional loci, dense population genetic data have the potential to reveal genomic elements that are currently functional. Here, we assess the potential of this approach by examining an ultradeep sample of human mitochondrial genomes (n = 16,411). We show that the high density of polymorphism in this data set precisely delineates regions experiencing purifying selection. Furthermore, we show that the number of segregating alleles at a site is strongly correlated with its divergence across species after accounting for known mutational biases in human mitochondrial DNA (ρ = 0.51; P < 2.2 × 10(-16)). These two measures track one another at a remarkably fine scale across many loci-a correlation that is purely the result of natural selection. Our results demonstrate that genetic variation has the potential to reveal with surprising precision which regions in the genome are currently performing important functions and likely to have deleterious fitness effects when mutated. As more complete human genomes are sequenced, similar power to reveal purifying selection may be achievable in the human nuclear genome. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Engineering modular ‘ON’ RNA switches using biological components

PubMed Central

Ceres, Pablo; Trausch, Jeremiah J.; Batey, Robert T.

2013-01-01

Riboswitches are cis-acting regulatory elements broadly distributed in bacterial mRNAs that control a wide range of critical metabolic activities. Expression is governed by two distinct domains within the mRNA leader: a sensory ‘aptamer domain’ and a regulatory ‘expression platform’. Riboswitches have also received considerable attention as important tools in synthetic biology because of their conceptually simple structure and the ability to obtain aptamers that bind almost any conceivable small molecule using in vitro selection (referred to as SELEX). In the design of artificial riboswitches, a significant hurdle has been to couple the two domains enabling their efficient communication. We previously demonstrated that biological transcriptional ‘OFF’ expression platforms are easily coupled to diverse aptamers, both biological and SELEX-derived, using simple design rules. Here, we present two modular transcriptional ‘ON’ riboswitch expression platforms that are also capable of hosting foreign aptamers. We demonstrate that these biological parts can be used to facilely generate artificial chimeric riboswitches capable of robustly regulating transcription both in vitro and in vivo. We expect that these modular expression platforms will be of great utility for various synthetic biological applications that use RNA-based biosensors. PMID:23999097

Optimization of biological sulfide removal in a CSTR bioreactor.

PubMed

Roosta, Aliakbar; Jahanmiri, Abdolhossein; Mowla, Dariush; Niazi, Ali; Sotoodeh, Hamidreza

2012-08-01

In this study, biological sulfide removal from natural gas in a continuous bioreactor is investigated for estimation of the optimal operational parameters. According to the carried out reactions, sulfide can be converted to elemental sulfur, sulfate, thiosulfate, and polysulfide, of which elemental sulfur is the desired product. A mathematical model is developed and was used for investigation of the effect of various parameters on elemental sulfur selectivity. The results of the simulation show that elemental sulfur selectivity is a function of dissolved oxygen, sulfide load, pH, and concentration of bacteria. Optimal parameter values are calculated for maximum elemental sulfur selectivity by using genetic algorithm as an adaptive heuristic search. In the optimal conditions, 87.76% of sulfide loaded to the bioreactor is converted to elemental sulfur.

Aquaporins Mediate Silicon Transport in Humans

PubMed Central

Garneau, Alexandre P.; Carpentier, Gabriel A.; Marcoux, Andrée-Anne; Frenette-Cotton, Rachelle; Simard, Charles F.; Rémus-Borel, Wilfried; Caron, Luc; Jacob-Wagner, Mariève; Noël, Micheline; Powell, Jonathan J.; Bélanger, Richard; Côté, François; Isenring, Paul

2015-01-01

In animals, silicon is an abundant and differentially distributed trace element that is believed to play important biological functions. One would thus expect silicon concentrations in body fluids to be regulated by silicon transporters at the surface of many cell types. Curiously, however, and even though they exist in plants and algae, no such transporters have been identified to date in vertebrates. Here, we show for the first time that the human aquaglyceroporins, i.e., AQP3, AQP7, AQP9 and AQP10 can act as silicon transporters in both Xenopus laevis oocytes and HEK-293 cells. In particular, heterologously expressed AQP7, AQP9 and AQP10 are all able to induce robust, saturable, phloretin-sensitive silicon transport activity in the range that was observed for low silicon rice 1 (lsi1), a silicon transporter in plant. Furthermore, we show that the aquaglyceroporins appear as relevant silicon permeation pathways in both mice and humans based on 1) the kinetics of substrate transport, 2) their presence in tissues where silicon is presumed to play key roles and 3) their transcriptional responses to changes in dietary silicon. Taken together, our data provide new evidence that silicon is a potentially important biological element in animals and that its body distribution is regulated. They should open up original areas of investigations aimed at deciphering the true physiological role of silicon in vertebrates. PMID:26313002

Aquaporins Mediate Silicon Transport in Humans.

PubMed

Garneau, Alexandre P; Carpentier, Gabriel A; Marcoux, Andrée-Anne; Frenette-Cotton, Rachelle; Simard, Charles F; Rémus-Borel, Wilfried; Caron, Luc; Jacob-Wagner, Mariève; Noël, Micheline; Powell, Jonathan J; Bélanger, Richard; Côté, François; Isenring, Paul

2015-01-01

In animals, silicon is an abundant and differentially distributed trace element that is believed to play important biological functions. One would thus expect silicon concentrations in body fluids to be regulated by silicon transporters at the surface of many cell types. Curiously, however, and even though they exist in plants and algae, no such transporters have been identified to date in vertebrates. Here, we show for the first time that the human aquaglyceroporins, i.e., AQP3, AQP7, AQP9 and AQP10 can act as silicon transporters in both Xenopus laevis oocytes and HEK-293 cells. In particular, heterologously expressed AQP7, AQP9 and AQP10 are all able to induce robust, saturable, phloretin-sensitive silicon transport activity in the range that was observed for low silicon rice 1 (lsi1), a silicon transporter in plant. Furthermore, we show that the aquaglyceroporins appear as relevant silicon permeation pathways in both mice and humans based on 1) the kinetics of substrate transport, 2) their presence in tissues where silicon is presumed to play key roles and 3) their transcriptional responses to changes in dietary silicon. Taken together, our data provide new evidence that silicon is a potentially important biological element in animals and that its body distribution is regulated. They should open up original areas of investigations aimed at deciphering the true physiological role of silicon in vertebrates.

Anomalous Rayleigh scattering with dilute concentrations of elements of biological importance

NASA Astrophysics Data System (ADS)

Hugtenburg, Richard P.; Bradley, David A.

2004-01-01

The anomalous scattering factor (ASF) correction to the relativistic form-factor approximation for Rayleigh scattering is examined in support of its utilization in radiographic imaging. ASF corrected total cross-section data have been generated for a low resolution grid for the Monte Carlo code EGS4 for the biologically important elements, K, Ca, Mn, Fe, Cu and Zn. Points in the fixed energy grid used by EGS4 as well as 8 other points in the vicinity of the K-edge have been chosen to achieve an uncertainty in the ASF component of 20% according to the Thomas-Reiche-Kuhn sum rule and an energy resolution of 20 eV. Such data is useful for analysis of imaging with a quasi-monoenergetic source. Corrections to the sampled distribution of outgoing photons, due to ASF, are given and new total cross-section data including that of the photoelectric effect have been computed using the Slater exchange self-consistent potential with the Latter tail. A measurement of Rayleigh scattering in a dilute aqueous solution of manganese (II) was performed, this system enabling determination of the absolute cross-section, although background subtraction was necessary to remove K β fluorescence and resonant Raman scattering occurring within several 100 eV of the edge. Measurements confirm the presence of below edge bound-bound structure and variation in the structure due to the ionic state that are not currently included in tabulations.

Biomimetic cellular metals-using hierarchical structuring for energy absorption.

PubMed

Bührig-Polaczek, A; Fleck, C; Speck, T; Schüler, P; Fischer, S F; Caliaro, M; Thielen, M

2016-07-19

Fruit walls as well as nut and seed shells typically perform a multitude of functions. One of the biologically most important functions consists in the direct or indirect protection of the seeds from mechanical damage or other negative environmental influences. This qualifies such biological structures as role models for the development of new materials and components that protect commodities and/or persons from damage caused for example by impacts due to rough handling or crashes. We were able to show how the mechanical properties of metal foam based components can be improved by altering their structure on various hierarchical levels inspired by features and principles important for the impact and/or puncture resistance of the biological role models, rather than by tuning the properties of the bulk material. For this various investigation methods have been established which combine mechanical testing with different imaging methods, as well as with in situ and ex situ mechanical testing methods. Different structural hierarchies especially important for the mechanical deformation and failure behaviour of the biological role models, pomelo fruit (Citrus maxima) and Macadamia integrifolia, were identified. They were abstracted and transferred into corresponding structural principles and thus hierarchically structured bio-inspired metal foams have been designed. A production route for metal based bio-inspired structures by investment casting was successfully established. This allows the production of complex and reliable structures, by implementing and combining different hierarchical structural elements found in the biological concept generators, such as strut design and integration of fibres, as well as by minimising casting defects. To evaluate the structural effects, similar investigation methods and mechanical tests were applied to both the biological role models and the metallic foams. As a result an even deeper quantitative understanding of the form-structure-function relationship of the biological concept generators as well as the bio-inspired metal foams was achieved, on deeper hierarchical levels and overarching different levels.

[The determination of the natural content of chemical elements in human biological objects (liver, kidney, stomach) by mass spectrometry with inductively coupled plasma].

PubMed

Luzanova, I S; Svetlolobov, D Iu; Zorin, Iu V

2014-01-01

The objective of the present work was to continue the studies of the sites of concentration of the chemical elements corresponding to normal homeostasis in human biological objects by mass spectrometry with inductively coupled plasma. The study yielded the data on the natural content of 27 elements in the cadaveric liver, kidney, and stomach. It is recommended to use these findings as the reference parameters corresponding to normal homeostasis.

Evolution of a Lowland Karst Landscape; A Mass-Balance Approach

NASA Astrophysics Data System (ADS)

Chamberlin, C.; Heffernan, J. B.; Cohen, M. J.; Quintero, C.; Pain, A.

2016-12-01

Karst landscapes are highly soluble, and are vulnerable to biological acid production as a major driving factor in their evolution. Big Cypress National Park (BICY) is a low-lying karst landscape in southern Florida displaying a distinctive morphology of isolated depressions likely influenced by biology. The goal of this study is to constrain timescales of landform development in BICY. This question was addressed through the construction of landscape-scale elemental budgets for both calcium and phosphorus. Precipitation and export fluxes were calculated using available chemistry and hydrology data, and stocks were calculated from a combination of existing data, field measurements, and laboratory chemical analysis. Estimates of expected mass export given no biological acid production and given an equivalent production of 100% of GPP were compared with observed rates. Current standing stocks of phosphorus are dominated by a large soil pool, and contain 500 Gg P. Inputs are largely dominated by precipitation, and 8000 years are necessary to accumulate standing stocks of phosphorus given modern fluxes. Calcium flux is vastly dominated by dissolution of the limestone bedrock, and though some calcium is retained in the soil, most is exported. Using LiDAR generated estimates of volume loss across the landscape and current export rates, an estimated 15,000 years would be necessary to create the modern landscape. Both of these estimates indicate that the BICY landscape is geologically very young. The different behaviors of these elements (calcium is largely exported, while phosphorus is largely retained) lend additional confidence to estimates of denudation rates of the landscape. These estimates can be even closer reconciled if calcium redistribution over the landscape is allowed for. This estimate is compared to the two bounding conditions for biological weathering to indicate a likely level of biological importance to landscape development in this system.

Combining content and elements of communication into an upper-level biochemistry course.

PubMed

Whittington, Carli P; Pellock, Samuel J; Cunningham, Rebecca L; Cox, James R

2014-01-01

This report describes how a science communication module was incorporated into an advanced biochemistry course. Elements of communication were taught synergistically with biochemistry content in this course in an effort to expose students to a variety of effective oral communication strategies. Students were trained to use these established techniques and incorporated them into various presentations throughout the course. Three students describe their use of specific resources and how the skills learned relate to their future career. The importance and relevance of science communication are receiving unprecedented national attention. The academic scientific community must respond by incorporating more communication-centered instruction and opportunities in the classroom and laboratory. © 2013 by The International Union of Biochemistry and Molecular Biology.

Pathways to Identity: Aiding Law Enforcement in Identification Tasks With Visual Analytics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bruce, Joseph R.; Scholtz, Jean; Hodges, Duncan

The nature of identity has changed dramatically in recent years, and has grown in complexity. Identities are defined in multiple domains: biological and psychological elements strongly contribute, but also biographical and cyber elements are necessary to complete the picture. Law enforcement is beginning to adjust to these changes, recognizing its importance in criminal justice. The SuperIdentity project seeks to aid law enforcement officials in their identification tasks through research of techniques for discovering identity traits, generation of statistical models of identity and analysis of identity traits through visualization. We present use cases compiled through user interviews in multiple fields, includingmore » law enforcement, as well as the modeling and visualization tools design to aid in those use cases.« less

Pathways to Identity. Using Visualization to Aid Law Enforcement in Identification Tasks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bruce, Joseph R.; Scholtz, Jean; Hodges, Duncan

The nature of identity has changed dramatically in recent years and has grown in complexity. Identities are defined in multiple domains: biological and psychological elements strongly contribute, but biographical and cyber elements also are necessary to complete the picture. Law enforcement is beginning to adjust to these changes, recognizing identity’s importance in criminal justice. The SuperIdentity project seeks to aid law enforcement officials in their identification tasks through research of techniques for discovering identity traits, generation of statistical models of identity and analysis of identity traits through visualization. We present use cases compiled through user interviews in multiple fields, includingmore » law enforcement, and describe the modeling and visualization tools design to aid in those use cases.« less

On the mechanics of growing thin biological membranes

NASA Astrophysics Data System (ADS)

Rausch, Manuel K.; Kuhl, Ellen

2014-02-01

Despite their seemingly delicate appearance, thin biological membranes fulfill various crucial roles in the human body and can sustain substantial mechanical loads. Unlike engineering structures, biological membranes are able to grow and adapt to changes in their mechanical environment. Finite element modeling of biological growth holds the potential to better understand the interplay of membrane form and function and to reliably predict the effects of disease or medical intervention. However, standard continuum elements typically fail to represent thin biological membranes efficiently, accurately, and robustly. Moreover, continuum models are typically cumbersome to generate from surface-based medical imaging data. Here we propose a computational model for finite membrane growth using a classical midsurface representation compatible with standard shell elements. By assuming elastic incompressibility and membrane-only growth, the model a priori satisfies the zero-normal stress condition. To demonstrate its modular nature, we implement the membrane growth model into the general-purpose non-linear finite element package Abaqus/Standard using the concept of user subroutines. To probe efficiently and robustness, we simulate selected benchmark examples of growing biological membranes under different loading conditions. To demonstrate the clinical potential, we simulate the functional adaptation of a heart valve leaflet in ischemic cardiomyopathy. We believe that our novel approach will be widely applicable to simulate the adaptive chronic growth of thin biological structures including skin membranes, mucous membranes, fetal membranes, tympanic membranes, corneoscleral membranes, and heart valve membranes. Ultimately, our model can be used to identify diseased states, predict disease evolution, and guide the design of interventional or pharmaceutic therapies to arrest or revert disease progression.

On the mechanics of growing thin biological membranes

PubMed Central

Rausch, Manuel K.; Kuhl, Ellen

2013-01-01

Despite their seemingly delicate appearance, thin biological membranes fulfill various crucial roles in the human body and can sustain substantial mechanical loads. Unlike engineering structures, biological membranes are able to grow and adapt to changes in their mechanical environment. Finite element modeling of biological growth holds the potential to better understand the interplay of membrane form and function and to reliably predict the effects of disease or medical intervention. However, standard continuum elements typically fail to represent thin biological membranes efficiently, accurately, and robustly. Moreover, continuum models are typically cumbersome to generate from surface-based medical imaging data. Here we propose a computational model for finite membrane growth using a classical midsurface representation compatible with standard shell elements. By assuming elastic incompressibility and membrane-only growth, the model a priori satisfies the zero-normal stress condition. To demonstrate its modular nature, we implement the membrane growth model into the general-purpose non-linear finite element package Abaqus/Standard using the concept of user subroutines. To probe efficiently and robustness, we simulate selected benchmark examples of growing biological membranes under different loading conditions. To demonstrate the clinical potential, we simulate the functional adaptation of a heart valve leaflet in ischemic cardiomyopathy. We believe that our novel approach will be widely applicable to simulate the adaptive chronic growth of thin biological structures including skin membranes, mucous membranes, fetal membranes, tympanic membranes, corneoscleral membranes, and heart valve membranes. Ultimately, our model can be used to identify diseased states, predict disease evolution, and guide the design of interventional or pharmaceutic therapies to arrest or revert disease progression. PMID:24563551

DEPPDB - DNA electrostatic potential properties database. Electrostatic properties of genome DNA elements.

PubMed

Osypov, Alexander A; Krutinin, Gleb G; Krutinina, Eugenia A; Kamzolova, Svetlana G

2012-04-01

Electrostatic properties of genome DNA are important to its interactions with different proteins, in particular, related to transcription. DEPPDB - DNA Electrostatic Potential (and other Physical) Properties Database - provides information on the electrostatic and other physical properties of genome DNA combined with its sequence and annotation of biological and structural properties of genomes and their elements. Genomes are organized on taxonomical basis, supporting comparative and evolutionary studies. Currently, DEPPDB contains all completely sequenced bacterial, viral, mitochondrial, and plastids genomes according to the NCBI RefSeq, and some model eukaryotic genomes. Data for promoters, regulation sites, binding proteins, etc., are incorporated from established DBs and literature. The database is complemented by analytical tools. User sequences calculations are available. Case studies discovered electrostatics complementing DNA bending in E.coli plasmid BNT2 promoter functioning, possibly affecting host-environment metabolic switch. Transcription factors binding sites gravitate to high potential regions, confirming the electrostatics universal importance in protein-DNA interactions beyond the classical promoter-RNA polymerase recognition and regulation. Other genome elements, such as terminators, also show electrostatic peculiarities. Most intriguing are gene starts, exhibiting taxonomic correlations. The necessity of the genome electrostatic properties studies is discussed.

Quantitative approaches to the study of bistability in the lac operon of Escherichia coli.

PubMed

Santillán, Moisés; Mackey, Michael C

2008-08-06

In this paper, the history and importance of the lac operon in the development of molecular and systems biology are briefly reviewed. We start by presenting a description of the regulatory mechanisms in this operon, taking into account the most recent discoveries. Then we offer a survey of the history of the lac operon, including the discovery of its main elements and the subsequent influence on the development of molecular and systems biology. Next the bistable behaviour of the operon is discussed, both with respect to its discovery and its molecular origin. A review of the literature in which this bistable phenomenon has been studied from a mathematical modelling viewpoint is then given. We conclude with some brief remarks.

Desmosomes in acquired disease

PubMed Central

Stahley, Sara N.; Kowalczyk, Andrew P.

2015-01-01

Desmosomes are cell-cell junctions that mediate adhesion and couple the intermediate filament cytoskeleton to sites of cell-cell contact. This architectural arrangement functions to integrate adhesion and cytoskeletal elements of adjacent cells. The importance of this robust adhesion system is evident in numerous human diseases, both inherited and acquired, that occur when desmosome function is compromised. This review focuses on autoimmune and infectious diseases that impair desmosome function. In addition, we discuss emerging evidence that desmosomal genes are often misregulated in cancer. The emphasis of our discussion is placed on how human diseases inform our understanding of basic desmosome biology, and in turn, how fundamental advances in the cell biology of desmosomes may lead to new treatments for acquired diseases of the desmosome. PMID:25795143

Silvics of North America: 1. Conifers; 2. Hardwoods

Treesearch

Russell M. Burns; Barbara H. (tech. Coords.) Honkala

1990-01-01

The total environment of a tree is a complex integration of physical and biological elements. The physical elements are related to climate and soil and include radiation, precipitation, and the movement and composition of air; as well as the texture of the soil and its structure, depth, moisture capacity, drainage, nutrient content, and topographic position. Biological...

Biological X-ray absorption spectroscopy (BioXAS): a valuable tool for the study of trace elements in the life sciences.

PubMed

Strange, Richard W; Feiters, Martin C

2008-10-01

Using X-ray absorption spectroscopy (XAS) the binding modes (type and number of ligands, distances and geometry) and oxidation states of metals and other trace elements in crystalline as well as non-crystalline samples can be revealed. The method may be applied to biological systems as a 'stand-alone' technique, but it is particularly powerful when used alongside other X-ray and spectroscopic techniques and computational approaches. In this review, we highlight how biological XAS is being used in concert with crystallography, spectroscopy and computational chemistry to study metalloproteins in crystals, and report recent applications on relatively rare trace elements utilised by living organisms and metals involved in neurodegenerative diseases.

Analysis of biological materials using a nuclear microprobe

NASA Astrophysics Data System (ADS)

Mulware, Stephen Juma

The use of nuclear microprobe techniques including: Particle induced x-ray emission (PIXE) and Rutherford backscattering spectrometry (RBS) for elemental analysis and quantitative elemental imaging of biological samples is especially useful in biological and biomedical research because of its high sensitivity for physiologically important trace elements or toxic heavy metals. The nuclear microprobe of the Ion Beam Modification and Analysis Laboratory (IBMAL) has been used to study the enhancement in metal uptake of two different plants. The roots of corn (Zea mays) have been analyzed to study the enhancement of iron uptake by adding Fe (II) or Fe(III) of different concentrations to the germinating medium of the seeds. The Fe uptake enhancement effect produced by lacing the germinating medium with carbon nanotubes has also been investigated. The aim of this investigation is to ensure not only high crop yield but also Fe-rich food products especially from calcareous soil which covers 30% of world's agricultural land. The result will help reduce iron deficiency anemia, which has been identified as the leading nutritional disorder especially in developing countries by the World Health Organization. For the second plant, Mexican marigold (Tagetes erecta ), the effect of an arbuscular mycorrhizal fungi (Glomus intraradices ) for the improvement of lead phytoremediation of lead contaminated soil has been investigated. Phytoremediation provides an environmentally safe technique of removing toxic heavy metals (like lead), which can find their way into human food, from lands contaminated by human activities like mining or by natural disasters like earthquakes. The roots of Mexican marigold have been analyzed to study the role of arbuscular mycorrhizal fungi in enhancement of lead uptake from the contaminated rhizosphere.

Physical, chemical, and biological data for detailed study of the Sun River Irrigation Project, Freezout Lake Wildlife Management Area, and Benton Lake National Wildlife Refuge, west-central Montana, 1990-92, with selected data for 1987-89

USGS Publications Warehouse

Lambing, J.H.; Nimick, D.A.; Knapton, J.R.; Palawski, D.U.

1994-01-01

Physical chemical, and biological data were collected in the lower Sun River area of west-central Montana during 1990-92 as part of a U.S. Department of the Interior detailed study of the extent, magnitude, sources, and potential biological impacts of contaminants associated with irrigation drainage. Physical and chemical data were collected from areas within and near the Sun River Irrigation Project and from wetland areas receiving irrigation drainage. Biological data were collected from areas in and near Freezout Lake Wildlife Management Area and Benton Lake National Wildlife Refuge. Additional biological data were collected previously during 1987-89 as part of a U.S. Fish and Wildlife Service program. This report presents data for selenium and other potentially toxic constituents in solid-phase, water, and biological media. Data consist of concentrations of major and trace elements in soil and drill cores; concen- trations of major ions, nutrients, and trace elements in ground water and surface water; and trace-element concentrations in bottom sediment and biological tissue. Hydrogeologic data for domestic and test wells and daily streamflow data for selected sites also are included.

Nutritional Systems Biology Modeling: From Molecular Mechanisms to Physiology

PubMed Central

de Graaf, Albert A.; Freidig, Andreas P.; De Roos, Baukje; Jamshidi, Neema; Heinemann, Matthias; Rullmann, Johan A.C.; Hall, Kevin D.; Adiels, Martin; van Ommen, Ben

2009-01-01

The use of computational modeling and simulation has increased in many biological fields, but despite their potential these techniques are only marginally applied in nutritional sciences. Nevertheless, recent applications of modeling have been instrumental in answering important nutritional questions from the cellular up to the physiological levels. Capturing the complexity of today's important nutritional research questions poses a challenge for modeling to become truly integrative in the consideration and interpretation of experimental data at widely differing scales of space and time. In this review, we discuss a selection of available modeling approaches and applications relevant for nutrition. We then put these models into perspective by categorizing them according to their space and time domain. Through this categorization process, we identified a dearth of models that consider processes occurring between the microscopic and macroscopic scale. We propose a “middle-out” strategy to develop the required full-scale, multilevel computational models. Exhaustive and accurate phenotyping, the use of the virtual patient concept, and the development of biomarkers from “-omics” signatures are identified as key elements of a successful systems biology modeling approach in nutrition research—one that integrates physiological mechanisms and data at multiple space and time scales. PMID:19956660

ModeLang: a new approach for experts-friendly viral infections modeling.

PubMed

Wasik, Szymon; Prejzendanc, Tomasz; Blazewicz, Jacek

2013-01-01

Computational modeling is an important element of systems biology. One of its important applications is modeling complex, dynamical, and biological systems, including viral infections. This type of modeling usually requires close cooperation between biologists and mathematicians. However, such cooperation often faces communication problems because biologists do not have sufficient knowledge to understand mathematical description of the models, and mathematicians do not have sufficient knowledge to define and verify these models. In many areas of systems biology, this problem has already been solved; however, in some of these areas there are still certain problematic aspects. The goal of the presented research was to facilitate this cooperation by designing seminatural formal language for describing viral infection models that will be easy to understand for biologists and easy to use by mathematicians and computer scientists. The ModeLang language was designed in cooperation with biologists and its computer implementation was prepared. Tests proved that it can be successfully used to describe commonly used viral infection models and then to simulate and verify them. As a result, it can make cooperation between biologists and mathematicians modeling viral infections much easier, speeding up computational verification of formulated hypotheses.

ModeLang: A New Approach for Experts-Friendly Viral Infections Modeling

PubMed Central

Blazewicz, Jacek

2013-01-01

Computational modeling is an important element of systems biology. One of its important applications is modeling complex, dynamical, and biological systems, including viral infections. This type of modeling usually requires close cooperation between biologists and mathematicians. However, such cooperation often faces communication problems because biologists do not have sufficient knowledge to understand mathematical description of the models, and mathematicians do not have sufficient knowledge to define and verify these models. In many areas of systems biology, this problem has already been solved; however, in some of these areas there are still certain problematic aspects. The goal of the presented research was to facilitate this cooperation by designing seminatural formal language for describing viral infection models that will be easy to understand for biologists and easy to use by mathematicians and computer scientists. The ModeLang language was designed in cooperation with biologists and its computer implementation was prepared. Tests proved that it can be successfully used to describe commonly used viral infection models and then to simulate and verify them. As a result, it can make cooperation between biologists and mathematicians modeling viral infections much easier, speeding up computational verification of formulated hypotheses. PMID:24454531

A Genome-Wide Identification of the WRKY Family Genes and a Survey of Potential WRKY Target Genes in Dendrobium officinale.

PubMed

He, Chunmei; Teixeira da Silva, Jaime A; Tan, Jianwen; Zhang, Jianxia; Pan, Xiaoping; Li, Mingzhi; Luo, Jianping; Duan, Jun

2017-08-23

The WRKY family, one of the largest families of transcription factors, plays important roles in the regulation of various biological processes, including growth, development and stress responses in plants. In the present study, 63 DoWRKY genes were identified from the Dendrobium officinale genome. These were classified into groups I, II, III and a non-group, each with 14, 28, 10 and 11 members, respectively. ABA-responsive, sulfur-responsive and low temperature-responsive elements were identified in the 1-k upstream regulatory region of DoWRKY genes. Subsequently, the expression of the 63 DoWRKY genes under cold stress was assessed, and the expression profiles of a large number of these genes were regulated by low temperature in roots and stems. To further understand the regulatory mechanism of DoWRKY genes in biological processes, potential WRKY target genes were investigated. Among them, most stress-related genes contained multiple W-box elements in their promoters. In addition, the genes involved in polysaccharide synthesis and hydrolysis contained W-box elements in their 1-k upstream regulatory regions, suggesting that DoWRKY genes may play a role in polysaccharide metabolism. These results provide a basis for investigating the function of WRKY genes and help to understand the downstream regulation network in plants within the Orchidaceae.

Electrochemical Biosensors - Sensor Principles and Architectures

PubMed Central

Grieshaber, Dorothee; MacKenzie, Robert; Vörös, Janos; Reimhult, Erik

2008-01-01

Quantification of biological or biochemical processes are of utmost importance for medical, biological and biotechnological applications. However, converting the biological information to an easily processed electronic signal is challenging due to the complexity of connecting an electronic device directly to a biological environment. Electrochemical biosensors provide an attractive means to analyze the content of a biological sample due to the direct conversion of a biological event to an electronic signal. Over the past decades several sensing concepts and related devices have been developed. In this review, the most common traditional techniques, such as cyclic voltammetry, chronoamperometry, chronopotentiometry, impedance spectroscopy, and various field-effect transistor based methods are presented along with selected promising novel approaches, such as nanowire or magnetic nanoparticle-based biosensing. Additional measurement techniques, which have been shown useful in combination with electrochemical detection, are also summarized, such as the electrochemical versions of surface plasmon resonance, optical waveguide lightmode spectroscopy, ellipsometry, quartz crystal microbalance, and scanning probe microscopy. The signal transduction and the general performance of electrochemical sensors are often determined by the surface architectures that connect the sensing element to the biological sample at the nanometer scale. The most common surface modification techniques, the various electrochemical transduction mechanisms, and the choice of the recognition receptor molecules all influence the ultimate sensitivity of the sensor. New nanotechnology-based approaches, such as the use of engineered ion-channels in lipid bilayers, the encapsulation of enzymes into vesicles, polymersomes, or polyelectrolyte capsules provide additional possibilities for signal amplification. In particular, this review highlights the importance of the precise control over the delicate interplay between surface nano-architectures, surface functionalization and the chosen sensor transducer principle, as well as the usefulness of complementary characterization tools to interpret and to optimize the sensor response. PMID:27879772

BFL: a node and edge betweenness based fast layout algorithm for large scale networks

PubMed Central

Hashimoto, Tatsunori B; Nagasaki, Masao; Kojima, Kaname; Miyano, Satoru

2009-01-01

Background Network visualization would serve as a useful first step for analysis. However, current graph layout algorithms for biological pathways are insensitive to biologically important information, e.g. subcellular localization, biological node and graph attributes, or/and not available for large scale networks, e.g. more than 10000 elements. Results To overcome these problems, we propose the use of a biologically important graph metric, betweenness, a measure of network flow. This metric is highly correlated with many biological phenomena such as lethality and clusters. We devise a new fast parallel algorithm calculating betweenness to minimize the preprocessing cost. Using this metric, we also invent a node and edge betweenness based fast layout algorithm (BFL). BFL places the high-betweenness nodes to optimal positions and allows the low-betweenness nodes to reach suboptimal positions. Furthermore, BFL reduces the runtime by combining a sequential insertion algorim with betweenness. For a graph with n nodes, this approach reduces the expected runtime of the algorithm to O(n2) when considering edge crossings, and to O(n log n) when considering only density and edge lengths. Conclusion Our BFL algorithm is compared against fast graph layout algorithms and approaches requiring intensive optimizations. For gene networks, we show that our algorithm is faster than all layout algorithms tested while providing readability on par with intensive optimization algorithms. We achieve a 1.4 second runtime for a graph with 4000 nodes and 12000 edges on a standard desktop computer. PMID:19146673

Junk DNA and the long non-coding RNA twist in cancer genetics

PubMed Central

Ling, Hui; Vincent, Kimberly; Pichler, Martin; Fodde, Riccardo; Berindan-Neagoe, Ioana; Slack, Frank J.; Calin, George A

2015-01-01

The central dogma of molecular biology states that the flow of genetic information moves from DNA to RNA to protein. However, in the last decade this dogma has been challenged by new findings on non-coding RNAs (ncRNAs) such as microRNAs (miRNAs). More recently, long non-coding RNAs (lncRNAs) have attracted much attention due to their large number and biological significance. Many lncRNAs have been identified as mapping to regulatory elements including gene promoters and enhancers, ultraconserved regions, and intergenic regions of protein-coding genes. Yet, the biological function and molecular mechanisms of lncRNA in human diseases in general and cancer in particular remain largely unknown. Data from the literature suggest that lncRNA, often via interaction with proteins, functions in specific genomic loci or use their own transcription loci for regulatory activity. In this review, we summarize recent findings supporting the importance of DNA loci in lncRNA function, and the underlying molecular mechanisms via cis or trans regulation, and discuss their implications in cancer. In addition, we use the 8q24 genomic locus, a region containing interactive SNPs, DNA regulatory elements and lncRNAs, as an example to illustrate how single nucleotide polymorphism (SNP) located within lncRNAs may be functionally associated with the individual’s susceptibility to cancer. PMID:25619839

Tracing Tellurium and Its Nanostructures in Biology.

PubMed

Zare, Bijan; Nami, Mohammad; Shahverdi, Ahmad-Reza

2017-12-01

Tellurium (Te) is a semimetal rare element in nature. Together with oxygen, sulfur (S), and selenium (Se), Te is considered a member of chalcogen group. Over recent decades, Te applications continued to emerge in different fields including metallurgy, glass industry, electronics, and applied chemical industries. Along these lines, Te has recently attracted research attention in various fields. Though Te exists in biologic organisms such as microbes, yeast, and human body, its importance and role and some of its potential implications have long been ignored. Some promising applications of Te using its inorganic and organic derivatives including novel Te nanostructures are being introduced. Before discovery and straightforward availability of antibiotics, Te had considered and had been used as an antibacterial element. Antilishmaniasis, antiinflammatory, antiatherosclerotic, and immuno-modulating properties of Te have been described for many years, while the innovative applications of Te have started to emerge along with nanotechnological advances over the recent years. Te quantum dots (QDs) and related nanostructures have proposed novel applications in the biological detection systems such as biosensors. In addition, Te nanostructures are used in labeling, imaging, and targeted drug delivery systems and are tested for antibacterial or antifungal properties. In addition, Te nanoparticles show novel lipid-lowering, antioxidant, and free radical scavenging properties. This review presents an overview on the novel forms of Te, their potential applications, as well as related toxicity profiles.

Functional and mechanistic diversity of distal transcription enhancers

PubMed Central

Bulger, Michael; Groudine, Mark

2013-01-01

Biological differences among metazoans, and between cell types in a given organism, arise in large part due to differences in gene expression patterns. The sequencing of multiple metazoan genomes, coupled with recent advances in genome-wide analysis of histone modifications and transcription factor binding, has revealed that among regulatory DNA sequences, gene-distal enhancers appear to exhibit the greatest diversity and cell-type specificity. Moreover, such elements are emerging as important targets for mutations that can give rise to disease and to genetic variability that underlies evolutionary change. Studies of long-range interactions between distal genomic sequences in the nucleus indicate that enhancers are often important determinants of nuclear organization, contributing to a general model for enhancer function that involves direct enhancer-promoter contact. In a number of systems, however, mechanisms for enhancer function are emerging that do not fit solely within such a model, suggesting that enhancers as a class of DNA regulatory element may be functionally and mechanistically diverse. PMID:21295696

Micro-PIXE investigation of bean seeds to assist micronutrient biofortification

NASA Astrophysics Data System (ADS)

Cvitanich, Cristina; Przybyłowicz, Wojciech J.; Mesjasz-Przybyłowicz, Jolanta; Blair, Matthew W.; Astudillo, Carolina; Orłowska, Elżbieta; Jurkiewicz, Anna M.; Jensen, Erik Ø.; Stougaard, Jens

2011-10-01

This study compares the distribution and concentrations of micro- and macronutrients in different bean cultivars with the aim of optimizing the biofortification, a sustainable approach towards improving dietary quality. Micro-PIXE was used to reveal the distribution of Fe, Zn, Mn, Ca, P, S in seeds of common beans (Phaseolus vulgaris) and runner beans (Phaseolus coccineus). Average concentrations of elements in different tissues were obtained using ICP-AES. The highest concentrations of Zn in the studied beans were found in the embryonic axis, but an increased concentration of this element was also detected in the provascular bundles of the cotyledons. The first layer of cells surrounding provascular bundles accumulated high concentrations of Fe, while the next cell layer had an increased concentration of Mn. The analysis showed that the provascular bundles and the first cell layers surrounding them could have a significant role in the storage of important seed micronutrients - Zn, Fe, and Mn. This information has important implications for molecular biology studies aimed at seed biofortification.

Elemental distribution in ascending aortic after radiotherapy and chemotherapy by Low Energy X-ray Fluorescence spectroscopy

NASA Astrophysics Data System (ADS)

Mantuano, A.; Mota, C. L.; Pickler, A.; Sena, G.; Braz, D.; Salata, C.; de Almeida, C. E.; Costa, F. N.; Barroso, R. C.

2018-05-01

Breast cancer (BC) is the most frequent cancer and the leading cause of cancer-related mortality in women. The treatment techniques for the BC include chemotherapy (CT) and/or radiotherapy (RT) and can modify elementary the cell matrix by calcificating tissues due to biological and morphological changes. Also, treatments for BC induce cardiotoxicity and it is important to understand the mechanisms involved in order to prevent this late effect in treated breast cancer patients. The high incidence of cardiovascular mortality in breast cancer patients is partially credited to increased intimal and medial calcifications of the aorta. The aim of this work is to investigate the distibution of low atomic number elements such as Magnesium (Mg), due to its importance for the cardiac metabolism; iron (Fe), since BC treatment may be associated with oxidative stress; and Sodium (Na), that is extremely related to the damage of endothelial cells. An optimal technique to observe these changes in aorta tissue is soft X-ray FLuorescence that can provide elemental maps of these important elements. The results performed by Low Energy X-ray Fluorescence LEXRF analyses showed that when the tissue is submitted to treatments with CT and/or RT, some normal structures become disorganized, and consequently the intensity of elemental compounds can be changed. All the experiments were carried out at the TwinMic beamline at Elettra Synchrotron facility using as animal model Wistar rats in order to evaluate the distribution of Na, Mg and Fe in aorta walls of Wistar rats, after BC treatment. Simultaneous acquisition of LEXRF and attenuation coefficient maps suggest that the combined chemotherapy and radiotherapy caused more damage to the aortic tissue as compared to radiation therapy alone. These findings add an in-depth understanding of elemental lack or excess in the tissue and contribute to locate these changes.

Bridging Food Webs, Ecosystem Metabolism, and Biogeochemistry Using Ecological Stoichiometry Theory.

PubMed

Welti, Nina; Striebel, Maren; Ulseth, Amber J; Cross, Wyatt F; DeVilbiss, Stephen; Glibert, Patricia M; Guo, Laodong; Hirst, Andrew G; Hood, Jim; Kominoski, John S; MacNeill, Keeley L; Mehring, Andrew S; Welter, Jill R; Hillebrand, Helmut

2017-01-01

Although aquatic ecologists and biogeochemists are well aware of the crucial importance of ecosystem functions, i.e., how biota drive biogeochemical processes and vice-versa, linking these fields in conceptual models is still uncommon. Attempts to explain the variability in elemental cycling consequently miss an important biological component and thereby impede a comprehensive understanding of the underlying processes governing energy and matter flow and transformation. The fate of multiple chemical elements in ecosystems is strongly linked by biotic demand and uptake; thus, considering elemental stoichiometry is important for both biogeochemical and ecological research. Nonetheless, assessments of ecological stoichiometry (ES) often focus on the elemental content of biota rather than taking a more holistic view by examining both elemental pools and fluxes (e.g., organismal stoichiometry and ecosystem process rates). ES theory holds the promise to be a unifying concept to link across hierarchical scales of patterns and processes in ecology, but this has not been fully achieved. Therefore, we propose connecting the expertise of aquatic ecologists and biogeochemists with ES theory as a common currency to connect food webs, ecosystem metabolism, and biogeochemistry, as they are inherently concatenated by the transfer of carbon, nitrogen, and phosphorous through biotic and abiotic nutrient transformation and fluxes. Several new studies exist that demonstrate the connections between food web ecology, biogeochemistry, and ecosystem metabolism. In addition to a general introduction into the topic, this paper presents examples of how these fields can be combined with a focus on ES. In this review, a series of concepts have guided the discussion: (1) changing biogeochemistry affects trophic interactions and ecosystem processes by altering the elemental ratios of key species and assemblages; (2) changing trophic dynamics influences the transformation and fluxes of matter across environmental boundaries; (3) changing ecosystem metabolism will alter the chemical diversity of the non-living environment. Finally, we propose that using ES to link nutrient cycling, trophic dynamics, and ecosystem metabolism would allow for a more holistic understanding of ecosystem functions in a changing environment.

The industrial melanism mutation in British peppered moths is a transposable element.

PubMed

Van't Hof, Arjen E; Campagne, Pascal; Rigden, Daniel J; Yung, Carl J; Lingley, Jessica; Quail, Michael A; Hall, Neil; Darby, Alistair C; Saccheri, Ilik J

2016-06-02

Discovering the mutational events that fuel adaptation to environmental change remains an important challenge for evolutionary biology. The classroom example of a visible evolutionary response is industrial melanism in the peppered moth (Biston betularia): the replacement, during the Industrial Revolution, of the common pale typica form by a previously unknown black (carbonaria) form, driven by the interaction between bird predation and coal pollution. The carbonaria locus has been coarsely localized to a 200-kilobase region, but the specific identity and nature of the sequence difference controlling the carbonaria-typica polymorphism, and the gene it influences, are unknown. Here we show that the mutation event giving rise to industrial melanism in Britain was the insertion of a large, tandemly repeated, transposable element into the first intron of the gene cortex. Statistical inference based on the distribution of recombined carbonaria haplotypes indicates that this transposition event occurred around 1819, consistent with the historical record. We have begun to dissect the mode of action of the carbonaria transposable element by showing that it increases the abundance of a cortex transcript, the protein product of which plays an important role in cell-cycle regulation, during early wing disc development. Our findings fill a substantial knowledge gap in the iconic example of microevolutionary change, adding a further layer of insight into the mechanism of adaptation in response to natural selection. The discovery that the mutation itself is a transposable element will stimulate further debate about the importance of 'jumping genes' as a source of major phenotypic novelty.

Identification & Characterization of Fungal Ice Nucleation Proteins

NASA Astrophysics Data System (ADS)

Scheel, Jan Frederik; Kunert, Anna Theresa; Kampf, Christopher Johannes; Mauri, Sergio; Weidner, Tobias; Pöschl, Ulrich; Fröhlich-Nowoisky, Janine

2016-04-01

Freezing of water at relatively warm subfreezing temperatures is dependent on ice nucleation catalysis facilitated by ice nuclei (IN). These IN can be of various origins and although extensive research was done and progress was achieved, the nature and mechanisms leading to an effective IN are to date still poorly understood. Some of the most important processes of our geosphere like the water cycle are highly dependent on effective ice nucleation at temperatures between -2°C - -8°C, a temperature range which is almost exclusively covered by biological IN (BioIN). BioIN are usually macromolecular structures of biological polymers. Sugars as well as proteins have been reported to serve as IN and the best characterized BioIN are ice nucleation proteins (IN-P) from gram negative bacteria. Fungal strains from Fusarium spp. were described to be effective IN at subfreezing temperatures up to -2°C already 25 years ago and more and more fungal species are described to serve as efficient IN. Fungal IN are also thought to be proteins or at least contain a proteinaceous compound, but to date the fungal IN-P primary structure as well as their coding genetic elements of all IN active fungi are unknown. The aim of this study is a.) to identify the proteins and their coding genetic elements from IN active fungi (F. acuminatum, F. avenaceum, M. alpina) and b.) to characterize the mechanisms by which fungal IN serve as effective IN. We designed an interdisciplinary approach using biological, analytical and physical methods to identify fungal IN-P and describe their biological, chemical, and physical properties.

Reading the tea leaves: Dead transposon copies reveal novel host and transposon biology.

PubMed

McLaughlin, Richard N

2018-03-01

Transposable elements comprise a huge portion of most animal genomes. Unlike many pathogens, these elements leave a mark of their impact via their insertion into host genomes. With proper teasing, these sequences can relay information about the evolutionary history of transposons and their hosts. In a new publication, Larson and colleagues describe a previously unappreciated density of long interspersed element-1 (LINE-1) sequences that have been spliced (LINE-1 and other reverse transcribing elements are necessarily intronless). They provide data to suggest that the retention of these potentially deleterious splice sites in LINE-1 results from the sites' overlap with an important transcription factor binding site. These spliced LINE-1s (i.e., spliced integrated retrotransposed elements [SpiREs]) lose their ability to replicate, suggesting they are evolutionary dead ends. However, the lethality of this splicing could be an efficient means of blocking continued replication of LINE-1. In this way, the record of inactive LINE-1 sequences in the human genome revealed a new, though infrequent, event in the LINE-1 replication cycle and motivates future studies to test whether splicing might be another weapon in the anti-LINE-1 arsenal of host genomes.

Vitamin D, Essential Minerals, and Toxic Elements: Exploring Interactions between Nutrients and Toxicants in Clinical Medicine

PubMed Central

Schwalfenberg, Gerry K.; Genuis, Stephen J.

2015-01-01

In clinical medicine, increasing attention is being directed towards the important areas of nutritional biochemistry and toxicant bioaccumulation as they relate to human health and chronic disease. Optimal nutritional status, including healthy levels of vitamin D and essential minerals, is requisite for proper physiological function; conversely, accrual of toxic elements has the potential to impair normal physiology. It is evident that vitamin D intake can facilitate the absorption and assimilation of essential inorganic elements (such as calcium, magnesium, copper, zinc, iron, and selenium) but also the uptake of toxic elements (such as lead, arsenic, aluminum, cobalt, and strontium). Furthermore, sufficiency of essential minerals appears to resist the uptake of toxic metals. This paper explores the literature to determine a suitable clinical approach with regard to vitamin D and essential mineral intake to achieve optimal biological function and to avoid harm in order to prevent and overcome illness. It appears preferable to secure essential mineral status in conjunction with adequate vitamin D, as intake of vitamin D in the absence of mineral sufficiency may result in facilitation of toxic element absorption with potential adverse clinical outcomes. PMID:26347061

Mass exchange in an experimental new-generation life support system model based on biological regeneration of environment.

PubMed

Tikhomirov, A A; Ushakova, S A; Manukovsky, N S; Lisovsky, G M; Kudenko, Yu A; Kovalev, V S; Gubanov, V G; Barkhatov, Yu V; Gribovskaya, I V; Zolotukhin, I G; Gros, J B; Lasseur, Ch

2003-01-01

An experimental model of a biological life support system was used to evaluate qualitative and quantitative parameters of the internal mass exchange. The photosynthesizing unit included the higher plant component (wheat and radish), and the heterotrophic unit consisted of a soil-like substrate, California worms, mushrooms and microbial microflora. The gas mass exchange involved evolution of oxygen by the photosynthesizing component and its uptake by the heterotroph component along with the formation and maintaining of the SLS structure, growth of mushrooms and California worms, human respiration, and some other processes. Human presence in the system in the form of "virtual human" that at regular intervals took part in the respirative gas exchange during the experiment. Experimental data demonstrated good oxygen/carbon dioxide balance, and the closure of the cycles of these gases was almost complete. The water cycle was nearly 100% closed. The main components in the water mass exchange were transpiration water and the watering solution with mineral elements. Human consumption of the edible plant biomass (grains and roots) was simulated by processing these products by a unique physicochemical method of oxidizing them to inorganic mineral compounds, which were then returned into the system and fully assimilated by the plants. The oxidation was achieved by "wet combustion" of organic biomass, using hydrogen peroxide following a special procedure, which does not require high temperature and pressure. Hydrogen peroxide is produced from the water inside the system. The closure of the cycle was estimated for individual elements and compounds. Stoichiometric proportions are given for the main components included in the experimental model of the system. Approaches to the mathematical modeling of the cycling processes are discussed, using the data of the experimental model. Nitrogen, as a representative of biogenic elements, shows an almost 100% closure of the cycle inside the system. The proposed experimental model of a biological system is discussed as a candidate for potential application in the investigations aimed at creating ecosystems with largely closed cycles of the internal mass exchange. The formation and maintenance of sustainable cycling of vitally important chemical elements and compounds in biological life support systems (BLSS) is an extremely pressing problem. To attain the stable functioning of biological life support systems (BLSS) and to maintain a high degree of closure of material cycles in than, it is essential to understand the character of mass exchange processes and stoichiometnc proportions of the initial and synthesized components of the system. c2003 COSPAR. Published by Elsevier Science Ltd. All rights reserved.

Periodic Table Target: A Game that Introduces the Biological Significance of Chemical Element Periodicity

ERIC Educational Resources Information Center

Sevcik, Richard S.; McGinty, Ragan L.; Schultz, Linda D.; Alexander, Susan V.

2008-01-01

Periodic Table Target, a game for middle school or high school students, familiarizes students with the form of the periodic table and the biological significance of different elements. The Periodic Table Target game board is constructed as a class project, and the game is played to reinforce the content. Students are assigned several elements…

Detection and quantification of proteins and cells by use of elemental mass spectrometry: progress and challenges.

PubMed

Yan, Xiaowen; Yang, Limin; Wang, Qiuquan

2013-07-01

Much progress has been made in identification of the proteins in proteomes, and quantification of these proteins has attracted much interest. In addition to popular tandem mass spectrometric methods based on soft ionization, inductively coupled plasma mass spectrometry (ICPMS), a typical example of mass spectrometry based on hard ionization, usually used for analysis of elements, has unique advantages in absolute quantification of proteins by determination of an element with a definite stoichiometry in a protein or attached to the protein. In this Trends article, we briefly describe state-of-the-art ICPMS-based methods for quantification of proteins, emphasizing protein-labeling and element-tagging strategies developed on the basis of chemically selective reactions and/or biospecific interactions. Recent progress from protein to cell quantification by use of ICPMS is also discussed, and the possibilities and challenges of ICPMS-based protein quantification for universal, selective, or targeted quantification of proteins and cells in a biological sample are also discussed critically. We believe ICPMS-based protein quantification will become ever more important in targeted quantitative proteomics and bioanalysis in the near future.

The fate of minor alkali elements in the chemical evolution of salt lakes

PubMed Central

2011-01-01

Alkaline earth elements and alkali metals (Mg, Ca, Na and K) play an important role in the geochemical evolution of saline lakes as the final brine type is defined by the abundance of these elements. The role of major ions in brine evolution has been studied in great detail, but little has been done to investigate the behaviour of minor alkali elements in these systems despite their similar chemical affinities to the major cations. We have examined three major anionic brine types, chloride, sulphate, and bicarbonate-carbonate, in fifteen lakes in North America and Antarctica to determine the geochemical behaviour of lithium, rubidium, strontium, and barium. Lithium and rubidium are largely conservative in all water types, and their concentrations are the result of long-term solute input and concentration through evaporation and/or sublimation. Strontium and barium behaviours vary with anionic brine type. Strontium can be removed in sulphate and carbonate-rich lakes by the precipitation of carbonate minerals. Barium may be removed in chloride and sulphate brines by either the precipitation of barite and perhaps biological uptake. PMID:21992434

Electron microprobe analysis program for biological specimens: BIOMAP

NASA Technical Reports Server (NTRS)

Edwards, B. F.

1972-01-01

BIOMAP is a Univac 1108 compatible program which facilitates the electron probe microanalysis of biological specimens. Input data are X-ray intensity data from biological samples, the X-ray intensity and composition data from a standard sample and the electron probe operating parameters. Outputs are estimates of the weight percentages of the analyzed elements, the distribution of these estimates for sets of red blood cells and the probabilities for correlation between elemental concentrations. An optional feature statistically estimates the X-ray intensity and residual background of a principal standard relative to a series of standards.

Biomolecular electrostatics and solvation: a computational perspective

PubMed Central

Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G.; Schnieders, Michael J.; Marucho, Marcelo; Zhang, Jiajing; Baker, Nathan A.

2012-01-01

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view towards describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g., solvent structure, polarization, ion binding, and nonpolar behavior) in order to provide a background to understand the different types of solvation models. PMID:23217364

Biomolecular electrostatics and solvation: a computational perspective.

PubMed

Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G; Schnieders, Michael J; Marucho, Marcelo; Zhang, Jiajing; Baker, Nathan A

2012-11-01

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.

SREBP-regulated lipid metabolism: convergent physiology - divergent pathophysiology.

PubMed

Shimano, Hitoshi; Sato, Ryuichiro

2017-12-01

Cellular lipid metabolism and homeostasis are controlled by sterol regulatory-element binding proteins (SREBPs). In addition to performing canonical functions in the transcriptional regulation of genes involved in the biosynthesis and uptake of lipids, genome-wide system analyses have revealed that these versatile transcription factors act as important nodes of convergence and divergence within biological signalling networks. Thus, they are involved in myriad physiological and pathophysiological processes, highlighting the importance of lipid metabolism in biology. Changes in cell metabolism and growth are reciprocally linked through SREBPs. Anabolic and growth signalling pathways branch off and connect to multiple steps of SREBP activation and form complex regulatory networks. In addition, SREBPs are implicated in numerous pathogenic processes such as endoplasmic reticulum stress, inflammation, autophagy and apoptosis, and in this way, they contribute to obesity, dyslipidaemia, diabetes mellitus, nonalcoholic fatty liver disease, nonalcoholic steatohepatitis, chronic kidney disease, neurodegenerative diseases and cancers. This Review aims to provide a comprehensive understanding of the role of SREBPs in physiology and pathophysiology at the cell, organ and organism levels.

Systems biology, adverse outcome pathways, and ecotoxicology in the 21st century

EPA Science Inventory

While many definitions of systems biology exist, the majority of these contain most (if not all) of the following elements: global measurements of biological molecules to the extent technically feasible, dynamic measurements of key biological molecules to establish quantitative r...

A Global Overview of Exposure Levels and Biological Effects of Trace Elements in Penguins.

PubMed

Espejo, Winfred; Celis, José E; GonzÃlez-Acuña, Daniel; Banegas, Andiranel; Barra, Ricardo; Chiang, Gustavo

2018-01-01

Trace elements are chemical contaminants that can be present almost anywhere on the planet. The study of trace elements in biotic matrices is a topic of great relevance for the implications that it can have on wildlife and human health. Penguins are very useful, since they live exclusively in the Southern Hemisphere and represent about 90% of the biomass of birds of the Southern Ocean. The levels of trace elements (dry weight) in different biotic matrices of penguins were reviewed here. Maps of trace element records in penguins were included. Data on exposure and effects of trace elements in penguins were collected from the literature. The most reported trace elements in penguins are aluminum, arsenic, cadmium, lead, mercury, copper, zinc, and manganese. Trace elements have been measured in 11 of the 18 species of penguins. The most studied biotic matrices are feathers and excreta. Most of the studies have been performed in Antarctica and subantarctic Islands. Little is known about the interaction among metals, which could provide better knowledge about certain mechanisms of detoxification in penguins. Future studies of trace elements in penguins must incorporate other metals such as vanadium, cobalt, nickel, and chromium. Data of metals in the species such as Eudyptes pachyrhynchus, Eudyptes moseleyi, Eudyptes sclateri, Eudyptes robustus, Eudyptes schlegeli, Spheniscus demersus, Spheniscus mendiculus, and Megadyptes antipodes are urged. It is important to correlate levels of metals in different biotic matrices with the effects on different species and in different geographic locations.

Elemental imaging at the nanoscale: NanoSIMS and complementary techniques for element localisation in plants.

PubMed

Moore, Katie L; Lombi, Enzo; Zhao, Fang-Jie; Grovenor, Chris R M

2012-04-01

The ability to locate and quantify elemental distributions in plants is crucial to understanding plant metabolisms, the mechanisms of uptake and transport of minerals and how plants cope with toxic elements or elemental deficiencies. High-resolution secondary ion mass spectrometry (SIMS) is emerging as an important technique for the analysis of biological material at the subcellular scale. This article reviews recent work using the CAMECA NanoSIMS to determine elemental distributions in plants. The NanoSIMS is able to map elemental distributions at high resolution, down to 50 nm, and can detect very low concentrations (milligrams per kilogram) for some elements. It is also capable of mapping almost all elements in the periodic table (from hydrogen to uranium) and can distinguish between stable isotopes, which allows the design of tracer experiments. In this review, particular focus is placed upon studying the same or similar specimens with both the NanoSIMS and a wide range of complementary techniques, showing how the advantages of each technique can be combined to provide a fuller data set to address complex scientific questions. Techniques covered include optical microscopy, synchrotron techniques, including X-ray fluorescence and X-ray absorption spectroscopy, transmission electron microscopy, electron probe microanalysis, particle-induced X-ray emission and inductively coupled plasma mass spectrometry. Some of the challenges associated with sample preparation of plant material for SIMS analysis, the artefacts and limitations of the technique and future trends are also discussed.

Mapping of native inorganic elements and injected nanoparticles in a biological organ with laser-induced plasma

NASA Astrophysics Data System (ADS)

Motto-Ros, V.; Sancey, L.; Ma, Q. L.; Lux, F.; Bai, X. S.; Wang, X. C.; Yu, Jin; Panczer, G.; Tillement, O.

2012-11-01

Emission spectroscopy of laser-induced plasma from a thin section of mouse kidney successfully detected inorganic elements, Na, Ca, Cu, and Gd, naturally contained in the organ or artificially injected in the form of Gd-based nanoparticle. A two-dimensional scan of the sample allowed the laser beam to explore its surface with a resolution of 100 μm, resulting in a quantitative elemental mapping of the organ with sub-mM sensitivity. The compatibility of the setup with standard optical microscopy emphasizes the potential to provide multiple images of a same biological tissue with different types of response which can be elemental, molecular, or cellular.

[Valorization of biological resources in tumour libraries].

PubMed

Keelaghan, Thérèse

2006-01-01

The transfer and commercialization of biological materials, whether in the form of tumour samples, tissue samples or chemicals, and of the data base pertaining to such material have become a subject of considerable importance for both the private and public sectors involved in medical research. In order to fully appreciate and apprehend the process for the protection and the valuation of the transferred material, intellectual property law must be taken into account. As a result, a distinction is made between the tangible and intangible elements of the biological material and of the attached data base, thus providing the transferring entity the possibility to claim property rights to future intellectual property arising from the research regarding the transferred material. The transfer of biological material and attached data base without such contractual provisions can lead to the loss of this potential value as well as of physical and legal control over the material transferred by the providing entity. The intentions and the assumptions of the parties must be negotiated and written into terms of contract, at the risk of losing future value due to unexpressed assumptions concerning intangible property rights.

Simulation of CNT-AFM tip based on finite element analysis for targeted probe of the biological cell

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yousefi, Amin Termeh, E-mail: at.tyousefi@gmail.com; Miyake, Mikio, E-mail: miyakejaist@gmail.com; Ikeda, Shoichiro, E-mail: sho16.ikeda@gmail.com

Carbon nanotubes (CNTs) are potentially ideal tips for atomic force microscopy (AFM) due to the robust mechanical properties, nano scale diameter and also their ability to be functionalized by chemical and biological components at the tip ends. This contribution develops the idea of using CNTs as an AFM tip in computational analysis of the biological cell’s. Finite element analysis employed for each section and displacement of the nodes located in the contact area was monitored by using an output database (ODB). This reliable integration of CNT-AFM tip process provides a new class of high performance nanoprobes for single biological cellmore » analysis.« less

Efficient finite element modeling of radiation forces on elastic particles of arbitrary size and geometry.

PubMed

Glynne-Jones, Peter; Mishra, Puja P; Boltryk, Rosemary J; Hill, Martyn

2013-04-01

A finite element based method is presented for calculating the acoustic radiation force on arbitrarily shaped elastic and fluid particles. Importantly for future applications, this development will permit the modeling of acoustic forces on complex structures such as biological cells, and the interactions between them and other bodies. The model is based on a non-viscous approximation, allowing the results from an efficient, numerical, linear scattering model to provide the basis for the second-order forces. Simulation times are of the order of a few seconds for an axi-symmetric structure. The model is verified against a range of existing analytical solutions (typical accuracy better than 0.1%), including those for cylinders, elastic spheres that are of significant size compared to the acoustic wavelength, and spheroidal particles.

Variable-Threshold Threshold Elements,

DTIC Science & Technology

A threshold element is a mathematical model of certain types of logic gates and of a biological neuron. Much work has been done on the subject of... threshold elements with fixed thresholds; this study concerns itself with elements in which the threshold may be varied, variable- threshold threshold ...elements. Physical realizations include resistor-transistor elements, in which the threshold is simply a voltage. Variation of the threshold causes the

[Important issues of biological safety].

PubMed

Onishchenko, G G

2007-01-01

The problem of biological security raises alarm due to the real growth of biological threats. Biological security includes a wide scope of problems, the solution of which becomes a part of national security as a necessary condition for the constant development of the country. A number of pathogens, such as human immunodeficiency virus, exotic Ebola and Lassa viruses causing hemorrhagic fever,rotaviruses causing acute intestinal diseases, etc. were first discovered in the last century. Terrorist actions committed in the USA in 2001 using the anthrax pathogen made the problem of biological danger even more important. In Russian Federation, biological threats are counteracted through the united state policy being a part of general state security policy. The biological Security legislation of Russian Federation is chiefly based on the 1992 Federal Law on Security. On the basis of cumulated experience, the President of Russia ratified Basics of Russian Federation's State Policy for Chemical and Biological Security for the Period through 2010 and Beyond on 4 December, 2003. The document determines the main directions and stages of the state development in the area of chemical and biological security. The Federal target program Russian Federation's National Program for Chemical and Biological Security is being developed, and its development is to be completed soon in order to perfect the national system for biological security and fulfill Basics of Russian Federation's State Policy for Chemical and Biological Security for the Period through 2010 and Beyond, ratified by the President. The new global strategy for control over infectious diseases, presented in the materials of Saint Petersburg summit of the Group of Eight, as well as the substantive part of its elements in Sanitary International Standards, are to a large degree an acknowledgement of the Russian Federation's experience and the algorithm for fighting extremely dangerous infections. This Russia's experience has resulted in the following global achievements: smallpox elimination in the USSR (1936); the USSR's suggestions on the program of smallpox elimination in the world and 2 billion doses of the vaccine transferred to the possession of the WHO (since 1958); the global elimination of the disease (1980); effective control over avian influenza at the epizootic stage, recognized internationally at Beijing International Congress, 17-18 January, 2006.

Seawater as the source of minor elements in black shales, phosphorites and other sedimentary rocks

USGS Publications Warehouse

Piper, D.Z.

1994-01-01

Many of the minor elements in seawater today have a concentration-depth profile similar to that of the biologically essential nutrients, NO-3 and PO3-4. They show a relative depletion in the photic zone and enrichment in the deep ocean. The difference between their surface- and deep-ocean values, normalized to the change in PO3-4, approaches the average of measured minor-element: P ratios in marine plankton, although individual analyses of the latter show extreme scatter for a variety of reasons. Despite this scatter in the minor-element analyses of plankton, agreement between the two sets of data shows unequivocally that an important marine flux of many minor elements through the ocean is in the form of biogenic matter, with a composition approaching that of plankton. This interpretation is further supported by sediment studies, particularly of sediments which accumulate in shelf-slope environments where biological productivity in the photic zone is exceptionally high and organic carbon contents of the underlying sediment elevated. The interelement relations observed for some of these sediments approach the average values of plankton. These same interelement relations are observed in many marine sedimentary rocks such as metalliferous black shales and phosphorites, rocks which have a high content of marine fractions (e.g., organic matter, apatite, biogenic silica and carbonates). Many previous studies of the geochemistry of these rocks have concluded that local hydrothermal activity, and/or seawater with an elemental content different from that of the modern ocean, was required to account for their minor-element contents. However, the similarity in several of the minor-element ratios in many of these formations to minor-element ratios in modern plankton demonstrates that these sedimentary rocks accumulated in environments whose marine chemistry was virtually identical to that seen on continental shelf-slopes, or in marginal seas, of the ocean today. The accumulation of the marine fraction of minor elements on these ancient sea floors was determined largely by the accumulation of organic matter, settling from the photic zone and with a composition of average plankton. A second marine fraction of minor elements in these rocks accumulated through precipitation and adsorption from seawater. The suite of elements in this fraction reflects redox conditions in the bottom water, as determined by bacterial respiration. For example, high Mn, high Cr+V and high Mo concentrations, above those which can be attributed to the accumulation of planktonic matter, characterize accumulation under bottom-water oxidizing, denitrifying and sulfate-reducing conditions, respectively. ?? 1994.

Force-controlled manipulation of single cells: from AFM to FluidFM.

PubMed

Guillaume-Gentil, Orane; Potthoff, Eva; Ossola, Dario; Franz, Clemens M; Zambelli, Tomaso; Vorholt, Julia A

2014-07-01

The ability to perturb individual cells and to obtain information at the single-cell level is of central importance for addressing numerous biological questions. Atomic force microscopy (AFM) offers great potential for this prospering field. Traditionally used as an imaging tool, more recent developments have extended the variety of cell-manipulation protocols. Fluidic force microscopy (FluidFM) combines AFM with microfluidics via microchanneled cantilevers with nano-sized apertures. The crucial element of the technology is the connection of the hollow cantilevers to a pressure controller, allowing their operation in liquid as force-controlled nanopipettes under optical control. Proof-of-concept studies demonstrated a broad spectrum of single-cell applications including isolation, deposition, adhesion and injection in a range of biological systems. Copyright © 2014 Elsevier Ltd. All rights reserved.

Top-down causation by information control: from a philosophical problem to a scientific research programme

PubMed Central

Auletta, G; Ellis, G.F.R; Jaeger, L

2008-01-01

It has been claimed that different types of causes must be considered in biological systems, including top-down as well as same-level and bottom-up causation, thus enabling the top levels to be causally efficacious in their own right. To clarify this issue, the important distinctions between information and signs are introduced here and the concepts of information control and functional equivalence classes in those systems are rigorously defined and used to characterize when top-down causation by feedback control happens, in a way that is testable. The causally significant elements we consider are equivalence classes of lower level processes, realized in biological systems through different operations having the same outcome within the context of information control and networks. PMID:18319208

Ecology, Ecosystem Management and Biology Teaching. Biology and Human Welfare.

ERIC Educational Resources Information Center

Spellerberg, Ian F.; Pritchard, Alan J.

This six-chapter document (part of a series on biology and human welfare) focuses on ecology, ecosystem management, and biology teaching. Chapter 1 discusses the basic elements of ecology (considering organisms and their environment, populations, and communities and ecosystems). Chapter 2 describes several aspects of human ecology and resources…

Responses of infaunal populations to benthoscape structure and the potential importance of transition zones

USGS Publications Warehouse

Zajac, R.N.; Lewis, R.S.; Poppe, L.J.; Twichell, D.C.; Vozarik, J.; DiGiacomo-Cohen, M. L.

2003-01-01

Relationships between population abundance and seafloor landscape, or benthoscape, structure were examined for 16 infaunal taxa in eastern Long Island Sound. Based on analyses of a side-scan sonar mosaic, the 19.4-km2 study area was comprised of six distinct large-scale (> km2) benthoscape elements, with varying levels of mesoscale (km2-m2) and small-scale (2) physical and biological habitat heterogeneity. Transition zones among elements varied from ~50 to 200 m in width, comprised ~32% of the benthoscape, and added to overall benthoscape heterogeneity. Population abundances of nine taxa varied significantly among the large-scale elements. Most species were found at high abundances only in one benthoscape element, but three had several foci of elevated abundances. Analyses of population responses to habitat heterogeneity at different spatial scales indicated that abundances of eight taxa varied significantly among spatial scales, but the significant scales were mixed among these species. Relatively large residual variations suggest significant amounts of mesoscale spatial variation were unaccounted for, varying from ~1 km2 to several m2. Responses to transition zones were mixed as well. Abundances of nine taxa varied significantly among transition zones and interiors of benthoscape elements, most with elevated abundances in transition zones. Our results show that infaunal populations exhibit complex and spatially varying patterns of abundance in relation to benthoscape structure and suggest that mesoscale variation may be particularly critical in this regard. Also, transition zones among benthoscape features add considerably to this variation and may be ecological important areas in seafloor environments.

Shedding light into the function of the earliest vertebrate skeleton

NASA Astrophysics Data System (ADS)

Martinez-Perez, Carlos; Purnell, Mark; Rayfield, Emily; Donoghue, Philip

2016-04-01

Conodonts are an extinct group of jawless vertebrates, the first in our evolutionary lineage to develop a biomineralized skeleton. As such, the conodont skeleton is of great significance because of the insights it provides concerning the biology and function of the primitive vertebrate skeleton. Conodont function has been debated for a century and a half on the basis of its paleocological importance in the Palaezoic ecosystems. However, due to the lack of extanct close representatives and the small size of the conodont element (under a milimiter in length) strongly limited their functional analysis, traditional restricted to analogy. More recently, qualitative approaches have been developed, facilitating tests of element function based on occlusal performance and analysis of microwear and microstructure. In this work we extend these approaches using novel quantitative experimental methods including Synchrotron Radiation X-ray Tomographic Microscopy or Finite Element Analysis to test hypotheses of conodont function. The development of high resolution virtual models of conodont elements, together with biomechanical approaches using Finite Element analysis, informed by occlusal and microwear analyses, provided conclusive support to test hypothesis of structural adaptation within the crown tissue microstructure, showing a close topological co-variation patterns of compressive and tensile stress distribution with different crystallite orientation. In addition, our computational analyses strongly support a tooth-like function for many conodont species. Above all, our study establishes a framework (experimental approach) in which the functional ecology of conodonts can be read from their rich taxonomy and phylogeny, representing an important attempt to understand the role of this abundant and diverse clade in the Phanerozoic marine ecosystems.

Adaptation, allometry, and hypertension.

PubMed

Weder, A B; Schork, N J

1994-08-01

Essential hypertension is a "disease of civilization" but has a clear genetic component. From an evolutionary perspective, persistence in the human genome of elements capable of raising blood pressure presupposes their adaptive significance. Recently, two hypotheses that explicitly appeal to selectionist arguments, the "slavery" and "thrifty gene" theories, have been forwarded. We find neither completely successful, and we advance an alternative explanation of the adaptive importance of genes responsible for hypertension. We propose that blood pressure rises during childhood and adolescence to subserve homeostatic needs of the organism. Specifically, we contend that blood pressure is a flexible element in the repertoire of renal homeostatic mechanisms serving to match renal function to growth. The effect of modern diet and lifestyle on human growth stimulates earlier and more vigorous development, straining biologically necessary relationships between renal and general somatic growth and requiring compensation via homeostatic mechanisms preserved during evolution. Prime among such mechanisms is blood pressure, which rises as a compensation to maintain renal function in the face of greater growth. Since virtually all members of acculturated societies share in the modern lifestyle, the demands imposed by accelerated growth and development result in a populational shift to higher blood pressures, with a consequent increase in the prevalence of hypertension. We propose that hypertension is the product of maladaptation of highly genetically conserved mechanisms subserving important biological homeostatic needs. Elucidation of the mechanisms underlying hypertension will require approaches that examine the developmental processes linking growth to blood pressure.

Toward mapping the biology of the genome.

PubMed

Chanock, Stephen

2012-09-01

This issue of Genome Research presents new results, methods, and tools from The ENCODE Project (ENCyclopedia of DNA Elements), which collectively represents an important step in moving beyond a parts list of the genome and promises to shape the future of genomic research. This collection sheds light on basic biological questions and frames the current debate over the optimization of tools and methodological challenges necessary to compare and interpret large complex data sets focused on how the genome is organized and regulated. In a number of instances, the authors have highlighted the strengths and limitations of current computational and technical approaches, providing the community with useful standards, which should stimulate development of new tools. In many ways, these papers will ripple through the scientific community, as those in pursuit of understanding the "regulatory genome" will heavily traverse the maps and tools. Similarly, the work should have a substantive impact on how genetic variation contributes to specific diseases and traits by providing a compendium of functional elements for follow-up study. The success of these papers should not only be measured by the scope of the scientific insights and tools but also by their ability to attract new talent to mine existing and future data.

Feasibility of an integrated X-ray instrument for Mars exobiology and geology. [Abstract only

NASA Technical Reports Server (NTRS)

Fonda, M. L.; Schwartz, D. E.; Koppel, L. N.; Franco, E. D.; Kerner, J. A.

1994-01-01

By employing an integrated X-ray instrument on a future Mars mission, data obtained will greatly augment those returned by Viking; details relevant to the possibility of the origin and evolution of life on Mars will be acquired. An integrated combined X Ray Fluorescence/X Ray Detection (XRF/XRD) instrument has been breadboarded and demonstrated to accommodate important exobiology and geology experiment objectives outlined for Mars Environmental Survey (MESUR) and future Mars missions. Among others, primary objectives for the exploration of Mars include: the intense study of local areas on Mars to 'establish the chemical, mineralogical, and petrological character of different components of the surface material; to determine the distribution, abundance and sources and sinks of volatile materials, including an assessment of the biologic potential, now and during past epochs; and to establish the global chemical and physical characteristics of the Martian surface'. The XRF/XRD breadboard instrument identifies and quantifies soil surface elemental, mineralogical, and petrological characteristics and acquires data necessary to address questions on volatile abundance and distribution. Additionally, the breadboard is able to characterize the biogenic element constituents of soil samples providing information on the biologic potential of the Mars environment.

Nanobiotechnology with S-layer proteins as building blocks.

PubMed

Sleytr, Uwe B; Schuster, Bernhard; Egelseer, Eva M; Pum, Dietmar; Horejs, Christine M; Tscheliessnig, Rupert; Ilk, Nicola

2011-01-01

One of the key challenges in nanobiotechnology is the utilization of self- assembly systems, wherein molecules spontaneously associate into reproducible aggregates and supramolecular structures. In this contribution, we describe the basic principles of crystalline bacterial surface layers (S-layers) and their use as patterning elements. The broad application potential of S-layers in nanobiotechnology is based on the specific intrinsic features of the monomolecular arrays composed of identical protein or glycoprotein subunits. Most important, physicochemical properties and functional groups on the protein lattice are arranged in well-defined positions and orientations. Many applications of S-layers depend on the capability of isolated subunits to recrystallize into monomolecular arrays in suspension or on suitable surfaces (e.g., polymers, metals, silicon wafers) or interfaces (e.g., lipid films, liposomes, emulsomes). S-layers also represent a unique structural basis and patterning element for generating more complex supramolecular structures involving all major classes of biological molecules (e.g., proteins, lipids, glycans, nucleic acids, or combinations of these). Thus, S-layers fulfill key requirements as building blocks for the production of new supramolecular materials and nanoscale devices as required in molecular nanotechnology, nanobiotechnology, biomimetics, and synthetic biology. Copyright © 2011 Elsevier Inc. All rights reserved.

Biological cell classification by multiangle light scattering

DOEpatents

Salzman, G.C.; Crowell, J.M.; Mullaney, P.F.

1975-06-03

The specification is directed to an apparatus and method for detecting light scattering from a biological cell. Light, preferably from a coherent source of radiation, intercepts an individual biological cell in a stream of cells passing through the beam. Light scattered from the cell is detected at a selected number of angles between 0 and 90/sup 0/ to the longitudinal axis of the beam with a circular array of light responsive elements which produce signals representative of the intensity of light incident thereon. Signals from the elements are processed to determine the light-scattering pattern of the cell and therefrom its identity.

Distribution and Phase Association of Some Major and Trace Elements in the Arabian Gulf Sediments

NASA Astrophysics Data System (ADS)

Basaham, A. S.; El-Sayed, M. A.

1998-02-01

Twenty-four sediment samples were collected from the Arabian Gulf (ROPME Sea) and analysed for their grain size distribution and carbonate contents as well as the major elements Ca, Mg, Fe and Al and macro and trace elements Mn, Sr, Ba, Zn, Cu, Cr, V, Ni and Hg. Concentration of trace elements are found comparable to previous data published for samples taken before and after the Gulf War, and reflect the natural background level. Grain size analyses, aluminium and carbonate measurements support the presence of two major sediment types: (1) a terrigenous, fine-grained and Al rich type predominating along the Iranian side; and (2) a coarse-grained and carbonate rich type predominating along the Arabian side of the Gulf. Investigation of the correlation of the elements analysed with the sediment type indicates that they could be grouped under two distinct associations: (1) carbonate association including Ca and Sr; and (2) terrigenous association comprising Al, Fe, Mg, Ba, Mn, Zn, Cu, Cr, V, Ni and Hg. Element/Al ratios calculated for the mud non-carbonate fraction indicate that the Euphrates and Tigris rivers have minor importance as sediment sources to the Gulf. Most of the elements have exceptionally high aluminium ratios in sediments containing more than 85-90% carbonate. These sediments are restricted to the southern and south-eastern part of the area where depth is shallow and temperature and salinity are high. Both biological accumulation and chemical and biochemical coprecipitation could be responsible for this anomaly.

Elemental Education.

ERIC Educational Resources Information Center

Daniel, Esther Gnanamalar Sarojini; Saat, Rohaida Mohd.

2001-01-01

Introduces a learning module integrating three disciplines--physics, chemistry, and biology--and based on four elements: carbon, oxygen, hydrogen, and silicon. Includes atomic model and silicon-based life activities. (YDS)

Repetitive element transcripts are elevated in the brain of C9orf72 ALS/FTLD patients.

PubMed

Prudencio, Mercedes; Gonzales, Patrick K; Cook, Casey N; Gendron, Tania F; Daughrity, Lillian M; Song, Yuping; Ebbert, Mark T W; van Blitterswijk, Marka; Zhang, Yong-Jie; Jansen-West, Karen; Baker, Matthew C; DeTure, Michael; Rademakers, Rosa; Boylan, Kevin B; Dickson, Dennis W; Petrucelli, Leonard; Link, Christopher D

2017-09-01

Significant transcriptome alterations are detected in the brain of patients with amyotrophic lateral sclerosis (ALS), including carriers of the C9orf72 repeat expansion and C9orf72-negative sporadic cases. Recently, the expression of repetitive element transcripts has been associated with toxicity and, while increased repetitive element expression has been observed in several neurodegenerative diseases, little is known about their contribution to ALS. To assess whether aberrant expression of repetitive element sequences are observed in ALS, we analysed RNA sequencing data from C9orf72-positive and sporadic ALS cases, as well as healthy controls. Transcripts from multiple classes and subclasses of repetitive elements (LINEs, endogenous retroviruses, DNA transposons, simple repeats, etc.) were significantly increased in the frontal cortex of C9orf72 ALS patients. A large collection of patient samples, representing both C9orf72 positive and negative ALS, ALS/FTLD, and FTLD cases, was used to validate the levels of several repetitive element transcripts. These analyses confirmed that repetitive element expression was significantly increased in C9orf72-positive compared to C9orf72-negative or control cases. While previous studies suggest an important link between TDP-43 and repetitive element biology, our data indicate that TDP-43 pathology alone is insufficient to account for the observed changes in repetitive elements in ALS/FTLD. Instead, we found that repetitive element expression positively correlated with RNA polymerase II activity in postmortem brain, and pharmacologic modulation of RNA polymerase II activity altered repetitive element expression in vitro. We conclude that increased RNA polymerase II activity in ALS/FTLD may lead to increased repetitive element transcript expression, a novel pathological feature of ALS/FTLD. © The Author 2017. Published by Oxford University Press.

What is microbial community ecology?

PubMed

Konopka, Allan

2009-11-01

The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered as a community property.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Konopka, Allan

The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbesmore » possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered a community property.« less

The Mediator Complex and Lipid Metabolism.

PubMed

Zhang, Yi; Xiaoli; Zhao, Xiaoping; Yang, Fajun

2013-03-01

The precise control of gene expression is essential for all biological processes. In addition to DNA-binding transcription factors, numerous transcription cofactors contribute another layer of regulation of gene transcription in eukaryotic cells. One of such transcription cofactors is the highly conserved Mediator complex, which has multiple subunits and is involved in various biological processes through directly interacting with relevant transcription factors. Although the current understanding on the biological functions of Mediator remains incomplete, research in the past decade has revealed an important role of Mediator in regulating lipid metabolism. Such function of Mediator is dependent on specific transcription factors, including peroxisome proliferator-activated receptor-gamma (PPARγ) and sterol regulatory element-binding proteins (SREBPs), which represent the master regulators of lipid metabolism. The medical significance of these findings is apparent, as aberrant lipid metabolism is intimately linked to major human diseases, such as type 2 diabetes and cardiovascular disease. Here, we briefly review the functions and molecular mechanisms of Mediator in regulation of lipid metabolism.

A Biobehavioral Model of Cancer Stress and Disease Course

PubMed Central

Andersen, Barbara L.; Kiecolt-Glaser, Janice K.; Glaser, Ronald

2009-01-01

Approximately 1 million Americans are diagnosed with cancer each year and must cope with the disease and treatments. Many studies have documented the deteriorations in quality of life that occur. These data suggest that the adjustment process is burdensome and lengthy. There is ample evidence showing that adults experiencing other long-term stressors experience not only high rates of adjustment difficulties (e.g., syndromal depression) but important biologic effects, such as persistent downregulation of elements of the immune system, and adverse health outcomes, such as higher rates of respiratory tract infections. Thus, deteriorations in quality of life with cancer are underscored if they have implications for biological processes, such as the immune system, relating to disease progression and spread. Considering these and other data, a biobehavioral model of adjustment to the stresses of cancer is offered, and mechanisms by which psychological and behavioral responses may influence biological processes and, perhaps, health outcomes are proposed. Finally, strategies for testing the model via experiments testing psychological interventions are offered. PMID:8024167

Deciphering the relationship among phosphate dynamics, electron-dense body and lipid accumulation in the green alga Parachlorella kessleri

PubMed Central

Ota, Shuhei; Yoshihara, Mai; Yamazaki, Tomokazu; Takeshita, Tsuyoshi; Hirata, Aiko; Konomi, Mami; Oshima, Kenshiro; Hattori, Masahira; Bišová, Kateřina; Zachleder, Vilém; Kawano, Shigeyuki

2016-01-01

Phosphorus is an essential element for life on earth and is also important for modern agriculture, which is dependent on inorganic fertilizers from phosphate rock. Polyphosphate is a biological polymer of phosphate residues, which is accumulated in organisms during the biological wastewater treatment process to enhance biological phosphorus removal. Here, we investigated the relationship between polyphosphate accumulation and electron-dense bodies in the green alga Parachlorella kessleri. Under sulfur-depleted conditions, in which some symporter genes were upregulated, while others were downregulated, total phosphate accumulation increased in the early stage of culture compared to that under sulfur-replete conditions. The P signal was detected only in dense bodies by energy dispersive X-ray analysis. Transmission electron microscopy revealed marked ultrastructural variations in dense bodies with and without polyphosphate. Our findings suggest that the dense body is a site of polyphosphate accumulation, and P. kessleri has potential as a phosphate-accumulating organism. PMID:27180903

Charge-transfer interaction of drug quinidine with quinol, picric acid and DDQ: Spectroscopic characterization and biological activity studies towards understanding the drug-receptor mechanism.

PubMed

Eldaroti, Hala H; Gadir, Suad A; Refat, Moamen S; Adam, Abdel Majid A

2014-04-01

Investigation of charge-transfer (CT) complexes of drugs has been recognized as an important phenomenon in understanding of the drug-receptor binding mechanism. Structural, thermal, morphological and biological behavior of CT complexes formed between drug quinidine (Qui) as a donor and quinol (QL), picric acid (PA) or dichlorodicyanobenzoquinone (DDQ) as acceptors were reported. The newly synthesized CT complexes have been spectroscopically characterized via elemental analysis; infrared (IR), Raman, 1 H NMR and electronic absorption spectroscopy; powder X-ray diffraction (PXRD); thermogravimetric (TG) analysis and scanning electron microscopy (SEM). It was found that the obtained complexes are nanoscale, semi-crystalline particles, thermally stable and spontaneous. The molecular composition of the obtained complexes was determined using spectrophotometric titration method and was found to be 1:1 ratios (donor:acceptor). Finally, the biological activities of the obtained CT complexes were tested for their antibacterial activities. The results obtained herein are satisfactory for estimation of drug Qui in the pharmaceutical form.

Moving beyond the van Krevelen Diagram: A New Stoichiometric Approach for Compound Classification in Organisms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rivas-Ubach, Albert; Liu, Yina; Bianchi, Thomas S.

van Krevelen diagrams (O:C vs H:C ratios of elemental formulas) have been widely used in studies to obtain an estimation of the main compound categories present in environmental samples. However, the limits defining a specific compound category based solely on O:C and H:C ratios of elemental formulas have never been accurately listed or proposed to classify metabolites in biological samples. Furthermore, while O:C vs. H:C ratios of elemental formulas can provide an overview of the compound categories, such classification is inefficient because of the large overlap among different compound categories along both axes. We propose a more accurate compound classificationmore » for biological samples analyzed by high-resolution mass spectrometry-based on an assessment of the C:H:O:N:P stoichiometric ratios of over 130,000 elemental formulas of compounds classified in 6 main categories: lipids, peptides, amino-sugars, carbohydrates, nucleotides and phytochemical compounds (oxy-aromatic compounds). Our multidimensional stoichiometric compound classification (MSCC) constraints showed a highly accurate categorization of elemental formulas to the main compound categories in biological samples with over 98% of accuracy representing a substantial improvement over any classification based on the classic van Krevelen diagram. This method represents a significant step forward in environmental research, especially ecological stoichiometry and eco-metabolomics studies, by providing a novel and robust tool to further our understanding the ecosystem structure and function through the chemical characterization of different biological samples.« less

Water-quality, bed-sediment, and biological data (October 1993 through September 1994) and statistical summaries of data for streams in the Upper Clark Fork basin, Montana

USGS Publications Warehouse

Lambing, J.H.; Hornberger, Michelle I.; Axtmann, E.V.; Dodge, K.A.

1995-01-01

Water, bed sediment, and biota were sampled in streams from Butte to below Missoula as part of a program to characterize aquatic resources in the upper Clark Fork basin of western Montana. Water- quality data were obtained periodically at 16 stations during October 1993 through September 1994 (water year 1994); daily suspended-sediment data were obtained at six of these stations. Bed-sediment and biological data were obtained at 11 stations in August 1994. Sampling stations were located on the Clark Fork and major tributaries. The primary constituents analyzed were trace elements associated with mine tailings from historical mining and smelting activities. Water-quality data include concentrations of major ions, trace elements, and suspended sediment in samples collected periodically during water year 1994. Daily values of streamflow, suspended-sediment concentration, and suspended- sediment discharge are given for six stations. Bed- sediment data include trace-element concentrations in the fine and bulk fractions. Biological data include trace-element concentrations in whole-body tissue of aquatic benthic insects. Quality-assurance data are reported for analytical results of water, bed sediment, and biota. Statistical summaries of bed sediment, and biological data are provided for the period of record at each station since 1985.

Application of an ecosystem model to evaluate the importance of different processes and food web structure for transfer of 13 elements in a shallow lake.

PubMed

Konovalenko, L; Bradshaw, C; Andersson, E; Kautsky, U

2017-04-01

In environmental risk assessments of nuclear waste, there is need to estimate the potential risks of a large number of radionuclides over a long time period during which the environment is likely to change. Usually concentration ratios (CRs) are used to calculate the activity concentrations in organisms. However, CRs are not available for all radionuclides and they are not easily scalable to the varying environment. Here, an ecosystem transport model of elements, which estimates concentrations in organisms using carbon flows and food transfer instead of CR is presented. It is a stochastic compartment model developed for Lake Eckarfjärden at Forsmark in Sweden. The model was based on available data on carbon circulation, physical and biological processes from the site and identifies 11 functional groups of organisms. The ecosystem model was used to estimate the environmental transfer of 13 elements (Al, Ca, Cd, Cl, Cs, I, Ni, Nb, Pb, Se, Sr, Th, U) to various aquatic organisms, using element-specific distribution coefficients for suspended particles (K d PM ) and upper sediment (K d sed ), and subsequent transfer in the foodweb. The modelled CRs for different organism groups were compared with measured CRs from the lake and literature data, and showed good agreement for many elements and organisms, particularly for lower trophic levels. The model is, therefore, proposed as an alternative to measured CR, though it is suggested to further explore active uptake, assimilation and elimination processes to get better correspondence for some of the elements. The benthic organisms (i.e. bacteria, microphytobenthos and macroalgae) were identified as more important than pelagic organisms for transfer of elements to top predators. The element transfer model revealed that most of the radionuclides were channelled through the microbial loop, despite the fact that macroalgae dominated the carbon fluxes in this lake. Thus, element-specific adsorption of elements to the surface of aquatic species, that may be food sources for organisms at higher trophic levels, needs to be considered in combination with generic processes described by carbon fluxes. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Symposium: The Role of Biological Sciences in the Optometric Curriculum.

ERIC Educational Resources Information Center

And Others; Rapp, Jerry

1980-01-01

Papers from a symposium probing some of the curricular elements of the program in biological sciences at a school or college of optometry are provided. The overall program sequence in the biological sciences, microbiology, pharmacology, and the curriculum in the biological sciences from a clinical perspective are discussed. (Author/MLW)

Trace element bias in the use of CO2 vents as analogues for low pH environments: Implications for contamination levels in acidified oceans

NASA Astrophysics Data System (ADS)

Vizzini, S.; Di Leonardo, R.; Costa, V.; Tramati, C. D.; Luzzu, F.; Mazzola, A.

2013-12-01

Research into the effects of ocean acidification on marine ecosystems has increasingly focused on natural CO2 vents, although their intrinsic environmental complexity means observations from these areas may not relate exclusively to pH gradients. In order to assess trace element levels and distribution in the Levante Bay (Vulcano Island, NE Sicily, Italy) and its suitability for studying biological effects of pH decline, Ba, Fe and trace elements (As, Cd, Co, Cr, Cu, Hg, Mn, Mo, Ni, Pb, V and Zn) in sediment were analysed from 7 transects. Where present, Cymodocea nodosa leaves and epiphytes were also analysed. At the spatial scale of the bay, trace element concentrations in sediments and biota showed wide variability, possibly related to both input from fluid emissions and seawater physico-chemical variables (i.e. pH and Eh), which may considerably affect the solubility and bioavailability of potentially harmful trace elements. According to two pollution indices (MSPI: Marine Sediment Pollution Index and SQG-Q: Sediment Quality Guideline Quotient), the bay can be considered to be affected by low contamination with moderate potential for adverse biological effects, especially in the area between about 150 and 350 m from the primary vent, where localized detrimental effects on biota may occur. Generally, biological samples showed concentrations that were comparable with the lower values of seagrass ranges. The overall results of this study support the complex spatial dynamics of trace elements in the CO2 vent studied, which are constrained by both direct input from the vent and/or biogeochemical processes affecting element precipitation at the sediment-seawater interface. Consequently, great caution should be used when relating biological changes along pH gradients to the unifactorial effect of pH only, as interactions with concurrent, multiple stressors, including trace element enrichments, may occur. This finding has implications for the use of CO2 vents as analogues in ocean acidification research. They should be considered more appropriately as analogues for low pH environments with non-negligible trace element contamination which, in a scenario of continuous increase in anthropogenic pollution, may be very common.

Hydrothermal impacts on trace element and isotope ocean biogeochemistry.

PubMed

German, C R; Casciotti, K A; Dutay, J-C; Heimbürger, L E; Jenkins, W J; Measures, C I; Mills, R A; Obata, H; Schlitzer, R; Tagliabue, A; Turner, D R; Whitby, H

2016-11-28

Hydrothermal activity occurs in all ocean basins, releasing high concentrations of key trace elements and isotopes (TEIs) into the oceans. Importantly, the calculated rate of entrainment of the entire ocean volume through turbulently mixing buoyant hydrothermal plumes is so vigorous as to be comparable to that of deep-ocean thermohaline circulation. Consequently, biogeochemical processes active within deep-ocean hydrothermal plumes have long been known to have the potential to impact global-scale biogeochemical cycles. More recently, new results from GEOTRACES have revealed that plumes rich in dissolved Fe, an important micronutrient that is limiting to productivity in some areas, are widespread above mid-ocean ridges and extend out into the deep-ocean interior. While Fe is only one element among the full suite of TEIs of interest to GEOTRACES, these preliminary results are important because they illustrate how inputs from seafloor venting might impact the global biogeochemical budgets of many other TEIs. To determine the global impact of seafloor venting, however, requires two key questions to be addressed: (i) What processes are active close to vent sites that regulate the initial high-temperature hydrothermal fluxes for the full suite of TEIs that are dispersed through non-buoyant hydrothermal plumes? (ii) How do those processes vary, globally, in response to changing geologic settings at the seafloor and/or the geochemistry of the overlying ocean water? In this paper, we review key findings from recent work in this realm, highlight a series of key hypotheses arising from that research and propose a series of new GEOTRACES modelling, section and process studies that could be implemented, nationally and internationally, to address these issues.This article is part of the themed issue 'Biological and climatic impacts of ocean trace element chemistry'. © 2015 The Authors.

Hydrothermal impacts on trace element and isotope ocean biogeochemistry

PubMed Central

Dutay, J.-C.; Heimbürger, L. E.; Jenkins, W. J.; Measures, C. I.; Mills, R. A.; Obata, H.; Turner, D. R.; Whitby, H.

2016-01-01

Hydrothermal activity occurs in all ocean basins, releasing high concentrations of key trace elements and isotopes (TEIs) into the oceans. Importantly, the calculated rate of entrainment of the entire ocean volume through turbulently mixing buoyant hydrothermal plumes is so vigorous as to be comparable to that of deep-ocean thermohaline circulation. Consequently, biogeochemical processes active within deep-ocean hydrothermal plumes have long been known to have the potential to impact global-scale biogeochemical cycles. More recently, new results from GEOTRACES have revealed that plumes rich in dissolved Fe, an important micronutrient that is limiting to productivity in some areas, are widespread above mid-ocean ridges and extend out into the deep-ocean interior. While Fe is only one element among the full suite of TEIs of interest to GEOTRACES, these preliminary results are important because they illustrate how inputs from seafloor venting might impact the global biogeochemical budgets of many other TEIs. To determine the global impact of seafloor venting, however, requires two key questions to be addressed: (i) What processes are active close to vent sites that regulate the initial high-temperature hydrothermal fluxes for the full suite of TEIs that are dispersed through non-buoyant hydrothermal plumes? (ii) How do those processes vary, globally, in response to changing geologic settings at the seafloor and/or the geochemistry of the overlying ocean water? In this paper, we review key findings from recent work in this realm, highlight a series of key hypotheses arising from that research and propose a series of new GEOTRACES modelling, section and process studies that could be implemented, nationally and internationally, to address these issues. This article is part of the themed issue ‘Biological and climatic impacts of ocean trace element chemistry’. PMID:29035265

Deciphering the Complex Chemistry of Deep-Ocean Particles Using Complementary Synchrotron X-ray Microscope and Microprobe Instruments.

PubMed

Toner, Brandy M; German, Christopher R; Dick, Gregory J; Breier, John A

2016-01-19

The reactivity and mobility of natural particles in aquatic systems have wide ranging implications for the functioning of Earth surface systems. Particles in the ocean are biologically and chemically reactive, mobile, and complex in composition. The chemical composition of marine particles is thought to be central to understanding processes that convert globally relevant elements, such as C and Fe, among forms with varying bioavailability and mobility in the ocean. The analytical tools needed to measure the complex chemistry of natural particles are the subject of this Account. We describe how a suite of complementary synchrotron radiation instruments with nano- and micrometer focusing, and X-ray absorption spectroscopy (XAS) and X-ray diffraction (XRD) capabilities are changing our understanding of deep-ocean chemistry and life. Submarine venting along mid-ocean ridges creates hydrothermal plumes where dynamic particle-forming reactions occur as vent fluids mix with deep-ocean waters. Whether plumes are net sources or sinks of elements in ocean budgets depends in large part on particle formation, reactivity, and transport properties. Hydrothermal plume particles have been shown to host microbial communities and exhibit complex size distributions, aggregation behavior, and composition. X-ray microscope and microprobe instruments can address particle size and aggregation, but their true strength is in measuring chemical composition. Plume particles comprise a stunning array of inorganic and organic phases, from single-crystal sulfides to poorly ordered nanophases and polymeric organic matrices to microbial cells. X-ray microscopes and X-ray microprobes with elemental imaging, XAS, and XRD capabilities are ideal for investigating these complex materials because they can (1) measure the chemistry of organic and inorganic constituents in complex matrices, usually within the same particle or aggregate, (2) provide strong signal-to-noise data with exceedingly small amounts of material, (3) simplify the chemical complexity of particles or sets of particles with a focused-beam, providing spatial resolution over 6 orders of magnitude (nanometer to millimeter), (4) provide elemental specificity for elements in the soft-, tender-, and hard-X-ray energies, (5) switch rapidly among elements of interest, and (6) function in the presence of water and gases. Synchrotron derived data sets are discussed in the context of important advances in deep-ocean technology, sample handling and preservation, molecular microbiology, and coupled physical-chemical-biological modeling. Particle chemistry, size, and morphology are all important in determining whether particles are reactive with dissolved constituents, provide substrates for microbial respiration and growth, and are delivered to marine sediments or dispersed by deep-ocean currents.

The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery.

PubMed

Papaleo, Elena; Saladino, Giorgio; Lambrughi, Matteo; Lindorff-Larsen, Kresten; Gervasio, Francesco Luigi; Nussinov, Ruth

2016-06-08

Proteins are dynamic entities that undergo a plethora of conformational changes that may take place on a wide range of time scales. These changes can be as small as the rotation of one or a few side-chain dihedral angles or involve concerted motions in larger portions of the three-dimensional structure; both kinds of motions can be important for biological function and allostery. It is becoming increasingly evident that "connector regions" are important components of the dynamic personality of protein structures. These regions may be either disordered loops, i.e., poorly structured regions connecting secondary structural elements, or linkers that connect entire protein domains. Experimental and computational studies have, however, revealed that these regions are not mere connectors, and their role in allostery and conformational changes has been emerging in the last few decades. Here we provide a detailed overview of the structural properties and classification of loops and linkers, as well as a discussion of the main computational methods employed to investigate their function and dynamical properties. We also describe their importance for protein dynamics and allostery using as examples key proteins in cellular biology and human diseases such as kinases, ubiquitinating enzymes, and transcription factors.

[Network structures in biological systems].

PubMed

Oleskin, A V

2013-01-01

Network structures (networks) that have been extensively studied in the humanities are characterized by cohesion, a lack of a central control unit, and predominantly fractal properties. They are contrasted with structures that contain a single centre (hierarchies) as well as with those whose elements predominantly compete with one another (market-type structures). As far as biological systems are concerned, their network structures can be subdivided into a number of types involving different organizational mechanisms. Network organization is characteristic of various structural levels of biological systems ranging from single cells to integrated societies. These networks can be classified into two main subgroups: (i) flat (leaderless) network structures typical of systems that are composed of uniform elements and represent modular organisms or at least possess manifest integral properties and (ii) three-dimensional, partly hierarchical structures characterized by significant individual and/or intergroup (intercaste) differences between their elements. All network structures include an element that performs structural, protective, and communication-promoting functions. By analogy to cell structures, this element is denoted as the matrix of a network structure. The matrix includes a material and an immaterial component. The material component comprises various structures that belong to the whole structure and not to any of its elements per se. The immaterial (ideal) component of the matrix includes social norms and rules regulating network elements' behavior. These behavioral rules can be described in terms of algorithms. Algorithmization enables modeling the behavior of various network structures, particularly of neuron networks and their artificial analogs.

Growth responses of five desert plants as influenced by biological soil crusts from a temperate desert, China

USGS Publications Warehouse

Zhang, Yuanming; Belnap, Jayne

2015-01-01

In almost all dryland systems, biological soil crusts (biocrusts) coexist alongside herbaceous and woody vegetation, creating landscape mosaics of vegetated and biocrusted patches. Results from past studies on the interaction between biocrusts and vascular plants have been contradictory. In the Gurbantunggut desert, a large temperate desert in northwestern China, well-developed lichen-dominated crusts dominate the areas at the base and between the sand dunes. We examined the influence of these lichen-dominated biocrusts on the germination, growth, biomass accumulation, and elemental content of five common plants in this desert: two shrubs (Haloxylon persicum, Ephedra distachya) and three herbaceous plants (Ceratocarpus arenarius, Malcolmia africana and Lappula semiglabra) under greenhouse conditions. The influence of biocrusts on seed germination was species-specific. Biocrusts did not affect percent germination in plants with smooth seeds, but inhibited germination of seeds with appendages that reduced or eliminated contact with the soil surface or prevented seeds from slipping into soil cracks. Once seeds had germinated, biocrusts had different influences on growth of shrub and herbaceous plants. The presence of biocrusts increased concentrations of nitrogen but did not affect phosphorus or potassium in tissue of all tested species, while the uptake of the other tested nutrients was species-specific. Our study showed that biocrusts can serve as a biological filter during seed germination and also can influence growth and elemental uptake. Therefore, they may be an important trigger for determining desert plant diversity and community composition in deserts.

Selenite modulates the level of phenolics and nutrient element to alleviate the toxicity of arsenite in rice (Oryza sativa L.).

PubMed

Chauhan, Reshu; Awasthi, Surabhi; Tripathi, Preeti; Mishra, Seema; Dwivedi, Sanjay; Niranjan, Abhishek; Mallick, Shekhar; Tripathi, Pratibha; Pande, Veena; Tripathi, Rudra Deo

2017-04-01

Arsenic (As) contamination of paddy rice is a serious threat all over the world particularly in South East Asia. Selenium (Se) plays important role in protection of plants against various abiotic stresses including heavy metals. Moreover, arsenite (AsIII) and selenite (SeIV) can be biologically antagonistic due to similar electronic configuration and sharing the common transporter for their uptake in plant. In the present study, the response of oxidative stress, phenolic compounds and nutrient elements was analyzed to investigate Se mediated As tolerance in rice seedlings during AsIII and SeIV exposure in hydroponics. Selenite (25µM) significantly decreased As accumulation in plant than As (25µM) alone treated plants. Level of oxidative stress related parameters viz., reactive oxygen species (ROS), lipid peroxidation, electrical conductivity, nitric oxide and pro-oxidant enzyme (NADPH oxidase), were in the order of As>As+Se>control>Se. Selenium ameliorated As phytotoxicity by increased level of phenolic compounds particularly gallic acid, protocatechuic acid, ferulic acid and rutin and thiol metabolism related enzymes viz., serine acetyl transferase (SAT) and cysteine synthase (CS). Selenium supplementation enhanced the uptake of nutrient elements viz., Fe, Mn, Co, Cu, Zn, Mo, and improved plant growth. The results concluded that Se addition in As contaminated environment might be an important strategy to reduce As uptake and associated phytotoxicity in rice plant by modulation of phenolic compounds and increased uptake of nutrient elements. Copyright © 2016 Elsevier Inc. All rights reserved.

Genome Scale Modeling in Systems Biology: Algorithms and Resources

PubMed Central

Najafi, Ali; Bidkhori, Gholamreza; Bozorgmehr, Joseph H.; Koch, Ina; Masoudi-Nejad, Ali

2014-01-01

In recent years, in silico studies and trial simulations have complemented experimental procedures. A model is a description of a system, and a system is any collection of interrelated objects; an object, moreover, is some elemental unit upon which observations can be made but whose internal structure either does not exist or is ignored. Therefore, any network analysis approach is critical for successful quantitative modeling of biological systems. This review highlights some of most popular and important modeling algorithms, tools, and emerging standards for representing, simulating and analyzing cellular networks in five sections. Also, we try to show these concepts by means of simple example and proper images and graphs. Overall, systems biology aims for a holistic description and understanding of biological processes by an integration of analytical experimental approaches along with synthetic computational models. In fact, biological networks have been developed as a platform for integrating information from high to low-throughput experiments for the analysis of biological systems. We provide an overview of all processes used in modeling and simulating biological networks in such a way that they can become easily understandable for researchers with both biological and mathematical backgrounds. Consequently, given the complexity of generated experimental data and cellular networks, it is no surprise that researchers have turned to computer simulation and the development of more theory-based approaches to augment and assist in the development of a fully quantitative understanding of cellular dynamics. PMID:24822031

New Developments in Hard X-ray Fluorescence Microscopy for In-situ Investigations of Trace Element Distributions in Aqueous Systems of Soil Colloids

NASA Astrophysics Data System (ADS)

Gleber, Sophie-Charlotte; Weinhausen, Britta; Köster, Sarah; Ward, Jesse; Vine, David; Finney, Lydia; Vogt, Stefan

2013-10-01

The distribution, binding and release of trace elements on soil colloids determine matter transport through the soil matrix, and necessitates an aqueous environment and short length and time scales for their study. However, not many microscopy techniques allow for that. We previously showed hard x-ray fluorescence microscopy capabilities to image aqueous colloidal soil samples [1]. As this technique provides attogram sensitivity for transition elements like Cu, Zn, and other geochemically relevant trace elements at sub micrometer spatial resolution (currently down to 150 nm at 2-ID-E [2]; below 50nm at Bionanoprobe, cf. G.Woloschak et al, this volume) combined with the capability to penetrate tens of micrometer of water, it is ideally suited for imaging the elemental content of soil colloids. To address the question of binding and release processes of trace elements on the surface of soil colloids, we developed a microfluidics based XRF flow cytometer, and expanded the applied methods of hard x-ray fluorescence microscopy towards three dimensional imaging. Here, we show (a) the 2-D imaged distributions of Si, K and Fe on soil colloids of Pseudogley samples; (b) how the trace element distribution is a dynamic, pH-dependent process; and (c) x-ray tomographic applications to render the trace elemental distributions in 3-D. We conclude that the approach presented here shows the remarkable potential to image and quantitate elemental distributions from samles within their natural aqueous microenvironment, particularly important in the environmental, medical, and biological sciences.

Metal accumulation screening of the Río Tinto flora (Huelva, Spain).

PubMed

de la Fuente, Vicenta; Rufo, Lourdes; Rodríguez, Nuria; Amils, Ricardo; Zuluaga, Javier

2010-06-01

Río Tinto (Huelva, Spain) is located in one of the most important mining regions in the world. Its soils are characterized by their extreme acidity and elevated concentrations of heavy metals. Due to these characteristics, the Tinto ecosystem is considered unique and an ideal location to study biological adaptations to this type of habitat. Plant species that present these adaptations might be useful to mining and other metal pollution restoration programs. This study reports the results for the screening of Ca, Mg, Na, Mn, Fe, Ni, Cu, Zn, As, and Pb in aerial tissues of 97 plant species from the Tinto basin flora. In addition, plant-soil relationships were analyzed using the biological absorption coefficient (BAC) to detect the main plant adaptations in the Tinto flora. The species selected are representative of the biomass of the main dominant edaphophile and climatophile vegetation communities of the three river sections, forest, and subseral stages. Plant and soil elemental analyses were performed using inductively coupled plasma-mass spectrometry technique (ICP-MS). The results indicate that in general, Tinto flora shows a pattern of accumulation of the analyzed elements in aerial tissues which agrees with the nutritional requirements of vascular plants (macronutrients > micronutrients > indifferent or toxic elements). Among macronutrients, Ca seems to be an essential element in this habitat. This element accumulates in the aerial plant tissues. Basically, the Río Tinto flora is made of Fe, Cu, Zn, Ni, As, and Pb excluders, although some analyzed species of Erica, Quercus, Lavandula, Cistus, Genista, and Cytisus genera can be considered Mn accumulators. The results of this study make up a body of fundamental knowledge of the strategies used by plants to thrive in habitats with high concentrations of toxic heavy metals. This information is vital when it comes to planning a restoration program. Plants must be selected and used according to the requirements, always respecting the characteristics of the territory and facilitating the development of suitable vegetation.

Monolithically Integrated, Mechanically Resilient Carbon-Based Probes for Scanning Probe Microscopy

NASA Technical Reports Server (NTRS)

Kaul, Anupama B.; Megerian, Krikor G.; Jennings, Andrew T.; Greer, Julia R.

2010-01-01

Scanning probe microscopy (SPM) is an important tool for performing measurements at the nanoscale in imaging bacteria or proteins in biology, as well as in the electronics industry. An essential element of SPM is a sharp, stable tip that possesses a small radius of curvature to enhance spatial resolution. Existing techniques for forming such tips are not ideal. High-aspect-ratio, monolithically integrated, as-grown carbon nanofibers (CNFs) have been formed that show promise for SPM applications by overcoming the limitations present in wet chemical and separate substrate etching processes.

LA-iMageS: a software for elemental distribution bioimaging using LA-ICP-MS data.

PubMed

López-Fernández, Hugo; de S Pessôa, Gustavo; Arruda, Marco A Z; Capelo-Martínez, José L; Fdez-Riverola, Florentino; Glez-Peña, Daniel; Reboiro-Jato, Miguel

2016-01-01

The spatial distribution of chemical elements in different types of samples is an important field in several research areas such as biology, paleontology or biomedicine, among others. Elemental distribution imaging by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is an effective technique for qualitative and quantitative imaging due to its high spatial resolution and sensitivity. By applying this technique, vast amounts of raw data are generated to obtain high-quality images, essentially making the use of specific LA-ICP-MS imaging software that can process such data absolutely mandatory. Since existing solutions are usually commercial or hard-to-use for average users, this work introduces LA-iMageS, an open-source, free-to-use multiplatform application for fast and automatic generation of high-quality elemental distribution bioimages from LA-ICP-MS data in the PerkinElmer Elan XL format, whose results can be directly exported to external applications for further analysis. A key strength of LA-iMageS is its substantial added value for users, with particular regard to the customization of the elemental distribution bioimages, which allows, among other features, the ability to change color maps, increase image resolution or toggle between 2D and 3D visualizations.

Evidence for contrasting accumulation pattern of cadmium in relation to other elements in Senilia senilis and Tagelus adansoni from the Bijagós archipelago, Guinea-Bissau.

PubMed

Catry, Teresa; Figueira, Paula; Carvalho, Lina; Monteiro, Rui; Coelho, Pedro; Lourenço, Pedro Miguel; Catry, Paulo; Tchantchalam, Quintino; Catry, Inês; Botelho, Maria J; Pereira, Eduarda; Granadeiro, José Pedro; Vale, Carlos

2017-11-01

Shellfish harvesting in intertidal areas is a widespread and economically important activity in many countries across West Africa. However, in some areas, there is virtually no information concerning the levels of contaminants (and other elements related to nutritional aspects) in the harvested species. We collected sediments and several individuals of the West African bloody cockle Senilia senilis and of the razor clam Tagelus adansoni during the dry season of 2015 nearby three islands in the Bijagós archipelago, Guinea-Bissau. Aluminium, Ca, Fe, Mg, As, Cd, Co, Cr, Cu, Mn, Ni, Pb and Zn were determined in sediments and whole soft tissues of the two bivalves. Sediments showed uniformly low trace element concentrations, pointing to an ecosystem with low levels of trace element contamination. T. adansoni presented higher concentrations of most elements than S. senilis, with the exception of Cd that showed up to 40 times higher values in S. senilis than in T. adansoni from the same sites. Furthermore, Cd concentrations (25±8.7 mg kg -1 , dw) in S. senilis are clearly above the maximum level established for human consumption. Future studies should clarify whether biological factors are the major responsible for this unusual situation.

Quantitative analysis of biomedical samples using synchrotron radiation microbeams

NASA Astrophysics Data System (ADS)

Ektessabi, Ali; Shikine, Shunsuke; Yoshida, Sohei

2001-07-01

X-ray fluorescence (XRF) using a synchrotron radiation (SR) microbeam was applied to investigate distributions and concentrations of elements in single neurons of patients with neurodegenerative diseases. In this paper we introduce a computer code that has been developed to quantify the trace elements and matrix elements at the single cell level. This computer code has been used in studies of several important neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD) and parkinsonism-dementia complex (PDC), as well as in basic biological experiments to determine the elemental changes in cells due to incorporation of foreign metal elements. The substantial nigra (SN) tissue obtained from the autopsy specimens of patients with Guamanian parkinsonism-dementia complex (PDC) and control cases were examined. Quantitative XRF analysis showed that neuromelanin granules of Parkinsonian SN contained higher levels of Fe than those of the control. The concentrations were in the ranges of 2300-3100 ppm and 2000-2400 ppm respectively. On the contrary, Zn and Ni in neuromelanin granules of SN tissue from the PDC case were lower than those of the control. Especially Zn was less than 40 ppm in SN tissue from the PDC case while it was 560-810 ppm in the control. These changes are considered to be closely related to the neuro-degeneration and cell death.

Water-quality, bed-sediment, and biological data (October 2012 through September 2013) and statistical summaries of data for streams in the Clark Fork Basin, Montana

USGS Publications Warehouse

Dodge, Kent A.; Hornberger, Michelle I.; Dyke, Jessica

2014-01-01

This report presents the analytical results and quality-assurance data for water-quality, bed-sediment, and biota samples collected at sites from October 2012 through September 2013. Water-quality data include concentrations of selected major ions, trace elements, and suspended sediment. Turbidity and dissolved organic carbon were analyzed for water samples collected at the four sites where seasonal daily values of turbidity were being determined. Daily values of mean suspended-sediment concentration and suspended-sediment discharge were determined for four sites. Bed-sediment data include trace-element concentrations in the fine-grained fraction. Biological data include trace-element concentrations in whole-body tissue of aquatic benthic insects. Statistical sum-maries of water-quality, bed-sediment, and biological data for sites in the upper Clark Fork Basin are provided for the period of record.

Speciation in Metal Toxicity and Metal-Based Therapeutics

PubMed Central

Templeton, Douglas M.

2015-01-01

Metallic elements, ions and compounds produce varying degrees of toxicity in organisms with which they come into contact. Metal speciation is critical to understanding these adverse effects; the adjectives “heavy” and “toxic” are not helpful in describing the biological properties of individual elements, but detailed chemical structures are. As a broad generalization, the metallic form of an element is inert, and the ionic salts are the species that show more significant bioavailability. Yet the salts and other chelates of a metal ion can give rise to quite different toxicities, as exemplified by a range of carcinogenic potential for various nickel species. Another important distinction comes when a metallic element is organified, increasing its lipophilicity and hence its ability to penetrate the blood brain barrier, as is seen, for example, with organic mercury and tin species. Some metallic elements, such as gold and platinum, are themselves useful therapeutic agents in some forms, while other species of the same element can be toxic, thus focusing attention on species interconversions in evaluating metal-based drugs. The therapeutic use of metal-chelating agents introduces new species of the target metal in vivo, and this can affect not only its desired detoxification, but also introduce a potential for further mechanisms of toxicity. Examples of therapeutic iron chelator species are discussed in this context, as well as the more recent aspects of development of chelation therapy for uranium exposure. PMID:29056656

The Moon: Biogenic elements

NASA Technical Reports Server (NTRS)

Gibson, Everett K., Jr.; Chang, Sherwood

1992-01-01

The specific objectives of the organic chemical exploration of the Moon involve the search for molecules of possible biological or prebiological origin. Detailed knowledge of the amount, distribution, and exact structure of organic compounds present on the Moon is extremely important to our understanding of the origin and history of the Moon and to its relationship to the history of the Earth and solar system. Specifically, such knowledge is essential for determining whether life on the Moon exists, ever did exist, or could develop. In the absence of life or organic matter, it is still essential to determine the abundance, distribution, and origin of the biogenic elements (e.g., H, C, O, N, S, P) in order to understand how the planetary environment may have influenced the course of chemical evolution. The history and scope of this effort is presented.

Participation of Xenopus Elr-type Proteins in Vegetal mRNA Localization during Oogenesis*

PubMed Central

Arthur, Patrick K.; Claussen, Maike; Koch, Susanne; Tarbashevich, Katsiaryna; Jahn, Olaf; Pieler, Tomas

2009-01-01

Directional transport of specific mRNAs is of primary biological relevance. In Xenopus oocytes, mRNA localization to the vegetal pole is important for germ layer formation and germ cell development. Using a biochemical approach, we identified Xenopus Elr-type proteins, homologs of the Hu/ELAV proteins, as novel components of the vegetal mRNA localization machinery. They bind specifically to the localization elements of several different vegetally localizing Xenopus mRNAs, and they are part of one RNP together with other localization proteins, such as Vg1RBP and XStaufen 1. Blocking Elr-type protein binding by either localization element mutagenesis or antisense morpholino oligonucleotide-mediated masking of their target RNA structures, as well as overexpression of wild type and mutant ElrB proteins, interferes with vegetal localization in Xenopus oocytes. PMID:19458392

Design principles for elementary gene circuits: Elements, methods, and examples

NASA Astrophysics Data System (ADS)

Savageau, Michael A.

2001-03-01

The control of gene expression involves complex circuits that exhibit enormous variation in design. For years the most convenient explanation for these variations was historical accident. According to this view, evolution is a haphazard process in which many different designs are generated by chance; there are many ways to accomplish the same thing, and so no further meaning can be attached to such different but equivalent designs. In recent years a more satisfying explanation based on design principles has been found for at least certain aspects of gene circuitry. By design principle we mean a rule that characterizes some biological feature exhibited by a class of systems such that discovery of the rule allows one not only to understand known instances but also to predict new instances within the class. The central importance of gene regulation in modern molecular biology provides strong motivation to search for more of these underlying design principles. The search is in its infancy and there are undoubtedly many design principles that remain to be discovered. The focus of this three-part review will be the class of elementary gene circuits in bacteria. The first part reviews several elements of design that enter into the characterization of elementary gene circuits in prokaryotic organisms. Each of these elements exhibits a variety of realizations whose meaning is generally unclear. The second part reviews mathematical methods used to represent, analyze, and compare alternative designs. Emphasis is placed on particular methods that have been used successfully to identify design principles for elementary gene circuits. The third part reviews four design principles that make specific predictions regarding (1) two alternative modes of gene control, (2) three patterns of coupling gene expression in elementary circuits, (3) two types of switches in inducible gene circuits, and (4) the realizability of alternative gene circuits and their response to phased environmental cues. In each case, the predictions are supported by experimental evidence. These results are important for understanding the function, design, and evolution of elementary gene circuits.

Simultaneously Synchrotron X-ray Fluorescence and Ptychographic Imaging of Frozen Biological Single Cells

DOE PAGES

Chen, S.; Deng, J.; Nashed, Y. S. G.; ...

2016-07-25

Bionanoprobe (BNP), a hard x-ray fluorescence sample-scanning nanoprobe at the Advanced Photon Source of Argonne National Laboratory, has been used to quantitatively study elemental distributions in biological cells with sub-100 nm spatial resolution and high sensitivity. Cryogenic conditions enable biological samples to be studied in their frozen-hydrated state with both ultrastructure and elemental distributions more faithfully preserved compared to conventional chemical fixation or dehydration methods. Furthermore, radiation damage is reduced in two ways: the diffusion rate of free radicals is decreased at low temperatures; and the sample is embedded in vitrified ice, which reduces mass loss.

Genomic identification of regulatory elements by evolutionary sequence comparison and functional analysis.

PubMed

Loots, Gabriela G

2008-01-01

Despite remarkable recent advances in genomics that have enabled us to identify most of the genes in the human genome, comparable efforts to define transcriptional cis-regulatory elements that control gene expression are lagging behind. The difficulty of this task stems from two equally important problems: our knowledge of how regulatory elements are encoded in genomes remains elementary, and there is a vast genomic search space for regulatory elements, since most of mammalian genomes are noncoding. Comparative genomic approaches are having a remarkable impact on the study of transcriptional regulation in eukaryotes and currently represent the most efficient and reliable methods of predicting noncoding sequences likely to control the patterns of gene expression. By subjecting eukaryotic genomic sequences to computational comparisons and subsequent experimentation, we are inching our way toward a more comprehensive catalog of common regulatory motifs that lie behind fundamental biological processes. We are still far from comprehending how the transcriptional regulatory code is encrypted in the human genome and providing an initial global view of regulatory gene networks, but collectively, the continued development of comparative and experimental approaches will rapidly expand our knowledge of the transcriptional regulome.

Disorders of metal metabolism

PubMed Central

Ferreira, Carlos R.; Gahl, William A.

2017-01-01

Trace elements are chemical elements needed in minute amounts for normal physiology. Some of the physiologically relevant trace elements include iodine, copper, iron, manganese, zinc, selenium, cobalt and molybdenum. Of these, some are metals, and in particular, transition metals. The different electron shells of an atom carry different energy levels, with those closest to the nucleus being lowest in energy. The number of electrons in the outermost shell determines the reactivity of such an atom. The electron shells are divided in sub-shells, and in particular the third shell has s, p and d sub-shells. Transition metals are strictly defined as elements whose atom has an incomplete d sub-shell. This incomplete d sub-shell makes them prone to chemical reactions, particularly redox reactions. Transition metals of biologic importance include copper, iron, manganese, cobalt and molybdenum. Zinc is not a transition metal, since it has a complete d sub-shell. Selenium, on the other hand, is strictly speaking a nonmetal, although given its chemical properties between those of metals and nonmetals, it is sometimes considered a metalloid. In this review, we summarize the current knowledge on the inborn errors of metal and metalloid metabolism. PMID:29354481

Emergy of the Global Biogeochemical Cycles of Biologically Active Elements

EPA Science Inventory

Accurate estimates of the emergy of elemental flows are needed to accurately evaluate the far field effects of anthropogenic wastes. The transformity and specific emergy of the elements and of their different chemical species is also needed to quantify the inputs to many producti...

Skin melanocytes: biology and development

PubMed Central

Wachulska, Małgorzata; Stasiewicz, Aneta; Tymińska, Agata

2013-01-01

In the human skin, melanocytes are present in the epidermis and hair follicles. The basic features of these cells are the ability to melanin production and the origin from neural crest cells. This last element is important because there are other cells able to produce melanin but of different embryonic origin (pigmented epithelium of retina, some neurons, adipocytes). The life cycle of melanocyte consists of several steps including differentiation of melanocyte lineage/s from neural crest, migration and proliferation of melanoblasts, differentiation of melanoblasts into melanocytes, proliferation and maturation of melanocytes at the target places (activity of melanogenic enzymes, melanosome formation and transport to keratinocytes) and eventual cell death (hair melanocytes). Melanocytes of the epidermis and hair are cells sharing some common features but in general they form biologically different populations living in unique niches of the skin. PMID:24278043

Life sciences research on the space station: An introduction

NASA Technical Reports Server (NTRS)

1985-01-01

The Space Station will provide an orbiting, low gravity, permanently manned facility for scientific research, starting in the 1990s. The facilities for life sciences research are being designed to allow scientific investigators to perform research in Space Medicine and Space Biology, to study the consequences of long-term exposure to space conditions, and to allow for the permanent presence of humans in space. This research, using humans, animals, and plants, will provide an understanding of the effects of the space environment on the basic processes of life. In addition, facilities are being planned for remote observations to study biologically important elements and compounds in space and on other planets (exobiology), and Earth observations to study global ecology. The life sciences community is encouraged to plan for participation in scientific research that will be made possible by the Space Station research facility.

Multiphysics of bone remodeling: A 2D mesoscale activation simulation.

PubMed

Spingarn, C; Wagner, D; Rémond, Y; George, D

2017-01-01

In this work, we present an evolutive trabecular model for bone remodeling based on a boundary detection algorithm accounting for both biology and applied mechanical forces, known to be an important factor in bone evolution. A finite element (FE) numerical model using the Abaqus/Standard® software was used with a UMAT subroutine to solve the governing coupled mechanical-biological non-linear differential equations of the bone evolution model. The simulations present cell activation on a simplified trabeculae configuration organization with trabecular thickness of 200µm. For this activation process, the results confirm that the trabeculae are mainly oriented in the active direction of the principal mechanical stresses and according to the principal applied mechanical load directions. The trabeculae surface activation is clearly identified and can provide understanding of the different bone cell activations in more complex geometries and load conditions.

Functional impact of splice isoform diversity in individual cells

PubMed Central

Yap, Karen; Makeyev, Eugene V.

2016-01-01

Alternative pre-mRNA splicing provides an effective means for expanding coding capacity of eukaryotic genomes. Recent studies suggest that co-expression of different splice isoforms may increase diversity of RNAs and proteins at a single-cell level. A pertinent question in the field is whether such co-expression is biologically meaningful or, rather, represents insufficiently stringent splicing regulation. Here we argue that isoform co-expression may produce functional outcomes that are difficult and sometimes impossible to achieve using other regulation strategies. Far from being a ‘splicing noise’, co-expression is often established through co-ordinated activity of specific cis-elements and trans-acting factors. Further work in this area may uncover new biological functions of alternative splicing (AS) and generate important insights into mechanisms allowing different cell types to attain their unique molecular identities. PMID:27528755

Functional impact of splice isoform diversity in individual cells.

PubMed

Yap, Karen; Makeyev, Eugene V

2016-08-15

Alternative pre-mRNA splicing provides an effective means for expanding coding capacity of eukaryotic genomes. Recent studies suggest that co-expression of different splice isoforms may increase diversity of RNAs and proteins at a single-cell level. A pertinent question in the field is whether such co-expression is biologically meaningful or, rather, represents insufficiently stringent splicing regulation. Here we argue that isoform co-expression may produce functional outcomes that are difficult and sometimes impossible to achieve using other regulation strategies. Far from being a 'splicing noise', co-expression is often established through co-ordinated activity of specific cis-elements and trans-acting factors. Further work in this area may uncover new biological functions of alternative splicing (AS) and generate important insights into mechanisms allowing different cell types to attain their unique molecular identities. © 2016 The Author(s).

Effects of dam construction and increasing pollutants on the ecohydrological evolution of a shallow freshwater lake in the Yangtze floodplain.

PubMed

Zeng, Linghan; McGowan, Suzanne; Cao, Yanmin; Chen, Xu

2018-04-15

Large river-floodplain systems which provide a variety of societal, economic and biological benefits are undergoing extensive and intensive human disturbance. However, floodplain lakes responses to multiple stressors are poorly understood. The Yangtze River and its floodplain which provide water and food resources for more than 300 million people are an important region in China. Hydrological regulation as well as socio-economic development have brought profound negative influence on this ecologically important area. To improve understanding of decadal-scale responses of floodplain lakes to multiple stressors, lake sediment proxies including particle size, geochemical elements, diatoms and chironomids were analysed in a lead-210 dated core from Futou Lake. The analyses show that dams constructed in 1935 and the early 1970s stabilized hydrological conditions in Futou Lake and impeded the interaction with the Yangtze River, resulting in a decrease in major elements (e.g., Mg, Al, Fe) transported into the lake and an increase of macrophyte-related chironomids (C. sylvestris-type, P. penicillatus-type and Paratanytarsus sp.). After the late 1990s, further decreases in major elements and increases in median grain size are attributed to the erosion of the Yangtze riverbed and declining supply of major elements-enriched sediments from the upper Yangtze caused by the impoundment of the Three Gorges Dam. Chironomid and diatom assemblages indicate that hydrological stabilization caused by dam constructions stimulated the growth of macrophytes, which may be important in buffering against an ecosystem state change towards a phytoplankton-dominated and turbid state with ongoing eutrophication. However, a recent increase in Zn, TP and the emergence of eutrophic diatom and chironomid species indicate initial signs of water quality deterioration which may be related to the combined effects of hydrological stabilization and aquaculture. Over all, the sediment record from Futou Lake emphasizes the importance of interactions between hydrological change and pollutant loads in determining floodplain lake ecosystem state. Copyright © 2017 Elsevier B.V. All rights reserved.

Elemental and isotopic imaging of biological samples using NanoSIMS.

PubMed

Kilburn, Matt R; Clode, Peta L

2014-01-01

With its low detection limits and the ability to analyze most of the elements in the periodic table, secondary ion mass spectrometry (SIMS) represents one of the most versatile in situ analytical techniques available, and recent developments have resulted in significant advantages for the use of imaging mass spectrometry in biological and biomedical research. Increases in spatial resolution and sensitivity allow detailed interrogation of samples at relevant scales and chemical concentrations. Advances in dynamic SIMS, specifically with the advent of NanoSIMS, now allow the tracking of stable isotopes within biological systems at subcellular length scales, while static SIMS combines subcellular imaging with molecular identification. In this chapter, we present an introduction to the SIMS technique, with particular reference to NanoSIMS, and discuss its application in biological and biomedical research.

Promoter and Terminator Discovery and Engineering.

PubMed

Deaner, Matthew; Alper, Hal S

Control of gene expression is crucial to optimize metabolic pathways and synthetic gene networks. Promoters and terminators are stretches of DNA upstream and downstream (respectively) of genes that control both the rate at which the gene is transcribed and the rate at which mRNA is degraded. As a result, both of these elements control net protein expression from a synthetic construct. Thus, it is highly important to discover and engineer promoters and terminators with desired characteristics. This chapter highlights various approaches taken to catalogue these important synthetic elements. Specifically, early strategies have focused largely on semi-rational techniques such as saturation mutagenesis to diversify native promoters and terminators. Next, in an effort to reduce the length of the synthetic biology design cycle, efforts in the field have turned towards the rational design of synthetic promoters and terminators. In this vein, we cover recently developed methods such as hybrid engineering, high throughput characterization, and thermodynamic modeling which allow finer control in the rational design of novel promoters and terminators. Emphasis is placed on the methodologies used and this chapter showcases the utility of these methods across multiple host organisms.

Polymer monolithic capillary microextraction combined on-line with inductively coupled plasma MS for the determination of trace rare earth elements in biological samples.

PubMed

Zhang, Lin; Chen, Beibei; He, Man; Hu, Bin

2013-07-01

A rapid and sensitive method based on polymer monolithic capillary microextraction combined on-line with microconcentric nebulization inductively coupled plasma MS has been developed for the determination of trace/ultratrace rare earth elements in biological samples. For this purpose, the iminodiacetic acid modified poly(glycidyl methacrylate-trimethylolpropane trimethacrylate) monolithic capillary was prepared and characterized by SEM and FTIR spectroscopy. Factors affecting the extraction efficiency, such as sample pH, sample flow rate, sample/eluent volume, and coexisting ions were investigated in detail. Under the optimal conditions, the LODs for rare earth elements were in the range of 0.08 (Er) to 0.97 ng/L (Nd) with a sampling frequency of 8.5 h(-1), and the RSDs were between 1.5% (Sm) and 7.4% (Nd) (c = 20 ng/L, n = 7). The proposed method was successfully applied to the analysis of trace/ultratrace rare earth elements in human urine and serum samples, and the recoveries for the spiked samples were in the range of 82-105%. The developed method was simple, rapid, sensitive, and favorable for the analysis of trace/ultratrace rare earth elements in biological samples with limited sample volume. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Linear ordered collagen scaffolds loaded with collagen-binding basic fibroblast growth factor facilitate recovery of sciatic nerve injury in rats.

PubMed

Ma, Fukai; Xiao, Zhifeng; Chen, Bing; Hou, Xianglin; Dai, Jianwu; Xu, Ruxiang

2014-04-01

Natural biological functional scaffolds, consisting of biological materials filled with promoting elements, provide a promising strategy for the regeneration of peripheral nerve defects. Collagen conduits have been used widely due to their excellent biological properties. Linear ordered collagen scaffold (LOCS) fibers are good lumen fillers that can guide nerve regeneration in an ordered direction. In addition, basic fibroblast growth factor (bFGF) is important in the recovery of nerve injury. However, the traditional method for delivering bFGF to the lesion site has no long-term effect because of its short half-life and rapid diffusion. Therefore, we fused a specific collagen-binding domain (CBD) peptide to the N-terminal of native basic fibroblast growth factor (NAT-bFGF) to retain bFGF on the collagen scaffolds. In this study, a natural biological functional scaffold was constructed using collagen tubes filled with collagen-binding bFGF (CBD-bFGF)-loaded LOCS to promote regeneration in a 5-mm rat sciatic nerve transection model. Functional evaluation, histological investigation, and morphometric analysis indicated that the natural biological functional scaffold retained more bFGF at the injury site, guided axon growth, and promoted nerve regeneration as well as functional restoration.

Elemental content of Vietnamese rice. Part 2. Multivariate data analysis.

PubMed

Kokot, S; Phuong, T D

1999-04-01

Rice samples were obtained from the Red River region and some other parts of Vietnam as well as from Yanco, Australia. These samples were analysed for 14 elements (P, K, Mg, Ca, Mn, Zn, Fe, Cu, Al, Na, Ni, As, Mo and Cd) by ICP-AES, ICP-MS and FAAS as described in Part 1. This data matrix was then submitted to multivariate data analysis by principal component analysis to investigate the influences of environmental and crop cultivation variables on the elemental content of rice. Results revealed that geographical location, grain variety, seasons and soil conditions are the most likely significant factors causing changes in the elemental content between the rice samples. To assess rice quality according to its elemental content and physio-biological properties, a multicriteria decision making method (PROMETHEE) was applied. With the Vietnamese rice, the sticky rice appeared to contain somewhat higher levels of nutritionally significant elements such as P, K and Mg than the non-sticky rice. Also, rice samples grown during the wet season have better levels of nutritionally significant mineral elements than those of the dry season, but in general, the wet season seemed to provide better overall elemental and physio-biological rice quality.

Healthy Watersheds Protection

MedlinePlus

... chemical water quality conditions able to support healthy biological communities. Natural vegetative cover in the landscape, including ... habitat habitat A place where the physical and biological elements of ecosystems provide a suitable environment including ...

Bridging Food Webs, Ecosystem Metabolism, and Biogeochemistry Using Ecological Stoichiometry Theory

PubMed Central

Welti, Nina; Striebel, Maren; Ulseth, Amber J.; Cross, Wyatt F.; DeVilbiss, Stephen; Glibert, Patricia M.; Guo, Laodong; Hirst, Andrew G.; Hood, Jim; Kominoski, John S.; MacNeill, Keeley L.; Mehring, Andrew S.; Welter, Jill R.; Hillebrand, Helmut

2017-01-01

Although aquatic ecologists and biogeochemists are well aware of the crucial importance of ecosystem functions, i.e., how biota drive biogeochemical processes and vice-versa, linking these fields in conceptual models is still uncommon. Attempts to explain the variability in elemental cycling consequently miss an important biological component and thereby impede a comprehensive understanding of the underlying processes governing energy and matter flow and transformation. The fate of multiple chemical elements in ecosystems is strongly linked by biotic demand and uptake; thus, considering elemental stoichiometry is important for both biogeochemical and ecological research. Nonetheless, assessments of ecological stoichiometry (ES) often focus on the elemental content of biota rather than taking a more holistic view by examining both elemental pools and fluxes (e.g., organismal stoichiometry and ecosystem process rates). ES theory holds the promise to be a unifying concept to link across hierarchical scales of patterns and processes in ecology, but this has not been fully achieved. Therefore, we propose connecting the expertise of aquatic ecologists and biogeochemists with ES theory as a common currency to connect food webs, ecosystem metabolism, and biogeochemistry, as they are inherently concatenated by the transfer of carbon, nitrogen, and phosphorous through biotic and abiotic nutrient transformation and fluxes. Several new studies exist that demonstrate the connections between food web ecology, biogeochemistry, and ecosystem metabolism. In addition to a general introduction into the topic, this paper presents examples of how these fields can be combined with a focus on ES. In this review, a series of concepts have guided the discussion: (1) changing biogeochemistry affects trophic interactions and ecosystem processes by altering the elemental ratios of key species and assemblages; (2) changing trophic dynamics influences the transformation and fluxes of matter across environmental boundaries; (3) changing ecosystem metabolism will alter the chemical diversity of the non-living environment. Finally, we propose that using ES to link nutrient cycling, trophic dynamics, and ecosystem metabolism would allow for a more holistic understanding of ecosystem functions in a changing environment. PMID:28747904

Model scientists

PubMed Central

Staves, Mark

2008-01-01

There is an increasing trend for the focus of biology to be determined more by administrators who have short-term pecuniary interests in science rather than by individuals who are “doing science” to further the fundamental human desire to understand ourselves, the natural environment, and our place in the world, though questioning. We feel that this ceding of the scope of science from the questioners to the administrators is at variance with the traditions of science, which heretofore have resulted in the remarkable advancements made in the field of biology. In contrast to the plethora of day-to-day conversations on how to fit into the administrators' directives, this essay provides a historical context, particularly though its extensive bibliography, to encourage today's biologists to question authority and question nature. “If it be of importance and of use to us to know the principles of the element we breathe, surely it is not of much less importance nor of much less use to comprehend the principles, and endeavour at the improvement of those laws, by which alone we breathe it in security.”—Jeremy Bentham1 PMID:19513206

Conversion of KEGG metabolic pathways to SBGN maps including automatic layout

PubMed Central

2013-01-01

Background Biologists make frequent use of databases containing large and complex biological networks. One popular database is the Kyoto Encyclopedia of Genes and Genomes (KEGG) which uses its own graphical representation and manual layout for pathways. While some general drawing conventions exist for biological networks, arbitrary graphical representations are very common. Recently, a new standard has been established for displaying biological processes, the Systems Biology Graphical Notation (SBGN), which aims to unify the look of such maps. Ideally, online repositories such as KEGG would automatically provide networks in a variety of notations including SBGN. Unfortunately, this is non‐trivial, since converting between notations may add, remove or otherwise alter map elements so that the existing layout cannot be simply reused. Results Here we describe a methodology for automatic translation of KEGG metabolic pathways into the SBGN format. We infer important properties of the KEGG layout and treat these as layout constraints that are maintained during the conversion to SBGN maps. Conclusions This allows for the drawing and layout conventions of SBGN to be followed while creating maps that are still recognizably the original KEGG pathways. This article details the steps in this process and provides examples of the final result. PMID:23953132

Implementing Best Practices and Validation of Cryopreservation Techniques for Microorganisms

PubMed Central

Smith, David; Ryan, Matthew

2012-01-01

Authentic, well preserved living organisms are basic elements for research in the life sciences and biotechnology. They are grown and utilized in laboratories around the world and are key to many research programmes, industrial processes and training courses. They are vouchers for publications and must be available for confirmation of results, further study or reinvestigation when new technologies become available. These biological resources must be maintained without change in biological resource collections. In order to achieve best practice in the maintenance and provision of biological materials for industry, research and education the appropriate standards must be followed. Cryopreservation is often the best preservation method available to achieve these aims, allowing long term, stable storage of important microorganisms. To promulgate best practice the Organisation for Economic Development and Co-operation (OECD published the best practice guidelines for BRCs. The OECD best practice consolidated the efforts of the UK National Culture Collections, the European Common Access to Biological Resources and Information (CABRI) project consortium and the World Federation for Culture Collections. The paper discusses quality management options and reviews cryopreservation of fungi, describing how the reproducibility and quality of the technique is maintained in order to retain the full potential of fungi. PMID:22629202

Drawing-to-Learn: A Framework for Using Drawings to Promote Model-Based Reasoning in Biology

PubMed Central

Quillin, Kim; Thomas, Stephen

2015-01-01

The drawing of visual representations is important for learners and scientists alike, such as the drawing of models to enable visual model-based reasoning. Yet few biology instructors recognize drawing as a teachable science process skill, as reflected by its absence in the Vision and Change report’s Modeling and Simulation core competency. Further, the diffuse research on drawing can be difficult to access, synthesize, and apply to classroom practice. We have created a framework of drawing-to-learn that defines drawing, categorizes the reasons for using drawing in the biology classroom, and outlines a number of interventions that can help instructors create an environment conducive to student drawing in general and visual model-based reasoning in particular. The suggested interventions are organized to address elements of affect, visual literacy, and visual model-based reasoning, with specific examples cited for each. Further, a Blooming tool for drawing exercises is provided, as are suggestions to help instructors address possible barriers to implementing and assessing drawing-to-learn in the classroom. Overall, the goal of the framework is to increase the visibility of drawing as a skill in biology and to promote the research and implementation of best practices. PMID:25713094

The nitrogen cycle on Mars

NASA Technical Reports Server (NTRS)

Mancinelli, Rocco L.

1989-01-01

Nirtogen is an essential element for the evolution of life, because it is found in a variety of biologically important molecules. Therefore, N is an important element to study from a exobiological perspective. In particular, fixed nitrogen is the biologically useful form of nitrogen. Fixed nitrogen is generally defines as NH3, NH4(+), NO(x), or N that is chemically bound to either inorganic or organic molecules, and releasable by hydrolysis to NH3 or NH4(+). On Earth, the vast majority of nitrogen exists as N2 in the atmosphere, and not in the fixes form. On early Mars the same situations probably existed. The partial pressure of N2 on early Mars was thought to be 18 mb, significantly less than that of Earth. Dinitrogen can be fixed abiotically by several mechanisms. These mechanisms include thernal shock from meteoritic infall and lightning, as well as the interaction of light and sand containing TiO2 which produces NH3 that would be rapidly destroyed by photolysis and reaction with OH radicals. These mechanisms could have been operative on primitive Mars.The chemical processes effecting these compounds and possible ways of fixing or burying N in the Martian environment are described. Data gathered in this laboratory suggest that the low abundance of nitrogen along (compared to primitive Earth) may not significantly deter the origin and early evolution of a nitrogen utilizing organisms. However, the conditions on current Mars with respect to nitrogen are quite different, and organisms may not be able to utilize all of the available nitrogen.

Multiscale smeared finite element model for mass transport in biological tissue: From blood vessels to cells and cellular organelles.

PubMed

Kojic, M; Milosevic, M; Simic, V; Koay, E J; Kojic, N; Ziemys, A; Ferrari, M

2018-05-21

One of the basic and vital processes in living organisms is mass exchange, which occurs on several levels: it goes from blood vessels to cells and organelles within cells. On that path, molecules, as oxygen, metabolic products, drugs, etc. Traverse different macro and micro environments - blood, extracellular/intracellular space, and interior of organelles; and also biological barriers such as walls of blood vessels and membranes of cells and organelles. Many aspects of this mass transport remain unknown, particularly the biophysical mechanisms governing drug delivery. The main research approach relies on laboratory and clinical investigations. In parallel, considerable efforts have been directed to develop computational tools for additional insight into the intricate process of mass exchange and transport. Along these lines, we have recently formulated a composite smeared finite element (CSFE) which is composed of the smeared continuum pressure and concentration fields of the capillary and lymphatic system, and of these fields within tissue. The element offers an elegant and simple procedure which opens up new lines of inquiry and can be applied to large systems such as organs and tumors models. Here, we extend this concept to a multiscale scheme which concurrently couples domains that span from large blood vessels, capillaries and lymph, to cell cytosol and further to organelles of nanometer size. These spatial physical domains are coupled by the appropriate connectivity elements representing biological barriers. The composite finite element has "degrees of freedom" which include pressures and concentrations of all compartments of the vessels-tissue assemblage. The overall model uses the standard, measurable material properties of the continuum biological environments and biological barriers. It can be considered as a framework into which we can incorporate various additional effects (such as electrical or biochemical) for transport through membranes or within cells. This concept and the developed FE software within our package PAK offers a computational tool that can be applied to whole-organ systems, while also including specific domains such as tumors. The solved examples demonstrate the accuracy of this model and its applicability to large biological systems. Copyright © 2018. Published by Elsevier Ltd.

Pigmentation in Xiphophorus: an emerging system in ecological and evolutionary genetics.

PubMed

Culumber, Zachary W

2014-02-01

The genus Xiphophorus has great potential to contribute to the study of vertebrate pigmentation and elucidating the relative influence of ecology, physiology, and behavior on evolution at the molecular level. More importantly, the association between pigmentation and a functional oncogene offers the potential to understand the evolution and maintenance of cancer-causing genetic elements. Using criteria laid out recently in the literature, I demonstrate the power of the Xiphophorus system for studying pigment evolution through integrative organismal biology. Using the most recent phylogeny, the phylogenetic distribution of several important pigmentation loci are reevaluated. I then review support for existing hypotheses of the functional importance of pigmentation. Finally, new observations and hypotheses regarding some of the characteristics of pigment patterns in natural populations and open questions and future directions in the study of the evolution of these traits are discussed.

The elements of life and medicines

PubMed Central

Chellan, Prinessa; Sadler, Peter J

2015-01-01

Which elements are essential for human life? Here we make an element-by-element journey through the periodic table and attempt to assess whether elements are essential or not, and if they are, whether there is a relevant code for them in the human genome. There are many difficulties such as the human biochemistry of several so-called essential elements is not well understood, and it is not clear how we should classify elements that are involved in the destruction of invading microorganisms, or elements which are essential for microorganisms with which we live in symbiosis. In general, genes do not code for the elements themselves, but for specific chemical species, i.e. for the element, its oxidation state, type and number of coordinated ligands, and the coordination geometry. Today, the biological periodic table is in a position somewhat similar to Mendeleev's chemical periodic table of 1869: there are gaps and we need to do more research to fill them. The periodic table also offers potential for novel therapeutic and diagnostic agents, based on not only essential elements, but also non-essential elements, and on radionuclides. Although the potential for inorganic chemistry in medicine was realized more than 2000 years ago, this area of research is still in its infancy. Future advances in the design of inorganic drugs require more knowledge of their mechanism of action, including target sites and metabolism. Temporal speciation of elements in their biological environments at the atomic level is a major challenge, for which new methods are urgently needed. PMID:25666066

The elements of life and medicines.

PubMed

Chellan, Prinessa; Sadler, Peter J

2015-03-13

Which elements are essential for human life? Here we make an element-by-element journey through the periodic table and attempt to assess whether elements are essential or not, and if they are, whether there is a relevant code for them in the human genome. There are many difficulties such as the human biochemistry of several so-called essential elements is not well understood, and it is not clear how we should classify elements that are involved in the destruction of invading microorganisms, or elements which are essential for microorganisms with which we live in symbiosis. In general, genes do not code for the elements themselves, but for specific chemical species, i.e. for the element, its oxidation state, type and number of coordinated ligands, and the coordination geometry. Today, the biological periodic table is in a position somewhat similar to Mendeleev's chemical periodic table of 1869: there are gaps and we need to do more research to fill them. The periodic table also offers potential for novel therapeutic and diagnostic agents, based on not only essential elements, but also non-essential elements, and on radionuclides. Although the potential for inorganic chemistry in medicine was realized more than 2000 years ago, this area of research is still in its infancy. Future advances in the design of inorganic drugs require more knowledge of their mechanism of action, including target sites and metabolism. Temporal speciation of elements in their biological environments at the atomic level is a major challenge, for which new methods are urgently needed.

Morphomics: An integral part of systems biology of the human placenta.

PubMed

Mayhew, T M

2015-04-01

The placenta is a transient organ the functioning of which has health consequences far beyond the embryo/fetus. Understanding the biology of any system (organ, organism, single cell, etc) requires a comprehensive and inclusive approach which embraces all the biomedical disciplines and 'omic' technologies and then integrates information obtained from all of them. Among the latest 'omics' is morphomics. The terms morphome and morphomics have been applied incoherently in biology and biomedicine but, recently, they have been given clear and widescale definitions. Morphomics is placed in the context of other 'omics' and its pertinent technologies and tools for sampling and quantitation are reviewed. Emphasis is accorded to the importance of random sampling principles in systems biology and the value of combining 3D quantification with alternative imaging techniques to advance knowledge and understanding of the human placental morphome. By analogy to other 'omes', the morphome is the totality of morphological features within a system and morphomics is the systematic study of those structures. Information about structure is required at multiple levels of resolution in order to understand better the processes by which a given system alters with time, experimental treatment or environmental insult. Therefore, morphomics research includes all imaging techniques at all levels of achievable resolution from gross anatomy and medical imaging, via optical and electron microscopy, to molecular characterisation. Quantification is an important element of all 'omics' studies and, because biological systems exist and operate in 3-dimensional (3D) space, precise descriptions of form, content and spatial relationships require the quantification of structure in 3D. These considerations are relevant to future study contributions to the Human Placenta Project. Copyright © 2015 Elsevier Ltd. All rights reserved.

Monitoring of airborne biological particles in outdoor atmosphere. Part 1: Importance, variability and ratios.

PubMed

Núñez, Andrés; Amo de Paz, Guillermo; Rastrojo, Alberto; García, Ana M; Alcamí, Antonio; Gutiérrez-Bustillo, A Montserrat; Moreno, Diego A

2016-03-01

The first part of this review ("Monitoring of airborne biological particles in outdoor atmosphere. Part 1: Importance, variability and ratios") describes the current knowledge on the major biological particles present in the air regarding their global distribution, concentrations, ratios and influence of meteorological factors in an attempt to provide a framework for monitoring their biodiversity and variability in such a singular environment as the atmosphere. Viruses, bacteria, fungi, pollen and fragments thereof are the most abundant microscopic biological particles in the air outdoors. Some of them can cause allergy and severe diseases in humans, other animals and plants, with the subsequent economic impact. Despite the harsh conditions, they can be found from land and sea surfaces to beyond the troposphere and have been proposed to play a role also in weather conditions and climate change by acting as nucleation particles and inducing water vapour condensation. In regards to their global distribution, marine environments act mostly as a source for bacteria while continents additionally provide fungal and pollen elements. Within terrestrial environments, their abundances and diversity seem to be influenced by the land-use type (rural, urban, coastal) and their particularities. Temporal variability has been observed for all these organisms, mostly triggered by global changes in temperature, relative humidity, et cetera. Local fluctuations in meteorological factors may also result in pronounced changes in the airbiota. Although biological particles can be transported several hundreds of meters from the original source, and even intercontinentally, the time and final distance travelled are strongly influenced by factors such as wind speed and direction. [Int Microbiol 2016; 19(1):1-1 3]. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

Two-Element Transducer for Ultrasound

NASA Technical Reports Server (NTRS)

Lecroissette, D. H.; Heyser, R. C.

1986-01-01

Separation of transmitting and receiving units improves probing of deep tissue. Ultrasonic transducer has dual elements to increase depth at which sonic images are made of biological tissue. Transducer uses separate transmitting and receiving elements, and frequency response of receiving element independently designed to accommodate attenuation of higher frequencies by tissue. New transducer intended for pulse-echo ultrasonic systems in which reflected sound pulses reveal features in tissue.

Transposon integration enhances expression of stress response genes.

PubMed

Feng, Gang; Leem, Young-Eun; Levin, Henry L

2013-01-01

Transposable elements possess specific patterns of integration. The biological impact of these integration profiles is not well understood. Tf1, a long-terminal repeat retrotransposon in Schizosaccharomyces pombe, integrates into promoters with a preference for the promoters of stress response genes. To determine the biological significance of Tf1 integration, we took advantage of saturated maps of insertion activity and studied how integration at hot spots affected the expression of the adjacent genes. Our study revealed that Tf1 integration did not reduce gene expression. Importantly, the insertions activated the expression of 6 of 32 genes tested. We found that Tf1 increased gene expression by inserting enhancer activity. Interestingly, the enhancer activity of Tf1 could be limited by Abp1, a host surveillance factor that sequesters transposon sequences into structures containing histone deacetylases. We found the Tf1 promoter was activated by heat treatment and, remarkably, only genes that themselves were induced by heat could be activated by Tf1 integration, suggesting a synergy of Tf1 enhancer sequence with the stress response elements of target promoters. We propose that the integration preference of Tf1 for the promoters of stress response genes and the ability of Tf1 to enhance the expression of these genes co-evolved to promote the survival of cells under stress.

An Integrated XRF/XRD Instrument for Mars Exobiology and Geology Experiments

NASA Technical Reports Server (NTRS)

Koppel, L. N.; Franco, E. D.; Kerner, J. A.; Fonda, M. L.; Schwartz, D. E.; Marshall, J. R.

1993-01-01

By employing an integrated x-ray instrument on a future Mars mission, data obtained will greatly augment those returned by Viking; details characterizing the past and present environment on Mars and those relevant to the possibility of the origin and evolution of life will be acquired. A combined x-ray fluorescence/x-ray diffraction (XRF/XRD) instrument was breadboarded and demonstrated to accommodate important exobiology and geology experiment objectives outlined for MESUR and future Mars missions. Among others, primary objectives for the exploration of Mars include the intense study of local areas on Mars to establish the chemical, mineralogical, and petrological character of different components of the surface material; to determine the distribution, abundance, and sources and sinks of volatile materials, including an assessment of the biologic potential, now and during past epoches; and to establish the global chemical and physical characteristics of the Martian surface. The XRF/XRD breadboard instrument identifies and quantifies soil surface elemental, mineralogical, and petrological characteristics and acquires data necessary to address questions on volatile abundance and distribution. Additionally, the breadboard is able to characterize the biogenic element constituents of soil samples providing information on the biologic potential of the Mars environment. Preliminary breadboard experiments confirmed the fundamental instrument design approach and measurement performance.

Transposon integration enhances expression of stress response genes

PubMed Central

Feng, Gang; Leem, Young-Eun; Levin, Henry L.

2013-01-01

Transposable elements possess specific patterns of integration. The biological impact of these integration profiles is not well understood. Tf1, a long-terminal repeat retrotransposon in Schizosaccharomyces pombe, integrates into promoters with a preference for the promoters of stress response genes. To determine the biological significance of Tf1 integration, we took advantage of saturated maps of insertion activity and studied how integration at hot spots affected the expression of the adjacent genes. Our study revealed that Tf1 integration did not reduce gene expression. Importantly, the insertions activated the expression of 6 of 32 genes tested. We found that Tf1 increased gene expression by inserting enhancer activity. Interestingly, the enhancer activity of Tf1 could be limited by Abp1, a host surveillance factor that sequesters transposon sequences into structures containing histone deacetylases. We found the Tf1 promoter was activated by heat treatment and, remarkably, only genes that themselves were induced by heat could be activated by Tf1 integration, suggesting a synergy of Tf1 enhancer sequence with the stress response elements of target promoters. We propose that the integration preference of Tf1 for the promoters of stress response genes and the ability of Tf1 to enhance the expression of these genes co-evolved to promote the survival of cells under stress. PMID:23193295

Boron uptake, localization, and speciation in marine brown algae.

PubMed

Miller, Eric P; Wu, Youxian; Carrano, Carl J

2016-02-01

In contrast to the generally boron-poor terrestrial environment, the concentration of boron in the marine environment is relatively high (0.4 mM) and while there has been extensive interest in its use as a surrogate of pH in paleoclimate studies in the context of climate change-related questions, the relatively depth independent, and the generally non-nutrient-like concentration profile of this element have led to boron being neglected as a potentially biologically relevant element in the ocean. Among the marine plant-like organisms the brown algae (Phaeophyta) are one of only five lineages of photosynthetic eukaryotes to have evolved complex multicellularity. Many of unusual and often unique features of brown algae are attributable to this singular evolutionary history. These adaptations are a reflection of the marine coastal environment which brown algae dominate in terms of biomass. Consequently, brown algae are of fundamental importance to oceanic ecology, geochemistry, and coastal industry. Our results indicate that boron is taken up by a facilitated diffusion mechanism against a considerable concentration gradient. Furthermore, in both Ectocarpus and Macrocystis some boron is most likely bound to cell wall constituent alginate and the photoassimilate mannitol located in sieve cells. Herein, we describe boron uptake, speciation, localization and possible biological function in two species of brown algae, Macrocystis pyrifera and Ectocarpus siliculosus.

Photonic structures in biology

NASA Astrophysics Data System (ADS)

Vukusic, Pete; Sambles, J. Roy

2003-08-01

Millions of years before we began to manipulate the flow of light using synthetic structures, biological systems were using nanometre-scale architectures to produce striking optical effects. An astonishing variety of natural photonic structures exists: a species of Brittlestar uses photonic elements composed of calcite to collect light, Morpho butterflies use multiple layers of cuticle and air to produce their striking blue colour and some insects use arrays of elements, known as nipple arrays, to reduce reflectivity in their compound eyes. Natural photonic structures are providing inspiration for technological applications.

Dual fiber microprobe for mapping elemental distributions in biological cells

DOEpatents

Martin, Rodger C [Powell, TN; Martin, Madhavi Z [Powell, TN

2007-07-31

Laser-induced breakdown spectroscopy (LIBS) is applied on a microscale for in situ elemental analysis and spatial mapping in biological cells. A high power laser beam is focused onto a cell surface using a dual branching optical fiber probe for optical excitation of the cell constituents. Dual spectrometers and ICCD detectors capture the emission spectra from the excited cell(s). Repeated probing or repositioning of the laser beam with respect to the cell can provide 2-D or 3-D mapping of the cell.

Biological Effects of Laser Radiation. Volume I. Review of the Literature on Biological Effects of Laser Radiation-to 1965.

DTIC Science & Technology

1978-10-17

because of the rapid progress made in laser technology to date. The use of the Laser Microprobe in spectrochemical analysis of the elements is based on...spectroscopy to vaporize microscopic amounts of samples for elemental analysis . On the other hand, the intense, highly monochromatic laser beam is being...employed as a light source for Raman spectroscopy to study molecular structure. These two uses of lasers in spectroscopic analysis have been sucessful

Optical fiber-based biosensors.

PubMed

Monk, David J; Walt, David R

2004-08-01

This review outlines optical fiber-based biosensor research from January 2001 through September 2003 and was written to complement the previous review in this journal by Marazuela and Moreno-Bondi. Optical fiber-based biosensors combine the use of a biological recognition element with an optical fiber or optical fiber bundle. They are classified by the nature of the biological recognition element used for sensing: enzyme, antibody/antigen (immunoassay), nucleic acid, whole cell, and biomimetic, and may be used for a variety of analytes ranging from metals and chemicals to physiological materials.

Overview of the mechanisms that could explain the 'Boundary Exchange' at the land-ocean contact.

PubMed

Jeandel, Catherine

2016-11-28

Land to ocean transfer of material largely controls the chemical composition of seawater and the global element cycles. Oceanic isotopic budgets of chemical species, macro- and micronutrients (e.g. Nd, Sr, Si, Mg, Zn, Mo and Ni) have revealed an imbalance between their sources and sinks. Radiogenic isotope budgets underlined the importance of taking into account continental margins as a source of elements to oceans. They also highlighted that the net land-ocean inputs of chemical species probably result from particle-dissolved exchange processes, named 'Boundary Exchange'. Yet, locations where 'Boundary Exchange' occurs are not clearly identified and reviewed here: discharge of huge amount of freshly weathered particles at the river mouths, submarine weathering of deposited sediments along the margins, submarine groundwater discharges and subterranean estuaries. As a whole, we conclude that all of them might contribute to 'Boundary Exchange'. Highlighting their specific roles and the processes at play is a key scientific issue for the second half of GEOTRACES.This article is part of the themed issue 'Biological and climatic impacts of ocean trace element chemistry'. © 2016 The Author(s).

Determination of Se in soil samples using the proton induced X-ray emission technique

NASA Astrophysics Data System (ADS)

Cruvinel, Paulo E.; Flocchini, Robert G.

1993-04-01

An alternative method for the direct determination of total Se in soil samples is presented. A large number of trace elements is present in soil at concentration values in the range of part per billion and tenths of parts of million. The most common are the trace elements of Al, Si, K, Ca, Ti, V, Cr, Fe, Cu, Zn, Br, Rb, Mo, Cd and Pb. As for biological samples many of these elements are of great importance for the nutrition of plants, while others are toxic and others have an unknown role. Selenium is an essential micronutrient for humans and animals but it is also known that in certain areas Se deficiency or toxicity has caused endemic disease to livestock and humans through the soil-plant-animal linkage. In this work the suitability of the proton induced X-ray emission (PIXE) technique as a fast and nondestructive technique useful to measure total the Se content in soil samples is demonstrated. To validate the results a comparison of data collected using the conventional atomic absorption spectrophotometry (AAS) method was performed.

A versatile transfection assay system to evaluate the biological effects of diverse industrial chemicals.

PubMed

Koizumi, Shinji; Ohno, Shotaro; Otsuka, Fuminori

2012-01-01

Gene expression processes are now recognized as important targets of the toxic effects exerted by industrial chemicals. The transient transfection assay is a powerful tool to evaluate such effects. Thus, we developed a versatile assay system by constructing a basic reporter plasmid in which the regulatory DNA sequence to be studied can easily be substituted. To verify the performance of this system, reporter plasmids carrying any of the three distinct regulatory sequences, estrogen responsive element (ERE), glucocorticoid responsive element (GRE) and xenobiotic responsive element (XRE) were constructed. After transfection of human cells, these plasmids successfully expressed the relevant reporter genes in response to specific inducers, β-estradiol, dexamethasone and 3-methylcholanthrene, respectively. Several industrial chemicals were assayed using these reporter plasmids, and the ability of p-dimethylaminoazobenzene to elevate GRE- and XRE-mediated transcription was detected. α-Naphthylamine and o-tolidine were also observed to increase the XRE-mediated response. The transfection assay system established here will be useful to evaluate the effects of a wide variety of industrial chemicals.

The effect of fault-bend folding on seismic velocity in the marginal ridge of accretionary prisms

USGS Publications Warehouse

Cai, Y.; Wang, Chun-Yong; Hwang, W.-t.; Cochrane, G.R.

1995-01-01

Fluid venting in accretionary prisms, which feeds chemosynthetic biological communities, occurs mostly on the marginal thrust ridge. New seismic data for the marginal ridge of the Cascadia prism show significantly lower velocity than that in the adjacent oceanic basin and place important constraints on the interpretations of why fluid venting occurs mostly on the marginal ridge. We employed a finite-element method to analyze a typical fault-bend folding model to explain the phenomenon. The fault in the model is simulated by contact elements. The elements are characterized not only by finite sliding along a slide line, but also by elastoplastic deformation. We present the results of a stress analysis which show that the marginal ridge is under subhorizontal extension and the frontal thrust is under compression. This state of stress favors the growth of tensile cracks in the marginal ridge, facilitates fluid flow and reduces seismic velocities therein; on the other hand, it may close fluid pathways along the frontal thrust and divert fluid flow to the marginal ridge. ?? 1995 Birkha??user Verlag.

Overview of the mechanisms that could explain the ‘Boundary Exchange’ at the land–ocean contact

PubMed Central

2016-01-01

Land to ocean transfer of material largely controls the chemical composition of seawater and the global element cycles. Oceanic isotopic budgets of chemical species, macro- and micronutrients (e.g. Nd, Sr, Si, Mg, Zn, Mo and Ni) have revealed an imbalance between their sources and sinks. Radiogenic isotope budgets underlined the importance of taking into account continental margins as a source of elements to oceans. They also highlighted that the net land–ocean inputs of chemical species probably result from particle-dissolved exchange processes, named ‘Boundary Exchange’. Yet, locations where ‘Boundary Exchange’ occurs are not clearly identified and reviewed here: discharge of huge amount of freshly weathered particles at the river mouths, submarine weathering of deposited sediments along the margins, submarine groundwater discharges and subterranean estuaries. As a whole, we conclude that all of them might contribute to ‘Boundary Exchange’. Highlighting their specific roles and the processes at play is a key scientific issue for the second half of GEOTRACES. This article is part of the themed issue ‘Biological and climatic impacts of ocean trace element chemistry’. PMID:29035253

Clusters of Monoisotopic Elements for Calibration in (TOF) Mass Spectrometry

NASA Astrophysics Data System (ADS)

Kolářová, Lenka; Prokeš, Lubomír; Kučera, Lukáš; Hampl, Aleš; Peňa-Méndez, Eladia; Vaňhara, Petr; Havel, Josef

2017-03-01

Precise calibration in TOF MS requires suitable and reliable standards, which are not always available for high masses. We evaluated inorganic clusters of the monoisotopic elements gold and phosphorus (Au n +/Au n - and P n +/P n -) as an alternative to peptides or proteins for the external and internal calibration of mass spectra in various experimental and instrumental scenarios. Monoisotopic gold or phosphorus clusters can be easily generated in situ from suitable precursors by laser desorption/ionization (LDI) or matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Their use offers numerous advantages, including simplicity of preparation, biological inertness, and exact mass determination even at lower mass resolution. We used citrate-stabilized gold nanoparticles to generate gold calibration clusters, and red phosphorus powder to generate phosphorus clusters. Both elements can be added to samples to perform internal calibration up to mass-to-charge ( m/z) 10-15,000 without significantly interfering with the analyte. We demonstrated the use of the gold and phosphorous clusters in the MS analysis of complex biological samples, including microbial standards and total extracts of mouse embryonic fibroblasts. We believe that clusters of monoisotopic elements could be used as generally applicable calibrants for complex biological samples.

Selenium. Role of the Essential Metalloid in Health

PubMed Central

Kurokawa, Suguru; Berry, Marla J.

2015-01-01

Selenium is an essential micronutrient in mammals, but is also recognized as toxic in excess. It is a non-metal with properties that are intermediate between the chalcogen elements sulfur and tellurium. Selenium exerts its biological functions through selenoproteins. Selenoproteins contain selenium in the form of the 21st amino acid, selenocysteine (Sec), which is an analog of cysteine with the sulfur-containing side chain replaced by a Se-containing side chain. Sec is encoded by the codon UGA, which is one of three termination codons for mRNA translation in non-selenoprotein genes. Recognition of the UGA codon as a Sec insertion site instead of stop requires a Sec insertion sequence (SECIS) element in selenoprotein mRNAs and a unique selenocysteyl-tRNA, both of which are recognized by specialized protein factors. Unlike the 20 standard amino acids, Sec is biosynthesized from serine on its tRNA. Twenty-five selenoproteins are encoded in the human genome. Most of the selenoprotein genes were discovered by bioinformatics approaches, searching for SECIS elements downstream of in-frame UGA codons. Sec has been described as having stronger nucleophilic and electrophilic properties than cysteine, and Sec is present in the catalytic site of all selenoenzymes. Most selenoproteins, whose functions are known, are involved in redox systems and signaling pathways. However, several selenoproteins are not well characterized in terms of their function. The selenium field has grown dramatically in the last few decades, and research on selenium biology is providing extensive new information regarding its importance for human health. PMID:24470102

Astrobiological stoichiometry.

PubMed

Young, Patrick A; Desch, Steven J; Anbar, Ariel D; Barnes, Rory; Hinkel, Natalie R; Kopparapu, Ravikumar; Madhusudhan, Nikku; Monga, Nikhil; Pagano, Michael D; Riner, Miriam A; Scannapieco, Evan; Shim, Sang-Heon; Truitt, Amanda

2014-07-01

Chemical composition affects virtually all aspects of astrobiology, from stellar astrophysics to molecular biology. We present a synopsis of the research results presented at the "Stellar Stoichiometry" Workshop Without Walls hosted at Arizona State University April 11-12, 2013, under the auspices of the NASA Astrobiology Institute. The results focus on the measurement of chemical abundances and the effects of composition on processes from stellar to planetary scales. Of particular interest were the scientific connections between processes in these normally disparate fields. Measuring the abundances of elements in stars and giant and terrestrial planets poses substantial difficulties in technique and interpretation. One of the motivations for this conference was the fact that determinations of the abundance of a given element in a single star by different groups can differ by more than their quoted errors. The problems affecting the reliability of abundance estimations and their inherent limitations are discussed. When these problems are taken into consideration, self-consistent surveys of stellar abundances show that there is still substantial variation (factors of ∼ 2) in the ratios of common elements (e.g., C, O, Na, Al, Mg, Si, Ca) important in rock-forming minerals, atmospheres, and biology. We consider how abundance variations arise through injection of supernova nucleosynthesis products into star-forming material and through photoevaporation of protoplanetary disks. The effects of composition on stellar evolution are substantial, and coupled with planetary atmosphere models can result in predicted habitable zone extents that vary by many tens of percent. Variations in the bulk composition of planets can affect rates of radiogenic heating and substantially change the mineralogy of planetary interiors, affecting properties such as convection and energy transport.

Speciation of Phosphorus by coupled HPLC-ICPMS: Application for quantification of reduced forms of phosphorus in rocks and natural waters.

NASA Astrophysics Data System (ADS)

Atlas, Z. D.; Pasek, M. A.; Sampson, J.

2014-12-01

Phosphorus is a geologically important element making up approximately 0.12 % of the Earth's crust. It is commonly found as relatively insoluble apatite and this causes phosphorus to be a limiting nutrient in biologic processes. Despite this, phosphorus is a key element in DNA, RNA and other cellular materials. Recent works suggest that reduced phosphorus played a substantial role in the development of life on the early Earth. Reduced phosphorus is considerably more soluble than oxidized phosphorus, and reduced phosphorus may continue to play a role in biologic productivity. This study examines a new methodology for quantification of reduced phosphorus separated by coupled HPLC - ICP-MS. We show that phosphorus species (P1+, P3+ and P5+) are cleanly separated in the HPLC and coupled with the ICP-MS reaction cell (using O2 gas) effectively convert elemental P to P-O producing lower background and flatter baseline chromatography. Results suggest very low detection limits (0.05 mM) for P species analyzed as P-O at M/Z = 47. Additionally this technique has potential to speciate at least 5 other metastable forms of phosphorus. We verified this method on numerous materials including leached Archean rocks to suburban retention pond waters and many samples show small but detectible levels of reduced phosphorus. These data highlight a significant role of redox processing of phosphorus throughout the history of the Earth, with the reduced oxidation state phosphorus compounds, phosphite and hypophosphite, potentially acting as significant constituents in the anaerobic environment.

Functional analysis of a large set of BRCA2 exon 7 variants highlights the predictive value of hexamer scores in detecting alterations of exonic splicing regulatory elements.

PubMed

Di Giacomo, Daniela; Gaildrat, Pascaline; Abuli, Anna; Abdat, Julie; Frébourg, Thierry; Tosi, Mario; Martins, Alexandra

2013-11-01

Exonic variants can alter pre-mRNA splicing either by changing splice sites or by modifying splicing regulatory elements. Often these effects are difficult to predict and are only detected by performing RNA analyses. Here, we analyzed, in a minigene assay, 26 variants identified in the exon 7 of BRCA2, a cancer predisposition gene. Our results revealed eight new exon skipping mutations in this exon: one directly altering the 5' splice site and seven affecting potential regulatory elements. This brings the number of splicing regulatory mutations detected in BRCA2 exon 7 to a total of 11, a remarkably high number considering the total number of variants reported in this exon (n = 36), all tested in our minigene assay. We then exploited this large set of splicing data to test the predictive value of splicing regulator hexamers' scores recently established by Ke et al. (). Comparisons of hexamer-based predictions with our experimental data revealed high sensitivity in detecting variants that increased exon skipping, an important feature for prescreening variants before RNA analysis. In conclusion, hexamer scores represent a promising tool for predicting the biological consequences of exonic variants and may have important applications for the interpretation of variants detected by high-throughput sequencing. © 2013 WILEY PERIODICALS, INC.

Light rare earth element depletion during Deepwater Horizon blowout methanotrophy.

PubMed

Shiller, A M; Chan, E W; Joung, D J; Redmond, M C; Kessler, J D

2017-09-04

Rare earth elements have generally not been thought to have a biological role. However, recent work has demonstrated that the light REEs (LREEs: La, Ce, Pr, and Nd) are essential for at least some methanotrophs, being co-factors in the XoxF type of methanol dehydrogenase (MDH). We show here that dissolved LREEs were significantly removed in a submerged plume of methane-rich water during the Deepwater Horizon (DWH) well blowout. Furthermore, incubation experiments conducted with naturally methane-enriched waters from hydrocarbon seeps in the vicinity of the DWH wellhead also showed LREE removal concurrent with methane consumption. Metagenomic sequencing of incubation samples revealed that LREE-containing MDHs were present. Our field and laboratory observations provide further insight into the biochemical pathways of methanotrophy during the DWH blowout. Additionally, our results are the first observations of direct biological alteration of REE distributions in oceanic systems. In view of the ubiquity of LREE-containing MDHs in oceanic systems, our results suggest that biological uptake of LREEs is an overlooked aspect of the oceanic geochemistry of this group of elements previously thought to be biologically inactive and an unresolved factor in the flux of methane, a potent greenhouse gas, from the ocean.

Scanning transmission ion microscopy mass measurements for quantitative trace element analysis within biological samples and validation using atomic force microscopy thickness measurements

NASA Astrophysics Data System (ADS)

Devès, Guillaume; Cohen-Bouhacina, Touria; Ortega, Richard

2004-10-01

We used the nuclear microprobe techniques, micro-PIXE (particle-induced X-ray emission), micro-RBS (Rutherford backscattering spectrometry) and scanning transmission ion microscopy (STIM) in order to perform the characterization of trace element content and spatial distribution within biological samples (dehydrated cultured cells, tissues). The normalization of PIXE results was usually expressed in terms of sample dry mass as determined by micro-RBS recorded simultaneously to micro-PIXE. However, the main limit of RBS mass measurement is the sample mass loss occurring during irradiation and which could be up to 30% of the initial sample mass. We present here a new methodology for PIXE normalization and quantitative analysis of trace element within biological samples based on dry mass measurement performed by mean of STIM. The validation of STIM cell mass measurements was obtained in comparison with AFM sample thickness measurements. Results indicated the reliability of STIM mass measurement performed on biological samples and suggested that STIM should be performed for PIXE normalization. Further information deriving from direct confrontation of AFM and STIM analysis could as well be obtained, like in situ measurements of cell specific gravity within cells compartment (nucleolus and cytoplasm).

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.

PubMed

Hucka, Michael; Bergmann, Frank T; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M; Le Novère, Nicolas; Myers, Chris J; Olivier, Brett G; Sahle, Sven; Schaff, James C; Smith, Lucian P; Waltemath, Dagmar; Wilkinson, Darren J

2018-03-09

Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. The design of Version 2 differs from Version 1 principally in allowing new MathML constructs, making more child elements optional, and adding identifiers to all SBML elements instead of only selected elements. Other materials and software are available from the SBML project website at http://sbml.org/.

Personal reflections on a galvanizing trail.

PubMed

O'Dell, B L

1998-01-01

This article encompasses my perception of, and experience in, an exciting segment of the trace element era in nutrition research: the role of zinc in the nutrition of animals and humans. Zinc has been a major player on the stage of trace element research, and it has left a trail that galvanized the attention of many researchers, including myself. It is ubiquitous in biological systems, and it plays a multitude of physiologic and biochemical functions. A brief historical overview is followed by a discussion of the contributions the work done in my laboratory has made toward understanding the physiological and biochemical functions of zinc. The effort of 40 years has led to the belief that one of zinc's major roles, and perhaps its first limiting role, is to preserve plasma-membrane function as regards ion channels and signal transduction. Although substantial knowledge has been gained relating to the importance of zinc in nutrition, much remains to be discovered.

[Mobile genetic elements in plant sex evolution].

PubMed

Gerashchenkov, G A; Rozhnova, N A

2010-11-01

The most significant theories of the appearance and maintenance of sex are presented. However, in the overwhelming majority of existing theories, the problem of sex, which is the central problem of evolutionary biology, is considered primarily through the prism of reproductive features of living organisms, whereas the issue of molecular driving forces of sexual reproduction id restricted to the possible role of mobile genetic elements (MGEs) in the appearance of sexual reproduction. The structural and functional significance of MGEs in the genomic organization of plants is illustrated. It is shown that MGEs could act as important molecular drivers of sex evolution in plants. The involvement of MGEs in the formation of sex chromosomes and possible participation in seeds-without-sex reproduction (apomixis) is discussed. Thus, the hypothesis on the active MGE participation in sex evolution is in good agreement with the modern views on pathways and directions of sex evolution in plants.

Modeling tabular icebergs submerged in the ocean

NASA Astrophysics Data System (ADS)

Stern, A. A.; Adcroft, A.; Sergienko, O.; Marques, G.

2017-08-01

Large tabular icebergs calved from Antarctic ice shelves have long lifetimes (due to their large size), during which they drift across large distances, altering ambient ocean circulation, bottom-water formation, sea-ice formation, and biological primary productivity in the icebergs' vicinity. However, despite their importance, the current generation of ocean circulation models usually do not represent large tabular icebergs. In this study, we develop a novel framework to model large tabular icebergs submerged in the ocean. In this framework, tabular icebergs are represented by pressure-exerting Lagrangian elements that drift in the ocean. The elements are held together and interact with each other via bonds. A breaking of these bonds allows the model to emulate calving events (i.e., detachment of a tabular iceberg from an ice shelf) and tabular icebergs breaking up into smaller pieces. Idealized simulations of a calving tabular iceberg, its drift, and its breakup demonstrate capabilities of the developed framework.

A central role for vesicle trafficking in epithelial neoplasia: Intracellular highways to carcinogenesis

PubMed Central

Goldenring, James R.

2014-01-01

Epithelial cell carcinogenesis involves the loss of polarity, alteration of polarized protein presentation, dynamic cell morphology changes, increased proliferation and increased cell motility and invasion. Elements of membrane vesicle trafficking underlie all of these processes. Specific membrane trafficking regulators, including Rab small GTPases, through the coordinated dynamics of intracellular trafficking along cytoskeletal pathways, determine cell surface presentation of proteins and overall function of both differentiated and neoplastic cells. While mutations in vesicle trafficking proteins may not be direct drivers of transformation, elements of the machinery of vesicle movement play critical roles in the phenotypes of neoplastic cells. Therefore, the regulators of membrane vesicle trafficking decisions are critical mediators of the full spectrum of cell physiologies driving cancer cell biology, including initial loss of polarity, invasion and metastasis. Targeting of these fundamental intracellular processes may provide important points for manipulation of cancer cell behaviour. PMID:24108097

Evaluation of cryoanalysis as a tool for analyzing elemental distribution in "live" tardigrades using micro-PIXE

NASA Astrophysics Data System (ADS)

Nilsson, E. J. C.; Pallon, J.; Przybylowicz, W. J.; Wang, Y. D.; Jönsson, K. I.

2014-08-01

Although heavy on labor and equipment, thus not often applied, cryoanalysis of frozen hydrated biological specimens can provide information that better reflects the living state of the organism, compared with analysis in the freeze-dried state. In this paper we report a study where the cryoanalysis facility with cryosectioning capabilities at Materials Research Department, iThemba LABS, South Africa was employed to evaluate the usefulness of combining three ion beam analytical methods (μPIXE, RBS and STIM) to analyze a biological target where a better elemental compositional description is needed - the tardigrade. Imaging as well as quantification results are of interest. In a previous study, the element composition and redistribution of elements in the desiccated and active states of two tardigrade species was investigated. This study included analysis of both whole and sectioned tardigrades, and the aim was to analyze each specimen twice; first frozen hydrated and later freeze-dried. The combination of the three analytical techniques proved useful: elements from C to Rb in the tardigrades could be determined and certain differences in distribution of elements between the frozen hydrated and the freeze-dried states were observed. RBS on frozen hydrated specimens provided knowledge of matrix elements.

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

PubMed

Baillie, J Kenneth; Bretherick, Andrew; Haley, Christopher S; Clohisey, Sara; Gray, Alan; Neyton, Lucile P A; Barrett, Jeffrey; Stahl, Eli A; Tenesa, Albert; Andersson, Robin; Brown, J Ben; Faulkner, Geoffrey J; Lizio, Marina; Schaefer, Ulf; Daub, Carsten; Itoh, Masayoshi; Kondo, Naoto; Lassmann, Timo; Kawai, Jun; Mole, Damian; Bajic, Vladimir B; Heutink, Peter; Rehli, Michael; Kawaji, Hideya; Sandelin, Albin; Suzuki, Harukazu; Satsangi, Jack; Wells, Christine A; Hacohen, Nir; Freeman, Thomas C; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R; Hume, David A

2018-03-01

Genetic variants underlying complex traits, including disease susceptibility, are enriched within the transcriptional regulatory elements, promoters and enhancers. There is emerging evidence that regulatory elements associated with particular traits or diseases share similar patterns of transcriptional activity. Accordingly, shared transcriptional activity (coexpression) may help prioritise loci associated with a given trait, and help to identify underlying biological processes. Using cap analysis of gene expression (CAGE) profiles of promoter- and enhancer-derived RNAs across 1824 human samples, we have analysed coexpression of RNAs originating from trait-associated regulatory regions using a novel quantitative method (network density analysis; NDA). For most traits studied, phenotype-associated variants in regulatory regions were linked to tightly-coexpressed networks that are likely to share important functional characteristics. Coexpression provides a new signal, independent of phenotype association, to enable fine mapping of causative variants. The NDA coexpression approach identifies new genetic variants associated with specific traits, including an association between the regulation of the OCT1 cation transporter and genetic variants underlying circulating cholesterol levels. NDA strongly implicates particular cell types and tissues in disease pathogenesis. For example, distinct groupings of disease-associated regulatory regions implicate two distinct biological processes in the pathogenesis of ulcerative colitis; a further two separate processes are implicated in Crohn's disease. Thus, our functional analysis of genetic predisposition to disease defines new distinct disease endotypes. We predict that patients with a preponderance of susceptibility variants in each group are likely to respond differently to pharmacological therapy. Together, these findings enable a deeper biological understanding of the causal basis of complex traits.

Genome-wide inference of regulatory networks in Streptomyces coelicolor.

PubMed

Castro-Melchor, Marlene; Charaniya, Salim; Karypis, George; Takano, Eriko; Hu, Wei-Shou

2010-10-18

The onset of antibiotics production in Streptomyces species is co-ordinated with differentiation events. An understanding of the genetic circuits that regulate these coupled biological phenomena is essential to discover and engineer the pharmacologically important natural products made by these species. The availability of genomic tools and access to a large warehouse of transcriptome data for the model organism, Streptomyces coelicolor, provides incentive to decipher the intricacies of the regulatory cascades and develop biologically meaningful hypotheses. In this study, more than 500 samples of genome-wide temporal transcriptome data, comprising wild-type and more than 25 regulatory gene mutants of Streptomyces coelicolor probed across multiple stress and medium conditions, were investigated. Information based on transcript and functional similarity was used to update a previously-predicted whole-genome operon map and further applied to predict transcriptional networks constituting modules enriched in diverse functions such as secondary metabolism, and sigma factor. The predicted network displays a scale-free architecture with a small-world property observed in many biological networks. The networks were further investigated to identify functionally-relevant modules that exhibit functional coherence and a consensus motif in the promoter elements indicative of DNA-binding elements. Despite the enormous experimental as well as computational challenges, a systems approach for integrating diverse genome-scale datasets to elucidate complex regulatory networks is beginning to emerge. We present an integrated analysis of transcriptome data and genomic features to refine a whole-genome operon map and to construct regulatory networks at the cistron level in Streptomyces coelicolor. The functionally-relevant modules identified in this study pose as potential targets for further studies and verification.

Antimicrobial and biological activity of leachate from light curable pulp capping materials.

PubMed

Arias-Moliz, Maria Teresa; Farrugia, Cher; Lung, Christie Y K; Wismayer, Pierre Schembri; Camilleri, Josette

2017-09-01

Characterization of a number of pulp capping materials and assessment of the leachate for elemental composition, antimicrobial activity and cell proliferation and expression. Three experimental light curable pulp-capping materials, Theracal and Biodentine were characterized by scanning electron microscopy, energy dispersive spectroscopy and X-ray diffraction. The elemental composition of the leachate formed after 24h was assessed by inductively coupled plasma (ICP). The antimicrobial activity of the leachate was determined by the minimum inhibitory concentration (MIC) against multispecies suspensions of Streptococcus mutans ATCC 25175, Streptococcus gordonii ATCC 33478 and Streptococcus sobrinus ATCC 33399. Cell proliferation and cell metabolic function over the material leachate was assessed by an indirect contact test using 3-(4,5 dimethylthiazolyl-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The hydration behavior of the test materials varied with Biodentine being the most reactive and releasing the highest amount of calcium ions in solution. All materials tested except the unfilled resin exhibited depletion of phosphate ions from the solution indicating interaction of the materials with the media. Regardless the different material characteristics, there was a similar antimicrobial activity and cellular activity. All the materials exhibited no antimicrobial activity and were initially cytotoxic with cell metabolic function improving after 3days. The development of light curable tricalcium silicate-based pulp capping materials is important to improve the bonding to the final resin restoration. Testing of both antimicrobial activity and biological behavior is critical for material development. The experimental light curable materials exhibited promising biological properties but require further development to enhance the antimicrobial characteristics. Copyright © 2017 Elsevier Ltd. All rights reserved.

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease

PubMed Central

Gray, Alan; Neyton, Lucile P. A.; Barrett, Jeffrey; Stahl, Eli A.; Tenesa, Albert; Andersson, Robin; Brown, J. Ben; Faulkner, Geoffrey J.; Lizio, Marina; Schaefer, Ulf; Daub, Carsten; Kondo, Naoto; Lassmann, Timo; Kawai, Jun; Kawaji, Hideya; Suzuki, Harukazu; Satsangi, Jack; Wells, Christine A.; Hacohen, Nir; Freeman, Thomas C.; Hayashizaki, Yoshihide; Forrest, Alistair R. R.; Hume, David A.

2018-01-01

Genetic variants underlying complex traits, including disease susceptibility, are enriched within the transcriptional regulatory elements, promoters and enhancers. There is emerging evidence that regulatory elements associated with particular traits or diseases share similar patterns of transcriptional activity. Accordingly, shared transcriptional activity (coexpression) may help prioritise loci associated with a given trait, and help to identify underlying biological processes. Using cap analysis of gene expression (CAGE) profiles of promoter- and enhancer-derived RNAs across 1824 human samples, we have analysed coexpression of RNAs originating from trait-associated regulatory regions using a novel quantitative method (network density analysis; NDA). For most traits studied, phenotype-associated variants in regulatory regions were linked to tightly-coexpressed networks that are likely to share important functional characteristics. Coexpression provides a new signal, independent of phenotype association, to enable fine mapping of causative variants. The NDA coexpression approach identifies new genetic variants associated with specific traits, including an association between the regulation of the OCT1 cation transporter and genetic variants underlying circulating cholesterol levels. NDA strongly implicates particular cell types and tissues in disease pathogenesis. For example, distinct groupings of disease-associated regulatory regions implicate two distinct biological processes in the pathogenesis of ulcerative colitis; a further two separate processes are implicated in Crohn’s disease. Thus, our functional analysis of genetic predisposition to disease defines new distinct disease endotypes. We predict that patients with a preponderance of susceptibility variants in each group are likely to respond differently to pharmacological therapy. Together, these findings enable a deeper biological understanding of the causal basis of complex traits. PMID:29494619

Geochemical and Isotopic Estimates of Eolian Dust in Soils of the San Juan Mountains, USA.

NASA Astrophysics Data System (ADS)

Lawrence, C. R.; Neff, J. C.; Farmer, L.; Painter, T. H.; Landry, C.

2007-12-01

Eolian dust deposition in the San Juan Mountain Range in southern Colorado has increased 5-7 fold in the past two centuries. This dust deposition contributes an exogenous supply of biologically relevant elements such as Ca, K, Mg, and P to these alpine ecosystems in the form of fine textured mineral particulates. The deposition of eolian dust may be an underestimated factor of soil formation and soil chemistry in these alpine settings. The importance of eolian dust relative to the weathering of local bedrock likely varies across bedrock types. The San Juan Range is geologically diverse with distinct regions of Meso-proterozic crystalline granites in the Weminuche Wilderness, Mesozoic sedimentary layers near Molas Pass in the San Juan National Forest, and Tertiary volcanic geology found on Red Mountain Pass in the Uncompahgre National Forest. Principle component analysis of element chemistry shows that bedrock and soils from these sites cluster by geology. In addition, these groups are chemically distinct from eolian dust collected from snow in the San Juan Range. Several elements seem to drive the difference of dust from soils and bedrock including Ca, Sr, Cu and Cd. The purpose of this research was to estimate the relative contribution of eolian dust to alpine soil element pools in the San Juan Mountains across a range of local geologic parent material. A calculation of element mass- balance shows that Cu and Cd are enriched in the surface soils of both volcanic and sedimentary soils relative to concentrations in local bedrock. However, Ca is enriched only in volcanic soils. These observations support the notion that eolian dust contributes to soil formation and that the relative contribution of dust across the landscape varies with geology. In addition to element mass-balance estimates we utilize Sr and Nd isotope measurements of soil, bedrock, and dust to further constrain the importance of eolian dust to these alpine soils.

Exploring High School Biology Students' Engagement with More and Less Epistemologically Considerate Texts

ERIC Educational Resources Information Center

Kloser, Matthew

2013-01-01

Texts play an integral role in science research and science classrooms yet biology textbooks have traditionally failed to reflect the epistemic elements of the discipline such as justification of claims and visual representations of empirical data. This study investigates high school biology students' reading experiences when engaging more…

Conceptual Elements: A Detailed Framework to Support and Assess Student Learning of Biology Core Concepts

ERIC Educational Resources Information Center

Cary, Tawnya; Branchaw, Janet

2017-01-01

The "Vision and Change in Undergraduate Biology Education: Call to Action" report has inspired and supported a nationwide movement to restructure undergraduate biology curricula to address overarching disciplinary concepts and competencies. The report outlines the concepts and competencies generally but does not provide a detailed…

Biological conversion of anglesite (PbSO(4)) and lead waste from spent car batteries to galena (PbS).

PubMed

Weijma, Jan; De Hoop, Klaas; Bosma, Wobby; Dijkman, Henk

2002-01-01

Lead paste, a solid mixture containing PbSO(4), PbO(2), PbO/Pb(OH)(2) precipitate, and elemental Pb, is one of the main waste fractions from spent car batteries. Biological sulfidation represents a new process for recovery of lead from this waste. In this process the lead salts in lead paste are converted to galena (PbS) by sulfate-reducing bacteria. This paper investigates a continuous process for sulfidation of anglesite (PbSO(4)), the main constituent of lead paste, and lead paste, consisting of a laboratory-scale gas-lift bioreactor to which a slurry of anglesite or lead paste was supplied. Sulfate or elemental sulfur was added as an additional sulfur source. Hydrogen gas served as an electron donor for the biological reduction of sulfate and elemental sulfur to sulfide by sulfate- and sulfur-reducing bacteria. Anglesite was almost completely converted to galena at a loading rate of 19 kg of PbSO(4) m(-)(3) day(-)(1), producing a sludge of which the crystalline lead phases consisted of >98% PbS (galena) and 1-2% elemental Pb. With lead paste, stable sulfidation rates of up to 17 kg of lead paste m(-)(3) day(-)(1) were demonstrated, producing a sludge of which the crystalline lead phases consisted of an estimated >96% PbS, 1-2% elemental Pb, and 1-2% PbO(2).

Particulate Trace Element Cycling in a Diatom Bloom at Station ALOHA

NASA Astrophysics Data System (ADS)

Weisend, R.; Morton, P. L.; Landing, W. M.; Fitzsimmons, J. N.; Hayes, C. T.; Boyle, E. A.

2014-12-01

Phytoplankton in oligotrophic marine deserts depend on remote sources to supply trace nutrients. To examine these sources, marine particulate matter samples from the central North Pacific (Station ALOHA) were collected during the July-August 2012 HOE-DYLAN cruises and analyzed for a suite of trace (e.g., Fe, Mn) and major (e.g. Al, P) elements. Daily surface SPM samples were examined for evidence of atmospheric deposition and biological uptake, while five vertical profiles were examined for evidence of surface vertical export and subsurface horizontal transport from nearby sources (e.g., margin sediments, hydrothermal plumes). Maxima in surface particulate P (a biological tracer) corresponded with a diatom bloom, and surprisingly also coincided with maxima in particulate Al (typically a tracer for lithogenic inputs). The surface particulate Al distributions likely result from the adsorption of dissolved Al onto diatom silica frustules, not from atmospheric dust deposition. In addition, a subsurface maximum in particulate Al and P was observed four days later at 75m, possibly resulting from vertical export of the surface diatom bloom. The distributions of other bioactive trace elements (e.g. Cd, Co, Cu) will be presented in the context of the diatom bloom and other biological, chemical and physical features. A second, complementary poster is also being presented which examines the cycling of trace elements in lithogenic particles (Morton et al., "Trace Element Cycling in Lithogenic Particles at Station ALOHA").

Spatial distribution and potential biological risk of some metals in relation to granulometric content in core sediments from Chilika Lake, India.

PubMed

Barik, Saroja K; Muduli, Pradipta R; Mohanty, Bita; Rath, Prasanta; Samanta, Srikanta

2018-01-01

The article presents first systematic report on the concentration of selected major elements [iron (Fe) and manganese (Mn)] and minor elements [zinc (Zn), copper (Cu), chromium (Cr), lead (Pb), nickel (Ni), and cobalt (Co)] from the core sediment of Chilika Lake, India. The analyzed samples revealed higher content of Pb than the background levels in the entire study area. The extent of contamination from minor and major elements is expressed by assessing (i) the metal enrichments in the sediment through the calculations of anthropogenic factor (AF), pollution load index (PLI), Enrichment factor (EF), and geoaccumulation index (Igeo) and (ii) potential biological risks by the use of sediment quality guidelines like effect range median (ERM) and effect range low (ERL) benchmarks. The estimated indices indicated that sediment is enriched with Pb, Ni, Cr, Cu and Co. The enrichment of these elements seems to be due to the fine granulometric characteristics of the sediment with Fe and Mn oxyhydroxides being the main metal carriers and fishing boats using low grade paints, fuel, and fishing technology using lead beads fixed to fishing nets. Trace element input to the Chilika lake needs to be monitored with due emphasis on Cr and Pb contaminations since the ERM and ERL benchmarks indicated potential biological risk with these metals.

Effects of Different Zinc Species on Cellar Zinc Distribution, Cell Cycle, Apoptosis and Viability in MDAMB231 Cells.

PubMed

Wang, Yan-hong; Zhao, Wen-jie; Zheng, Wei-juan; Mao, Li; Lian, Hong-zhen; Hu, Xin; Hua, Zi-chun

2016-03-01

Intracellular metal elements exist in mammalian cells with the concentration range from picomoles per litre to micromoles per litre and play a considerable role in various biological procedures. Element provided by different species can influence the availability and distribution of the element in a cell and could lead to different biological effects on the cell's growth and function. Zinc as an abundant and widely distributed essential trace element, is involved in numerous and relevant physiological functions. Zinc homeostasis in cells, which is regulated by metallothioneins, zinc transporter/SLC30A, Zrt-/Irt-like proteins/SLC39A and metal-response element-binding transcription factor-1 (MTF-1), is crucial for normal cellular functioning. In this study, we investigated the influences of different zinc species, zinc sulphate, zinc gluconate and bacitracin zinc, which represented inorganic, organic and biological zinc species, respectively, on cell cycle, viability and apoptosis in MDAMB231 cells. It was found that the responses of cell cycle, apoptosis and death to different zinc species in MDAMB231 cells are different. Western blot analysis of the expression of several key proteins in regulating zinc-related transcription, cell cycle, apoptosis, including MTF-1, cyclin B1, cyclin D1, caspase-8 and caspase-9 in treated cells further confirmed the observed results on cell level.

Mammalian lipoxygenases and their biological relevance

PubMed Central

Kuhn, Hartmut; Banthiya, Swathi; van Leyen, Klaus

2015-01-01

Lipoxygenases (LOXs) form a heterogeneous class of lipid peroxidizing enzymes, which have been implicated in cell proliferation and differentiation but also in the pathogenesis of various diseases with major public health relevance. As other fatty acid dioxygenases LOX oxidize polyunsaturated fatty acids to their corresponding hydroperoxy derivatives, which are further transformed to bioactive lipid mediators (eicosanoids and related substances). On the other hand, lipoxygenases are key players in regulation of the cellular redox homeostasis, which is an important element in gene expression regulation. Although the first mammalian lipoxygenases were discovered 40 years ago and although the enzymes have been well characterized with respect to their structural and functional properties the biological roles of the different lipoxygenase isoforms are not completely understood. This review is aimed at summarizing the current knowledge on the physiological roles of different mammalian LOX-isoforms and their patho-physiological function in inflammatory, metabolic, hyperproliferative, neurodegenerative and infectious disorders. PMID:25316652

Computer support for physiological cell modelling using an ontology on cell physiology.

PubMed

Takao, Shimayoshi; Kazuhiro, Komurasaki; Akira, Amano; Takeshi, Iwashita; Masanori, Kanazawa; Tetsuya, Matsuda

2006-01-01

The development of electrophysiological whole cell models to support the understanding of biological mechanisms is increasing rapidly. Due to the complexity of biological systems, comprehensive cell models, which are composed of many imported sub-models of functional elements, can get quite complicated as well, making computer modification difficult. Here, we propose a computer support to enhance structural changes of cell models, employing the markup languages CellML and our original PMSML (physiological model structure markup language), in addition to a new ontology for cell physiological modelling. In particular, a method to make references from CellML files to the ontology and a method to assist manipulation of model structures using markup languages together with the ontology are reported. Using these methods three software utilities, including a graphical model editor, are implemented. Experimental results proved that these methods are effective for the modification of electrophysiological models.

Infant toxicology: state of the science and considerations in evaluation of safety.

PubMed

Neal-Kluever, April; Aungst, Jason; Gu, Yan; Hatwell, Karen; Muldoon-Jacobs, Kristi; Liem, Ayesha; Ogungbesan, Adejoke; Shackelford, Mary

2014-08-01

Differences in the physiology and biological susceptibilities of adults and infants have led to growing interest in safety evaluation methods for exposures from infant formula packaging. In addition to potential physiological differences, infants aged 0-6 months may consume a sole source of food, infant formula or breast milk, and consume higher amounts of food relative to body weight compared to adults. While the duration of the exposure is short compared to the expected lifespan of the individual, it occurs during a period of important developmental processes. The purpose of this document is to (1) review key biological and exposure elements that may impact the evaluation of safety for food contact products intended for use by infants, (2) summarize the current reproductive and developmental toxicity testing protocols available, and (3) identify potential data gaps concerning this period of development. Published by Elsevier Ltd.

Negotiation of mutualism: rhizobia and legumes

PubMed Central

Akçay, Erol; Roughgarden, Joan

2006-01-01

The evolution and persistence of biological cooperation have been an important puzzle in evolutionary theory. Here, we suggest a new approach based on bargaining theory to tackle the question. We present a mechanistic model for negotiation of benefits between a nitrogen-fixing nodule and a legume plant. To that end, we first derive growth rates for the nodule and plant from metabolic models of each as a function of material fluxes between them. We use these growth rates as pay-off functions in the negotiation process, which is analogous to collective bargaining between a firm and a workers' union. Our model predicts that negotiations lead to the Nash bargaining solution, maximizing the product of players' pay-offs. This work introduces elements of cooperative game theory into the field of mutualistic interactions. In the discussion of the paper, we argue for the benefits of such an approach in studying the question of biological cooperation. PMID:17015340

Decoding the genome beyond sequencing: the new phase of genomic research.

PubMed

Heng, Henry H Q; Liu, Guo; Stevens, Joshua B; Bremer, Steven W; Ye, Karen J; Abdallah, Batoul Y; Horne, Steven D; Ye, Christine J

2011-10-01

While our understanding of gene-based biology has greatly improved, it is clear that the function of the genome and most diseases cannot be fully explained by genes and other regulatory elements. Genes and the genome represent distinct levels of genetic organization with their own coding systems; Genes code parts like protein and RNA, but the genome codes the structure of genetic networks, which are defined by the whole set of genes, chromosomes and their topological interactions within a cell. Accordingly, the genetic code of DNA offers limited understanding of genome functions. In this perspective, we introduce the genome theory which calls for the departure of gene-centric genomic research. To make this transition for the next phase of genomic research, it is essential to acknowledge the importance of new genome-based biological concepts and to establish new technology platforms to decode the genome beyond sequencing. Copyright © 2011 Elsevier Inc. All rights reserved.

Resonant soft X-ray scattering on protein solutions

NASA Astrophysics Data System (ADS)

Ye, Dan; Le, Thinh; Wang, Cheng; Zwart, Peter; Gomez, Esther; Gomez, Enrique

Protein structure is crucial for biological function, such that characterizing protein folding and packing is important for the design of therapeutics and enzymes. We propose resonant soft X-ray scattering (RSOXS) as an approach to study proteins and other biological assemblies in solution. Calculations of the scattering contrast suggest that soft X-ray scattering is more sensitive than hard X-ray scattering, because of contrast generated at the absorption edges of constituent elements such as carbon, nitrogen and oxygen. We have examined the structure of bovine serum albumin (BSA) in solution by RSOXS. We find that by varying incident X-ray energies, we are able to achieve higher scattering contrast near the absorption edge. From our RSOXS scattering result we are able to reconstruct the structure of BSA in 3D. These RSOXS results also agree with hard X-ray experiments, including crystallographic data. Our study demonstrates the potential of RSOXS for studying protein structure in solution.

RNA Characterization by Solid-State NMR Spectroscopy.

PubMed

Yang, Yufei; Wang, Shenlin

2018-06-21

The structures of RNAs, which play critical roles in various biological processes, provide important clues and insights into the biological functions of these molecules. However, RNA structure determination remains a challenging topic. In recent years, magic-angle-spinning solid-state NMR (MAS SSNMR) has emerged as an alternative technique for structural and dynamic characterization of RNA. MAS SSNMR has been successfully applied to provide atomic-level structural information about several RNA molecules and RNA-protein complexes. In this Minireview, we give an overview of recent progress in the field of MAS SSNMR based RNA structural characterization, and introduce sample preparation strategies and SSNMR spectroscopic techniques that have been incorporated to identify RNA structural elements. We also highlight a few impressive examples of RNAs that have been investigated extensively by SSNMR. Finally, we briefly discuss future technical trends in the use of MAS SSNMR to facilitate RNA structure determination. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Without it no music: cognition, biology and evolution of musicality.

PubMed

Honing, Henkjan; ten Cate, Carel; Peretz, Isabelle; Trehub, Sandra E

2015-03-19

Musicality can be defined as a natural, spontaneously developing trait based on and constrained by biology and cognition. Music, by contrast, can be defined as a social and cultural construct based on that very musicality. One critical challenge is to delineate the constituent elements of musicality. What biological and cognitive mechanisms are essential for perceiving, appreciating and making music? Progress in understanding the evolution of music cognition depends upon adequate characterization of the constituent mechanisms of musicality and the extent to which they are present in non-human species. We argue for the importance of identifying these mechanisms and delineating their functions and developmental course, as well as suggesting effective means of studying them in human and non-human animals. It is virtually impossible to underpin the evolutionary role of musicality as a whole, but a multicomponent perspective on musicality that emphasizes its constituent capacities, development and neural cognitive specificity is an excellent starting point for a research programme aimed at illuminating the origins and evolution of musical behaviour as an autonomous trait. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Without it no music: cognition, biology and evolution of musicality

PubMed Central

Honing, Henkjan; ten Cate, Carel; Peretz, Isabelle; Trehub, Sandra E.

2015-01-01

Musicality can be defined as a natural, spontaneously developing trait based on and constrained by biology and cognition. Music, by contrast, can be defined as a social and cultural construct based on that very musicality. One critical challenge is to delineate the constituent elements of musicality. What biological and cognitive mechanisms are essential for perceiving, appreciating and making music? Progress in understanding the evolution of music cognition depends upon adequate characterization of the constituent mechanisms of musicality and the extent to which they are present in non-human species. We argue for the importance of identifying these mechanisms and delineating their functions and developmental course, as well as suggesting effective means of studying them in human and non-human animals. It is virtually impossible to underpin the evolutionary role of musicality as a whole, but a multicomponent perspective on musicality that emphasizes its constituent capacities, development and neural cognitive specificity is an excellent starting point for a research programme aimed at illuminating the origins and evolution of musical behaviour as an autonomous trait. PMID:25646511

Rupturing of Biological Spores As a Source of Secondary Particles in Amazonia

DOE Office of Scientific and Technical Information (OSTI.GOV)

China, Swarup; Wang, Bingbing; Weis, Johannes

Airborne biological particles, such as fungal spores and pollen, are ubiquitous in the Earth’s atmosphere and play an important role in the atmospheric environment and climate, impacting air quality, cloud formation, and the Earth’s radiation budget. The atmospheric transformations of airborne biological spores at elevated relative humidity remain poorly understood and their climatic role is uncertain. Using an environmental scanning electron microscope (ESEM), we observed rupturing of Amazonian fungal spores and subsequent release of nanometer to submicron size fragments after exposure to high humidity. We find that fungal fragments contain elements of inorganic salts (e.g., Na and Cl). They aremore » hygroscopic in nature with a growth factor up to 2.3 at 96% relative humidity, thus they may potentially influence cloud formation. Due to their hygroscopic growth, light scattering cross sections of the fragments are enhanced by up to a factor of 10. Furthermore, rupturing of fungal spores at high humidity may explain the bursting events of nanoparticles and may provide insight into new particle formation in Amazonia.« less

Mammalian lipoxygenases and their biological relevance.

PubMed

Kuhn, Hartmut; Banthiya, Swathi; van Leyen, Klaus

2015-04-01

Lipoxygenases (LOXs) form a heterogeneous class of lipid peroxidizing enzymes, which have been implicated not only in cell proliferation and differentiation but also in the pathogenesis of various diseases with major public health relevance. As other fatty acid dioxygenases LOXs oxidize polyunsaturated fatty acids to their corresponding hydroperoxy derivatives, which are further transformed to bioactive lipid mediators (eicosanoids and related substances). On the other hand, lipoxygenases are key players in the regulation of the cellular redox homeostasis, which is an important element in gene expression regulation. Although the first mammalian lipoxygenases were discovered 40 years ago and although the enzymes have been well characterized with respect to their structural and functional properties the biological roles of the different lipoxygenase isoforms are not completely understood. This review is aimed at summarizing the current knowledge on the physiological roles of different mammalian LOX-isoforms and their patho-physiological function in inflammatory, metabolic, hyperproliferative, neurodegenerative and infectious disorders. This article is part of a Special Issue entitled "Oxygenated metabolism of PUFA: analysis and biological relevance". Copyright © 2014 Elsevier B.V. All rights reserved.

Computational studies of Ras and PI3K

NASA Technical Reports Server (NTRS)

Ren, Lei; Cucinotta, Francis A.

2004-01-01

Until recently, experimental techniques in molecular cell biology have been the primary means to investigate biological risk upon space radiation. However, computational modeling provides an alternative theoretical approach, which utilizes various computational tools to simulate proteins, nucleotides, and their interactions. In this study, we are focused on using molecular mechanics (MM) and molecular dynamics (MD) to study the mechanism of protein-protein binding and to estimate the binding free energy between proteins. Ras is a key element in a variety of cell processes, and its activation of phosphoinositide 3-kinase (PI3K) is important for survival of transformed cells. Different computational approaches for this particular study are presented to calculate the solvation energies and binding free energies of H-Ras and PI3K. The goal of this study is to establish computational methods to investigate the roles of different proteins played in the cellular responses to space radiation, including modification of protein function through gene mutation, and to support the studies in molecular cell biology and theoretical kinetics models for our risk assessment project.

Biomarkers as Common Data Elements for Symptom and Self-Management Science.

PubMed

Page, Gayle G; Corwin, Elizabeth J; Dorsey, Susan G; Redeker, Nancy S; McCloskey, Donna Jo; Austin, Joan K; Guthrie, Barbara J; Moore, Shirley M; Barton, Debra; Kim, Miyong T; Docherty, Sharron L; Waldrop-Valverde, Drenna; Bailey, Donald E; Schiffman, Rachel F; Starkweather, Angela; Ward, Teresa M; Bakken, Suzanne; Hickey, Kathleen T; Renn, Cynthia L; Grady, Patricia

2018-05-01

Biomarkers as common data elements (CDEs) are important for the characterization of biobehavioral symptoms given that once a biologic moderator or mediator is identified, biologically based strategies can be investigated for treatment efforts. Just as a symptom inventory reflects a symptom experience, a biomarker is an indicator of the symptom, though not the symptom per se. The purposes of this position paper are to (a) identify a "minimum set" of biomarkers for consideration as CDEs in symptom and self-management science, specifically biochemical biomarkers; (b) evaluate the benefits and limitations of such a limited array of biomarkers with implications for symptom science; (c) propose a strategy for the collection of the endorsed minimum set of biologic samples to be employed as CDEs for symptom science; and (d) conceptualize this minimum set of biomarkers consistent with National Institute of Nursing Research (NINR) symptoms of fatigue, depression, cognition, pain, and sleep disturbance. From May 2016 through January 2017, a working group consisting of a subset of the Directors of the NINR Centers of Excellence funded by P20 or P30 mechanisms and NINR staff met bimonthly via telephone to develop this position paper suggesting the addition of biomarkers as CDEs. The full group of Directors reviewed drafts, provided critiques and suggestions, recommended the minimum set of biomarkers, and approved the completed document. Best practices for selecting, identifying, and using biological CDEs as well as challenges to the use of biological CDEs for symptom and self-management science are described. Current platforms for sample outcome sharing are presented. Finally, biological CDEs for symptom and self-management science are proposed along with implications for future research and use of CDEs in these areas. The recommended minimum set of biomarker CDEs include pro- and anti-inflammatory cytokines, a hypothalamic-pituitary-adrenal axis marker, cortisol, the neuropeptide brain-derived neurotrophic factor, and DNA polymorphisms. It is anticipated that this minimum set of biomarker CDEs will be refined as knowledge regarding biologic mechanisms underlying symptom and self-management science further develop. The incorporation of biological CDEs may provide insights into mechanisms of symptoms, effectiveness of proposed interventions, and applicability of chosen theoretical frameworks. Similarly, as for the previously suggested NINR CDEs for behavioral symptoms and self-management of chronic conditions, biological CDEs offer the potential for collaborative efforts that will strengthen symptom and self-management science. The use of biomarker CDEs in biobehavioral symptoms research will facilitate the reproducibility and generalizability of research findings and benefit symptom and self-management science. © 2018 Sigma Theta Tau International.

Official Methods for the Determination of Minerals and Trace Elements in Infant Formula and Milk Products: A Review.

PubMed

Poitevin, Eric

2016-01-01

The minerals and trace elements that account for about 4% of total human body mass serve as materials and regulators in numerous biological activities in body structure building. Infant formula and milk products are important sources of endogenic and added minerals and trace elements and hence, must comply with regulatory as well as nutritional and safety requirements. In addition, reliable analytical data are necessary to support product content and innovation, health claims, or declaration and specific safety issues. Adequate analytical platforms and methods must be implemented to demonstrate both the compliance and safety assessment of all declared and regulated minerals and trace elements, especially trace-element contaminant surveillance. The first part of this paper presents general information on the mineral composition of infant formula and milk products and their regulatory status. In the second part, a survey describes the main techniques and related current official methods determining minerals and trace elements in infant formula and milk products applied for by various international organizations (AOAC INTERNATIONAL, the International Organization for Standardization, the International Dairy Federation, and the European Committe for Standardization). The third part summarizes method officialization activities by Stakeholder Panels on Infant Formula and Adult Nutritionals and Stakeholder Panel on Strategic Food Analytical Methods. The final part covers a general discussion focusing on analytical gaps and future trends in inorganic analysis that have been applied for in infant formula and milk-based products.

Psychiatry outside the framework of empiricism.

PubMed

Mume, Celestine Okorome

2017-01-01

Science is interested in whatever that is empirical and objective. Any claim that cannot be objectively demonstrated has no place in science, because the subject does not deviate from the role, which it has set out to play in the life of mankind. Psychiatry, as a scientific discipline, plays along these basic principles. In the etiology, symptomatology, and management of psychiatric disorders, the biopsychosocial model recognizes the role of biological, psychological, and social factors. This essay views psychiatry from the biopsychosocial perspective and asserts that certain elements, which may not be readily and empirically verifiable, are important in the practice of psychiatry.

Crystal structure of enolase from Drosophila melanogaster.

PubMed

Sun, Congcong; Xu, Baokui; Liu, Xueyan; Zhang, Zhen; Su, Zhongliang

2017-04-01

Enolase is an important enzyme in glycolysis and various biological processes. Its dysfunction is closely associated with diseases. Here, the enolase from Drosophila melanogaster (DmENO) was purified and crystallized. A crystal of DmENO diffracted to 2.0 Å resolution and belonged to space group R32. The structure was solved by molecular replacement. Like most enolases, DmENO forms a homodimer with conserved residues in the dimer interface. DmENO possesses an open conformation in this structure and contains conserved elements for catalytic activity. This work provides a structural basis for further functional and evolutionary studies of enolase.

Analysis of sDMA modifications of PIWI proteins

PubMed Central

Honda, Shozo; Kirino, Yoriko; Kirino, Yohei

2015-01-01

Summary Arginine methylation is an important post-translational protein modification that modulates protein function for a wide range of biological processes. PIWI proteins, a subclade of the Argonaute family proteins, contain evolutionarily conserved symmetrical dimethylarginines (sDMAs). It has become increasingly apparent that the sDMAs of PIWI proteins serve as binding elements for TUDOR-domain containing proteins and that sDMA-dependent protein interactions play crucial roles in the biogenesis and function of PIWI-interacting RNAs (piRNAs). We describe a method for detecting PIWI sDMAs and purifying PIWI/piRNA complexes using anti-sDMA antibodies. PMID:24178562

Bioforensics: Characterization of biological weapons agents by NanoSIMS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weber, P K; Ghosal, S; Leighton, T J

2007-02-26

The anthrax attacks of Fall 2001 highlight the need to develop forensic methods based on multiple identifiers to determine the origin of biological weapons agents. Genetic typing methods (i.e., DNA and RNA-based) provide one attribution technology, but genetic information alone is not usually sufficient to determine the provenance of the material. Non-genetic identifiers, including elemental and isotopic signatures, provide complementary information that can be used to identify the means, geographic location and date of production. Under LDRD funding, we have successfully developed the techniques necessary to perform bioforensic characterization with the NanoSIMS at the individual spore level. We have developedmore » methods for elemental and isotopic characterization at the single spore scale. We have developed methods for analyzing spore sections to map elemental abundance within spores. We have developed rapid focused ion beam (FIB) sectioning techniques for spores to preserve elemental and structural integrity. And we have developed a high-resolution depth profiling method to characterize the elemental distribution in individual spores without sectioning. We used these newly developed methods to study the controls on elemental abundances in spores, characterize the elemental distribution of in spores, and to study elemental uptake by spores. Our work under this LDRD project attracted FBI and DHS funding for applied purposes.« less

Changes in the Bacterial Community of Soil from a Neutral Mine Drainage Channel

PubMed Central

Pereira, Letícia Bianca; Vicentini, Renato; Ottoboni, Laura M. M.

2014-01-01

Mine drainage is an important environmental disturbance that affects the chemical and biological components in natural resources. However, little is known about the effects of neutral mine drainage on the soil bacteria community. Here, a high-throughput 16S rDNA pyrosequencing approach was used to evaluate differences in composition, structure, and diversity of bacteria communities in samples from a neutral drainage channel, and soil next to the channel, at the Sossego copper mine in Brazil. Advanced statistical analyses were used to explore the relationships between the biological and chemical data. The results showed that the neutral mine drainage caused changes in the composition and structure of the microbial community, but not in its diversity. The Deinococcus/Thermus phylum, especially the Meiothermus genus, was in large part responsible for the differences between the communities, and was positively associated with the presence of copper and other heavy metals in the environmental samples. Other important parameters that influenced the bacterial diversity and composition were the elements potassium, sodium, nickel, and zinc, as well as pH. The findings contribute to the understanding of bacterial diversity in soils impacted by neutral mine drainage, and demonstrate that heavy metals play an important role in shaping the microbial population in mine environments. PMID:24796430

NMR studies of protein-nucleic acid interactions.

PubMed

Varani, Gabriele; Chen, Yu; Leeper, Thomas C

2004-01-01

Protein-DNA and protein-RNA complexes play key functional roles in every living organism. Therefore, the elucidation of their structure and dynamics is an important goal of structural and molecular biology. Nuclear magnetic resonance (NMR) studies of protein and nucleic acid complexes have common features with studies of protein-protein complexes: the interaction surfaces between the molecules must be carefully delineated, the relative orientation of the two species needs to be accurately and precisely determined, and close intermolecular contacts defined by nuclear Overhauser effects (NOEs) must be obtained. However, differences in NMR properties (e.g., chemical shifts) and biosynthetic pathways for sample productions generate important differences. Chemical shift differences between the protein and nucleic acid resonances can aid the NMR structure determination process; however, the relatively limited dispersion of the RNA ribose resonances makes the process of assigning intermolecular NOEs more difficult. The analysis of the resulting structures requires computational tools unique to nucleic acid interactions. This chapter summarizes the most important elements of the structure determination by NMR of protein-nucleic acid complexes and their analysis. The main emphasis is on recent developments (e.g., residual dipolar couplings and new Web-based analysis tools) that have facilitated NMR studies of these complexes and expanded the type of biological problems to which NMR techniques of structural elucidation can now be applied.

Conceptual Elements: A Detailed Framework to Support and Assess Student Learning of Biology Core Concepts

PubMed Central

Cary, Tawnya; Branchaw, Janet

2017-01-01

The Vision and Change in Undergraduate Biology Education: Call to Action report has inspired and supported a nationwide movement to restructure undergraduate biology curricula to address overarching disciplinary concepts and competencies. The report outlines the concepts and competencies generally but does not provide a detailed framework to guide the development of the learning outcomes, instructional materials, and assessment instruments needed to create a reformed biology curriculum. In this essay, we present a detailed Vision and Change core concept framework that articulates key components that transcend subdisciplines and scales for each overarching biological concept, the Conceptual Elements (CE) Framework. The CE Framework was developed using a grassroots approach of iterative revision and incorporates feedback from more than 60 biologists and undergraduate biology educators from across the United States. The final validation step resulted in strong national consensus, with greater than 92% of responders agreeing that each core concept list was ready for use by the biological sciences community, as determined by scientific accuracy and completeness. In addition, we describe in detail how educators and departments can use the CE Framework to guide and document reformation of individual courses as well as entire curricula. PMID:28450444

Uncovering the Repertoire of Endogenous Flaviviral Elements in Aedes Mosquito Genomes

PubMed Central

Suzuki, Yasutsugu; Frangeul, Lionel; Dickson, Laura B.; Blanc, Hervé; Verdier, Yann; Vinh, Joelle

2017-01-01

ABSTRACT Endogenous viral elements derived from nonretroviral RNA viruses have been described in various animal genomes. Whether they have a biological function, such as host immune protection against related viruses, is a field of intense study. Here, we investigated the repertoire of endogenous flaviviral elements (EFVEs) in Aedes mosquitoes, the vectors of arboviruses such as dengue and chikungunya viruses. Previous studies identified three EFVEs from Aedes albopictus cell lines and one from Aedes aegypti cell lines. However, an in-depth characterization of EFVEs in wild-type mosquito populations and individual mosquitoes in vivo has not been performed. We detected the full-length DNA sequence of the previously described EFVEs and their respective transcripts in several A. albopictus and A. aegypti populations from geographically distinct areas. However, EFVE-derived proteins were not detected by mass spectrometry. Using deep sequencing, we detected the production of PIWI-interacting RNA-like small RNAs, in an antisense orientation, targeting the EFVEs and their flanking regions in vivo. The EFVEs were integrated in repetitive regions of the mosquito genomes, and their flanking sequences varied among mosquito populations. We bioinformatically predicted several new EFVEs from a Vietnamese A. albopictus population and observed variation in the occurrence of those elements among mosquitoes. Phylogenetic analysis of an A. aegypti EFVE suggested that it integrated prior to the global expansion of the species and subsequently diverged among and within populations. The findings of this study together reveal the substantial structural and nucleotide diversity of flaviviral integrations in Aedes genomes. Unraveling this diversity will help to elucidate the potential biological function of these EFVEs. IMPORTANCE Endogenous viral elements (EVEs) are whole or partial viral sequences integrated in host genomes. Interestingly, some EVEs have important functions for host fitness and antiviral defense. Because mosquitoes also have EVEs in their genomes, characterizing these EVEs is a prerequisite for their potential use to manipulate the mosquito antiviral response. In the study described here, we focused on EVEs related to the Flavivirus genus, to which dengue and Zika viruses belong, in individual Aedes mosquitoes from geographically distinct areas. We show the existence in vivo of flaviviral EVEs previously identified in mosquito cell lines, and we detected new ones. We show that EVEs have evolved differently in each mosquito population. They produce transcripts and small RNAs but not proteins, suggesting a function at the RNA level. Our study uncovers the diverse repertoire of flaviviral EVEs in Aedes mosquito populations and contributes to an understanding of their role in the host antiviral system. PMID:28539440

Uncovering the Repertoire of Endogenous Flaviviral Elements in Aedes Mosquito Genomes.

PubMed

Suzuki, Yasutsugu; Frangeul, Lionel; Dickson, Laura B; Blanc, Hervé; Verdier, Yann; Vinh, Joelle; Lambrechts, Louis; Saleh, Maria-Carla

2017-08-01

Endogenous viral elements derived from nonretroviral RNA viruses have been described in various animal genomes. Whether they have a biological function, such as host immune protection against related viruses, is a field of intense study. Here, we investigated the repertoire of endogenous flaviviral elements (EFVEs) in Aedes mosquitoes, the vectors of arboviruses such as dengue and chikungunya viruses. Previous studies identified three EFVEs from Aedes albopictus cell lines and one from Aedes aegypti cell lines. However, an in-depth characterization of EFVEs in wild-type mosquito populations and individual mosquitoes in vivo has not been performed. We detected the full-length DNA sequence of the previously described EFVEs and their respective transcripts in several A. albopictus and A. aegypti populations from geographically distinct areas. However, EFVE-derived proteins were not detected by mass spectrometry. Using deep sequencing, we detected the production of PIWI-interacting RNA-like small RNAs, in an antisense orientation, targeting the EFVEs and their flanking regions in vivo The EFVEs were integrated in repetitive regions of the mosquito genomes, and their flanking sequences varied among mosquito populations. We bioinformatically predicted several new EFVEs from a Vietnamese A. albopictus population and observed variation in the occurrence of those elements among mosquitoes. Phylogenetic analysis of an A. aegypti EFVE suggested that it integrated prior to the global expansion of the species and subsequently diverged among and within populations. The findings of this study together reveal the substantial structural and nucleotide diversity of flaviviral integrations in Aedes genomes. Unraveling this diversity will help to elucidate the potential biological function of these EFVEs. IMPORTANCE Endogenous viral elements (EVEs) are whole or partial viral sequences integrated in host genomes. Interestingly, some EVEs have important functions for host fitness and antiviral defense. Because mosquitoes also have EVEs in their genomes, characterizing these EVEs is a prerequisite for their potential use to manipulate the mosquito antiviral response. In the study described here, we focused on EVEs related to the Flavivirus genus, to which dengue and Zika viruses belong, in individual Aedes mosquitoes from geographically distinct areas. We show the existence in vivo of flaviviral EVEs previously identified in mosquito cell lines, and we detected new ones. We show that EVEs have evolved differently in each mosquito population. They produce transcripts and small RNAs but not proteins, suggesting a function at the RNA level. Our study uncovers the diverse repertoire of flaviviral EVEs in Aedes mosquito populations and contributes to an understanding of their role in the host antiviral system. Copyright © 2017 Suzuki et al.

Solving the forward problem of magnetoacoustic tomography with magnetic induction by means of the finite element method

NASA Astrophysics Data System (ADS)

Li, Xun; Li, Xu; Zhu, Shanan; He, Bin

2009-05-01

Magnetoacoustic tomography with magnetic induction (MAT-MI) is a recently proposed imaging modality to image the electrical impedance of biological tissue. It combines the good contrast of electrical impedance tomography with the high spatial resolution of sonography. In this paper, a three-dimensional MAT-MI forward problem was investigated using the finite element method (FEM). The corresponding FEM formulae describing the forward problem are introduced. In the finite element analysis, magnetic induction in an object with conductivity values close to biological tissues was first carried out. The stimulating magnetic field was simulated as that generated from a three-dimensional coil. The corresponding acoustic source and field were then simulated. Computer simulation studies were conducted using both concentric and eccentric spherical conductivity models with different geometric specifications. In addition, the grid size for finite element analysis was evaluated for the model calibration and evaluation of the corresponding acoustic field.

The CGTCA sequence motif is essential for biological activity of the vasoactive intestinal peptide gene cAMP-regulated enhancer.

PubMed Central

Fink, J S; Verhave, M; Kasper, S; Tsukada, T; Mandel, G; Goodman, R H

1988-01-01

cAMP-regulated transcription of the human vasoactive intestinal peptide gene is dependent upon a 17-base-pair DNA element located 70 base pairs upstream from the transcriptional initiation site. This element is similar to sequences in other genes known to be regulated by cAMP and to sequences in several viral enhancers. We have demonstrated that the vasoactive intestinal peptide regulatory element is an enhancer that depends upon the integrity of two CGTCA sequence motifs for biological activity. Mutations in either of the CGTCA motifs diminish the ability of the element to respond to cAMP. Enhancers containing the CGTCA motif from the somatostatin and adenovirus genes compete for binding of nuclear proteins from C6 glioma and PC12 cells to the vasoactive intestinal peptide enhancer, suggesting that CGTCA-containing enhancers interact with similar transacting factors. Images PMID:2842787

Solving the Forward Problem of Magnetoacoustic Tomography with Magnetic Induction by Means of the Finite Element Method

PubMed Central

Li, Xun; Li, Xu; Zhu, Shanan; He, Bin

2010-01-01

Magnetoacoustic Tomography with Magnetic Induction (MAT-MI) is a recently proposed imaging modality to image the electrical impedance of biological tissue. It combines the good contrast of electrical impedance tomography with the high spatial resolution of sonography. In this paper, three-dimensional MAT-MI forward problem was investigated using the finite element method (FEM). The corresponding FEM formulas describing the forward problem are introduced. In the finite element analysis, magnetic induction in an object with conductivity values close to biological tissues was first carried out. The stimulating magnetic field was simulated as that generated from a three-dimensional coil. The corresponding acoustic source and field were then simulated. Computer simulation studies were conducted using both concentric and eccentric spherical conductivity models with different geometric specifications. In addition, the grid size for finite element analysis was evaluated for model calibration and evaluation of the corresponding acoustic field. PMID:19351978

Imaging Electric Properties of Biological Tissues by RF Field Mapping in MRI

PubMed Central

Zhang, Xiaotong; Zhu, Shanan; He, Bin

2010-01-01

The electric properties (EPs) of biological tissue, i.e., the electric conductivity and permittivity, can provide important information in the diagnosis of various diseases. The EPs also play an important role in specific absorption rate (SAR) calculation, a major concern in high-field Magnetic Resonance Imaging (MRI), as well as in non-medical areas such as wireless-telecommunications. The high-field MRI system is accompanied by significant wave propagation effects, and the radio frequency (RF) radiation is dependent on the EPs of biological tissue. Based on the measurement of the active transverse magnetic component of the applied RF field (known as B1-mapping technique), we propose a dual-excitation algorithm, which uses two sets of measured B1 data to noninvasively reconstruct the electric properties of biological tissues. The Finite Element Method (FEM) was utilized in three-dimensional (3D) modeling and B1 field calculation. A series of computer simulations were conducted to evaluate the feasibility and performance of the proposed method on a 3D head model within a transverse electromagnetic (TEM) coil and a birdcage (BC) coil. Using a TEM coil, when noise free, the reconstructed EP distribution of tissues in the brain has relative errors of 12% ∼ 28% and correlated coefficients of greater than 0.91. Compared with other B1-mapping based reconstruction algorithms, our approach provides superior performance without the need for iterative computations. The present simulation results suggest that good reconstruction of electric properties from B1 mapping can be achieved. PMID:20129847

Stochasticity versus determinism: consequences for realistic gene regulatory network modelling and evolution.

PubMed

Jenkins, Dafyd J; Stekel, Dov J

2010-02-01

Gene regulation is one important mechanism in producing observed phenotypes and heterogeneity. Consequently, the study of gene regulatory network (GRN) architecture, function and evolution now forms a major part of modern biology. However, it is impossible to experimentally observe the evolution of GRNs on the timescales on which living species evolve. In silico evolution provides an approach to studying the long-term evolution of GRNs, but many models have either considered network architecture from non-adaptive evolution, or evolution to non-biological objectives. Here, we address a number of important modelling and biological questions about the evolution of GRNs to the realistic goal of biomass production. Can different commonly used simulation paradigms, in particular deterministic and stochastic Boolean networks, with and without basal gene expression, be used to compare adaptive with non-adaptive evolution of GRNs? Are these paradigms together with this goal sufficient to generate a range of solutions? Will the interaction between a biological goal and evolutionary dynamics produce trade-offs between growth and mutational robustness? We show that stochastic basal gene expression forces shrinkage of genomes due to energetic constraints and is a prerequisite for some solutions. In systems that are able to evolve rates of basal expression, two optima, one with and one without basal expression, are observed. Simulation paradigms without basal expression generate bloated networks with non-functional elements. Further, a range of functional solutions was observed under identical conditions only in stochastic networks. Moreover, there are trade-offs between efficiency and yield, indicating an inherent intertwining of fitness and evolutionary dynamics.

Undergraduate Students’ Initial Ability in Understanding Phylogenetic Tree

NASA Astrophysics Data System (ADS)

Sa'adah, S.; Hidayat, T.; Sudargo, Fransisca

2017-04-01

The Phylogenetic tree is a visual representation depicts a hypothesis about the evolutionary relationship among taxa. Evolutionary experts use this representation to evaluate the evidence for evolution. The phylogenetic tree is currently growing for many disciplines in biology. Consequently, learning about the phylogenetic tree has become an important part of biological education and an interesting area of biology education research. Skill to understanding and reasoning of the phylogenetic tree, (called tree thinking) is an important skill for biology students. However, research showed many students have difficulty in interpreting, constructing, and comparing among the phylogenetic tree, as well as experiencing a misconception in the understanding of the phylogenetic tree. Students are often not taught how to reason about evolutionary relationship depicted in the diagram. Students are also not provided with information about the underlying theory and process of phylogenetic. This study aims to investigate the initial ability of undergraduate students in understanding and reasoning of the phylogenetic tree. The research method is the descriptive method. Students are given multiple choice questions and an essay that representative by tree thinking elements. Each correct answer made percentages. Each student is also given questionnaires. The results showed that the undergraduate students’ initial ability in understanding and reasoning phylogenetic tree is low. Many students are not able to answer questions about the phylogenetic tree. Only 19 % undergraduate student who answered correctly on indicator evaluate the evolutionary relationship among taxa, 25% undergraduate student who answered correctly on indicator applying concepts of the clade, 17% undergraduate student who answered correctly on indicator determines the character evolution, and only a few undergraduate student who can construct the phylogenetic tree.

Mosaic, self-similarity logic, and biological attraction principles: three explanatory instruments in biology.

PubMed

Agnati, Luigi F; Baluska, Frantisek; Barlow, Peter W; Guidolin, Diego

2009-11-01

From a structural standpoint, living organisms are organized like a nest of Russian matryoshka dolls, in which structures are buried within one another. From a temporal point of view, this type of organization is the result of a history comprised of a set of time backcloths which have accompanied the passage of living matter from its origins up to the present day. The aim of the present paper is to indicate a possible course of this 'passage through time, and suggest how today's complexity has been reached by living organisms. This investigation will employ three conceptual tools, namely the Mosaic, Self-Similarity Logic, and the Biological Attraction principles. Self-Similarity Logic indicates the self-consistency by which elements of a living system interact, irrespective of the spatiotemporal level under consideration. The term Mosaic indicates how, from the same set of elements assembled according to different patterns, it is possible to arrive at completely different constructions: hence, each system becomes endowed with different emergent properties. The Biological Attraction principle states that there is an inherent drive for association and merging of compatible elements at all levels of biological complexity. By analogy with the gravitation law in physics, biological attraction is based on the evidence that each living organism creates an attractive field around itself. This field acts as a sphere of influence that actively attracts similar fields of other biological systems, thereby modifying salient features of the interacting organisms. Three specific organizational levels of living matter, namely the molecular, cellular, and supracellular levels, have been considered in order to analyse and illustrate the interpretative as well as the predictive roles of each of these three explanatory principles.

Carbon nanotubes allow capture of krypton, barium and lead for multichannel biological X-ray fluorescence imaging

NASA Astrophysics Data System (ADS)

Serpell, Christopher J.; Rutte, Reida N.; Geraki, Kalotina; Pach, Elzbieta; Martincic, Markus; Kierkowicz, Magdalena; de Munari, Sonia; Wals, Kim; Raj, Ritu; Ballesteros, Belén; Tobias, Gerard; Anthony, Daniel C.; Davis, Benjamin G.

2016-10-01

The desire to study biology in situ has been aided by many imaging techniques. Among these, X-ray fluorescence (XRF) mapping permits observation of elemental distributions in a multichannel manner. However, XRF imaging is underused, in part, because of the difficulty in interpreting maps without an underlying cellular `blueprint' this could be supplied using contrast agents. Carbon nanotubes (CNTs) can be filled with a wide range of inorganic materials, and thus can be used as `contrast agents' if biologically absent elements are encapsulated. Here we show that sealed single-walled CNTs filled with lead, barium and even krypton can be produced, and externally decorated with peptides to provide affinity for sub-cellular targets. The agents are able to highlight specific organelles in multiplexed XRF mapping, and are, in principle, a general and versatile tool for this, and other modes of biological imaging.

Regulating Cancer Associated Fibroblast Biology in Prostate Cancer

DTIC Science & Technology

2016-10-01

AWARD NUMBER: W81XWH-15-1-0512 TITLE: Regulating Cancer-Associated Fibroblast Biology in Prostate Cancer PRINCIPAL INVESTIGATOR: Andrew...CONTRACT NUMBER Regulating Cancer-Associated Fibroblast Biology in Prostate Cancer 5b. GRANT NUMBER W81XWH-15-1-0512 5c. PROGRAM ELEMENT NUMBER 6... biology to modulate epithelial growth and that inhibitors of this protein kinase have the potential to block this process and thus inhibit tumor growth

Construction of 2,4,6-Trinitrotoluene Biosensors with Novel Sensing Elements from Escherichia coli K-12 MG1655.

PubMed

Tan, Junjie; Kan, Naipeng; Wang, Wei; Ling, Jingyi; Qu, Guolong; Jin, Jing; Shao, Yu; Liu, Gang; Chen, Huipeng

2015-06-01

Detection of 2,4,6-trinitrotoluene (TNT) has been extensively studied since it is a common explosive filling for landmines, posing significant threats to the environment and human safety. The rapid advances in synthetic biology give new hope to detect such toxic and hazardous compounds in a more sensitive and safe way. Biosensor construction anticipates finding sensing elements able to detect TNT. As TNT can induce some physiological responses in E. coli, it may be useful to define the sensing elements from E. coli to detect TNT. An E. coli MG1655 genomic promoter library containing nearly 5,400 elements was constructed. Five elements, yadG, yqgC, aspC, recE, and topA, displayed high sensing specificity to TNT and its indicator compounds 1,3-DNB and 2,4-DNT. Based on this, a whole cell biosensor was constructed using E. coli, in which green fluorescent protein was positioned downstream of the five sensing elements via genetic fusion. The threshold value, detection time, EC200 value, and other aspects of five sensing elements were determined and the minimum responding concentration to TNT was 4.75 mg/L. According to the synthetic biology, the five sensing elements enriched the reservoir of TNT-sensing elements, and provided a more applicable toolkit to be applied in genetic routes and live systems of biosensors in future.

Quantum biology at the cellular level--elements of the research program.

PubMed

Bordonaro, Michael; Ogryzko, Vasily

2013-04-01

Quantum biology is emerging as a new field at the intersection between fundamental physics and biology, promising novel insights into the nature and origin of biological order. We discuss several elements of QBCL (quantum biology at cellular level) - a research program designed to extend the reach of quantum concepts to higher than molecular levels of biological organization. We propose a new general way to address the issue of environmentally induced decoherence and macroscopic superpositions in biological systems, emphasizing the 'basis-dependent' nature of these concepts. We introduce the notion of 'formal superposition' and distinguish it from that of Schroedinger's cat (i.e., a superposition of macroscopically distinct states). Whereas the latter notion presents a genuine foundational problem, the former one contradicts neither common sense nor observation, and may be used to describe cellular 'decision-making' and adaptation. We stress that the interpretation of the notion of 'formal superposition' should involve non-classical correlations between molecular events in a cell. Further, we describe how better understanding of the physics of Life can shed new light on the mechanism driving evolutionary adaptation (viz., 'Basis-Dependent Selection', BDS). Experimental tests of BDS and the potential role of synthetic biology in closing the 'evolvability mechanism' loophole are also discussed. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Updated Lagrangian finite element formulations of various biological soft tissue non-linear material models: a comprehensive procedure and review.

PubMed

Townsend, Molly T; Sarigul-Klijn, Nesrin

2016-01-01

Simplified material models are commonly used in computational simulation of biological soft tissue as an approximation of the complicated material response and to minimize computational resources. However, the simulation of complex loadings, such as long-duration tissue swelling, necessitates complex models that are not easy to formulate. This paper strives to offer the updated Lagrangian formulation comprehensive procedure of various non-linear material models for the application of finite element analysis of biological soft tissues including a definition of the Cauchy stress and the spatial tangential stiffness. The relationships between water content, osmotic pressure, ionic concentration and the pore pressure stress of the tissue are discussed with the merits of these models and their applications.

A First Attempt to Bring Computational Biology into Advanced High School Biology Classrooms

PubMed Central

Gallagher, Suzanne Renick; Coon, William; Donley, Kristin; Scott, Abby; Goldberg, Debra S.

2011-01-01

Computer science has become ubiquitous in many areas of biological research, yet most high school and even college students are unaware of this. As a result, many college biology majors graduate without adequate computational skills for contemporary fields of biology. The absence of a computational element in secondary school biology classrooms is of growing concern to the computational biology community and biology teachers who would like to acquaint their students with updated approaches in the discipline. We present a first attempt to correct this absence by introducing a computational biology element to teach genetic evolution into advanced biology classes in two local high schools. Our primary goal was to show students how computation is used in biology and why a basic understanding of computation is necessary for research in many fields of biology. This curriculum is intended to be taught by a computational biologist who has worked with a high school advanced biology teacher to adapt the unit for his/her classroom, but a motivated high school teacher comfortable with mathematics and computing may be able to teach this alone. In this paper, we present our curriculum, which takes into consideration the constraints of the required curriculum, and discuss our experiences teaching it. We describe the successes and challenges we encountered while bringing this unit to high school students, discuss how we addressed these challenges, and make suggestions for future versions of this curriculum.We believe that our curriculum can be a valuable seed for further development of computational activities aimed at high school biology students. Further, our experiences may be of value to others teaching computational biology at this level. Our curriculum can be obtained at http://ecsite.cs.colorado.edu/?page_id=149#biology or by contacting the authors. PMID:22046118

A first attempt to bring computational biology into advanced high school biology classrooms.

PubMed

Gallagher, Suzanne Renick; Coon, William; Donley, Kristin; Scott, Abby; Goldberg, Debra S

2011-10-01

Computer science has become ubiquitous in many areas of biological research, yet most high school and even college students are unaware of this. As a result, many college biology majors graduate without adequate computational skills for contemporary fields of biology. The absence of a computational element in secondary school biology classrooms is of growing concern to the computational biology community and biology teachers who would like to acquaint their students with updated approaches in the discipline. We present a first attempt to correct this absence by introducing a computational biology element to teach genetic evolution into advanced biology classes in two local high schools. Our primary goal was to show students how computation is used in biology and why a basic understanding of computation is necessary for research in many fields of biology. This curriculum is intended to be taught by a computational biologist who has worked with a high school advanced biology teacher to adapt the unit for his/her classroom, but a motivated high school teacher comfortable with mathematics and computing may be able to teach this alone. In this paper, we present our curriculum, which takes into consideration the constraints of the required curriculum, and discuss our experiences teaching it. We describe the successes and challenges we encountered while bringing this unit to high school students, discuss how we addressed these challenges, and make suggestions for future versions of this curriculum.We believe that our curriculum can be a valuable seed for further development of computational activities aimed at high school biology students. Further, our experiences may be of value to others teaching computational biology at this level. Our curriculum can be obtained at http://ecsite.cs.colorado.edu/?page_id=149#biology or by contacting the authors.

Fast X-Ray Fluorescence Microtomography of Hydrated Biological Samples

PubMed Central

Lombi, Enzo; de Jonge, Martin D.; Donner, Erica; Kopittke, Peter M.; Howard, Daryl L.; Kirkham, Robin; Ryan, Chris G.; Paterson, David

2011-01-01

Metals and metalloids play a key role in plant and other biological systems as some of them are essential to living organisms and all can be toxic at high concentrations. It is therefore important to understand how they are accumulated, complexed and transported within plants. In situ imaging of metal distribution at physiological relevant concentrations in highly hydrated biological systems is technically challenging. In the case of roots, this is mainly due to the possibility of artifacts arising during sample preparation such as cross sectioning. Synchrotron x-ray fluorescence microtomography has been used to obtain virtual cross sections of elemental distributions. However, traditionally this technique requires long data acquisition times. This has prohibited its application to highly hydrated biological samples which suffer both radiation damage and dehydration during extended analysis. However, recent advances in fast detectors coupled with powerful data acquisition approaches and suitable sample preparation methods can circumvent this problem. We demonstrate the heightened potential of this technique by imaging the distribution of nickel and zinc in hydrated plant roots. Although 3D tomography was still impeded by radiation damage, we successfully collected 2D tomograms of hydrated plant roots exposed to environmentally relevant metal concentrations for short periods of time. To our knowledge, this is the first published example of the possibilities offered by a new generation of fast fluorescence detectors to investigate metal and metalloid distribution in radiation-sensitive, biological samples. PMID:21674049

Student Perceptions of the Cell Biology Laboratory Learning Environment in Four Undergraduate Science Courses in Spain

ERIC Educational Resources Information Center

De Juan, Joaquin; Pérez-Cañaveras, Rosa M.; Segovia, Yolanda; Girela, Jose Luis; Martínez-Ruiz, Noemi; Romero-Rameta, Alejandro; Gómez-Torres, Maria José; Vizcaya-Moreno, M. Flores

2016-01-01

Cell biology is an academic discipline that organises and coordinates the learning of the structure, function and molecular composition of cells in some undergraduate biomedical programs. Besides course content and teaching methodologies, the laboratory environment is considered a key element in the teaching of and learning of cell biology. The…

Evaluation of the Redesign of an Undergraduate Cell Biology Course

ERIC Educational Resources Information Center

McEwen, Laura April; Harris, dik; Schmid, Richard F.; Vogel, Jackie; Western, Tamara; Harrison, Paul

2009-01-01

This article offers a case study of the evaluation of a redesigned and redeveloped laboratory-based cell biology course. The course was a compulsory element of the biology program, but the laboratory had become outdated and was inadequately equipped. With the support of a faculty-based teaching improvement project, the teaching team redesigned the…

Characterization of the bionano interface and mapping extrinsic interactions of the corona of nanomaterials

NASA Astrophysics Data System (ADS)

O'Connell, D. J.; Bombelli, F. Baldelli; Pitek, A. S.; Monopoli, M. P.; Cahill, D. J.; Dawson, K. A.

2015-09-01

Nanoparticles in physiological environments are known to selectively adsorb proteins and other biomolecules forming a tightly bound biomolecular `corona' on their surface. Where the exchange times of the proteins are sufficiently long, it is believed that the protein corona constitutes the particle identity in biological milieu. Here we show that proteins in the corona retain their functional characteristics and can specifically bind to cognate proteins on arrays of thousands of immobilised human proteins. The biological identity of the nanomaterial is seen to be specific to the blood plasma concentration in which they are exposed. We show that the resulting in situ nanoparticle interactome is dependent on the protein concentration in plasma, with the emergence of a small number of dominant protein-protein interactions. These interactions are those driven by proteins that are adsorbed onto the particle surface and whose binding epitopes are subsequently expressed or presented suitably on the particle surface. We suggest that, since specific tailored protein arrays for target systems and organs can be designed, their use may be an important element in an overall study of the biomolecular corona.Nanoparticles in physiological environments are known to selectively adsorb proteins and other biomolecules forming a tightly bound biomolecular `corona' on their surface. Where the exchange times of the proteins are sufficiently long, it is believed that the protein corona constitutes the particle identity in biological milieu. Here we show that proteins in the corona retain their functional characteristics and can specifically bind to cognate proteins on arrays of thousands of immobilised human proteins. The biological identity of the nanomaterial is seen to be specific to the blood plasma concentration in which they are exposed. We show that the resulting in situ nanoparticle interactome is dependent on the protein concentration in plasma, with the emergence of a small number of dominant protein-protein interactions. These interactions are those driven by proteins that are adsorbed onto the particle surface and whose binding epitopes are subsequently expressed or presented suitably on the particle surface. We suggest that, since specific tailored protein arrays for target systems and organs can be designed, their use may be an important element in an overall study of the biomolecular corona. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr01970b

ReNE: A Cytoscape Plugin for Regulatory Network Enhancement

PubMed Central

Politano, Gianfranco; Benso, Alfredo; Savino, Alessandro; Di Carlo, Stefano

2014-01-01

One of the biggest challenges in the study of biological regulatory mechanisms is the integration, americanmodeling, and analysis of the complex interactions which take place in biological networks. Despite post transcriptional regulatory elements (i.e., miRNAs) are widely investigated in current research, their usage and visualization in biological networks is very limited. Regulatory networks are commonly limited to gene entities. To integrate networks with post transcriptional regulatory data, researchers are therefore forced to manually resort to specific third party databases. In this context, we introduce ReNE, a Cytoscape 3.x plugin designed to automatically enrich a standard gene-based regulatory network with more detailed transcriptional, post transcriptional, and translational data, resulting in an enhanced network that more precisely models the actual biological regulatory mechanisms. ReNE can automatically import a network layout from the Reactome or KEGG repositories, or work with custom pathways described using a standard OWL/XML data format that the Cytoscape import procedure accepts. Moreover, ReNE allows researchers to merge multiple pathways coming from different sources. The merged network structure is normalized to guarantee a consistent and uniform description of the network nodes and edges and to enrich all integrated data with additional annotations retrieved from genome-wide databases like NCBI, thus producing a pathway fully manageable through the Cytoscape environment. The normalized network is then analyzed to include missing transcription factors, miRNAs, and proteins. The resulting enhanced network is still a fully functional Cytoscape network where each regulatory element (transcription factor, miRNA, gene, protein) and regulatory mechanism (up-regulation/down-regulation) is clearly visually identifiable, thus enabling a better visual understanding of its role and the effect in the network behavior. The enhanced network produced by ReNE is exportable in multiple formats for further analysis via third party applications. ReNE can be freely installed from the Cytoscape App Store (http://apps.cytoscape.org/apps/rene) and the full source code is freely available for download through a SVN repository accessible at http://www.sysbio.polito.it/tools_svn/BioInformatics/Rene/releases/. ReNE enhances a network by only integrating data from public repositories, without any inference or prediction. The reliability of the introduced interactions only depends on the reliability of the source data, which is out of control of ReNe developers. PMID:25541727

Metal stable isotopes in low-temperature systems: A primer

USGS Publications Warehouse

Bullen, T.D.; Eisenhauer, A.

2009-01-01

Recent advances in mass spectrometry have allowed isotope scientists to precisely determine stable isotope variations in the metallic elements. Biologically infl uenced and truly inorganic isotope fractionation processes have been demonstrated over the mass range of metals. This Elements issue provides an overview of the application of metal stable isotopes to low-temperature systems, which extend across the borders of several science disciplines: geology, hydrology, biology, environmental science, and biomedicine. Information on instrumentation, fractionation processes, data-reporting terminology, and reference materials presented here will help the reader to better understand this rapidly evolving field.

Biological half-life of gaseous elemental iodine deposited onto rice grains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uchida, S.; Muramatsu, Y.; Sumiya, M.

In order to obtain the biological half-life (Tb) of iodine deposited on rough rice grains, rice plants of four different growing stages--heading, milky, dough, and yellow ripe--were exposed to elemental gaseous iodine. After the exposure, the rough rice samples were collected at different intervals and analyzed for iodine to estimate the value of Tb. The average value of Tb obtained by the experiments at the dough and yellow ripe stages was about 200 d. This value is considerably larger than those for pasture grass and leafy vegetables.

Creativity in tuberculosis research and discovery.

PubMed

Younga, Douglas; Verreck, Frank A W

2012-03-01

The remarkable advances in TB vaccinology over the last decade have been driven by a pragmatic approach to moving candidates along the development pipeline to clinical trials, fuelled by encouraging data on protection in animal models. Efficacy data from Phase IIb trials of the first generation of new candidates are anticipated over the next 1-2 years. As outlined in the TB Vaccines Strategic Blueprint, to exploit this information and to inspire design of next generation candidates, it is important that this empirical approach is complemented by progress in understanding of fundamental immune mechanisms and improved translational modalities. Current trends towards improved experimental and computational approaches for studying biological complexity will be an important element in the developing science of TB vaccinology. Copyright © 2012 Elsevier Ltd. All rights reserved.

Simulation Analysis of Temperature Field in the Heat Transfer Process of Shell

NASA Astrophysics Data System (ADS)

Zhang, Di; Luo, Zhen; Xuan, Wenbo

Sea temperature is the key factors that determines whether shellfish can maintain normal growth development and survival, as protective film, the shell is a very important part of structure of shellfish, so the research of heat transfer characteristics become very important. In this paper, we firstly make a comprehensive analysis on the appearance of the shell, for the next simulation builds a good foundation, and based on the large general finite element analysis software ANSYS, we analyze the thermodynamics of shells, study the effect of the shell thickness and structure on heat transfer time. And through apply different temperature load, analyze the heat transfer characteristics and temperature distribution of the shells, It is expected that the results is useful at the biological heat transfer of shellfish.

Measuring ocean acidification: new technology for a new era of ocean chemistry.

PubMed

Byrne, Robert H

2014-05-20

Human additions of carbon dioxide to the atmosphere are creating a cascade of chemical consequences that will eventually extend to the bottom of all the world's oceans. Among the best-documented seawater effects are a worldwide increase in open-ocean acidity and large-scale declines in calcium carbonate saturation states. The susceptibility of some young, fast-growing calcareous organisms to adverse impacts highlights the potential for biological and economic consequences. Many important aspects of seawater CO2 chemistry can be only indirectly observed at present, and important but difficult-to-observe changes can include shifts in the speciation and possibly bioavailability of some life-essential elements. Innovation and invention are urgently needed to develop the in situ instrumentation required to document this era of rapid ocean evolution.

Metals, minerals and microbes: geomicrobiology and bioremediation.

PubMed

Gadd, Geoffrey Michael

2010-03-01

Microbes play key geoactive roles in the biosphere, particularly in the areas of element biotransformations and biogeochemical cycling, metal and mineral transformations, decomposition, bioweathering, and soil and sediment formation. All kinds of microbes, including prokaryotes and eukaryotes and their symbiotic associations with each other and 'higher organisms', can contribute actively to geological phenomena, and central to many such geomicrobial processes are transformations of metals and minerals. Microbes have a variety of properties that can effect changes in metal speciation, toxicity and mobility, as well as mineral formation or mineral dissolution or deterioration. Such mechanisms are important components of natural biogeochemical cycles for metals as well as associated elements in biomass, soil, rocks and minerals, e.g. sulfur and phosphorus, and metalloids, actinides and metal radionuclides. Apart from being important in natural biosphere processes, metal and mineral transformations can have beneficial or detrimental consequences in a human context. Bioremediation is the application of biological systems to the clean-up of organic and inorganic pollution, with bacteria and fungi being the most important organisms for reclamation, immobilization or detoxification of metallic and radionuclide pollutants. Some biominerals or metallic elements deposited by microbes have catalytic and other properties in nanoparticle, crystalline or colloidal forms, and these are relevant to the development of novel biomaterials for technological and antimicrobial purposes. On the negative side, metal and mineral transformations by microbes may result in spoilage and destruction of natural and synthetic materials, rock and mineral-based building materials (e.g. concrete), acid mine drainage and associated metal pollution, biocorrosion of metals, alloys and related substances, and adverse effects on radionuclide speciation, mobility and containment, all with immense social and economic consequences. The ubiquity and importance of microbes in biosphere processes make geomicrobiology one of the most important concepts within microbiology, and one requiring an interdisciplinary approach to define environmental and applied significance and underpin exploitation in biotechnology.

Overview of integrative tools and methods in assessing ecological integrity in estuarine and coastal systems worldwide.

PubMed

Borja, Angel; Bricker, Suzanne B; Dauer, Daniel M; Demetriades, Nicolette T; Ferreira, João G; Forbes, Anthony T; Hutchings, Pat; Jia, Xiaoping; Kenchington, Richard; Carlos Marques, João; Zhu, Changbo

2008-09-01

In recent years, several sets of legislation worldwide (Oceans Act in USA, Australia or Canada; Water Framework Directive or Marine Strategy in Europe, National Water Act in South Africa, etc.) have been developed in order to address ecological quality or integrity, within estuarine and coastal systems. Most such legislation seeks to define quality in an integrative way, by using several biological elements, together with physico-chemical and pollution elements. Such an approach allows assessment of ecological status at the ecosystem level ('ecosystem approach' or 'holistic approach' methodologies), rather than at species level (e.g. mussel biomonitoring or Mussel Watch) or just at chemical level (i.e. quality objectives) alone. Increasing attention has been paid to the development of tools for different physico-chemical or biological (phytoplankton, zooplankton, benthos, algae, phanerogams, fishes) elements of the ecosystems. However, few methodologies integrate all the elements into a single evaluation of a water body. The need for such integrative tools to assess ecosystem quality is very important, both from a scientific and stakeholder point of view. Politicians and managers need information from simple and pragmatic, but scientifically sound methodologies, in order to show to society the evolution of a zone (estuary, coastal area, etc.), taking into account human pressures or recovery processes. These approaches include: (i) multidisciplinarity, inherent in the teams involved in their implementation; (ii) integration of biotic and abiotic factors; (iii) accurate and validated methods in determining ecological integrity; and (iv) adequate indicators to follow the evolution of the monitored ecosystems. While some countries increasingly use the establishment of marine parks to conserve marine biodiversity and ecological integrity, there is awareness (e.g. in Australia) that conservation and management of marine ecosystems cannot be restricted to Marine Protected Areas but must include areas outside such reserves. This contribution reviews the current situation of integrative ecological assessment worldwide, by presenting several examples from each of the continents: Africa, Asia, Australia, Europe and North America.

Transcriptional oscillation of canonical clock genes in mouse peripheral tissues

PubMed Central

Yamamoto, Takuro; Nakahata, Yasukazu; Soma, Haruhiko; Akashi, Makoto; Mamine, Takayoshi; Takumi, Toru

2004-01-01

Background The circadian rhythm of about 24 hours is a fundamental physiological function observed in almost all organisms from prokaryotes to humans. Identification of clock genes has allowed us to study the molecular bases for circadian behaviors and temporal physiological processes such as hormonal secretion, and has prompted the idea that molecular clocks reside not only in a central pacemaker, the suprachiasmatic nuclei (SCN) of hypothalamus in mammals, but also in peripheral tissues, even in immortalized cells. Furthermore, previous molecular dissection revealed that the mechanism of circadian oscillation at a molecular level is based on transcriptional regulation of clock and clock-controlled genes. Results We systematically analyzed the mRNA expression of clock and clock-controlled genes in mouse peripheral tissues. Eight genes (mBmal1, mNpas2, mRev-erbα, mDbp, mRev-erbβ, mPer3, mPer1 and mPer2; given in the temporal order of the rhythm peak) showed robust circadian expressions of mRNAs in all tissues except testis, suggesting that these genes are core molecules of the molecular biological clock. The bioinformatics analysis revealed that these genes have one or a combination of 3 transcriptional elements (RORE, DBPE, and E-box), which are conserved among human, mouse, and rat genome sequences, and indicated that these 3 elements may be responsible for the biological timing of expression of canonical clock genes. Conclusions The observation of oscillatory profiles of canonical clock genes is not only useful for physiological and pathological examination of the circadian clock in various organs but also important for systematic understanding of transcriptional regulation on a genome-wide basis. Our finding of the oscillatory expression of canonical clock genes with a temporal order provides us an interesting hypothesis, that cyclic timing of all clock and clock-controlled genes may be dependent on several transcriptional elements including 3 known elements, E-box, RORE, and DBPE. PMID:15473909

Sinking fluxes of minor and trace elements in the North Pacific Ocean measured during the VERTIGO program

NASA Astrophysics Data System (ADS)

Lamborg, C. H.; Buesseler, K. O.; Lam, P. J.

2008-07-01

As part of the Vertical Transport in the Global Ocean (VERTIGO) program, we collected and analyzed sinking particles using sediment traps at three depths in the oceanic mesopelagic zone and at two biogeochemically contrasting sites (N. Central Pacific at ALOHA; N. Pacific Western Subarctic Gyre at K2). In this paper, we present the results of minor and trace element determinations made on these samples. Minor and trace elements in the sinking material showed 2 trends in flux with depth: increasing and constant. The sinking particulate phase of some elements (Al, Fe, Mn) was dominated by material of lithogenic origin and exhibited flux that was constant with depth and consistent with eolian dust inputs (ALOHA), or increasing in flux with depth as a result of lateral inputs from a shelf (K2). This shelf-derived material also appears to have been confined to very small particles, whose inherent sinking rates are slow, and residence time within the mesopelagic "twilight zone" would be consequently long. Furthermore, the flux of this material did not change with substantial changes in the rain of biogenic material from the surface (K2), suggesting mechanistic decoupling from the flux of organic carbon and macronutrients. Micronutrient (Fe, Co, Zn and Cu) fluxes examined in a 1-D mass balance suggest widely differing sources and sinks in the water column as well as impacts from biological uptake and regeneration. For example, total Fe fluxes into and out of the euphotic zone appeared to be dominated by lithogenic material and far exceed biological requirements. The export flux of Fe, however, appeared to be balanced by the eolian input of soluble Fe. For Zn and Cu, the situation is reversed, with atmospheric inputs insufficient to support fluxes, and the cycling therefore dominated by the draw down of an internal pool. For Co, the situation lies in between, with important, but ultimately insufficient atmospheric inputs.

A bridge from physics to biology.

PubMed

Preparata, Giuliano

2010-01-01

Through molecular biology, the 'atomistic paradigm' tries to remove from the analysis of living matter every element of what appears as the distinguishing character of the chain of the biological processes: their cooperative, collective aspects. Living matter appears, on the contrary, governed by Quantum Field Theory (QFT), spontaneously creating order when the thermodynamical conditions are right. 'Electrodynamical coherence' (EC) is the most promising hint for the existence of a bridge between Physics and Biology.

History of the molecular biology of cytomegaloviruses.

PubMed

Stinski, Mark F

2014-01-01

The history of the molecular biology of cytomegaloviruses from the purification of the virus and the viral DNA to the cloning and expression of the viral genes is reviewed. A key genetic element of cytomegalovirus (the CMV promoter) contributed to our understanding of eukaryotic cell molecular biology and to the development of lifesaving therapeutic proteins. The study of the molecular biology of cytomegaloviruses also contributed to the development of antivirals to control the viral infection.

Considerations for designing chemical screening strategies in plant biology

PubMed Central

Serrano, Mario; Kombrink, Erich; Meesters, Christian

2015-01-01

Traditionally, biologists regularly used classical genetic approaches to characterize and dissect plant processes. However, this strategy is often impaired by redundancy, lethality or pleiotropy of gene functions, which prevent the isolation of viable mutants. The chemical genetic approach has been recognized as an alternative experimental strategy, which has the potential to circumvent these problems. It relies on the capacity of small molecules to modify biological processes by specific binding to protein target(s), thereby conditionally modifying protein function(s), which phenotypically resemble mutation(s) of the encoding gene(s). A successful chemical screening campaign comprises three equally important elements: (1) a reliable, robust, and quantitative bioassay, which allows to distinguish between potent and less potent compounds, (2) a rigorous validation process for candidate compounds to establish their selectivity, and (3) an experimental strategy for elucidating a compound's mode of action and molecular target. In this review we will discuss details of this general strategy and additional aspects that deserve consideration in order to take full advantage of the power provided by the chemical approach to plant biology. In addition, we will highlight some success stories of recent chemical screenings in plant systems, which may serve as teaching examples for the implementation of future chemical biology projects. PMID:25904921

Beryllium chemical speciation in elemental human biological fluids.

PubMed

Sutton, Mark; Burastero, Stephen R

2003-09-01

The understanding of beryllium chemistry in human body fluids is important for understanding the prevention and treatment of chronic beryllium disease. Thermodynamic modeling has traditionally been used to study environmental contaminant migration and rarely in the examination of metal (particularly beryllium) toxicology. In this work, a chemical thermodynamic speciation code (MINTEQA2) has been used to model and understand the chemistry of beryllium in simulated human biological fluids such as intracellular, interstitial, and plasma fluids, a number of airway surface fluids for patients with lung conditions, saliva, sweat, urine, bile, gastric juice, and pancreatic fluid. The results show that predicted beryllium solubility and speciation vary markedly between each simulated biological fluid. Formation of beryllium hydroxide and/or phosphate was observed in most of the modeled fluids, and results support the postulation that beryllium absorption in the gastrointestinal tract may be limited by the formation of beryllium phosphate solids. It is also postulated that beryllium is potentially 13% less soluble in the airway surface fluid of a patient with asthma when compared to a "normal" case. The results of this work, supported by experimental validation, can aid in the understanding of beryllium toxicology. Our results can potentially be applied to assessing the feasibility of biological monitoring or chelation treatment of beryllium body burden.

Spectral fingerprint of electrostatic forces between biological cells

NASA Astrophysics Data System (ADS)

Murovec, T.; Brosseau, C.

2015-10-01

The prediction of electrostatic forces (EFs) between biological cells still poses challenges of great scientific importance, e.g., cell recognition, electroporation (EP), and mechanosensing. Frequency-domain finite element simulations explore a variety of cell configurations in the range of parameters typical for eukaryotic cells. Here, by applying an electric field to a pair of layered concentric shells, a prototypical model of a biological cell, we provide numerical evidence that the instantaneous EF changes from repulsion to attraction as the drive frequency of the electric field is varied. We identify crossover frequencies and discuss their dependence as a function of field frequency, conductivity of the extracellular medium, and symmetry of the configuration of cells. We present findings which suggest that the spectrum of EFs depends sensitively on the configuration of cells. We discuss the signatures of the collective behavior of systems with many cells in the spectrum of the EF and highlight a few of the observational consequences that this behavior implies. By looking at different cell configurations, we are able to show that the repulsion-to-attraction transition phenomenon is largely associated with an asymmetric electrostatic screening at very small separation between cells. These findings pave the way for the experimental observation of the electromagnetic properties of efficient and simple models of biological tissues.

Novel Transcriptional Activities of Vitamin E: Inhibition of Cholesterol Biosynthesis

PubMed Central

Valastyan, Scott; Thakur, Varsha; Johnson, Amy; Kumar, Karan; Manor, Danny

2008-01-01

Vitamin E is a dietary lipid that is essential for vertebrate health and fertility. The biological activity of vitamin E is thought to reflect its ability to quench oxygen- and carbon- based free radicals, and thus to protect the organism from oxidative damage. However, recent reports suggest that vitamin E may also display other biological activities. Here, to examine possible mechanisms that may underlie such non-classical activities of vitamin E, we investigated the possibility that it functions as a specific modulator of gene expression. We show that treatment of cultured hepatocytes with RRR-α-tocopherol alters the expression of multiple genes and that these effects are distinct from those elicited by another antioxidant. Genes modulated by vitamin E include those that encode key enzymes in the cholesterol biosynthetic pathway. Correspondingly, vitamin E caused a pronounced inhibition of de novo cholesterol biosynthesis. The transcriptional activities of vitamin E were mediated by attenuating the post-translational processing of the transcription factor SREBP-2 that, in turn, led to a decreased transcriptional activity of sterol responsive elements in the promoters of target genes. These observations indicate that vitamin E possesses novel transcriptional activities that affect fundamental biological processes. Cross talk between tocopherol levels and cholesterol status may be an important facet of the biological activities of vitamin E. PMID:18095660

Spectral fingerprint of electrostatic forces between biological cells.

PubMed

Murovec, T; Brosseau, C

2015-10-01

The prediction of electrostatic forces (EFs) between biological cells still poses challenges of great scientific importance, e.g., cell recognition, electroporation (EP), and mechanosensing. Frequency-domain finite element simulations explore a variety of cell configurations in the range of parameters typical for eukaryotic cells. Here, by applying an electric field to a pair of layered concentric shells, a prototypical model of a biological cell, we provide numerical evidence that the instantaneous EF changes from repulsion to attraction as the drive frequency of the electric field is varied. We identify crossover frequencies and discuss their dependence as a function of field frequency, conductivity of the extracellular medium, and symmetry of the configuration of cells. We present findings which suggest that the spectrum of EFs depends sensitively on the configuration of cells. We discuss the signatures of the collective behavior of systems with many cells in the spectrum of the EF and highlight a few of the observational consequences that this behavior implies. By looking at different cell configurations, we are able to show that the repulsion-to-attraction transition phenomenon is largely associated with an asymmetric electrostatic screening at very small separation between cells. These findings pave the way for the experimental observation of the electromagnetic properties of efficient and simple models of biological tissues.

BioMetals: a historical and personal perspective.

PubMed

Silver, Simon

2011-06-01

Understanding of BioMetals developed basically from a starting point about 60 years ago to current mechanistic understanding of the biological behavior of many metal ions from protein structural and functional studies. Figure 1 shows a Biochemical Periodic Table, element by element, with requirements, roles and biochemistry of the specific ions indicated. With few exceptions, the biology is of the ions formed and not of the elemental state of each. Early BioMetals efforts defined nutritional growth needs for animals, plants and microbes for inorganic "macro-nutrients" such as magnesium, calcium, potassium, sodium, and phosphate and of "micronutrients" such as copper, iron, manganese and zinc. Surprises came early with regard to microbes, for example the finding that Escherichia coli (then and now the standard microbial model) grows happily in the apparent total absence of calcium, sodium, and chloride, which are certainly major animal nutrients. Some elements such as mercury and arsenic are never required by living cells, but are always toxic, often at very low levels. Therefore, the division into nutrient elements and toxic elements came soon. For most inorganic nutrients, excessive amounts can be toxic as well, for example for copper and iron.

Determination of selenium bioavailability to a benthic bivalve from particulate and solute pathways

USGS Publications Warehouse

Luoma, S.N.; Johns, C.; Fisher, N.S.; Steinberg, N.A.; Oremland, R.S.; Reinfelder, J.R.

1992-01-01

Particulate organo-Se was assimilated with 86% efficiency by the deposit feeding bivalve Macoma balthica, when the clam was fed 75Se-labeled diatoms. Absorption efficiencies of participate elemental Se were 22%, when the animals were fed 75Se-labeled sediments in which elemental Se was precipitated by microbial dissimilatory reduction. Precipitation of elemental Se did not eliminate biological availability of the element. Selenite was taken up from solution slowly by M. balthica (mean concentration factor was 712). Concentrations of selenite high enough to influence Se bioaccumulation by M. balthica did not occur in the oxidized water column of San Francisco Bay. However, 98-99% of the Se observed in M. balthica could be explained by ingestion of the concentrations of participate Se found in the bay. The potential for adverse biological effects occurred at much lower concentrations of environmental Se when food web transfer was considered than when predictions of effects were based upon bioassays with solute forms of the element. Selenium clearly requires a protective criterion based upon particulate concentrations or food web transfer. ?? 1992 American Chemical Society.

Predicting Protein Relationships to Human Pathways through a Relational Learning Approach Based on Simple Sequence Features.

PubMed

García-Jiménez, Beatriz; Pons, Tirso; Sanchis, Araceli; Valencia, Alfonso

2014-01-01

Biological pathways are important elements of systems biology and in the past decade, an increasing number of pathway databases have been set up to document the growing understanding of complex cellular processes. Although more genome-sequence data are becoming available, a large fraction of it remains functionally uncharacterized. Thus, it is important to be able to predict the mapping of poorly annotated proteins to original pathway models. We have developed a Relational Learning-based Extension (RLE) system to investigate pathway membership through a function prediction approach that mainly relies on combinations of simple properties attributed to each protein. RLE searches for proteins with molecular similarities to specific pathway components. Using RLE, we associated 383 uncharacterized proteins to 28 pre-defined human Reactome pathways, demonstrating relative confidence after proper evaluation. Indeed, in specific cases manual inspection of the database annotations and the related literature supported the proposed classifications. Examples of possible additional components of the Electron transport system, Telomere maintenance and Integrin cell surface interactions pathways are discussed in detail. All the human predicted proteins in the 2009 and 2012 releases 30 and 40 of Reactome are available at http://rle.bioinfo.cnio.es.

Phosphate toxicity: new insights into an old problem

PubMed Central

RAZZAQUE, M. Shawkat

2011-01-01

Phosphorus is an essential nutrient required for critical biological reactions that maintain the normal homoeostatic control of the cell. This element is an important component of different cellular structures, including nucleic acids and cell membranes. Adequate phosphorus balance is vital for maintaining basic cellular functions, ranging from energy metabolism to cell signalling. In addition, many intracellular pathways utilize phosphate ions for important cellular reactions; therefore, homoeostatic control of phosphate is one of the most delicate biological regulations. Impaired phosphorus balance can affect the functionality of almost every human system, including musculoskeletal and cardiovascular systems, ultimately leading to an increase in morbidity and mortality of the affected patients. Human and experimental studies have found that delicate balance among circulating factors, like vitamin D, PTH (parathyroid hormone) and FGF23 (fibroblast growth factor 23), are essential for regulation of physiological phosphate balance. Dysregulation of these factors, either alone or in combination, can induce phosphorus imbalance. Recent studies have shown that suppression of the FGF23–klotho system can lead to hyperphosphataemia with extensive tissue damage caused by phosphate toxicity. The cause and consequences of phosphate toxicity will be briefly summarized in the present review. PMID:20958267

Phosphate toxicity: new insights into an old problem.

PubMed

Razzaque, M Shawkat

2011-02-01

Phosphorus is an essential nutrient required for critical biological reactions that maintain the normal homoeostatic control of the cell. This element is an important component of different cellular structures, including nucleic acids and cell membranes. Adequate phosphorus balance is vital for maintaining basic cellular functions, ranging from energy metabolism to cell signalling. In addition, many intracellular pathways utilize phosphate ions for important cellular reactions; therefore, homoeostatic control of phosphate is one of the most delicate biological regulations. Impaired phosphorus balance can affect the functionality of almost every human system, including musculoskeletal and cardiovascular systems, ultimately leading to an increase in morbidity and mortality of the affected patients. Human and experimental studies have found that delicate balance among circulating factors, like vitamin D, PTH (parathyroid hormone) and FGF23 (fibroblast growth factor 23), are essential for regulation of physiological phosphate balance. Dysregulation of these factors, either alone or in combination, can induce phosphorus imbalance. Recent studies have shown that suppression of the FGF23-klotho system can lead to hyperphosphataemia with extensive tissue damage caused by phosphate toxicity. The cause and consequences of phosphate toxicity will be briefly summarized in the present review.

Discovery of simian virus 40 (SV40) and its relationship to poliomyelitis virus vaccines.

PubMed

Hilleman, M R

1998-01-01

Simian Virus 40 (SV40) was discovered in 1959 as a covert contaminant of poliovirus vaccines prepared using Macacus monkey renal cell cultures. This inapparent polyoma virus of monkeys was detected using Cercopithecus renal cell cultures and was eliminated from poliovaccines. There has been no evidence to implicate SV40 virus of vaccine origin in long- or short-term consequences in human subjects. Of importance, SV40 virus provided a new model for basic studies of viral pathogenesis and for cell transformation and neoplasia. Neoplastic transformation is fixed on the promiscuous binding of SV40 large T antigen to anti-oncogene cellular protein elements. SV40 also served as a valuable model for defining the immunology of virus-induced cancer and in its prevention and cure. Further, it has been a prime tool for elucidating the molecular details of eukaryotic cell processes. Numerous techniques now used in molecular biology were pioneered in the SV40 system. The SV40 promoter is commonly used in vector expression constructs and it has continued to be a model to develop new tools for site-specific mutagenesis. The virus has been critically important to studies in modern genetics and in molecular biology.

Rule-based programming paradigm: a formal basis for biological, chemical and physical computation.

PubMed

Krishnamurthy, V; Krishnamurthy, E V

1999-03-01

A rule-based programming paradigm is described as a formal basis for biological, chemical and physical computations. In this paradigm, the computations are interpreted as the outcome arising out of interaction of elements in an object space. The interactions can create new elements (or same elements with modified attributes) or annihilate old elements according to specific rules. Since the interaction rules are inherently parallel, any number of actions can be performed cooperatively or competitively among the subsets of elements, so that the elements evolve toward an equilibrium or unstable or chaotic state. Such an evolution may retain certain invariant properties of the attributes of the elements. The object space resembles Gibbsian ensemble that corresponds to a distribution of points in the space of positions and momenta (called phase space). It permits the introduction of probabilities in rule applications. As each element of the ensemble changes over time, its phase point is carried into a new phase point. The evolution of this probability cloud in phase space corresponds to a distributed probabilistic computation. Thus, this paradigm can handle tor deterministic exact computation when the initial conditions are exactly specified and the trajectory of evolution is deterministic. Also, it can handle probabilistic mode of computation if we want to derive macroscopic or bulk properties of matter. We also explain how to support this rule-based paradigm using relational-database like query processing and transactions.

Planar optical waveguide based sandwich assay sensors and processes for the detection of biological targets including protein markers, pathogens and cellular debris

DOEpatents

Martinez, Jennifer S [Santa Fe, NM; Swanson, Basil I [Los Alamos, NM; Grace, Karen M [Los Alamos, NM; Grace, Wynne K [Los Alamos, NM; Shreve, Andrew P [Santa Fe, NM

2009-06-02

An assay element is described including recognition ligands bound to a film on a single mode planar optical waveguide, the film from the group of a membrane, a polymerized bilayer membrane, and a self-assembled monolayer containing polyethylene glycol or polypropylene glycol groups therein and an assay process for detecting the presence of a biological target is described including injecting a biological target-containing sample into a sensor cell including the assay element, with the recognition ligands adapted for binding to selected biological targets, maintaining the sample within the sensor cell for time sufficient for binding to occur between selected biological targets within the sample and the recognition ligands, injecting a solution including a reporter ligand into the sensor cell; and, interrogating the sample within the sensor cell with excitation light from the waveguide, the excitation light provided by an evanescent field of the single mode penetrating into the biological target-containing sample to a distance of less than about 200 nanometers from the waveguide thereby exciting the fluorescent-label in any bound reporter ligand within a distance of less than about 200 nanometers from the waveguide and resulting in a detectable signal.

A Synopsis of Technical Issues of Concern for Monitoring Trace Elements in Highway and Urban Runoff

USGS Publications Warehouse

Breault, Robert F.; Granato, Gregory E.

2000-01-01

Trace elements, which are regulated for aquatic life protection, are a primary concern in highway- and urban-runoff studies because stormwater runoff may transport these constituents from the land surface to receiving waters. Many of these trace elements are essential for biological activity and become detrimental only when geologic or anthropogenic sources exceed concentrations beyond ranges typical of the natural environment. The Federal Highway Administration and State Transportation Agencies are concerned about the potential effects of highway runoff on the watershed scale and for the management and protection of watersheds. Transportation agencies need information that is documented as valid, current, and scientifically defensible to support planning and management decisions. There are many technical issues of concern for monitoring trace elements; therefore, trace-element data commonly are considered suspect, and the responsibility to provide data-quality information to support the validity of reported results rests with the data-collection agency. Paved surfaces are fundamentally different physically, hydraulically, and chemically from the natural surfaces typical of most freshwater systems that have been the focus of many traceelement- monitoring studies. Existing scientific conceptions of the behavior of trace elements in the environment are based largely upon research on natural systems, rather than on systems typical of pavement runoff. Additionally, the logistics of stormwater sampling are difficult because of the great uncertainty in the occurrence and magnitude of storm events. Therefore, trace-element monitoring programs may be enhanced if monitoring and sampling programs are automated. Automation would standardize the process and provide a continuous record of the variations in flow and water-quality characteristics. Great care is required to collect and process samples in a manner that will minimize potential contamination or attenuation of trace elements and other sources of bias and variability in the sampling process. Trace elements have both natural and anthropogenic sources that may affect the sampling process, including the sample-collection and handling materials used in many trace-element monitoring studies. Trace elements also react with these materials within the timescales typical for collection, processing and analysis of runoff samples. To study the characteristics and potential effects of trace elements in highway and urban runoff, investigators typically sample one or more operationally defined matrixes including: whole water, dissolved (filtered water), suspended sediment, bottom sediment, biological tissue, and contaminant sources. The sampling and analysis of each of these sample matrixes can provide specific information about the occurrence and distribution of trace elements in runoff and receiving waters. There are, however, technical concerns specific to each matrix that must be understood and addressed through use of proper collection and processing protocols. Valid protocols are designed to minimize inherent problems and to maximize the accuracy, precision, comparability, and representativeness of data collected. Documentation, including information about monitoring protocols, quality assurance and quality control efforts, and ancillary data also is necessary to establish data quality. This documentation is especially important for evaluation of historical traceelement monitoring data, because trace-element monitoring protocols and analysis methods have been constantly changing over the past 30 years.

Biological particle identification apparatus

DOEpatents

Salzman, Gary C.; Gregg, Charles T.; Grace, W. Kevin; Hiebert, Richard D.

1989-01-01

An apparatus and method for making multiparameter light scattering measurements from suspensions of biological particles is described. Fourteen of the sixteen Mueller matrix elements describing the particles under investigation can be substantially individually determined as a function of scattering angle and probing radiations wavelength, eight elements simultaneously for each of two apparatus configurations using an apparatus which incluees, in its simplest form, two polarization modulators each operating at a chosen frequency, one polarizer, a source of monochromatic electromagnetic radiation, a detector sensitive to the wavelength of radiation employed, eight phase-sensitive detectors, and appropriate electronics. A database of known biological particle suspensions can be assembled, and unknown samples can be quickly identified once measurements are performed on it according to the teachings of the subject invention, and a comparison is made with the database.

Methodological challenges of optical tweezers-based X-ray fluorescence imaging of biological model organisms at synchrotron facilities.

PubMed

Vergucht, Eva; Brans, Toon; Beunis, Filip; Garrevoet, Jan; Bauters, Stephen; De Rijcke, Maarten; Deruytter, David; Janssen, Colin; Riekel, Christian; Burghammer, Manfred; Vincze, Laszlo

2015-07-01

Recently, a radically new synchrotron radiation-based elemental imaging approach for the analysis of biological model organisms and single cells in their natural in vivo state was introduced. The methodology combines optical tweezers (OT) technology for non-contact laser-based sample manipulation with synchrotron radiation confocal X-ray fluorescence (XRF) microimaging for the first time at ESRF-ID13. The optical manipulation possibilities and limitations of biological model organisms, the OT setup developments for XRF imaging and the confocal XRF-related challenges are reported. In general, the applicability of the OT-based setup is extended with the aim of introducing the OT XRF methodology in all research fields where highly sensitive in vivo multi-elemental analysis is of relevance at the (sub)micrometre spatial resolution level.

Biologically mediated isotope fractionations - Biochemistry, geochemical significance and preservation in the earth's oldest sediments

NASA Technical Reports Server (NTRS)

Schidlowski, M.

1983-01-01

Preferential metabolization of isotopically light carbon and sulfur has resulted in a fractionation of the stable isotopes of these elements on a global scale, with the light species (C-12, S-32) markedly concentrated in biogenic materials. Since the biological effects are basically retained when carbon and sulfur are incorporated in sediments, the respective fractionations are propagated into the rock section of the geochemical cycle, this having consequently caused a characteristic bipartition of both elements between 'light' and 'heavy' crustal reservoirs. Preservation of the biological isotope effects in sedimentary rocks makes it possible to trace the underlying biochemical processes back over most of the geological record. According to the available evidence, biological (autotrophic) carbon fixation arose prior to 3.5(if not 3.8) billion years ago, while the emergence of dissimilatory sulfate reduction antedates the appearance of the oldest presumably bacteriogenic sulfur isotope patterns in rocks between 2.7 and 2.8 billion years old. Hence, biological control of the terrestrial carbon and sulfur cycles has been established very early in the earth's history.

Tinkering: a conceptual and historical evaluation.

PubMed

Laubichler, Manfred D

2007-01-01

Francois Jacob's article 'Evolution and Tinkering' published in Science in 1977 is still the locus classicus for the concept of tinkering in biology. It first introduced the notion of tinkering to a wide audience of scientists. Jacob drew on a variety of different sources ranging from molecular biology to evolutionary biology and cultural anthropology. The notion of tinkering, or more accurately, the concept of bricolage, are conceptual abstractions that allow for the theoretical analysis of a wide range of phenomena that are united by a shared underlying process--tinkering, or the opportunistic rearrangement and recombination of existing elements. This paper looks at Jacob's analysis as itself an example of conceptual tinkering. It traces the history of some of its elements and sketches how it has become part of an inclusive discourse of theoretical biology and evolutionary developmental biology that emerged over the last 30 years. I will argue that the theoretical power of Jacob's analysis lies in the fact that he captured a widespread phenomenon. His conceptual analysis is thus an example of an interdisciplinary synthesis that is based on a shared process rather than a shared object.

Period doubling induced by thermal noise amplification in genetic circuits.

PubMed

Ruocco, G; Fratalocchi, A

2014-11-18

Rhythms of life are dictated by oscillations, which take place in a wide rage of biological scales. In bacteria, for example, oscillations have been proven to control many fundamental processes, ranging from gene expression to cell divisions. In genetic circuits, oscillations originate from elemental block such as autorepressors and toggle switches, which produce robust and noise-free cycles with well defined frequency. In some circumstances, the oscillation period of biological functions may double, thus generating bistable behaviors whose ultimate origin is at the basis of intense investigations. Motivated by brain studies, we here study an "elemental" genetic circuit, where a simple nonlinear process interacts with a noisy environment. In the proposed system, nonlinearity naturally arises from the mechanism of cooperative stability, which regulates the concentration of a protein produced during a transcription process. In this elemental model, bistability results from the coherent amplification of environmental fluctuations due to a stochastic resonance of nonlinear origin. This suggests that the period doubling observed in many biological functions might result from the intrinsic interplay between nonlinearity and thermal noise.

Methodological issues in the use of individual brain measures to index trait liabilities: The example of noise-probe P3.

PubMed

Perkins, Emily R; Yancey, James R; Drislane, Laura E; Venables, Noah C; Balsis, Steve; Patrick, Christopher J

2017-01-01

Recent research initiatives have called for an increased use of biological concepts and measures in defining and studying mental health problems, but important measurement-related challenges confront efforts in this direction. This article highlights some of these challenges with reference to an intriguing measure of neural reactivity: the probe P3 response, a mid-latency brain potential evoked by an intense, unexpected acoustic-probe stimulus. Using data for a large adult sample (N=418), we report evidence that amplitude of probe P3 response to unwarned noise bursts occurring in a picture-viewing task exhibits robust, independent associations with two distinct trait constructs: weak inhibitory control (or disinhibition; DIS) and threat sensitivity (THT). Additionally, we report a selective association for THT with attentional suppression of probe P3 response during viewing of aversive pictures compared to neutral. These results point to separable elements of variance underlying the probe P3 response, including one element reflecting DIS-related variations in cognitive-elaborative processing, and others reflecting THT-related variations in aversive foreground engagement and abrupt defensive reorientation. Key measurement issues are considered in relation to these specific findings, and methodological and statistical approaches for addressing these issues are discussed in relation to advancement of a quantitatively sound, biologically informed science of psychopathology. Copyright © 2016 Elsevier B.V. All rights reserved.

Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb

DOE PAGES

Monti, Remo; Barozzi, Iros; Osterwalder, Marco; ...

2017-08-21

Epigenomic mapping of enhancer-associated chromatin modifications facilitates the genome-wide discovery of tissue-specific enhancers in vivo. However, reliance on single chromatin marks leads to high rates of false-positive predictions. More sophisticated, integrative methods have been described, but commonly suffer from limited accessibility to the resulting predictions and reduced biological interpretability. Here we present the Limb-Enhancer Genie (LEG), a collection of highly accurate, genome-wide predictions of enhancers in the developing limb, available through a user-friendly online interface. We predict limb enhancers using a combination of > 50 published limb-specific datasets and clusters of evolutionarily conserved transcription factor binding sites, taking advantage ofmore » the patterns observed at previously in vivo validated elements. By combining different statistical models, our approach outperforms current state-of-the-art methods and provides interpretable measures of feature importance. Our results indicate that including a previously unappreciated score that quantifies tissue-specific nuclease accessibility significantly improves prediction performance. We demonstrate the utility of our approach through in vivo validation of newly predicted elements. Moreover, we describe general features that can guide the type of datasets to include when predicting tissue-specific enhancers genome-wide, while providing an accessible resource to the general biological community and facilitating the functional interpretation of genetic studies of limb malformations.« less

Methodological Issues in the Use of Individual Brain Measures to Index Trait Liabilities: The Example of Noise-Probe P3

PubMed Central

Perkins, Emily R.; Yancey, James R.; Drislane, Laura E.; Venables, Noah C.; Balsis, Steve; Patrick, Christopher J.

2016-01-01

Recent research initiatives have called for an increased use of biological concepts and measures in defining and studying mental health problems, but important measurement-related challenges confront efforts in this direction. This article highlights some of these challenges with reference to an intriguing measure of neural reactivity: the probe P3 response, a mid-latency brain potential evoked by an intense, unexpected acoustic-probe stimulus. Using data for a large adult sample (N = 418), we report evidence that amplitude of probe P3 response to unwarned noise bursts occurring in a picture-viewing task exhibits robust, independent associations with two distinct trait constructs: weak inhibitory control (or disinhibition; DIS) and threat sensitivity (THT). Additionally, we report a selective association for THT with attentional suppression of probe P3 response during viewing of aversive pictures compared to neutral. These results point to separable elements of variance underlying the probe P3 response, including one element reflecting DIS-related variations in cognitive-elaborative processing, and others reflecting THT-related variations in aversive foreground engagement and abrupt defensive reorientation. Key measurement issues are considered in relation to these specific findings, and methodological and statistical approaches for addressing these issues are discussed in relation to advancement of a quantitatively sound, biologically informed science of psychopathology. PMID:27856400

FungalBraid: A GoldenBraid-based modular cloning platform for the assembly and exchange of DNA elements tailored to fungal synthetic biology.

PubMed

Hernanz-Koers, Miguel; Gandía, Mónica; Garrigues, Sandra; Manzanares, Paloma; Yenush, Lynne; Orzaez, Diego; Marcos, Jose F

2018-07-01

Current challenges in the study and biotechnological exploitation of filamentous fungi are the optimization of DNA cloning and fungal genetic transformation beyond model fungi, the open exchange of ready-to-use and standardized genetic elements among the research community, and the availability of universal synthetic biology tools and rules. The GoldenBraid (GB) cloning framework is a Golden Gate-based DNA cloning system developed for plant synthetic biology through Agrobacterium tumefaciens-mediated genetic transformation (ATMT). In this study, we develop reagents for the adaptation of GB version 3.0 from plants to filamentous fungi through: (i) the expansion of the GB toolbox with the domestication of fungal-specific genetic elements; (ii) the design of fungal-specific GB structures; and (iii) the ATMT and gene disruption of the plant pathogen Penicillium digitatum as a proof of concept. Genetic elements domesticated into the GB entry vector pUPD2 include promoters, positive and negative selection markers and terminators. Interestingly, some GB elements can be directly exchanged between plants and fungi, as demonstrated with the marker hph for Hyg R or the fluorescent protein reporter YFP. The iterative modular assembly of elements generates an endless number of diverse transcriptional units and other higher order combinations in the pDGB3α/pDGB3Ω destination vectors. Furthermore, the original plant GB syntax was adapted here to incorporate specific GB structures for gene disruption through homologous recombination and dual selection. We therefore have successfully adapted the GB technology for the ATMT of fungi. We propose the name of FungalBraid (FB) for this new branch of the GB technology that provides open, exchangeable and collaborative resources to the fungal research community. Copyright © 2018 Elsevier Inc. All rights reserved.

Treatment of high-strength sulfate wastewater using an autotrophic biocathode in view of elemental sulfur recovery.

PubMed

Blázquez, Enric; Gabriel, David; Baeza, Juan Antonio; Guisasola, Albert

2016-11-15

Treatment of high-strength sulfate wastewaters is becoming a research issue not only for its optimal management but also for the possibility of recovering elemental sulfur. Moreover, sulfate-rich wastewater production is expected to grow due to the increased SO 2 emission contained in flue gases which are treated by chemical absorption in water. Bioelectrochemical systems (BESs) are a promising alternative for sulfate reduction with a lack of electron donor, since hydrogen can be generated in situ from electricity. However, complete sulfate reduction leads to hydrogen sulfide as final sulfur compound. This work is the first to demonstrate that, in addition to an efficient sulfate-rich wastewater treatment, elemental sulfur could be recovered in a biocathode of a BES under oxygen limiting conditions. The key of the process is the biological oxidation of sulfide to elemental sulfur simultaneously to the sulfate reduction in the cathode using the oxygen produced in the anode that diffuses through the membrane. High sulfate reduction rates (up to 388 mg S-SO 4 2-  L -1  d -1 ) were observed linked to a low production of sulfide. Accumulation of elemental sulfur over graphite fibers of the biocathode was demonstrated by energy dispersive spectrometry, discarding the presence of metal sulfides. Microbial community analysis of the cathode biofilm demonstrated the presence of sulfate-reducing bacteria (mainly Desulfovibrio sp.) and sulfide-oxidizing bacteria (mainly Sulfuricurvum sp.). Hence, this biocathode allows simultaneous biological sulfate reduction and biological sulfide oxidation to elemental sulfur, opening up a novel process for recovering sulfur from sulfate-rich wastewaters. Copyright © 2016 Elsevier Ltd. All rights reserved.

The use of biomarkers as integrative tools for transitional water bodies monitoring in the Water Framework Directive context - A holistic approach in Minho river transitional waters.

PubMed

Capela, R; Raimundo, J; Santos, M M; Caetano, M; Micaelo, C; Vale, C; Guimarães, L; Reis-Henriques, M A

2016-01-01

The Water Framework Directive (WFD) provides an important legislative opportunity to promote and implement an integrated approach for the protection of inland surface waters, transitional waters, coastal waters and groundwaters. The transitional waters constitute a central piece as they are usually under high environmental pressure and by their inherent characteristics present monitoring challenges. Integrating water quality monitoring with biological monitoring can increase the cost-effectiveness of monitoring efforts. One way of doing this is with biomarkers, which effectively integrate physical-chemical status and biological quality elements, dealing holistically with adverse consequences on the health of water bodies. The new Marine Strategy Framework Directive (MSFD) already incorporates the biomarker approach. Given the recent activities of OSPAR and HELCOM to harmonize existing monitoring guidelines between MSFD and WFD the use of similar methodologies should be fostered. To illustrate the potential of the biomarker approach, juveniles of flounder (Platichthys flesus) were used to evaluate the quality of the Minho river-estuary water bodies. The use of juveniles instead of adults eliminates several confounding factors such changes on the biological responses associated with reproduction. Here, a panel of well-established biomarkers, EROD, AChE, SOD, CAT, GST, LPO, ENA and FACs (1-Hydroxyrene) were selected and measured along with a gradient of different physical conditions, and integrated with trace elements characterization on both biota and sediments. In general, a clear profile along the water bodies was found, with low seasonal and spatial variation, consistent with a low impacted area. Overall, the results support the use of both the battery of biomarkers and the use of juvenile flounders in the monitoring of the water quality status within the WFD. Copyright © 2015 Elsevier B.V. All rights reserved.

Geochemical and Mineralogical Analyses of Cold Spring Deposits at Borup Fiord Pass, a Sulfur-Dominated Arctic Analog for Planetary Environments on Mars and Europa

NASA Astrophysics Data System (ADS)

Lau, Graham Elliot

Sulfur is one of the most ubiquitous elements in the universe and one of those that is crucial for life, as we know it. This graduate dissertation presents the culmination of work conducted to better understand biological and geochemical processes related to sulfur cycling at a sulfur-dominated field site in the Canadian High Arctic. This site, situated in a valley called Borup Fiord Pass, provides a unique environment where sulfide-rich fluids emerge from a glacier and form large deposits of ice that become covered in elemental sulfur. The role of biology is compelling and yet challenging to define in each step of sulfur cycling at Borup Fiord pass, whether one considers the origin of the sulfide (presumed biological sulfate reduction in the subsurface) or one focuses on the processes driving sulfur oxidation and stabilization at the glacier's surface. This dissertation presents results from a field expedition in 2014 as well as detailed mineralogical and spectroscopic analyses of sulfur-rich materials returned from the field. The importance of sulfur and carbonate minerals at this site is considered. Also, analyses of materials within pyrite alteration features in the valley are explored. These features appear to represent emplaced subsurface sulfide ores, which have been subsequently leached near the surface, forming gossanous structures. The geochemistry and mineralogy of these features is explored, as well as is their potential to serve as analogs for the exploration of Mars. The dissertation then concludes with some consideration of potential future work to be considered as well as a recapitulation of the current state of knowledge of processes at Borup Fiord Pass.

MATLAB Algorithms for Rapid Detection and Embedding of Palindrome and Emordnilap Electronic Watermarks in Simulated Chemical and Biological Image Data

DTIC Science & Technology

2004-11-16

MATLAB Algorithms for Rapid Detection and Embedding of Palindrome and Emordnilap Electronic Watermarks in Simulated Chemical and Biological Image ...and Emordnilap Electronic Watermarks in Simulated Chemical and Biological Image Data 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT...Conference on Chemical and Biological Defense Research. Held in Hunt Valley, Maryland on 15-17 November 2004., The original document contains color images

Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates.

PubMed

Chalopin, Domitille; Naville, Magali; Plard, Floriane; Galiana, Delphine; Volff, Jean-Nicolas

2015-01-09

Transposable elements (TEs) are major components of vertebrate genomes, with major roles in genome architecture and evolution. In order to characterize both common patterns and lineage-specific differences in TE content and TE evolution, we have compared the mobilomes of 23 vertebrate genomes, including 10 actinopterygian fish, 11 sarcopterygians, and 2 nonbony vertebrates. We found important variations in TE content (from 6% in the pufferfish tetraodon to 55% in zebrafish), with a more important relative contribution of TEs to genome size in fish than in mammals. Some TE superfamilies were found to be widespread in vertebrates, but most elements showed a more patchy distribution, indicative of multiple events of loss or gain. Interestingly, loss of major TE families was observed during the evolution of the sarcopterygian lineage, with a particularly strong reduction in TE diversity in birds and mammals. Phylogenetic trends in TE composition and activity were detected: Teleost fish genomes are dominated by DNA transposons and contain few ancient TE copies, while mammalian genomes have been predominantly shaped by nonlong terminal repeat retrotransposons, along with the persistence of older sequences. Differences were also found within lineages: The medaka fish genome underwent more recent TE amplification than the related platyfish, as observed for LINE retrotransposons in the mouse compared with the human genome. This study allows the identification of putative cases of horizontal transfer of TEs, and to tentatively infer the composition of the ancestral vertebrate mobilome. Taken together, the results obtained highlight the importance of TEs in the structure and evolution of vertebrate genomes, and demonstrate their major impact on genome diversity both between and within lineages. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Fundamental Technical Elements of Freeze-fracture/Freeze-etch in Biological Electron Microscopy

EPA Science Inventory

Freeze-fracture/freeze-etch describes a process whereby specimens, typically biological or nanomaterial in nature, are frozen, fractured, and replicated to generate a carbon/platinum "cast" intended for examination by transmission electron microscopy. Specimens are subjected to u...

Bringing Life Processes to Life

ERIC Educational Resources Information Center

Souders, Hannah

2018-01-01

Protein synthesis, involving such abstract concepts as "DNA," "RNA," "transcription," and "translation," is one of many biological processes too small to be seen by the naked eye. This combination of scientific jargon and sub-microscopic elements can make biology seem overwhelming to any student--but…

A multi-level biological approach to evaluate impacts of a major municipal effluent in wild St. Lawrence River yellow perch (Perca flavescens).

PubMed

Houde, Magali; Giraudo, Maeva; Douville, Mélanie; Bougas, Bérénice; Couture, Patrice; De Silva, Amila O; Spencer, Christine; Lair, Stéphane; Verreault, Jonathan; Bernatchez, Louis; Gagnon, Christian

2014-11-01

The development of integrated ecotoxicological approaches is of great interest in the investigation of global concerns such as impacts of municipal wastewater effluents on aquatic ecosystems. The objective of this study was to investigate the effects of a major wastewater municipal effluent on fish using a multi-level biological approach, from gene transcription and enzyme activities to histological changes. Yellow perch (Perca flavescens) were selected based on their wide distribution, their commercial and recreational importance, and the availability of a customized microarray. Yellow perch were sampled upstream of a major municipal wastewater treatment plant (WWTP) and 4 km and 10 km downstream from its point of discharge in the St. Lawrence River (Quebec, Canada). Concentrations of perfluoroalkyl substances (PFASs), polybrominated diphenyl ethers (PBDEs) and metals/trace elements in whole body homogenates were comparable to those from other industrialized regions of the world. Genomic results indicated that the transcription level of 177 genes was significantly different (p<0.024) between exposed and non-exposed fish. Among these genes, 38 were found to be differentially transcribed at both downstream sites. Impacted genes were associated with biological processes and molecular functions such as immunity, detoxification, lipid metabolism/energy homeostasis (e.g., peroxisome proliferation), and retinol metabolism suggesting impact of WWTP on these systems. Moreover, antioxidant enzyme activities were more elevated in perch collected at the 4 km site. Biomarkers of lipid metabolism, biosynthetic activity, and aerobic capacities were significantly lower (p<0.05) in fish residing near the outfall of the effluent. Histological examination of the liver indicated no differences between sites. Correlations between PFAS, PBDE, and metal/trace element tissue concentrations and markers of peroxisomal proliferation, oxidative stress, and retinoid metabolism were found at the gene and cellular levels. Present results suggest that relating transcriptomic analyses to phenotypic responses is important to better understand impacts of environmental contamination on wild fish populations. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

Mosaic, Self-Similarity Logic, and Biological Attraction principles

PubMed Central

Baluška, František; Barlow, Peter W; Guidolin, Diego

2009-01-01

From a structural standpoint, living organisms are organized like a nest of Russian matryoshka dolls, in which structures are buried within one another. From a temporal point of view, this type of organization is the result of a history comprised of a set of time backcloths which have accompanied the passage of living matter from its origins up to the present day. The aim of the present paper is to indicate a possible course of this ‘passage through time, and suggest how today’s complexity has been reached by living organisms. This investigation will employ three conceptual tools, namely the Mosaic, Self-Similarity Logic, and the Biological Attraction principles. Self-Similarity Logic indicates the self-consistency by which elements of a living system interact, irrespective of the spatiotemporal level under consideration. The term Mosaic indicates how, from the same set of elements assembled according to different patterns, it is possible to arrive at completely different constructions: hence, each system becomes endowed with different emergent properties. The Biological Attraction principle states that there is an inherent drive for association and merging of compatible elements at all levels of biological complexity. By analogy with the gravitation law in physics, biological attraction is based on the evidence that each living organism creates an attractive field around itself. This field acts as a sphere of influence that actively attracts similar fields of other biological systems, thereby modifying salient features of the interacting organisms. Three specific organizational levels of living matter, namely the molecular, cellular, and supracellular levels, have been considered in order to analyse and illustrate the interpretative as well as the predictive roles of each of these three explanatory principles. PMID:20195461

Magnetic field-dependent molecular and chemical processes in biochemistry, genetics and medicine

NASA Astrophysics Data System (ADS)

Buchachenko, A. L.

2014-01-01

The molecular concept (paradigm) in magnetobiology seems to be most substantiated and significant for explaining the biomedical effects of electromagnetic fields, for the new medical technology of transcranial magnetic stimulation of cognitive activity, for the nuclear magnetic control of biochemical processes and for the search of new magnetic effects in biology and medicine. The key structural element of the concept is a radical ion pair as the receiver of magnetic fields and the source of magnetic effects. The existence of such pairs was recently detected in the two life-supporting processes of paramount importance — in enzymatic ATP and DNA syntheses. The bibliography includes 80 references.

[Natural factors influencing sleep].

PubMed

Jurkowski, Marek K; Bobek-Billewicz, Barbara

2007-01-01

Sleep is a universal phenomenon of human and animal lives, although the importance of sleep for homeo-stasis is still unknown. Sleep disturbances influence many behavioral and physiologic processes, leading to health complications including death. On the other hand, sleep improvement can beneficially influence the course of healing of many disorders and can be a prognostic of health recovery. The factors influencing sleep have different biological and chemical origins. They are classical hormones, hypothalamic releasing and inhibitory hormones, neuropeptides, peptides and others as cytokines, prostaglandins, oleamid, adenosine, nitric oxide. These factors regulate most physiologic processes and are likely elements integrating sleep with physiology and physiology with sleep in health and disorders.

Evaluation of methods for trace-element determination with emphasis on their usability in the clinical routine laboratory.

PubMed

Bolann, B J; Rahil-Khazen, R; Henriksen, H; Isrenn, R; Ulvik, R J

2007-01-01

Commonly used techniques for trace-element analysis in human biological material are flame atomic absorption spectrometry (FAAS), graphite furnace atomic absorption spectrometry (GFAAS), inductively coupled plasma atomic emission spectrometry (ICP-AES) and inductively coupled plasma mass spectrometry (ICP-MS). Elements that form volatile hydrides, first of all mercury, are analysed by hydride generation techniques. In the absorption techniques the samples are vaporized into free, neutral atoms and illuminated by a light source that emits the atomic spectrum of the element under analysis. The absorbance gives a quantitative measure of the concentration of the element. ICP-AES and ICP-MS are multi-element techniques. In ICP-AES the atoms of the sample are excited by, for example, argon plasma at very high temperatures. The emitted light is directed to a detector, and the optical signals are processed to values for the concentrations of the elements. In ICP-MS a mass spectrometer separates and detects ions produced by the ICP, according to their mass-to-charge ratio. Dilution of biological fluids is commonly needed to reduce the effect of the matrix. Digestion using acids and microwave energy in closed vessels at elevated pressure is often used. Matrix and spectral interferences may cause problems. Precautions should be taken against trace-element contamination during collection, storage and processing of samples. For clinical problems requiring the analysis of only one or a few elements, the use of FAAS may be sufficient, unless the higher sensitivity of GFAAS is required. For screening of multiple elements, however, the ICP techniques are preferable.

Genome Integration and Excision by a New Streptomyces Bacteriophage, ϕJoe

PubMed Central

Haley, Joshua A.; Stark, W. Marshall

2016-01-01

ABSTRACT Bacteriophages are the source of many valuable tools for molecular biology and genetic manipulation. In Streptomyces, most DNA cloning vectors are based on serine integrase site-specific DNA recombination systems derived from phage. Because of their efficiency and simplicity, serine integrases are also used for diverse synthetic biology applications. Here, we present the genome of a new Streptomyces phage, ϕJoe, and investigate the conditions for integration and excision of the ϕJoe genome. ϕJoe belongs to the largest Streptomyces phage cluster (R4-like) and encodes a serine integrase. The attB site from Streptomyces venezuelae was used efficiently by an integrating plasmid, pCMF92, constructed using the ϕJoe int-attP locus. The attB site for ϕJoe integrase was occupied in several Streptomyces genomes, including that of S. coelicolor, by a mobile element that varies in gene content and size between host species. Serine integrases require a phage-encoded recombination directionality factor (RDF) to activate the excision reaction. The ϕJoe RDF was identified, and its function was confirmed in vivo. Both the integrase and RDF were active in in vitro recombination assays. The ϕJoe site-specific recombination system is likely to be an important addition to the synthetic biology and genome engineering toolbox. IMPORTANCE Streptomyces spp. are prolific producers of secondary metabolites, including many clinically useful antibiotics. Bacteriophage-derived integrases are important tools for genetic engineering, as they enable integration of heterologous DNA into the Streptomyces chromosome with ease and high efficiency. Recently, researchers have been applying phage integrases for a variety of applications in synthetic biology, including rapid assembly of novel combinations of genes, biosensors, and biocomputing. An important requirement for optimal experimental design and predictability when using integrases, however, is the need for multiple enzymes with different specificities for their integration sites. In order to provide a broad platform of integrases, we identified and validated the integrase from a newly isolated Streptomyces phage, ϕJoe. ϕJoe integrase is active in vitro and in vivo. The specific recognition site for integration is present in a wide range of different actinobacteria, including Streptomyces venezuelae, an emerging model bacterium in Streptomyces research. PMID:28003200

DNA capture elements for rapid detection and identification of biological agents

NASA Astrophysics Data System (ADS)

Kiel, Johnathan L.; Parker, Jill E.; Holwitt, Eric A.; Vivekananda, Jeeva

2004-08-01

DNA capture elements (DCEs; aptamers) are artificial DNA sequences, from a random pool of sequences, selected for their specific binding to potential biological warfare agents. These sequences were selected by an affinity method using filters to which the target agent was attached and the DNA isolated and amplified by polymerase chain reaction (PCR) in an iterative, increasingly stringent, process. Reporter molecules were attached to the finished sequences. To date, we have made DCEs to Bacillus anthracis spores, Shiga toxin, Venezuelan Equine Encephalitis (VEE) virus, and Francisella tularensis. These DCEs have demonstrated specificity and sensitivity equal to or better than antibody.

Amplification of biological targets via on-chip culture for biosensing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harper, Jason C.; Edwards, Thayne L.; Carson, Bryan

The present invention, in part, relates to methods and apparatuses for on-chip amplification and/or detection of various targets, including biological targets and any amplifiable targets. In some examples, the microculture apparatus includes a single-use, normally-closed fluidic valve that is initially maintained in the closed position by a valve element bonded to an adhesive coating. The valve is opened using a magnetic force. The valve element includes a magnetic material or metal. Such apparatuses and methods are useful for in-field or real-time detection of targets, especially in limited resource settings.

NASA Human Research Program Space Radiation Program Element

NASA Technical Reports Server (NTRS)

Chappell, Lori; Huff, Janice; Patel, Janapriya; Wang, Minli; Hu, Shaowwen; Kidane, Yared; Myung-Hee, Kim; Li, Yongfeng; Nounu, Hatem; Plante, Ianik;

Metabolomic and elemental analysis of camel and bovine urine by GC-MS and ICP-MS.

PubMed

Ahamad, Syed Rizwan; Alhaider, Abdul Qader; Raish, Mohammad; Shakeel, Faiyaz

2017-01-01

Recent studies from the author's laboratory indicated that camel urine possesses antiplatelet activity and anti-cancer activity which is not present in bovine urine. The objective of this study is to compare the volatile and elemental components of bovine and camel urine using GC-MS and ICP-MS analysis. We are interested to know the component that performs these biological activities. The freeze dried urine was dissolved in dichloromethane and then derivatization process followed by using BSTFA for GC-MS analysis. Thirty different compounds were analyzed by the derivatization process in full scan mode. For ICP-MS analysis twenty eight important elements were analyzed in both bovine and camel urine. The results of GC-MS and ICP-MS analysis showed marked difference in the urinary metabolites. GC-MS evaluation of camel urine finds a lot of products of metabolism like benzene propanoic acid derivatives, fatty acid derivatives, amino acid derivatives, sugars, prostaglandins and canavanine. Several research reports reveal the metabolomics studies on camel urine but none of them completely reported the pharmacology related metabolomics. The present data of GC-MS suggest and support the previous studies and activities related to camel urine.

Selenium- and tellurium-containing fluorescent molecular probes for the detection of biologically important analytes.

PubMed

Manjare, Sudesh T; Kim, Youngsam; Churchill, David G

2014-10-21

As scientists in recent decades have discovered, selenium is an important trace element in life. The element is now known to play an important role in biology as an enzymatic antioxidant. In this case, it sits at the active site and converts biological hydrogen peroxides to water. Mimicking this reaction, chemists have synthesized several organoselenium compounds that undergo redox transformations. As such, these types of compounds are important in the future of both medicinal and materials chemistry. One main challenge for organochalcogen chemists has been to synthesize molecular probes that are soluble in water where a selenium or tellurium center can best modify electronics of the molecule based on a chemical oxidation or reduction event. In this Account, we discuss chemists' recent efforts to create chalcogen-based chemosensors through synthetic means and current photophysical understanding. Our work has focused on small chromophoric or fluorophoric molecules, in which we incorporate discrete organochalcogen atoms (e.g., R-Se-R, R-Te-R) in predesigned sites. These synthetic molecules, involving rational synthetic pathways, allow us to chemoselectively oxidize compounds and to study the level of analyte selectivity by way of their optical responses. All the reports we discussed here deal with well-defined and small synthetic molecular systems. With a large number of reports published over the last few years, many have notably originated from the laboratory of K. Han (P. R. China). This growing body of research has given chemists new ideas for the previously untenable reversible reactive oxygen species detection. While reversibility of the probe is technically important from the stand-point of the chalcogen center, facile regenerability of the probe using a secondary analyte to recover the initial probe is a very promising avenue. This is because (bio)chalcogen chemistry is extremely rich and bioinspired and continues to yield important developments across many scientific fields. Organochalcogen (R-E-R) chemistry in such chemical recognition and supramolecular pursuits is a fundamental tool to allow chemists to explore stable organic-based probe modalities of interest to develop better spectroscopic tools for (neuro)biological applications. Chalcogen donor sites also provide sites where metals can coordinate, and facile oxidation may extend to the sulfone analogues (R-EO2-R) or beyond. Consequently, chemists can then make use of reliable reversible chemical probing platforms based on the chemical redox properties valence state switching principally from 2 to 4 (and back to 2) of selenium and tellurium atoms. The main organic molecular skeletons have involved chemical frames including boron-dipyrromethene (BODIPY) systems, extended cyanine groups, naphthalimide, rhodamine, and fluorescein cores, and isoselenazolone, pyrene, coumarin, benzoselenadiazole, and selenoguanine systems. Our group has tested many such molecular probe systems in cellular milieu and under a series of conditions and competitive environments. We have found that the most important analytes have been reactive oxygen species (ROS) such as superoxide and hypochlorite. Reactive nitrogen species (RNS) such as peroxynitrite are also potential targets. In addition, we have also considered Fenton chemistry systems. Our research and that of others shows that the action of ROS is often reversible with H2S or biothiols such as glutathione (GSH). We have also found that a second class of analytes are the thiols (RSH), in particular, biothiols. Here, the target group might involve an R-Se-Se-R group. The study of analytes also extends to metal ions, for example, Hg(2+), and anions such as fluoride (F(-)), and we have developed NIR-based systems as well. These work through various photomechanisms, including photoinduced electron transfer (PET), twisted internal charge transfer (TICT), and internal charge transfer (ICT). The growing understanding of this class of probe suggests that there is much room for creative thinking regarding modular designs or unexpected organic chemical synthesis designs, interplay between analytes, new analyte selectivity, biological targeting, and chemical switching, which can also serve to further the neurological probing and molecular logic gating frontiers.

Biological forcing controls the chemistry of the coral exoskeleton

NASA Astrophysics Data System (ADS)

Meibom, A.; Mostefaoui, S.; Cuif, J.; Yurimoto, H.; Dauphin, Y.; Houlbreque, F.; Dunbar, R.; Constantz, B.

2006-12-01

A multitude of marine organisms produce calcium carbonate skeletons that are used extensively to reconstruct water temperature variability of the tropical and subtropical oceans - a key parameter in global climate-change models. Such paleo-climate reconstructions are based on the notion that skeletal oxygen isotopic composition and certain trace-element abundances (e.g., Sr/Ca and Mg/Ca ratios) vary in response to changes in the water temperature. However, it is a fundamental problem that poorly understood biological processes introduce large compositional deviations from thermodynamic equilibrium and hinder precise calibrations of many paleo-climate proxies. Indeed, the role of water temperature in controlling the composition of the skeleton is far from understood. We have studied trace-element abundances as well as oxygen and carbon isotopic compositions of individual skeletal components in the zooxanthellate and non-zooxanthellate corals at ultra-structural, i.e. micrometer to sub-micrometer length scales. From this body of work we draw the following, generalized conclusions: 1) Centers of calcification (COC) are not in equilibrium with seawater. Notably, the Sr/Ca ratio is higher than expected for aragonite equilibrium with seawater at the temperature at which the skeleton was formed. Furthermore, the COC are further away from equilibrium with seawater than fibrous skeleton in terms of stable isotope composition. 2) COC are dramatically different from the fibrous aragonite skeleton in terms of trace element composition. 3) Neither trace element nor stable isotope variations in the fibrous (bulk) part of the skeleton are directly related to changes in SST. In fact, changes in SST can have very little to do with the observed compositional variations. 4) Trace element variations in the fibrous (bulk) part of the skeleton are not related to the activity of zooxanthellae. These observations are directly relevant to the issue of biological versus non-biological control over skeleton composition and will be discussed.

Why do we study animal toxins?

PubMed Central

ZHANG, Yun

2015-01-01

Venom (toxins) is an important trait evolved along the evolutionary tree of animals. Our knowledges on venoms, such as their origins and loss, the biological relevance and the coevolutionary patterns with other organisms are greatly helpful in understanding many fundamental biological questions, i.e., the environmental adaptation and survival competition, the evolution shaped development and balance of venoms, and the sophisticated correlations among venom, immunity, body power, intelligence, their genetic basis, inherent association, as well as the cost-benefit and trade-offs of biological economy. Lethal animal envenomation can be found worldwide. However, from foe to friend, toxin studies have led lots of important discoveries and exciting avenues in deciphering and fighting human diseases, including the works awarded the Nobel Prize and lots of key clinic therapeutics. According to our survey, so far, only less than 0.1% of the toxins of the venomous animals in China have been explored. We emphasize on the similarities shared by venom and immune systems, as well as the studies of toxin knowledge-based physiological toxin-like proteins/peptides (TLPs). We propose the natural pairing hypothesis. Evolution links toxins with humans. Our mission is to find out the right natural pairings and interactions of our body elements with toxins, and with endogenous toxin-like molecules. Although, in nature, toxins may endanger human lives, but from a philosophical point of view, knowing them well is an effective way to better understand ourselves. So, this is why we study toxins. PMID:26228472

Biogeochemical Coupling between Ocean and Sea Ice

NASA Astrophysics Data System (ADS)

Wang, S.; Jeffery, N.; Maltrud, M. E.; Elliott, S.; Wolfe, J.

2016-12-01

Biogeochemical processes in ocean and sea ice are tightly coupled at high latitudes. Ongoing changes in Arctic and Antarctic sea ice domain likely influence the coupled system, not only through physical fields but also biogeochemical properties. Investigating the system and its changes requires representation of ocean and sea ice biogeochemical cycles, as well as their coupling in Earth System Models. Our work is based on ACME-HiLAT, a new offshoot of the Community Earth System Model (CESM), including a comprehensive representation of marine ecosystems in the form of the Biogeochemical Elemental Cycling Module (BEC). A full vertical column sea ice biogeochemical module has recently been incorporated into the sea ice component. We have further introduced code modifications to couple key growth-limiting nutrients (N, Si, Fe), dissolved and particulate organic matter, and phytoplankton classes that are important in polar regions between ocean and sea ice. The coupling of ocean and sea ice biology-chemistry will enable representation of key processes such as the release of important climate active constituents or seeding algae from melting sea ice into surface waters. Sensitivity tests suggest sea ice and ocean biogeochemical coupling influences phytoplankton competition, biological production, and the CO2 flux. Sea ice algal seeding plays an important role in determining phytoplankton composition of Arctic early spring blooms, since different groups show various responses to the seeding biomass. Iron coupling leads to increased phytoplankton biomass in the Southern Ocean, which also affects carbon uptake via the biological pump. The coupling of macronutrients and organic matter may have weaker influences on the marine ecosystem. Our developments will allow climate scientists to investigate the fully coupled responses of the sea ice-ocean BGC system to physical changes in polar climate.

Smart Phones: Platform Enabling Modular, Chemical, Biological, and Explosives Sensing

DTIC Science & Technology

2013-07-01

Smart phones: Platform Enabling Modular, Chemical, Biological, and Explosives Sensing by Amethist S. Finch , Matthew Coppock, Justin R...Chemical, Biological, and Explosives Sensing Amethist S. Finch , Matthew Coppock, Justin R. Bickford, Marvin A. Conn, Thomas J. Proctor, and...Explosives Sensing 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Amethist S. Finch , Matthew Coppock, Justin R

Removing the tree-ring width biological trend using expected basal area increment

Treesearch

Franco Biondi; Fares Qeadan

2008-01-01

One of the main elements of dendrochronological standardization is the removal of the biological trend, i.e., the progressive decline of ring width along a cross-sectional radius that is mostly caused by the corresponding increase in stem diameter over time. A very common option for removing this biological trend is to fit a modified negative exponential curve to the...

Physical and Biological Controls of Copepod Aggregation and Baleen Whale Distribution

DTIC Science & Technology

2010-09-30

1 DISTRIBUTION STATEMENT A: Approved for public release; distribution is unlimited. Physical and Biological Controls of Copepod Aggregation...distribution. OBJECTIVES The objectives of this study are to • Elucidate the mechanisms of copepod aggregation in the Great South Channel, a...Physical and Biological Controls of Copepod Aggregation and Baleen Whale Distribution 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT

Cell-Sediment Separation and Elemental Stoichiometries in Extreme Environments

NASA Astrophysics Data System (ADS)

Neveu, M.; Poret-peterson, A. T.; Lee, Z. M.; Anbar, A. D.; Elser, J. J.

2012-12-01

Better understanding of the coupling of major biogeochemical cycles requires knowledge of the cellular elemental composition of key microbes. This is difficult in benthic sediments and mats, because of the contributions of non-living components. We are particularly interested in microbial extremophiles, and therefore sought to determine and interpret bulk and cellular elemental ratios in complex field-collected sediment samples from diverse hot spring ecosystems of Yellowstone National Park (YNP). These samples covered a broad range of temperature, pH, and chemical composition. We also sought to extend stoichiometric analysis to a broader suite of elements, including metals (Fe, Ni, Cu, Zn, Mo, etc.) of biological importance (Sterner and Elser, 2002). To overcome the challenge of rigorously isolating communities from their complex mineral matrices (Havig et al., 2011), we adapted a cell-sediment separation procedure from Amalfitano and Fazi (2008). The method involves chemical (use of a detergent and a chelating agent) and physical methods (stirring, gentle sonication, and gradient centrifugation) to break the microbe-mineral bonds. C and N elemental and isotopic abundances were determined by elemental analysis - isotope ratio - mass spectrometry (EA-IR-MS), while P, Na, Mg, Al, K, Ca, V, Cr, Fe, Co, Ni, Cu, Zn, and Mo contents were determined by inductively coupled plasma - mass spectrometry (ICP-MS). We sought to assess the existence of an "Extended Redfield Ratio" (ERR) for these microbes; that is, to establish the multi-element stoichiometric envelope within which extremophilic microbes must operate. Elemental and isotopic mass balance analyses of cultured E. coli before and after separation showed that our procedure preserved cellular C, N, P, Fe, and trace metal contents: neither loss of these elements (e.g., by cell lysis) nor contamination by reagents were observed. On the other hand, cation-forming elements (Na, Mg, K, Ca), were not conserved. Cell counting by epifluorescence microscopy indicated a cell recovery yield between 6 and 40% in field-collected samples (95% for cultured E. coli). Aluminum, assumed to be non-biological in origin, was used to estimate the extent of mineral contamination of isolated cell communities. These results show that our method is successful at separating microbial cells from sediment collected in extreme environments and preserving them for analysis of a broad suite of elements. Photosynthetic sites yielded much more cell material than hotter, chemosynthetic sites (Cox et al., 2011). We are currently measuring cellular elemental abundances and ratios in samples from relatively low-temperature (25 to 65°C), photosynthetic areas, spanning a wide range of pH (2 to 9.5) and composition. These measurements will be compared to existing datasets on the bulk sediment stoichiometry of these ecosystems, and to previous observations of cellular elemental composition. References: Redfield, A.C. (1934) In Daniel, R.J. [Ed.], James Johnstone Memorial Volume, pp. 176-192, Univ. Press Liverpool. Sterner, R.W., Elser, J.J. (2002) Ecological Stoichiometry Princeton Univ. Press, 441p. Havig, J.R., et al. (2011) JGR 116, G01005. Amalfitano, S., Fazi, S. (2008) J. of Microbiol. Methods 75, 237-243. Cox, A., et al. (2011) Chem. Geol. 280, 344-351.

Bursts of transposable elements as an evolutionary driving force.

PubMed

Belyayev, A

2014-12-01

A burst of transposable elements (TEs) is a massive outbreak that may cause radical genomic rebuilding. This phenomenon has been reported in connection with the formation of taxonomic groups and species and has therefore been associated with major evolutionary events in the past. Over the past few years, several research groups have discovered recent stress-induced bursts of different TEs. The events for which bursts of TEs have been recorded include domestication, polyploidy, changes in mating systems, interspecific and intergeneric hybridization and abiotic stress. Cases involving abiotic stress, particularly bursts of TEs in natural populations driven by environmental change, are of special interest because this phenomenon may underlie micro- and macro-evolutionary events and ultimately support the maintenance and generation of biological diversity. This study reviews the known cases of bursts of TEs and their possible consequences, with particular emphasis on the speciation process. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Anopheline Reproductive Biology: Impacts on Vectorial Capacity and Potential Avenues for Malaria Control.

PubMed

Mitchell, Sara N; Catteruccia, Flaminia

2017-12-01

Vectorial capacity is a mathematical approximation of the efficiency of vector-borne disease transmission, measured as the number of new infections disseminated per case per day by an insect vector. Multiple elements of mosquito biology govern their vectorial capacity, including survival, population densities, feeding preferences, and vector competence. Intriguingly, biological pathways essential to mosquito reproductive fitness directly or indirectly influence a number of these elements. Here, we explore this complex interaction, focusing on how the interplay between mating and blood feeding in female Anopheles not only shapes their reproductive success but also influences their ability to sustain Plasmodium parasite development. Central to malaria transmission, mosquito reproductive biology has recently become the focus of research strategies aimed at malaria control, and we discuss promising new methods based on the manipulation of key reproductive steps. In light of widespread resistance to all public health-approved insecticides targeting mosquito reproduction may prove crucial to the success of malaria-eradication campaigns. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Protein-protein interactions in the regulation of WRKY transcription factors.

PubMed

Chi, Yingjun; Yang, Yan; Zhou, Yuan; Zhou, Jie; Fan, Baofang; Yu, Jing-Quan; Chen, Zhixiang

2013-03-01

It has been almost 20 years since the first report of a WRKY transcription factor, SPF1, from sweet potato. Great progress has been made since then in establishing the diverse biological roles of WRKY transcription factors in plant growth, development, and responses to biotic and abiotic stress. Despite the functional diversity, almost all analyzed WRKY proteins recognize the TTGACC/T W-box sequences and, therefore, mechanisms other than mere recognition of the core W-box promoter elements are necessary to achieve the regulatory specificity of WRKY transcription factors. Research over the past several years has revealed that WRKY transcription factors physically interact with a wide range of proteins with roles in signaling, transcription, and chromatin remodeling. Studies of WRKY-interacting proteins have provided important insights into the regulation and mode of action of members of the important family of transcription factors. It has also emerged that the slightly varied WRKY domains and other protein motifs conserved within each of the seven WRKY subfamilies participate in protein-protein interactions and mediate complex functional interactions between WRKY proteins and between WRKY and other regulatory proteins in the modulation of important biological processes. In this review, we summarize studies of protein-protein interactions for WRKY transcription factors and discuss how the interacting partners contribute, at different levels, to the establishment of the complex regulatory and functional network of WRKY transcription factors.

Real-time Measurements of Biological Particles at Several Continental Sites using the WIBS-4A

NASA Astrophysics Data System (ADS)

McMeeking, G. R.; Kok, G. L.; Petters, M. D.; Wright, T.; Hader, J.; Mccubbin, I. B.; Hallar, A. G.; Twohy, C. H.; Toohey, D. W.; DeMott, P. J.; McCluskey, C.; Baumgardner, D.

2013-12-01

Biological particles (bacteria, fungi/fungal spores, viruses, algae and fragments of biological material) may play a significant role in modifying cloud properties by acting as ice nuclei and thus have an indirect effect on climate forcing. Little is known, however, regarding the abundance and distribution of biological particles and their importance to cloud microphysics in different environments. On-line, continuous measurement systems offer the potential to measure biological systems at high time resolution and sensitivity, providing greater insight into their distribution in the atmosphere, dispersal mechanisms and potential soures. The WIBS-4A (Wideband Integrated Bioaerosol Sensor) detects fluorescent biological material in real-time associated with individual particles. It measures five properties: a) optical size via light scattering, b) fluorescent emissions in the wavelength range 310-400 following excitation by 280 nm light, c) fluorescent emissions in the wavelength range 420-650 following excitation by 280 nm light, d) fluorescent emissions in the wavelength range 420-650 following excitation by 370 nm light, and e) particle asymmetry factor based on intensities of forward scattered light onto a 4-element detector. Together, these properties aid the classification of sampled particles that contain biofluorophores such as tryptophan or NAD(P)H, which can be found in biological particles. Here we present results from a series of laboratory, ground- and aircraft-based measurements of biological particles using the WIBS-4A. The studies include airborne measurements over the United States, ground-based measurements at a coastal site, an urban site in the southeast US and a high alpine site, and laboratory measurements of a variety of biological and non-biological particles. Our analysis focused on both the characterization of the instrument response as well as an evaluation of its suitability for performing ambient measurements and potential artifacts. We also present recommendations for field operation of the instrument, sample system design considerations, and data analysis approaches.

QEEN Workshop: "Quantifying Exposure to Engineered Nano ...

EPA Pesticide Factsheets

The measurement and characterization of nanomaterials in biological tissues is complicated by a number of factors including: the sensitivity of the assay to small sized particles or low concentrations of materials; the ability to distinguish different forms and transformations of the materials related to the biological matrix; distinguishing exogenous nanomaterials, which may be composed of biologically common elements such as carbon,from normal biological tissues; differentiating particle from ionic phases for materials that dissolve; localization of sparsely distributed materials in a complex substrate (the

Drawing-to-learn: a framework for using drawings to promote model-based reasoning in biology.

PubMed

Quillin, Kim; Thomas, Stephen

2015-03-02

The drawing of visual representations is important for learners and scientists alike, such as the drawing of models to enable visual model-based reasoning. Yet few biology instructors recognize drawing as a teachable science process skill, as reflected by its absence in the Vision and Change report's Modeling and Simulation core competency. Further, the diffuse research on drawing can be difficult to access, synthesize, and apply to classroom practice. We have created a framework of drawing-to-learn that defines drawing, categorizes the reasons for using drawing in the biology classroom, and outlines a number of interventions that can help instructors create an environment conducive to student drawing in general and visual model-based reasoning in particular. The suggested interventions are organized to address elements of affect, visual literacy, and visual model-based reasoning, with specific examples cited for each. Further, a Blooming tool for drawing exercises is provided, as are suggestions to help instructors address possible barriers to implementing and assessing drawing-to-learn in the classroom. Overall, the goal of the framework is to increase the visibility of drawing as a skill in biology and to promote the research and implementation of best practices. © 2015 K. Quillin and S. Thomas. CBE—Life Sciences Education © 2015 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

The mammary gland in domestic ruminants: a systems biology perspective.

PubMed

Ferreira, Ana M; Bislev, Stine L; Bendixen, Emøke; Almeida, André M

2013-12-06

Milk and dairy products are central elements in the human diet. It is estimated that 108kg of milk per year are consumed per person worldwide. Therefore, dairy production represents a relevant fraction of the economies of many countries, being cattle, sheep, goat, water buffalo, and other ruminants the main species used worldwide. An adequate management of dairy farming cannot be achieved without the knowledge on the biological mechanisms behind lactation in ruminants. Thus, understanding the morphology, development and regulation of the mammary gland in health, disease and production is crucial. Presently, innovative and high-throughput technologies such as genomics, transcriptomics, proteomics and metabolomics allow a much broader and detailed knowledge on such issues. Additionally, the application of a systems biology approach to animal science is vastly growing, as new advances in one field of specialization or animal species lead to new lines of research in other areas or/and are expanded to other species. This article addresses how modern research approaches may help us understand long-known issues in mammary development, lactation biology and dairy production. Dairy production depends upon the knowledge of the morphology and regulation of the mammary gland and lactation. High-throughput technologies allow a much broader and detailed knowledge on the biology of the mammary gland. This paper reviews the major contributions that genomics, transcriptomics, metabolomics and proteomics approaches have provided to understand the regulation of the mammary gland in health, disease and production. In the context of mammary gland "omics"-based research, the integration of results using a Systems Biology Approach is of key importance. © 2013.

On the relationship between the dynamic behavior and nanoscale staggered structure of the bone

NASA Astrophysics Data System (ADS)

Qwamizadeh, Mahan; Zhang, Zuoqi; Zhou, Kun; Zhang, Yong Wei

2015-05-01

Bone, a typical load-bearing biological material, composed of ordinary base materials such as organic protein and inorganic mineral arranged in a hierarchical architecture, exhibits extraordinary mechanical properties. Up to now, most of previous studies focused on its mechanical properties under static loading. However, failure of the bone occurs often under dynamic loading. An interesting question is: Are the structural sizes and layouts of the bone related or even adapted to the functionalities demanded by its dynamic performance? In the present work, systematic finite element analysis was performed on the dynamic response of nanoscale bone structures under dynamic loading. It was found that for a fixed mineral volume fraction and unit cell area, there exists a nanoscale staggered structure at some specific feature size and layout which exhibits the fastest attenuation of stress waves. Remarkably, these specific feature sizes and layouts are in excellent agreement with those experimentally observed in the bone at the same scale, indicating that the structural size and layout of the bone at the nanoscale are evolutionarily adapted to its dynamic behavior. The present work points out the importance of dynamic effect on the biological evolution of load-bearing biological materials.

High-performance liquid chromatographic determination of histamine in biological samples: the cerebrospinal fluid challenge--a review.

PubMed

Wang, Zhaopin; Wu, Juanli; Wu, Shihua; Bao, Aimin

2013-04-24

Histamine, a neurotransmitter crucially involved in a number of basic physiological functions, undergoes changes in neuropsychiatric disorders. Detection of histamine in biological samples such as cerebrospinal fluid (CSF) is thus of clinical importance. The most commonly used method for measuring histamine levels is high performance liquid chromatography (HPLC). However, factors such as very low levels of histamine, the even lower CSF-histamine and CSF-histamine metabolite levels, especially in certain neuropsychiatric diseases, rapid formation of histamine metabolites, and other confounding elements during sample collection, make analysis of CSF-histamine and CSF-histamine metabolites a challenging task. Nonetheless, this challenge can be met, not only with respect to HPLC separation column, derivative reagent, and detector, but also in terms of optimizing the CSF sample collection. This review aims to provide a general insight into the quantitative analyses of histamine in biological samples, with an emphasis on HPLC instruments, methods, and hyphenated techniques, with the aim of promoting the development of an optimal and practical protocol for the determination of CSF-histamine and/or CSF-histamine metabolites. Copyright © 2013 Elsevier B.V. All rights reserved.

Swarm chondrosarcoma: a continued resource for chondroblastic-like extracellular matrix and chondrosarcoma biology research.

PubMed

Stevens, Jeff W

2013-01-01

Since its first description over four decades ago, the Swarm chondrosarcoma (Swarm rat chondrosarcoma, SRC) remains a valuable tool for studies of chondroblastic-like extracellular matrix (ECM) biology and as an animal model of human chondrosarcoma of histological grades I-III. Moreover, articular joints and skeletal anomalies such as arthritis as well as cartilage regeneration, skeletal development, tissue engineering, hard tissue tumorigenesis and space flight physiology are advanced through studies in hyaline cartilage-like models. With more than 500 articles published since the first report on the characteristics of mucopolysaccharides (glycosaminoglycans) of the tumor in 1971, several transplantable tumor and cell lines have been developed by multiple laboratories worldwide. This review describes the characterization of SRC tumors and cell lines, including the use of SRC lines as a resource for isolation and characterization of several ECM elements that have become vital for the advancement of our understanding of cartilage biology. Also presented is the importance of pertubation of ECM components and the influence of the tumor microenvironment on disease progression. Therapeutic failure and currently pursued avenues of intervention utilizing the SRC lines in treatment of chondrosarcoma are also discussed.

Exact solutions of a two parameter flux model and cryobiological applications.

PubMed

Benson, James D; Chicone, Carmen C; Critser, John K

2005-06-01

Solute-solvent transmembrane flux models are used throughout biological sciences with applications in plant biology, cryobiology (transplantation and transfusion medicine), as well as circulatory and kidney physiology. Using a standard two parameter differential equation model of solute and solvent transmembrane flux described by Jacobs [The simultaneous measurement of cell permeability to water and to dissolved substances, J. Cell. Comp. Physiol. 2 (1932) 427-444], we determine the functions that describe the intracellular water volume and moles of intracellular solute for every time t and every set of initial conditions. Here, we provide several novel biophysical applications of this theory to important biological problems. These include using this result to calculate the value of cell volume excursion maxima and minima along with the time at which they occur, a novel result that is of significant relevance to the addition and removal of permeating solutes during cryopreservation. We also present a methodology that produces extremely accurate sum of squares estimates when fitting data for cellular permeability parameter values. Finally, we show that this theory allows a significant increase in both accuracy and speed of finite element methods for multicellular volume simulations, which has critical clinical biophysical applications in cryosurgical approaches to cancer treatment.

Sucrose metabolism gene families and their biological functions

PubMed Central

Jiang, Shu-Ye; Chi, Yun-Hua; Wang, Ji-Zhou; Zhou, Jun-Xia; Cheng, Yan-Song; Zhang, Bao-Lan; Ma, Ali; Vanitha, Jeevanandam; Ramachandran, Srinivasan

2015-01-01

Sucrose, as the main product of photosynthesis, plays crucial roles in plant development. Although studies on general metabolism pathway were well documented, less information is available on the genome-wide identification of these genes, their expansion and evolutionary history as well as their biological functions. We focused on four sucrose metabolism related gene families including sucrose synthase, sucrose phosphate synthase, sucrose phosphate phosphatase and UDP-glucose pyrophosphorylase. These gene families exhibited different expansion and evolutionary history as their host genomes experienced differentiated rates of the whole genome duplication, tandem and segmental duplication, or mobile element mediated gene gain and loss. They were evolutionarily conserved under purifying selection among species and expression divergence played important roles for gene survival after expansion. However, we have detected recent positive selection during intra-species divergence. Overexpression of 15 sorghum genes in Arabidopsis revealed their roles in biomass accumulation, flowering time control, seed germination and response to high salinity and sugar stresses. Our studies uncovered the molecular mechanisms of gene expansion and evolution and also provided new insight into the role of positive selection in intra-species divergence. Overexpression data revealed novel biological functions of these genes in flowering time control and seed germination under normal and stress conditions. PMID:26616172

Using nuclear microscopy to characterize the interaction of textile-used silver nanoparticles with a biological wastewater treatment system

NASA Astrophysics Data System (ADS)

Bento, J. B.; Franca, R. D. G.; Pinheiro, T.; Alves, L. C.; Pinheiro, H. M.; Lourenço, N. D.

2017-08-01

The use of engineered nanoparticles in the textile industry has been rapidly increasing but their fate during biological wastewater treatment is largely unknown. The goal of the current study was to characterize the interaction of silver nanoparticles (AgNPs), used in the textile industry, with a biological wastewater treatment system based on aerobic granular sludge (AGS). The exposure tests were performed using a laboratory-scale sequencing batch reactor (SBR) system with AGS. The behavior and fate of textile AgNPs in the AGS system was studied with nuclear microscopy techniques. Elemental maps of AGS samples collected from the SBR showed that AgNPs typically clustered in agglomerates of small dimensions (<10 μm), which were preferentially associated with extracellular polymeric substances (EPS). This preliminary study highlights the potential application of nuclear microscopy for the characterization of the behavior and fate of AgNPs in AGS. The detailed compartmentalization of AgNPs in AGS components obtained with nuclear microscopy provides new and relevant information concerning AgNPs retention. This will be important in biotechnological terms to delineate strategies for AgNPs removal from textile wastewater.

Handling gene and protein names in the age of bioinformatics: the special challenge of secreted multimodular bacterial enzymes such as the cbhA/cbh9A gene of Clostridium thermocellum.

PubMed

Schwarz, Wolfgang H; Brunecky, Roman; Broeker, Jannis; Liebl, Wolfgang; Zverlov, Vladimir V

2018-02-26

An increasing number of researchers working in biology, biochemistry, biotechnology, bioengineering, bioinformatics and other related fields of science are using biological molecules. As the scientific background of the members of different scientific communities is more diverse than ever before, the number of scientists not familiar with the rules for non-ambiguous designation of genetic elements is increasing. However, with biological molecules gaining importance through biotechnology, their functional and unambiguous designation is vital. Unfortunately, naming genes and proteins is not an easy task. In addition, the traditional concepts of bioinformatics are challenged with the appearance of proteins comprising different modules with a respective function in each module. This article highlights basic rules and novel solutions in designation recently used within the community of bacterial geneticists, and we discuss the present-day handling of gene and protein designations. As an example we will utilize a recent mischaracterization of gene nomenclature. We make suggestions for better handling of names in future literature as well as in databases and annotation projects. Our methodology emphasizes the hydrolytic function of multi-modular genes and extracellular proteins from bacteria.

Structure investigation of three hydrazones Schiff's bases by spectroscopic, thermal and molecular orbital calculations and their biological activities

NASA Astrophysics Data System (ADS)

Belal, Arafa A. M.; Zayed, M. A.; El-Desawy, M.; Rakha, Sh. M. A. H.

2015-03-01

Three Schiff's bases AI (2(1-hydrazonoethyl)phenol), AII (2, 4-dibromo 6-(hydrazonomethyl)phenol) and AIII (2(hydrazonomethyl)phenol) were prepared as new hydrazone compounds via condensation reactions with molar ratio (1:1) of reactants. Firstly by reaction of 2-hydroxy acetophenone solution and hydrazine hydrate; it gives AI. Secondly condensation between 3,5-dibromo-salicylaldehyde and hydrazine hydrate gives AII. Thirdly condensation between salicylaldehyde and hydrazine hydrate gives AIII. The structures of AI-AIII were characterized by elemental analysis (EA), mass (MS), FT-IR and 1H NMR spectra, and thermal analyses (TG, DTG, and DTA). The activation thermodynamic parameters, such as, ΔE∗, ΔH∗, ΔS∗ and ΔG∗ were calculated from the TG curves using Coats-Redfern method. It is important to investigate their molecular structures to know the active groups and weak bond responsible for their biological activities. Consequently in the present work, the obtained thermal (TA) and mass (MS) practical results are confirmed by semi-empirical MO-calculations (MOCS) using PM3 procedure. Their biological activities have been tested in vitro against Escherichia coli, Proteus vulgaris, Bacillissubtilies and Staphylococcus aurous bacteria in order to assess their anti-microbial potential.

In vivo and in vitro characterization of σ70 constitutive promoters by real-time PCR and fluorescent measurements.

PubMed

Chappell, James; Freemont, Paul

2013-01-01

The characterization of DNA regulatory elements such as ribosome binding sites and transcriptional promoters is a fundamental aim of synthetic biology. Characterization of such DNA regulatory elements by monitoring the synthesis of fluorescent proteins is a commonly used technique to resolve the relative or absolute strengths. These measurements can be used in combination with mathematical models and computer simulation to rapidly assess performance of DNA regulatory elements both in isolation and in combination, to assist predictable and efficient engineering of complex novel biological devices and systems. Here we describe the construction and relative characterization of Escherichia coli (E. coli) σ(70) transcriptional promoters by monitoring the synthesis of green fluorescent protein (GFP) both in vivo in E. coli and in vitro in a E. coli cell-free transcription and translation reaction.

Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects.

PubMed

Dresch, Jacqueline M; Liu, Xiaozhou; Arnosti, David N; Ay, Ahmet

2010-10-24

Quantitative models of gene expression generate parameter values that can shed light on biological features such as transcription factor activity, cooperativity, and local effects of repressors. An important element in such investigations is sensitivity analysis, which determines how strongly a model's output reacts to variations in parameter values. Parameters of low sensitivity may not be accurately estimated, leading to unwarranted conclusions. Low sensitivity may reflect the nature of the biological data, or it may be a result of the model structure. Here, we focus on the analysis of thermodynamic models, which have been used extensively to analyze gene transcription. Extracted parameter values have been interpreted biologically, but until now little attention has been given to parameter sensitivity in this context. We apply local and global sensitivity analyses to two recent transcriptional models to determine the sensitivity of individual parameters. We show that in one case, values for repressor efficiencies are very sensitive, while values for protein cooperativities are not, and provide insights on why these differential sensitivities stem from both biological effects and the structure of the applied models. In a second case, we demonstrate that parameters that were thought to prove the system's dependence on activator-activator cooperativity are relatively insensitive. We show that there are numerous parameter sets that do not satisfy the relationships proferred as the optimal solutions, indicating that structural differences between the two types of transcriptional enhancers analyzed may not be as simple as altered activator cooperativity. Our results emphasize the need for sensitivity analysis to examine model construction and forms of biological data used for modeling transcriptional processes, in order to determine the significance of estimated parameter values for thermodynamic models. Knowledge of parameter sensitivities can provide the necessary context to determine how modeling results should be interpreted in biological systems.

High-resolution elemental mapping of human placental chorionic villi using synchrotron X-ray fluorescence spectroscopy

DOE PAGES

Punshon, Tracy; Chen, Si; Finney, Lydia; ...

2015-07-03

The placenta is the organ that mediates transport of nutrients and waste materials between mother and fetus. Synchrotron X-ray fluorescence (SXRF) microanalysis is a tool for imaging the distribution and quantity of elements in biological tissue, which can be used to study metal transport across biological membranes. Our aims were to pilot placental biopsy specimen preparation techniques that could be integrated into an ongoing epidemiology birth cohort study without harming rates of sample acquisition. We studied the effects of fixative (formalin or glutaraldehyde) and storage duration (30 days or immediate processing) on metal distribution and abundance and investigated a thaw-fixationmore » protocol for archived specimens stored at -80° C. We measured fixative elemental composition with and without a placental biopsy via inductively coupled plasma mass spectrometry (ICP-MS) to quantify fixative-induced elemental changes. Formalin-fixed specimens showed hemolysis of erythrocytes. The glutaraldehyde-paraformaldehyde solution in HEPES buffer (GTA-HEPES) had superior anatomical preservation, avoided hemolysis, and minimized elemental loss, although some cross-linking of exogenous Zn was evident. Elemental loss from tissue stored in fixative for 1 month showed variable losses (≈ 40 % with GTA-HEPES), suggesting storage duration be controlled for. Lastly, thawing of tissue held at -80 °C in a GTA-HEPES solution provided high-quality visual images and elemental images« less

An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance.

PubMed

Casimiro, Ana C; Vinga, Susana; Freitas, Ana T; Oliveira, Arlindo L

2008-02-07

Motif finding algorithms have developed in their ability to use computationally efficient methods to detect patterns in biological sequences. However the posterior classification of the output still suffers from some limitations, which makes it difficult to assess the biological significance of the motifs found. Previous work has highlighted the existence of positional bias of motifs in the DNA sequences, which might indicate not only that the pattern is important, but also provide hints of the positions where these patterns occur preferentially. We propose to integrate position uniformity tests and over-representation tests to improve the accuracy of the classification of motifs. Using artificial data, we have compared three different statistical tests (Chi-Square, Kolmogorov-Smirnov and a Chi-Square bootstrap) to assess whether a given motif occurs uniformly in the promoter region of a gene. Using the test that performed better in this dataset, we proceeded to study the positional distribution of several well known cis-regulatory elements, in the promoter sequences of different organisms (S. cerevisiae, H. sapiens, D. melanogaster, E. coli and several Dicotyledons plants). The results show that position conservation is relevant for the transcriptional machinery. We conclude that many biologically relevant motifs appear heterogeneously distributed in the promoter region of genes, and therefore, that non-uniformity is a good indicator of biological relevance and can be used to complement over-representation tests commonly used. In this article we present the results obtained for the S. cerevisiae data sets.

Multi-energy method of digital radiography for imaging of biological objects

NASA Astrophysics Data System (ADS)

Ryzhikov, V. D.; Naydenov, S. V.; Opolonin, O. D.; Volkov, V. G.; Smith, C. F.

2016-03-01

This work has been dedicated to the search for a new possibility to use multi-energy digital radiography (MER) for medical applications. Our work has included both theoretical and experimental investigations of 2-energy (2E) and 3- energy (3D) radiography for imaging the structure of biological objects. Using special simulation methods and digital analysis based on the X-ray interaction energy dependence for each element of importance to medical applications in the X-ray range of energy up to 150 keV, we have implemented a quasi-linear approximation for the energy dependence of the X-ray linear mass absorption coefficient μm (E) that permits us to determine the intrinsic structure of the biological objects. Our measurements utilize multiple X-ray tube voltages (50, 100, and 150 kV) with Al and Cu filters of different thicknesses to achieve 3-energy X-ray examination of objects. By doing so, we are able to achieve significantly improved imaging quality of the structure of the subject biological objects. To reconstruct and visualize the final images, we use both two-dimensional (2D) and three-dimensional (3D) palettes of identification. The result is a 2E and/or 3E representation of the object with color coding of each pixel according to the data outputs. Following the experimental measurements and post-processing, we produce a 3D image of the biological object - in the case of our trials, fragments or parts of chicken and turkey.

Non-integer viscoelastic constitutive law to model soft biological tissues to in-vivo indentation.

PubMed

Demirci, Nagehan; Tönük, Ergin

2014-01-01

During the last decades, derivatives and integrals of non-integer orders are being more commonly used for the description of constitutive behavior of various viscoelastic materials including soft biological tissues. Compared to integer order constitutive relations, non-integer order viscoelastic material models of soft biological tissues are capable of capturing a wider range of viscoelastic behavior obtained from experiments. Although integer order models may yield comparably accurate results, non-integer order material models have less number of parameters to be identified in addition to description of an intermediate material that can monotonically and continuously be adjusted in between an ideal elastic solid and an ideal viscous fluid. In this work, starting with some preliminaries on non-integer (fractional) calculus, the "spring-pot", (intermediate mechanical element between a solid and a fluid), non-integer order three element (Zener) solid model, finally a user-defined large strain non-integer order viscoelastic constitutive model was constructed to be used in finite element simulations. Using the constitutive equation developed, by utilizing inverse finite element method and in vivo indentation experiments, soft tissue material identification was performed. The results indicate that material coefficients obtained from relaxation experiments, when optimized with creep experimental data could simulate relaxation, creep and cyclic loading and unloading experiments accurately. Non-integer calculus viscoelastic constitutive models, having physical interpretation and modeling experimental data accurately is a good alternative to classical phenomenological viscoelastic constitutive equations.

Water-quality, bed-sediment, and biological data (October 1992 through September 1993) and statistical summaries of water-quality data (March 1985 through September 1993) for streams in the upper Clark Fork basin, Montana

USGS Publications Warehouse

Lambing, John H.

1994-01-01

Water, bed sediment, and biota were sampled in streams from Butte to below Missoula as part of a program to characterize aquatic resources in the upper Clark Fork basin of western Montana. Water-quality data were obtained periodically at 16 stations during October 1992 through September 1993 (water year 1993); daily suspended-sediment data were obtained at six of these stations. Bed-sediment and biological data were obtained at 11 stations in August 1993. Sampling stations were located on the Clark Fork and major tributaries. The primary constituents analyzed were trace elements associated with mine tailings from historic mining and smelting activities. Water-quality data include concentra- tions of major ions, trace elements, and suspended sediment in samples collected periodically during water year 1993. A statistical summary of water- quality data is provided for the period of record at each station since 1985. Daily values of streamflow, suspended-sediment concentration, and suspended-sediment discharge are given for six stations. Bed-sediment data include trace- element concentrations in the fine and bulk fractions. Biological data include trace-element concentrations in whole-body tissue of aquatic benthic insects. Quality-assurance data are reported for analytical results of water, bed sediment, and biota.

Trace Element Composition of Phytoplankton Along the US GEOTRACES Pacific Zonal Transect: Comparing Single-Cell SXRF Quotas, Chemical Leaching, and Bulk Particle Digestion

NASA Astrophysics Data System (ADS)

Ohnemus, D.; Rauschenberg, S.; Twining, B. S.

2014-12-01

The elemental stoichiometries of phytoplankton are critical ecological and chemical parameters due to biological participation in, if not control over, the marine cycles of many GEOTRACES trace elements and isotopes (TEI). Elemental stoichiometries in euphotic zone protists can be used as end-members in biogeochemical models for bioactive elements (e.g. Fe, Si) and can provide insight into relationships found in the deep ocean and sediments (e.g. Cd:P, Zn:Si) due to broad and organism-specific geochemical links. Though sub-euphotic zone (e.g. hydrothermal, margin-sourced lateral) inputs and processes are also interesting aspects of these cycles, biological incorporation of TEIs in the euphotic zone is, fundamentally, where "the rubber meets the road." Using the 2013 Pacific GEOTRACES super stations and Peruvian coastal transect as ecological waypoints, we present and compare results from three methods for studying trace elemental composition of phytoplankton: single-cell synchrotron x-ray fluorescence (SXRF); weak chemical leaching (acetic acid/hydroxylamine); and total chemical digestion (HNO3/HCl/HF). This combination of techniques allows examination of taxon-specific trends in biotic stoichiometry across the Eastern Pacific and also provides traditional bulk chemical metrics for both biotic and bulk shallow particulate composition.

7th Annual Systems Biology Symposium: Systems Biology and Engineering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Galitski, Timothy P.

2008-04-01

Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology has been hosted by the Institute for Systems Biology in Seattle, Washington, since 2002. The annual two-day event gathers the most influential researchers transforming biology into an integrative discipline investingating complex systems. Engineering and application of new technology is a central element of systems biology. Genome-scale, or very small-scale, biological questions drive the enigneering of new technologies, which enable new modes of experimentation and computational analysis, leading to new biological insights and questions. Concepts and analytical methods in engineering aremore » now finding direct applications in biology. Therefore, the 2008 Symposium, funded in partnership with the Department of Energy, featured global leaders in "Systems Biology and Engineering."« less

Should we treat the ionome as a combination of individual elements, or should we be deriving novel combined traits?

PubMed

Baxter, Ivan

2015-04-01

It has been more than 10 years since the concept of the ionome, all of the mineral nutrients in a cell tissue or organism, was introduced. In the intervening years, ionomics, high throughput elemental profiling, has been used to analyse over 400,000 samples from at least 10 different organisms. There are now multiple published examples where an ionomics approach has been used to find genes of novel function, find lines or environments that produce foods with altered nutritional profiles, or define gene by environmental effects on elemental accumulation. In almost all of these studies, the ionome has been treated as a collection of independent elements, with the analysis repeated on each measured element. However, many elements share chemical properties, are known to interact with each other, or have been shown to have similar interactions with biological molecules. Accordingly, there is strong evidence from ionomic studies that the elements of the ionome do not behave independently and that combinations of elements should be treated as the phenotypes of interest. In this review, I will consider the evidence that we have for the interdependence of the ionome, some of its causes, methods for incorporating this interdependence into analyses and the benefits, drawbacks, and challenges of taking these approaches. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Biogeochemical and hydrological constraints on concentration-discharge curves

NASA Astrophysics Data System (ADS)

Moatar, Florentina; Abbott, Ben; Minaudo, Camille; Curie, Florence; Pinay, Gilles

2017-04-01

The relationship between concentration and discharge (C-Q) can give insight into the location, abundance, rate of production or consumption, and transport dynamics of elements in coupled terrestrial-aquatic ecosystems. Consequently, the investigation of C-Q relationships for multiple elements at multiple spatial and temporal scales can be a powerful tool to address three of ecohydrology's fundamental questions: where does water comes from, how long does it stay, and what happens to the solutes and particulates it carries along the way. We analyzed long-term water quality data from 300 monitoring stations covering nearly half of France to investigate how elemental properties, catchment characteristics, and hydrological parameters influence C-Q. Based on previous work, we segmented the hydrograph, calculating independent C-Q slopes for flows above and below the median discharge. We found that most elements only expressed two of the nine possible C-Q modalities, indicating strong elemental control of C-Q shape. Catchment characteristics including land use and human population had a strong impact on concentration but typically did not influence the C-Q slopes, also suggesting inherent constraints on elemental production and transport. Biological processes appeared to regulate C-Q slope at low flows for biologically-reactive elements, but at high flows, these processes became unimportant, and most parameters expressed chemostatic behavior. This study provides a robust description of possible C-Q shapes for a wide variety of catchments and elements and demonstrates the value of low-frequency, long-term data collected by water quality agencies.

Tree biology and dendrochemistry

Treesearch

Kevin T. Smith; Walter C. Shortle

1996-01-01

Dendrochemistry, the interpretation of elemental analysis of dated tree rings, can provide a temporal record of environmental change. Using the dendrochemical record requires an understanding of tree biology. In this review, we pose four questions concerning assumptions that underlie recent dendrochemical research: 1) Does the chemical composition of the wood directly...

Physics and Size in Biological Systems.

ERIC Educational Resources Information Center

Barnes, George

1989-01-01

Described is the subject of biological scaling for physics teachers including examples and in-depth reading. Topics are elements of scaling, terminal velocities, Lilliputian and Brobdingnagian, brain evolution, dolphin echolocation, surface tension, gravity change, food and oxygen, and seeing. Ten references on physics and size, and ten questions…

New Trends in Impedimetric Biosensors for the Detection of Foodborne Pathogenic Bacteria

PubMed Central

Wang, Yixian; Ye, Zunzhong; Ying, Yibin

2012-01-01

The development of a rapid, sensitive, specific method for the foodborne pathogenic bacteria detection is of great importance to ensure food safety and security. In recent years impedimetric biosensors which integrate biological recognition technology and impedance have gained widespread application in the field of bacteria detection. This paper presents an overview on the progress and application of impedimetric biosensors for detection of foodborne pathogenic bacteria, particularly the new trends in the past few years, including the new specific bio-recognition elements such as bacteriophage and lectin, the use of nanomaterials and microfluidics techniques. The applications of these new materials or techniques have provided unprecedented opportunities for the development of high-performance impedance bacteria biosensors. The significant developments of impedimetric biosensors for bacteria detection in the last five years have been reviewed according to the classification of with or without specific bio-recognition element. In addition, some microfluidics systems, which were used in the construction of impedimetric biosensors to improve analytical performance, are introduced in this review. PMID:22737018

Genomic impact of eukaryotic transposable elements

PubMed Central

2012-01-01

The third international conference on the genomic impact of eukaryotic transposable elements (TEs) was held 24 to 28 February 2012 at the Asilomar Conference Center, Pacific Grove, CA, USA. Sponsored in part by the National Institutes of Health grant 5 P41 LM006252, the goal of the conference was to bring together researchers from around the world who study the impact and mechanisms of TEs using multiple computational and experimental approaches. The meeting drew close to 170 attendees and included invited floor presentations on the biology of TEs and their genomic impact, as well as numerous talks contributed by young scientists. The workshop talks were devoted to computational analysis of TEs with additional time for discussion of unresolved issues. Also, there was ample opportunity for poster presentations and informal evening discussions. The success of the meeting reflects the important role of Repbase in comparative genomic studies, and emphasizes the need for close interactions between experimental and computational biologists in the years to come. PMID:23171443

Genomic impact of eukaryotic transposable elements.

PubMed

Arkhipova, Irina R; Batzer, Mark A; Brosius, Juergen; Feschotte, Cédric; Moran, John V; Schmitz, Jürgen; Jurka, Jerzy

2012-11-21

The third international conference on the genomic impact of eukaryotic transposable elements (TEs) was held 24 to 28 February 2012 at the Asilomar Conference Center, Pacific Grove, CA, USA. Sponsored in part by the National Institutes of Health grant 5 P41 LM006252, the goal of the conference was to bring together researchers from around the world who study the impact and mechanisms of TEs using multiple computational and experimental approaches. The meeting drew close to 170 attendees and included invited floor presentations on the biology of TEs and their genomic impact, as well as numerous talks contributed by young scientists. The workshop talks were devoted to computational analysis of TEs with additional time for discussion of unresolved issues. Also, there was ample opportunity for poster presentations and informal evening discussions. The success of the meeting reflects the important role of Repbase in comparative genomic studies, and emphasizes the need for close interactions between experimental and computational biologists in the years to come.

Silicon as Versatile Player in Plant and Human Biology: Overlooked and Poorly Understood

PubMed Central

Farooq, Muhammad Ansar; Dietz, Karl-Josef

2015-01-01

Silicon (Si) serves as bioactive beneficial element. Si is highly abundant in soil, and occurs ubiquitously in all organisms including plants and humans. During the last three decades, nutritional significance of Si for plant and human health has received increasing attention. Plant Si plays a pivotal role in growth and development, and this beneficial effect depends usually on accumulation in plant tissues, which are then protected from various forms of biotic and abiotic stresses. Likewise, human exposure to Si imparts health benefits and essentially occurs through plant-derived food products. Si bioavailability in human diet, e.g., strengthens bones and improves immune response, as well as neuronal and connective tissue health. Despite this empiric knowledge, the essentiality of Si still remains enigmatic. Thus the link between Si availability for plant development and its profound implication for human welfare should receive attention. This review aims to provide a broad perspective on Si as important element for plant and human nutrition and to define research fields for interdisciplinary research. PMID:26617630

Role of riboswitches in gene regulation and their potential for algal biotechnology.

PubMed

Nguyen, Ginnie T D T; Scaife, Mark A; Helliwell, Katherine E; Smith, Alison G

2016-06-01

Riboswitches are regulatory elements in messenger RNA to which specific ligands can bind directly in the absence of proteins. Ligand binding alters the mRNA secondary structure, thereby affecting expression of the encoded protein. Riboswitches are widespread in prokaryotes, with over 20 different effector ligands known, including amino acids, cofactors, and Mg(2+) ions, and gene expression is generally regulated by affecting translation or termination of transcription. In plants, fungi, and microalgae, riboswitches have been found, but only those that bind thiamine pyrophosphate. These eukaryotic riboswitches operate by causing alternative splicing of the transcript. Here, we review the current status of riboswitch research with specific emphasis on microalgae. We discuss new riboswitch discoveries and insights into the underlying mechanism of action, and how next generation sequencing technology provides the motivation and opportunity to improve our understanding of these rare but important regulatory elements. We also highlight the potential of microalgal riboswitches as a tool for synthetic biology and industrial biotechnology. © 2016 Phycological Society of America.

Investigation of micrometre-sized fossil by laser mass spectrometer (LMS) designed for in situ space research

NASA Astrophysics Data System (ADS)

Tulej, Marek; Neubeck, Anna; Ivarsson, Magnus; Brigitte Neuland, Maike; Riedo, Andreas; Wurz, Peter

2015-04-01

Search for signatures of life on other planets is one of the most important goals of current planetary missions. Among various possible biomarkers, which can be investigated in situ on planetary surfaces, the detection of bio-relevant elements in planetary materials is of considerable interest and the abundance of isotopes can be important signatures of past and present bioactivities [1, 2]. We investigate the chemical composition of fossilised biological inclusions embedded in a carbonate host phase by a miniature laser ablation mass spectrometer (LMS) [3]. The LMS instrument combines a laser ablation ion source for ablation, atomisation and ionisation of surface material with a reflectron time-of-flight (TOF) mass spectrometer. LMS delivers mass spectra of almost all elements and their isotopes. In the current setup a fs-laser ablation ion source is applied with high lateral (15 um) and vertical (sub-um) resolution [4, 7] and the mass analyser supports mass resolution of 400-500 (at 56Fe mass peak) and dynamic range of eight orders of magnitude [5, 6]. From the 200 mass spectra recorded at 200 different locations on the carbonate sample surface, five mass spectra were identified which recorded the chemical composition of inclusions; from the other mass spectra the composition of the carbonate host matrix could be determined. The microscopic inspection of the sample surface and correlation with the coordinates of the laser ablation measurements made the confirmation to the location of the inclusion [8]. For the carbonate host matrix, the mass spectrometric analysis yielded the major elements H, C, O, Na, Mg, K and Ca and the trace elements Li, B and Cl. The measurements at the inclusion locations yielded in addition, the detection of F, Si, P, S, Mn, Fe, Ni, Co and Se. For most of the major elements the isotope ratios were found to be conform to the terrestrial values within a few per mills, while for minor and trace elements the determination of isotope ratios were less accurate due to low signal to noise ratios (SNR). The isotope abundances for the lightest isotope of B, S were observed to be larger than terrestrial, which is consistent with isotope fractionation by bio-relevant processes and a salty ocean. The studies demonstrates the current performance of the miniature LMS for in situ investigation of highly heterogeneous samples and its capabilities for the identification of fossilised biological matter. References: [1] Summons et al., Astrobiology, 11, 157, 2011. [2] Wurz et al., Sol. Sys. Res. 46 408, 2012. [3] Rohner et al.,Meas. Sci. Technol., 14, 2159, 2003. [4] Riedo et al., J. Anal. Atom. Spectrom. 28, 1256, 2013. [5] Riedo et al., J. Mass Spectrom.48, 1, 2013. [6] Neuland et al., Planet. Space. Sci. 101, 196, 2014. [7] Grimaudo et al., Anal. Chem. 2014, submitted. [8] Tulej et al. Geostand. Geoanal. Res., 2014; DOI: 10.1111/j.1751-908X.2014.00302.x

X-ray Microprobe Investigations of Elemental Distributions and Concentrations at Mineral-Microbe Interfaces

NASA Astrophysics Data System (ADS)

Kemner, K. M.; Kelly, S. D.; O'Loughlin, E. J.; Lai, B.; Maser, J.; Cai, Z.; Londer, Y.; Schiffer, M.; Nealson, K.

2003-12-01

Understanding the fate of heavy-metal contaminants in the environment is of fundamental importance in the development and evaluation of effective remediation and sequestration strategies. Bacteria and the extracellular material associated with them are thought to play a key role in determining a contaminant's speciation and thus its mobility in the environment. Additionally, the metabolism and surface properties of bacteria can be quite different depending upon whether the bacteria exhibit a planktonic (free-floating) or biofilm (surface adhered) habit. The microenvironment at and adjacent to actively metabolizing cells also can be significantly different from the bulk environment. Thus, to understand the microscopic physical, geological, chemical, and biological interfaces that determine a contaminant's macroscopic fate, the spatial distribution and chemical speciation of contaminants and elements that are key to biological processes must be characterized at micron and submicron lengthscales for bacteria in both planktonic and adhered states. Hard x-ray microimaging is a powerful technique for the element-specific investigation of complex environmental samples at the needed micron and submicron resolution. An important advantage of these techniques results from the large penetration depth of hard x-rays in water. This advantage minimizes the requirements for sample preparation and allows the detailed study of hydrated samples. The objectives of the studies to be presented are (1) to determine the spatial distribution, concentration, and chemical speciation of metals at, in, and near bacteria and bacteria-geosurface interfaces, (2) to use this information to identify the metabolic processes occurring within the microbes, and (3) to identify the interactions occurring near these interfaces among the metals, mineral surfaces, and bacteria under a variety of conditions. We have used x-ray fluorescence microscopy to investigate the spatial distribution of 3d elements in Pseudomonas fluorescens cells in both planktonic and surface-adhered states. We have used x-ray fluorescence spectromicroscopy to investigate the chemical speciation and distribution of Cr that was introduced to these cells as Cr(VI). Additionally, we have used these techniques to identify the distribution of an over expressed cytochrome c7 in individual E. coli. Finally, we have used x-ray fluorescence microscopy to investigate Shewanella oneidensis MR-1 cells adhered to iron oxyhydroxide thin films. The zone plate used in these microscopy experiments produced a focused beam with a cross section (and hence spatial resolution) of 100-300 nanometers. Results from x-ray fluorescence imaging experiments indicate that the distribution of P, S, Cl, Ca, Fe, Ni, Cu, and Zn can define the location of the microbe. Additionally, quantitative elemental analysis of individual microbes identified significant changes in concentration of 3d transition elements depending on the age of the culture and the type of electron acceptor presented to the microbes. These results and a discussion of the use of this technique for identifying metabolic states of individual microbes within communities and the chemical speciation of metal contaminants at the mineral-microbe interface will be presented.

Space geodiversity review: a case study in the southwestern region of Paraná State, Brazil.

NASA Astrophysics Data System (ADS)

Manosso, Fernando; Tauana Basso, Bruna; Alcindo Da Roza, Douglas; Souza dos Santos, Daniel

2015-04-01

Considering the strong global concern for nature protection, improvements emerge to support techniques to understand physical and biological means of selecting areas for environmental conservation. Most techniques take into consideration mainly the biological characteristics of nature, however as the nature is a complex of biotic and abiotic elements it becomes thus necessary the creation of parameters to understand the diversity of abiotic elements, their distribution, occurrence, threats and values as well. This paper aims to identify, quantify and perform a spatial analysis of the distribution of geodiversity in the southwestern region of Paraná State, Brazil, from the different concepts of geodiversity with the use of techniques on digital cartographic database in a Geographic Information System - GIS. Gray (2004) conceptualized geodiversity as the natural distribution of geology, including rocks, minerals, fossils, soil characteristics, land forms and processes (geomorphology), and their connections. Geodiversity is composed by the variability of abiotic nature, including lithological elements, tectonic, geomorphological, edaphic, hydrological, topographical and physical processes of the Earth surface, seas, oceans, together with natural endogenous, exogenous and anthropogenic processes that include a diversity of particles, elements and places (Serrano and Ruiz Flaño, 2007). Different methods of quantitative assessment of geodiversity in different territories were applied by Carcavilla et al (2007), Pellitero and González-Amuchastegui (2010), Navarro (2010), Katerina and Dušan (2008), Serrano et al (2007; 2009), Kozlowski (2010), Zwolinski and Stachowiak (2012), Thomas (2012), Hjort and Luoto (2010; 2012), Pellitero et al (2014), and Silva (2014). Considering geodiversity as the abiotic elements which constitute the landscape; it is important to mention that such set may vary spatially according to the occurrence of different geological formations, rock types, landforms, occurrence of fossils, drainage system, soil and other processes that outline the geodiversity. In addition to the wealth index number, which presents a quantity and area ratio, another way of analyzing the geodiversity of a case study is the abundance, dominance or the relative frequency of geodiversity (Carcavilla et al, 2007). As for the southwestern region of Paraná State case study, we used a set of cartographic databases at the 1:250.000 scale; for example: geomorphological and soil compartments, rivers, geological formations, structural lineaments, as well as temperature, rainfall and humidity average maps. The maps were organized relating the attribute tables, quantifying the sum of different elements each sample cell contained in a regular grid of 4km2. As a result, a map of the geodiversity wealth index of the region has been generated. High geodiversity wealth index comprises more carved valleys with steep slopes on some structural lines; on the other hand, less wealthy areas are located on softer relief plateaus with large hills, more homogeneous soils and lower relief structural control. These results, as well as adjustments and efficiency of the method seem to indicate an important tool for area management, especially regarding the selection of priority areas for nature conservation.

Final report for CCQM-K107: total elements and selenomethionine in human serum

NASA Astrophysics Data System (ADS)

Goenaga Infante, Heidi

2016-01-01

Routine tests that measure the concentration of electrolytes in serum are needed for diagnosis and management of renal, endocrine, acid-base, water balance and other conditions such as screening D- and A-vitamin disorders, kidney insufficiency, bone diseases and leukaemia. The diagnostic concentration ranges for many such markers are narrow, requiring reference methods with small uncertainty. Serum concentration of total selenium (Se) is important in health studies but there is increasing interest in the speciation of selenium compounds in clinical samples such as serum and individual Se- Species are bio-indicators of Se status. The last CCQM IAWG key comparison for elements in the clinical area (CCQM-K14: Ca in human serum) was organized in 2003 and the previous key comparison (CCQM-K60) for Se and Se species used a wheat flour sample. Therefore, the CCQM IAWG agreed that CCQM-K107 and a parallel pilot study CCQM-P146 should be carried out. The candidate human serum sample used for both CCQM-K107 and P146 is of high complexity and contains approximately 1000-fold lower concentrations of selenium methionine (SeMet) than those encountered in the CCQM-K60 wheat flour. This significantly broadens the scope and degree of difficulty of earlier measurements in this field. A total of eleven institutes participated in CCQM-K107 (11 participants for total elements and 7 for SeMet). The performance of the majority of the K107 participants for all the measurands was very good, illustrating their ability to obtain accurate results for analytes such as electrolytes at mg kg-1 level, essential elements at µg kg-1 level and selenium species at µg kg-1 level in a complex biological fluid. The range of agreement between participants was within the interval of ± 0.1% for Ca and up to ± 1.8% for Fe. CMC claims based on total elements in this study may include other elements with similar core competencies (e.g. Se, Cu, Zn) in a wide range of biological materials (including liquids and solids) at a similar level of performance using the same measurement technique applied in CCQM-K107 provided that there are no additional factors (e.g. blank or dissolution issues). CMC claims based on SeMet measurements in this study may be applied to other biological matrices (e.g., tissues) provided that the concentration range is similar and due diligence is taken to ensure an appropriate extraction process is achieved and species specific spikes are available for quantitation by isotope dilution. Indeed, having accepted such conditions, application to quantitation of other organometallic species and other elements in similar matrices should be possible with the same level of performance. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

How causal analysis can reveal autonomy in models of biological systems

NASA Astrophysics Data System (ADS)

Marshall, William; Kim, Hyunju; Walker, Sara I.; Tononi, Giulio; Albantakis, Larissa

2017-11-01

Standard techniques for studying biological systems largely focus on their dynamical or, more recently, their informational properties, usually taking either a reductionist or holistic perspective. Yet, studying only individual system elements or the dynamics of the system as a whole disregards the organizational structure of the system-whether there are subsets of elements with joint causes or effects, and whether the system is strongly integrated or composed of several loosely interacting components. Integrated information theory offers a theoretical framework to (1) investigate the compositional cause-effect structure of a system and to (2) identify causal borders of highly integrated elements comprising local maxima of intrinsic cause-effect power. Here we apply this comprehensive causal analysis to a Boolean network model of the fission yeast (Schizosaccharomyces pombe) cell cycle. We demonstrate that this biological model features a non-trivial causal architecture, whose discovery may provide insights about the real cell cycle that could not be gained from holistic or reductionist approaches. We also show how some specific properties of this underlying causal architecture relate to the biological notion of autonomy. Ultimately, we suggest that analysing the causal organization of a system, including key features like intrinsic control and stable causal borders, should prove relevant for distinguishing life from non-life, and thus could also illuminate the origin of life problem. This article is part of the themed issue 'Reconceptualizing the origins of life'.

Robust k-mer frequency estimation using gapped k-mers

PubMed Central

Ghandi, Mahmoud; Mohammad-Noori, Morteza

2013-01-01

Oligomers of fixed length, k, commonly known as k-mers, are often used as fundamental elements in the description of DNA sequence features of diverse biological function, or as intermediate elements in the constuction of more complex descriptors of sequence features such as position weight matrices. k-mers are very useful as general sequence features because they constitute a complete and unbiased feature set, and do not require parameterization based on incomplete knowledge of biological mechanisms. However, a fundamental limitation in the use of k-mers as sequence features is that as k is increased, larger spatial correlations in DNA sequence elements can be described, but the frequency of observing any specific k-mer becomes very small, and rapidly approaches a sparse matrix of binary counts. Thus any statistical learning approach using k-mers will be susceptible to noisy estimation of k-mer frequencies once k becomes large. Because all molecular DNA interactions have limited spatial extent, gapped k-mers often carry the relevant biological signal. Here we use gapped k-mer counts to more robustly estimate the ungapped k-mer frequencies, by deriving an equation for the minimum norm estimate of k-mer frequencies given an observed set of gapped k-mer frequencies. We demonstrate that this approach provides a more accurate estimate of the k-mer frequencies in real biological sequences using a sample of CTCF binding sites in the human genome. PMID:23861010

Robust k-mer frequency estimation using gapped k-mers.

PubMed

Ghandi, Mahmoud; Mohammad-Noori, Morteza; Beer, Michael A

2014-08-01

Oligomers of fixed length, k, commonly known as k-mers, are often used as fundamental elements in the description of DNA sequence features of diverse biological function, or as intermediate elements in the constuction of more complex descriptors of sequence features such as position weight matrices. k-mers are very useful as general sequence features because they constitute a complete and unbiased feature set, and do not require parameterization based on incomplete knowledge of biological mechanisms. However, a fundamental limitation in the use of k-mers as sequence features is that as k is increased, larger spatial correlations in DNA sequence elements can be described, but the frequency of observing any specific k-mer becomes very small, and rapidly approaches a sparse matrix of binary counts. Thus any statistical learning approach using k-mers will be susceptible to noisy estimation of k-mer frequencies once k becomes large. Because all molecular DNA interactions have limited spatial extent, gapped k-mers often carry the relevant biological signal. Here we use gapped k-mer counts to more robustly estimate the ungapped k-mer frequencies, by deriving an equation for the minimum norm estimate of k-mer frequencies given an observed set of gapped k-mer frequencies. We demonstrate that this approach provides a more accurate estimate of the k-mer frequencies in real biological sequences using a sample of CTCF binding sites in the human genome.