Effects of a weighted vest on attention to task and self-stimulatory behaviors in preschoolers with pervasive developmental disorders.

PubMed

Fertel-Daly, D; Bedell, G; Hinojosa, J

2001-01-01

This study examined the effectiveness of using a weighted vest for increasing attention to a fine motor task and decreasing self-stimulatory behaviors in preschool children with pervasive developmental disorders (PDD). Using an ABA single-subject design, the duration of attention to task and self-stimulatory behaviors and the number of distractions were measured in five preschool children with PDD over a period of 6 weeks. During the intervention phase, all participants displayed a decrease in the number of distractions and an increase in the duration of focused attention while wearing the weighted vest. All but 1 participant demonstrated a decrease in the duration of self-stimulatory behaviors while wearing a weighted vest; however, the type of self-stimulatory behaviors changed and became less self-abusive for this child while she wore the vest. During the intervention withdrawal phase, 3 participants experienced an increase in the duration of self-stimulatory behaviors, and all participants experienced an increase in the number of distractions and a decrease in the duration of focused attention. The increase or decrease, however, never returned to baseline levels for these behaviors. The findings suggest that for these 5 children with PDD, the use of a weighted vest resulted in an increase in attention to task and decrease in self-stimulatory behaviors. The most consistent improvement observed was the decreased number of distractions. Additional research is necessary to build consensus about the effectiveness of wearing a weighted vest to increase attention to task and decrease self-stimulatory behaviors for children with PDD.

D-Amino acid oxidase bio-functionalized platforms: Toward an enhanced enzymatic bio-activity

NASA Astrophysics Data System (ADS)

Herrera, Elisa; Valdez Taubas, Javier; Giacomelli, Carla E.

2015-11-01

The purpose of this work is to study the adsorption process and surface bio-activity of His-tagged D-amino acid oxidase (DAAO) from Rhodotorula gracilis (His6-RgDAAO) as the first step for the development of an electrochemical bio-functionalized platform. With such a purpose this work comprises: (a) the His6-RgDAAO bio-activity in solution determined by amperometry, (b) the adsorption mechanism of His6-RgDAAO on bare gold and carboxylated modified substrates in the absence (substrate/COO-) and presence of Ni(II) (substrate/COO- + Ni(II)) determined by reflectometry, and (c) the bio-activity of the His6-RgDAAO bio-functionalized platforms determined by amperometry. Comparing the adsorption behavior and bio-activity of His6-RgDAAO on these different solid substrates allows understanding the contribution of the diverse interactions responsible for the platform performance. His6-RgDAAO enzymatic performance in solution is highly improved when compared to the previously used pig kidney (pk) DAAO. His6-RgDAAO exhibits an amperometrically detectable bio-activity at concentrations as low as those expected on a bio-functional platform; hence, it is a viable bio-recognition element of D-amino acids to be coupled to electrochemical platforms. Moreover, His6-RgDAAO bio-functionalized platforms exhibit a higher surface activity than pkDAAO physically adsorbed on gold. The platform built on Ni(II) modified substrates present enhanced bio-activity because the surface complexes histidine-Ni(II) provide with site-oriented, native-like enzymes. The adsorption mechanism responsible of the excellent performance of the bio-functionalized platform takes place in two steps involving electrostatic and bio-affinity interactions whose prevalence depends on the degree of surface coverage.

Photobiology of Symbiodinium revisited: bio-physical and bio-optical signatures

NASA Astrophysics Data System (ADS)

Hennige, S. J.; Suggett, D. J.; Warner, M. E.; McDougall, K. E.; Smith, D. J.

2009-03-01

Light is often the most abundant resource within the nutrient-poor waters surrounding coral reefs. Consequently, zooxanthellae ( Symbiodinium spp.) must continually photoacclimate to optimise productivity and ensure coral success. In situ coral photobiology is becoming dominated by routine assessments using state-of-the-art non-invasive bio-optical or chlorophyll a fluorescence (bio-physical) techniques. Multiple genetic types of Symbiodinium are now known to exist; however, little focus has been given as to how these types differ in terms of characteristics that are observable using these techniques. Therefore, this investigation aimed to revisit and expand upon a pivotal study by Iglesias-Prieto and Trench (1994) by comparing the photoacclimation characteristics of different Symbiodinium types based on their bio-physical (chlorophyll a fluorescence, reaction centre counts) and bio-optical (optical absorption, pigment concentrations) ‘signatures’. Signatures described here are unique to Symbiodinium type and describe phenotypic responses to set conditions, and hence are not suitable to describe taxonomic structure of in hospite Symbiodinium communities. In this study, eight Symbiodinium types from clades and sub-clades (A-B, F) were grown under two PFDs (Photon Flux Density) and examined. The photoacclimation response by Symbiodinium was highly variable between algal types for all bio-physical and for many bio-optical measurements; however, a general preference to modifying reaction centre content over effective antennae-absorption was observed. Certain bio-optically derived patterns, such as light absorption, were independent of algal type and, when considered per photosystem, were matched by reaction centre stoichiometry. Only by better understanding genotypic and phenotypic variability between Symbiodinium types can future studies account for the relative taxonomic and physiological contribution by Symbiodinium to coral acclimation.

Governing at a distance: social marketing and the (bio) politics of responsibility.

PubMed

Crawshaw, Paul

2012-07-01

In the recently published lectures from the College de France series, The Birth of Bio-Politics, Foucault (2009) offers his most explicit analysis of neo-liberal governmentality and its impact upon states and societies in the late twentieth century. Framed in terms of the bio-political as a mode of governance of populations and its relationship to neo-liberalism, these lectures offer a rich seam of theoretical resources with which to interrogate contemporary forms of governmentality. This paper seeks to apply these and some recent critical analysis by Foucauldian scholars, to the study of health governance, with particular reference to the use of social marketing as a strategy to improve the health of populations 'at a distance'. Reflecting a broader decollectivisation of welfare, such strategies are identified as exemplars of neo-liberal methods of governance through inculcating self management and individualisation of responsibility for health and wellbeing. Drawing on original empirical data collected with a sample of fifty long term unemployed men in 2009, this paper critically examines social marketing as a newer feature of health governance and reflects upon participants' responses to it as a strategy in the context of their wider understandings of health, choice and responsibility. Copyright © 2012 Elsevier Ltd. All rights reserved.

A swinging seesaw as a novel model mechanism for time-dependent hormesis under dose-dependent stimulatory and inhibitory effects: A case study on the toxicity of antibacterial chemicals to Aliivibrio fischeri.

PubMed

Sun, Haoyu; Calabrese, Edward J; Zheng, Min; Wang, Dali; Pan, Yongzheng; Lin, Zhifen; Liu, Ying

2018-08-01

Hormesis occurs frequently in broadly ranging biological areas (e.g. plant biology, microbiology, biogerontology), toxicology, pharmacology and medicine. While numerous mechanisms (e.g. receptor and pathway mediated pathway responses) account for stimulatory and inhibitory features of hormetic dose responses, the vast majority emphasizes the inclusion of many doses but only one timepoint or use of a single optimized dose that is assessed over a broad range of timepoints. In this paper, a toxicity study was designed using a large number of properly spaced doses with responses determined over a large number of timepoints, which could help us reveal the underlying mechanism of hormesis. We present the results of a dose-time-response study on hormesis using five antibacterial chemicals on the bioluminescence of Aliivibrio fischeri, measuring expression of protein mRNA based on quorum sensing, simulating bioluminescent reaction and analyzing toxic actions of test chemicals. The findings show dose-time-dependent responses conforming to the hormetic dose-response model, while revealing unique response dynamics between agent induced stimulatory and inhibitory effects within bacterial growth phase dynamics. These dynamic dose-time features reveal a type of biological seesaw model that integrates stimulatory and inhibitory responses within unique growth phase, dose and time features, which has faultlessly explained the time-dependent hormetic phenomenon induced by five antibacterial chemicals (characterized by low-dose stimulation and high-dose inhibition). This study offers advances in understanding cellular dynamics, the biological integration of diverse and opposing responses and their role in evolutionary adaptive strategies to chemicals, which can provide new insight into the mechanistic investigation of hormesis. Copyright © 2018 Elsevier Ltd. All rights reserved.

Immunosuppressive Myeloid Cells' Blockade in the Glioma Microenvironment Enhances the Efficacy of Immune-Stimulatory Gene Therapy.

PubMed

Kamran, Neha; Kadiyala, Padma; Saxena, Meghna; Candolfi, Marianela; Li, Youping; Moreno-Ayala, Mariela A; Raja, Nicholas; Shah, Diana; Lowenstein, Pedro R; Castro, Maria G

2017-01-04

Survival of glioma (GBM) patients treated with the current standard of care remains dismal. Immunotherapeutic approaches that harness the cytotoxic and memory potential of the host immune system have shown great benefit in other cancers. GBMs have developed multiple strategies, including the accumulation of myeloid-derived suppressor cells (MDSCs) to induce immunosuppression. It is therefore imperative to develop multipronged approaches when aiming to generate a robust anti-tumor immune response. Herein, we tested whether combining MDSC depletion or checkpoint blockade would augment the efficacy of immune-stimulatory herpes simplex type-I thymidine kinase (TK) plus Fms-like tyrosine kinase ligand (Flt3L)-mediated immune stimulatory gene therapy. Our results show that MDSCs constitute >40% of the tumor-infiltrating immune cells. These cells express IL-4Rα, inducible nitric oxide synthase (iNOS), arginase, programmed death ligand 1 (PDL1), and CD80, molecules that are critically involved in antigen-specific T cell suppression. Depletion of MDSCs strongly enhanced the TK/Flt3L gene therapy-induced tumor-specific CD8 T cell response, which lead to increased median survival and percentage of long-term survivors. Also, combining PDL1 or CTLA-4 immune checkpoint blockade greatly improved the efficacy of TK/Flt3L gene therapy. Our results, therefore, indicate that blocking MDSC-mediated immunosuppression holds great promise for increasing the efficacy of gene therapy-mediated immunotherapies for GBM. Copyright © 2017 The American Society of Gene and Cell Therapy. Published by Elsevier Inc. All rights reserved.

GPER is involved in the stimulatory effects of aldosterone in breast cancer cells and breast tumor-derived endothelial cells.

PubMed

Rigiracciolo, Damiano Cosimo; Scarpelli, Andrea; Lappano, Rosamaria; Pisano, Assunta; Santolla, Maria Francesca; Avino, Silvia; De Marco, Paola; Bussolati, Benedetta; Maggiolini, Marcello; De Francesco, Ernestina Marianna

2016-01-05

Aldosterone induces relevant effects binding to the mineralcorticoid receptor (MR), which acts as a ligand-gated transcription factor. Alternate mechanisms can mediate the action of aldosterone such as the activation of epidermal growth factor receptor (EGFR), MAPK/ERK, transcription factors and ion channels. The G-protein estrogen receptor (GPER) has been involved in the stimulatory effects of estrogenic signalling in breast cancer. GPER has been also shown to contribute to certain responses to aldosterone, however the role played by GPER and the molecular mechanisms implicated remain to be fully understood. Here, we evaluated the involvement of GPER in the stimulatory action exerted by aldosterone in breast cancer cells and breast tumor derived endothelial cells (B-TEC). Competition assays, gene expression and silencing studies, immunoblotting and immunofluorescence experiments, cell proliferation and migration were performed in order to provide novel insights into the role of GPER in the aldosterone-activated signalling. Our results demonstrate that aldosterone triggers the EGFR/ERK transduction pathway in a MR- and GPER-dependent manner. Aldosterone does not bind to GPER, it however induces the direct interaction between MR and GPER as well as between GPER and EGFR. Next, we ascertain that the up-regulation of the Na+/H+ exchanger-1 (NHE-1) induced by aldosterone involves MR and GPER. Biologically, both MR and GPER contribute to the proliferation and migration of breast and endothelial cancer cells mediated by NHE-1 upon aldosterone exposure. Our data further extend the current knowledge on the molecular mechanisms through which GPER may contribute to the stimulatory action elicited by aldosterone in breast cancer.

Marked enhancement of the immune response to BioThrax® (Anthrax Vaccine Adsorbed) by the TLR9 agonist CPG 7909 in healthy volunteers.

PubMed

Rynkiewicz, Dianna; Rathkopf, Melinda; Sim, Iain; Waytes, A Thomas; Hopkins, Robert J; Giri, Lallan; DeMuria, Deborah; Ransom, Janet; Quinn, James; Nabors, Gary S; Nielsen, Carl J

2011-08-26

Immunization with BioThrax(®) (Anthrax Vaccine Adsorbed) is a safe and effective means of preventing anthrax. Animal studies have demonstrated that the addition of CpG DNA adjuvants to BioThrax can markedly increase the immunogenicity of the vaccine, increasing both serum anti-protective antigen (PA) antibody and anthrax toxin-neutralizing antibody (TNA) concentrations. The immune response to CpG-adjuvanted BioThrax in animals was not only stronger, but was also more rapid and led to higher levels of protection in spore challenge models. The B-class CpG DNA adjuvant CPG 7909, a 24-base synthetic, single-strand oligodeoxynucleotide, was evaluated for its safety profile and adjuvant properties in a Phase 1 clinical trial. A double-blind study was performed in which 69 healthy subjects, age 18-45 years, were randomized to receive three doses of either: (1) BioThrax alone, (2) 1 mg of CPG 7909 alone or (3) BioThrax plus 1 mg of CPG 7909, all given intramuscularly on study days 0, 14 and 28. Subjects were monitored for IgG to PA by ELISA and for TNA titers through study day 56 and for safety through month 6. CPG 7909 increased the antibody response by 6-8-fold at peak, and accelerated the response by 3 weeks compared to the response seen in subjects vaccinated with BioThrax alone. No serious adverse events related to study agents were reported, and the combination was considered to be reasonably well tolerated. The marked acceleration and enhancement of the immune response seen by combining BioThrax and CPG 7909 offers the potential to shorten the course of immunization and reduce the time to protection, and may be particularly useful in the setting of post-exposure prophylaxis. Copyright © 2011 Elsevier Ltd. All rights reserved.

Analysis of the bacterial community changes in soil for septic tank effluent treatment in response to bio-clogging.

PubMed

Nie, J Y; Zhu, N W; Zhao, K; Wu, L; Hu, Y H

2011-01-01

Soil columns were set up to survey the bacterial community in the soil for septic tank effluent treatment. When bio-clogging occurred in the soil columns, the effluent from the columns was in poorer quality. To evaluate changes of the soil bacterial community in response to bio-clogging, the bacterial community was characterized by DNA gene sequences from soil samples after polymerase chain reaction coupled with denaturing gradient gel electrophoresis process. Correspondence analysis showed that Proteobacteria related bacteria were the main bacteria within the soil when treating septic tank effluent. However, Betaproteobacteria related bacteria were the dominant microorganisms in the normal soil, whereas Alphaproteobacteria related bacteria were more abundant in the clogged soil. This study provided insight into changes of the soil bacterial community in response to bio-clogging. The results can supply some useful information for the design and management of soil infiltration systems.

PEGylated graphene oxide elicits strong immunological responses despite surface passivation

NASA Astrophysics Data System (ADS)

Luo, Nana; Weber, Jeffrey K.; Wang, Shuang; Luan, Binquan; Yue, Hua; Xi, Xiaobo; Du, Jing; Yang, Zaixing; Wei, Wei; Zhou, Ruhong; Ma, Guanghui

2017-02-01

Engineered nanomaterials promise to transform medicine at the bio-nano interface. However, it is important to elucidate how synthetic nanomaterials interact with critical biological systems before such products can be safely utilized in humans. Past evidence suggests that polyethylene glycol-functionalized (PEGylated) nanomaterials are largely biocompatible and elicit less dramatic immune responses than their pristine counterparts. We here report results that contradict these findings. We find that PEGylated graphene oxide nanosheets (nGO-PEGs) stimulate potent cytokine responses in peritoneal macrophages, despite not being internalized. Atomistic molecular dynamics simulations support a mechanism by which nGO-PEGs preferentially adsorb onto and/or partially insert into cell membranes, thereby amplifying interactions with stimulatory surface receptors. Further experiments demonstrate that nGO-PEG indeed provokes cytokine secretion by enhancing integrin β8-related signalling pathways. The present results inform that surface passivation does not always prevent immunological reactions to 2D nanomaterials but also suggest applications for PEGylated nanomaterials wherein immune stimulation is desired.

GPER is involved in the stimulatory effects of aldosterone in breast cancer cells and breast tumor-derived endothelial cells

PubMed Central

Rigiracciolo, Damiano Cosimo; Scarpelli, Andrea; Lappano, Rosamaria; Pisano, Assunta; Santolla, Maria Francesca; Avino, Silvia; De Marco, Paola; Bussolati, Benedetta; Maggiolini, Marcello; De Francesco, Ernestina Marianna

2016-01-01

Aldosterone induces relevant effects binding to the mineralcorticoid receptor (MR), which acts as a ligand-gated transcription factor. Alternate mechanisms can mediate the action of aldosterone such as the activation of epidermal growth factor receptor (EGFR), MAPK/ERK, transcription factors and ion channels. The G-protein estrogen receptor (GPER) has been involved in the stimulatory effects of estrogenic signalling in breast cancer. GPER has been also shown to contribute to certain responses to aldosterone, however the role played by GPER and the molecular mechanisms implicated remain to be fully understood. Here, we evaluated the involvement of GPER in the stimulatory action exerted by aldosterone in breast cancer cells and breast tumor derived endothelial cells (B-TEC). Competition assays, gene expression and silencing studies, immunoblotting and immunofluorescence experiments, cell proliferation and migration were performed in order to provide novel insights into the role of GPER in the aldosterone-activated signalling. Our results demonstrate that aldosterone triggers the EGFR/ERK transduction pathway in a MR- and GPER-dependent manner. Aldosterone does not bind to GPER, it however induces the direct interaction between MR and GPER as well as between GPER and EGFR. Next, we ascertain that the up-regulation of the Na+/H+ exchanger-1 (NHE-1) induced by aldosterone involves MR and GPER. Biologically, both MR and GPER contribute to the proliferation and migration of breast and endothelial cancer cells mediated by NHE-1 upon aldosterone exposure. Our data further extend the current knowledge on the molecular mechanisms through which GPER may contribute to the stimulatory action elicited by aldosterone in breast cancer. PMID:26646587

Prostate Cancer Cell Growth: Stimulatory Role of Neurotensin and Mechanism of Inhibition by Flavonoids as Related to Protein Kinase C

DTIC Science & Technology

2009-01-01

Stimulatory Role of Neurotensin and Mechanism of Inhibition by Flavonoids as Related to Protein Kinase C PRINCIPAL INVESTIGATOR: Robert E. Carraway...CONTRACT NUMBER Prostate Cancer Cell Growth: Stimulatory Role of Neurotensin and Mechanism of Inhibition by Flavonoids as Related to Protein Kinase C...relationship between neurotensin (NT) and protein kinases and to investigate the mechanism by which flavonoids (FLAV) inhibit NT growth signaling in PC3

Response of Surface Soil Hydrology to the Micro-Pattern of Bio-Crust in a Dry-Land Loess Environment, China

PubMed Central

Wei, Wei; Yu, Yun; Chen, Liding

2015-01-01

The specific bio-species and their spatial patterns play crucial roles in regulating eco-hydrologic process, which is significant for large-scale habitat promotion and vegetation restoration in many dry-land ecosystems. Such effects, however, are not yet fully studied. In this study, 12 micro-plots, each with size of 0.5 m in depth and 1 m in length, were constructed on a gentle grassy hill-slope with a mean gradient of 8° in a semiarid loess hilly area of China. Two major bio-crusts, including mosses and lichens, had been cultivated for two years prior to the field simulation experiments, while physical crusts and non-crusted bare soils were used for comparison. By using rainfall simulation method, four designed micro-patterns (i.e., upper bio-crust and lower bare soil, scattered bio-crust, upper bare soil and lower bio-crust, fully-covered bio-crust) to the soil hydrological response were analyzed. We found that soil surface bio-crusts were more efficient in improving soil structure, water holding capacity and runoff retention particularly at surface 10 cm layers, compared with physical soil crusts and non-crusted bare soils. We re-confirmed that mosses functioned better than lichens, partly due to their higher successional stage and deeper biomass accumulation. Physical crusts were least efficient in water conservation and erosion control, followed by non-crusted bare soils. More importantly, there were marked differences in the efficiency of the different spatial arrangements of bio-crusts in controlling runoff and sediment generation. Fully-covered bio-crust pattern provides the best option for soil loss reduction and runoff retention, while a combination of upper bio-crust and lower bare soil pattern is the least one. These findings are suggested to be significant for surface-cover protection, rainwater infiltration, runoff retention, and erosion control in water-restricted and degraded natural slopes. PMID:26207757

Response of Surface Soil Hydrology to the Micro-Pattern of Bio-Crust in a Dry-Land Loess Environment, China.

PubMed

Wei, Wei; Yu, Yun; Chen, Liding

2015-01-01

The specific bio-species and their spatial patterns play crucial roles in regulating eco-hydrologic process, which is significant for large-scale habitat promotion and vegetation restoration in many dry-land ecosystems. Such effects, however, are not yet fully studied. In this study, 12 micro-plots, each with size of 0.5 m in depth and 1 m in length, were constructed on a gentle grassy hill-slope with a mean gradient of 8° in a semiarid loess hilly area of China. Two major bio-crusts, including mosses and lichens, had been cultivated for two years prior to the field simulation experiments, while physical crusts and non-crusted bare soils were used for comparison. By using rainfall simulation method, four designed micro-patterns (i.e., upper bio-crust and lower bare soil, scattered bio-crust, upper bare soil and lower bio-crust, fully-covered bio-crust) to the soil hydrological response were analyzed. We found that soil surface bio-crusts were more efficient in improving soil structure, water holding capacity and runoff retention particularly at surface 10 cm layers, compared with physical soil crusts and non-crusted bare soils. We re-confirmed that mosses functioned better than lichens, partly due to their higher successional stage and deeper biomass accumulation. Physical crusts were least efficient in water conservation and erosion control, followed by non-crusted bare soils. More importantly, there were marked differences in the efficiency of the different spatial arrangements of bio-crusts in controlling runoff and sediment generation. Fully-covered bio-crust pattern provides the best option for soil loss reduction and runoff retention, while a combination of upper bio-crust and lower bare soil pattern is the least one. These findings are suggested to be significant for surface-cover protection, rainwater infiltration, runoff retention, and erosion control in water-restricted and degraded natural slopes.

A bio-injectable algin-aminocaproic acid thixogel with tri-stimuli responsiveness.

PubMed

Chejara, Dharmesh R; Mabrouk, Mostafa; Badhe, Ravindra V; Mulla, Jameel A S; Kumar, Pradeep; Choonara, Yahya E; du Toit, Lisa C; Pillay, Viness

2016-01-01

In this article a novel bio-injectable algin-aminocaproic acid (Alg-ACA) tri-stimuli responsive thixogel system is reported. The designed soft thixotrophic hydrogel (thixogel) was characterized using various analytical techniques such as FT-IR, NMR, SEM, AFM and DSC. The soft thixogel system was further investigated for stress responsiveness using different rheological studies which confirmed the thixotropic nature of the gel [Thixotropic area (Ar) of Alg-ACA (1:0.5), Alg-ACA (1:1) and Alg-ACA (1:2), were 23.5%, 43.1%, and 27.59%, respectively, which were higher than that of Na-Alg (2.08%)]. The thixogel also demonstrated temperature and ultrasonication responsiveness. This tri-stimuli responsive soft thixogel system was rendered flowable (fluid) on applying the described physical stimuli and recovered its "rigid" gel structure upon removal of the applied stimuli. This approach of synthesizing a thixogels may be applicable to a broad variety of other natural polymers and has the potential for use in biomedical applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

Prostate Cancer Cell Growth: Stimulatory Role of Neurotensin And Mechanism of Inhibition by Flavonoids as Related to Protein Kinase C

DTIC Science & Technology

2008-01-31

Stimulatory Role of Neurotensin And Mechanism of Inhibition by Flavonoids as Related to Protein Kinase C. PRINCIPAL INVESTIGATOR: Robert E...SUBTITLE Prostate Cancer Cell Growth: Stimulatory Role of Neurotensin and 5a. CONTRACT NUMBER Mechanism of Inhibition by Flavonoids as Related to...isotypes and to investigate the mechanism by which flavonoids (FLAV) inhibit NT growth signaling in PC3 cells. The long-range scope is to determine the

tmBioC: improving interoperability of text-mining tools with BioC.

PubMed

Khare, Ritu; Wei, Chih-Hsuan; Mao, Yuqing; Leaman, Robert; Lu, Zhiyong

2014-01-01

The lack of interoperability among biomedical text-mining tools is a major bottleneck in creating more complex applications. Despite the availability of numerous methods and techniques for various text-mining tasks, combining different tools requires substantial efforts and time owing to heterogeneity and variety in data formats. In response, BioC is a recent proposal that offers a minimalistic approach to tool interoperability by stipulating minimal changes to existing tools and applications. BioC is a family of XML formats that define how to present text documents and annotations, and also provides easy-to-use functions to read/write documents in the BioC format. In this study, we introduce our text-mining toolkit, which is designed to perform several challenging and significant tasks in the biomedical domain, and repackage the toolkit into BioC to enhance its interoperability. Our toolkit consists of six state-of-the-art tools for named-entity recognition, normalization and annotation (PubTator) of genes (GenNorm), diseases (DNorm), mutations (tmVar), species (SR4GN) and chemicals (tmChem). Although developed within the same group, each tool is designed to process input articles and output annotations in a different format. We modify these tools and enable them to read/write data in the proposed BioC format. We find that, using the BioC family of formats and functions, only minimal changes were required to build the newer versions of the tools. The resulting BioC wrapped toolkit, which we have named tmBioC, consists of our tools in BioC, an annotated full-text corpus in BioC, and a format detection and conversion tool. Furthermore, through participation in the 2013 BioCreative IV Interoperability Track, we empirically demonstrate that the tools in tmBioC can be more efficiently integrated with each other as well as with external tools: Our experimental results show that using BioC reduces >60% in lines of code for text-mining tool integration. The tmBioC toolkit

Effects of Punishment Procedures on the Self-Stimulatory Behavior of an Autistic Child.

ERIC Educational Resources Information Center

Friman, Patrick C.; And Others

1984-01-01

Three punishment procedures--contingent applications of water mist, lemon juice, and vinegar--were evaluated as aversive treatment methods for a self-stimulatory behavior exhibited by a severely retarded 11-year-old male. The water mist procedure was as effective as lemon juice or vinegar, presented less physical threat to the client, and was…

Effects of aluminum trichloride on the cartilage stimulatory growth factors in rats.

PubMed

Zhang, Fan; Sun, Xudong; Yu, Hongyan; Yang, Xu; Song, Miao; Han, Yanfei; Li, Yanfei; Zhu, Yanzhu

2017-02-01

Aluminum (Al) is considered to be a potentially toxic metal and inhibits cartilage formation. Transforming growth factor β1 (TGF-β1) and bone morphogenetic protein 2 (BMP-2) are cartilage stimulatory growth factors, which play important roles in regulating the cartilage formation. To investigate the effects of aluminum trichloride (AlCl 3 ) on the regulation of cartilage formation. Eighty Wistar rats were orally exposed to 0 (control group), 0.4 g/L (low-dose group), 0.8 g/L (mid-dose group) and 1.6 g/L (high-dose group) AlCl 3 for 120 days, respectively. The rats body weight were decreased, the cartilage histological structure were disrupted, the cartilage and serum contents of Al and the serum level of C-telopeptide of type II collagen were all increased, the serum level of type II collagen (Col II) and alkaline phosphatase (ALP), and the mRNA expressions of TGF-β1, BMP-2, ALP and Col II were all decreased in the AlCl 3 -treated groups compared with those in control group. These results indicate that AlCl 3 inhibits the cartilage formation through inhibition of the cartilage stimulatory growth factors expressions.

Co-stimulatory molecules in and beyond co-stimulation - tipping the balance in atherosclerosis?

PubMed

Gerdes, N; Zirlik, A

2011-11-01

A plethora of basic laboratory and clinical studies has uncovered the chronic inflammatory nature of atherosclerosis. The adaptive immune system with its front-runner, the T cell, drives the atherogenic process at all stages. T cell function is dependent on and controlled by a variety of either co-stimulatory or co-inhibitory signals. In addition, many of these proteins enfold T cell-independent pro-atherogenic functions on a variety of cell types. Accordingly they represent potential targets for immune-modulatory and/or anti-inflammatory therapy of atherosclerosis. This review focuses on the diverse role of co-stimulatory molecules of the B7 and tumour necrosis factor (TNF)-superfamily and their downstream signalling effectors in atherosclerosis. In particular, the contribution of CD28/CD80/CD86/CTLA4, ICOS/ICOSL, PD-1/PDL-1/2, TRAF, CD40/CD154, OX40/OX40L, CD137/CD137L, CD70/CD27, GITR/GITRL, and LIGHT to arterial disease is reviewed. Finally, the potential for a therapeutic exploitation of these molecules in the treatment of atherosclerosis is discussed.

Safety Aspects of Bio-Based Nanomaterials.

PubMed

Catalán, Julia; Norppa, Hannu

2017-12-01

Moving towards a bio-based and circular economy implies a major focus on the responsible and sustainable utilization of bio-resources. The emergence of nanotechnology has opened multiple possibilities, not only in the existing industrial sectors, but also for completely novel applications of nanoscale bio-materials, the commercial exploitation of which has only begun during the last few years. Bio-based materials are often assumed not to be toxic. However, this pre-assumption is not necessarily true. Here, we provide a short overview on health and environmental aspects associated with bio-based nanomaterials, and on the relevant regulatory requirements. We also discuss testing strategies that may be used for screening purposes at pre-commercial stages. Although the tests presently used to reveal hazards are still evolving, regarding modifi-cations required for nanomaterials, their application is needed before the upscaling or commercialization of bio-based nanomaterials, to ensure the market potential of the nanomaterials is not delayed by uncertainties about safety issues.

Functional tooth restoration by next-generation bio-hybrid implant as a bio-hybrid artificial organ replacement therapy

PubMed Central

Oshima, Masamitsu; Inoue, Kaoru; Nakajima, Kei; Tachikawa, Tetsuhiko; Yamazaki, Hiromichi; Isobe, Tomohide; Sugawara, Ayaka; Ogawa, Miho; Tanaka, Chie; Saito, Masahiro; Kasugai, Shohei; Takano-Yamamoto, Teruko; Inoue, Takashi; Tezuka, Katsunari; Kuboki, Takuo; Yamaguchi, Akira; Tsuji, Takashi

2014-01-01

Bio-hybrid artificial organs are an attractive concept to restore organ function through precise biological cooperation with surrounding tissues in vivo. However, in bio-hybrid artificial organs, an artificial organ with fibrous connective tissues, including muscles, tendons and ligaments, has not been developed. Here, we have enveloped with embryonic dental follicle tissue around a HA-coated dental implant, and transplanted into the lower first molar region of a murine tooth-loss model. We successfully developed a novel fibrous connected tooth implant using a HA-coated dental implant and dental follicle stem cells as a bio-hybrid organ. This bio-hybrid implant restored physiological functions, including bone remodelling, regeneration of severe bone-defect and responsiveness to noxious stimuli, through regeneration with periodontal tissues, such as periodontal ligament and cementum. Thus, this study represents the potential for a next-generation bio-hybrid implant for tooth loss as a future bio-hybrid artificial organ replacement therapy. PMID:25116435

Immune-Stimulatory Effects of Althaea rosea Flower Extracts through the MAPK Signaling Pathway in RAW264.7 Cells.

PubMed

Kim, Yon-Suk; Kim, Eun-Kyung; Nawarathna, Weligala Pahalagedara Amila Srilal; Dong, Xin; Shin, Woen-Bin; Park, Jin-Su; Moon, Sang-Ho; Park, Pyo-Jam

2017-04-25

Althaea rosea (Linn.) is a medicinal plant from China and Korea that has been traditionally used to control inflammation, to stop bedwetting and as a mouthwash in cases of bleeding gums. Its flowers are employed medicinally for their emollient, demulcent and diuretic properties, which make them useful in chest complaints. Furthermore, a flower extract decoction is used to improve blood circulation, for the treatment of constipation, dysmenorrhoea, haemorrhages, etc. However, the possible mechanisms of the immune-stimulatory effect remains to be elucidated. Therefore, we investigated the role of Althaea rosea flower (ARF) extracts in the immune-stimulatory effect of macrophages and the underlying mechanisms of action. ARF water extract (ARFW) could dose-dependently increase NO production and cytokines (IL-6 and TNF-α). We also found that ARFW significantly increased the expression of iNOS and COX-2 proteins in RAW264.7 cells. Consistent with these results, MAPK protein (JNK, ERK, p38) expression levels were induced after treatment with ARFW. Additionally, ARFW showed a marked increase in the phosphorylation level of IκBα and subsequent IκBα degradation allowing NF-κB nuclear translocation. These results suggest that the immune-stimulatory effect of A. rosea flower extracts is mediated through the translocation of NF-κB p65 subunit into the nucleus from the cytoplasm and subsequent activation of pro-inflammatory cytokines (IL-6 and TNF-α) and other mediators (iNOS and COX-2), which occurs mainly through MAPK signalling pathway. Thus, we suggest that ARFW could be considered as a potential therapeutic agent useful in the development of immune-stimulatory compounds.

The Initial Immune Reaction to a New Tumor Antigen Is Always Stimulatory and Probably Necessary for the Tumor's Growth

PubMed Central

Prehn, Richmond T.

2010-01-01

All nascent neoplasms probably elicit at least a weak immune reaction. However, the initial effect of the weak immune reaction on a nascent tumor is always stimulatory rather than inhibitory to tumor growth, assuming only that exposure to the tumor antigens did not antedate the initiation of the neoplasm (as may occur in some virally induced tumors). This conclusion derives from the observation that the relationship between the magnitude of an adaptive immune reaction and tumor growth is not linear but varies such that while large quantities of antitumor immune reactants tend to inhibit tumor growth, smaller quantities of the same reactants are, for unknown reasons, stimulatory. Any immune reaction must presumably be small before it can become large; hence the initial reaction to the first presentation of a tumor antigen must always be small and in the stimulatory portion of this nonlinear relationship. In mouse-skin carcinogenesis experiments it was found that premalignant papillomas were variously immunogenic, but that the carcinomas that arose in them were, presumably because of induced immune tolerance, nonimmunogenic in the animal of origin. PMID:20811480

The initial immune reaction to a new tumor antigen is always stimulatory and probably necessary for the tumor's growth.

PubMed

Prehn, Richmond T

2010-01-01

All nascent neoplasms probably elicit at least a weak immune reaction. However, the initial effect of the weak immune reaction on a nascent tumor is always stimulatory rather than inhibitory to tumor growth, assuming only that exposure to the tumor antigens did not antedate the initiation of the neoplasm (as may occur in some virally induced tumors). This conclusion derives from the observation that the relationship between the magnitude of an adaptive immune reaction and tumor growth is not linear but varies such that while large quantities of antitumor immune reactants tend to inhibit tumor growth, smaller quantities of the same reactants are, for unknown reasons, stimulatory. Any immune reaction must presumably be small before it can become large; hence the initial reaction to the first presentation of a tumor antigen must always be small and in the stimulatory portion of this nonlinear relationship. In mouse-skin carcinogenesis experiments it was found that premalignant papillomas were variously immunogenic, but that the carcinomas that arose in them were, presumably because of induced immune tolerance, nonimmunogenic in the animal of origin.

Targeting the T-cell co-stimulatory CD27/CD70 pathway in cancer immunotherapy: rationale and potential.

PubMed

van de Ven, Koen; Borst, Jannie

2015-01-01

In 2013, cancer immunotherapy was named 'breakthrough of the year' based on the outcome of clinical trials with blocking antibodies to the T-cell co-inhibitory receptors CTLA-4 and PD-1. This success has emphasized that cytotoxic T-cell responses to cancer can occur, but are limited by peripheral tolerance and by immunosuppression in the tumor microenvironment. Targeting of CTLA-4, PD-1 or its ligands partly overcomes these limitations and can now be applied in multiple immunogenic cancer types. Furthermore, an increased success rate is expected from combining CTLA-4 and/or PD-1 blocking with deliberate engagement of T-cell co-stimulatory receptors, particularly TNF receptor (R) family members. The TNFR family includes CD27 (Tnfrsf7), for which an agonistic antibody has recently entered clinical trials. In this review, we describe how CD27 co-stimulation impacts the T-cell response, with the purpose to illuminate how CD27 agonism can be exploited in cancer immunotherapy.

Antibodies to B7.1 define the GFCC'C" face of the N-terminal domain as critical for co-stimulatory interactions.

PubMed

Wang, Suyue; Veldman, Geertruida M; Stahl, Mark; Xing, Yuzhe; Tobin, James F; Erbe, David V

2002-09-02

Antagonists of the B7 family of co-stimulatory molecules have the potential for altering immune responses therapeutically. To better define the requirements for such inhibitors, we have mapped the binding of an entire panel of blocking antibodies specific for human B7.1. By mutagenesis, each of the residues critical for blocking antibody binding appeared to fall entirely within the N-terminal V-set domain of B7.1. Thus, although antibody-antigen interacting surfaces can be quite large, these results indicate that a relatively small portion of the GFCC'C" face of this domain is crucial for further antagonist development.

The bio-response of osteocytes and its regulation on osteoblasts under vibration.

PubMed

Wu, Xin-Tong; Sun, Lian-Wen; Qi, Hong-Yu; Shi, Hao; Fan, Yu-Bo

2016-04-01

Vibration, especially at low magnitude and high frequency (LMHF), was demonstrated to be anabolic for bone, but how the LMHF vibration signal is perceived by osteocytes is not fully studied. On the other hand, the mechanotransduction of osteocytes under shear stress has been scientists' primary focus for years. Due to the small strain caused by low-magnitude vibration, whether the previous explanation for shear stress will still work for LMHF vibration is unknown. In this study, a finite element method (FEM) model based on the real geometrical shape of an osteocyte was built to compare the mechanical behaviors of osteocytes under LMHF vibration and shear stress. The bio-response of osteocytes to vibration under different frequencies, including the secretion of soluble factors and the concentration of intracellular calcium, were studied. The regulating effect of the conditioned medium (CM) from vibrated osteocytes on osteoblasts was also studied. The FEM analysis result showed the cell membrane deformation under LMHF vibration was very small (with a peak value of 1.09%) as compared to the deformation caused by shear stress (with a peak value of 6.65%). The F-actin stress fibers of osteocytes were reorganized, especially on the nucleus periphery after LMHF vibration. The vibration at 30 Hz has a promoting effect on osteocytes and the osteogenesis of osteoblasts, whereas vibration at 90 Hz was suppressive. These results lead to a conclusion that the bio-response of osteocytes to LMHF vibration is frequency-dependent and is more related to the cytoskeleton on nuclear periphery rather than the membrane deformation. © 2016 International Federation for Cell Biology.

Merging high doxorubicin loading with pronounced magnetic response and bio-repellent properties in hybrid drug nanocarriers.

PubMed

Bakandritsos, Aristides; Papagiannopoulos, Aristeidis; Anagnostou, Eleni N; Avgoustakis, Konstantinos; Zboril, Radek; Pispas, Stergios; Tucek, Jiri; Ryukhtin, Vasyl; Bouropoulos, Nikolaos; Kolokithas-Ntoukas, Argiris; Steriotis, Theodore A; Keiderling, Uwe; Winnefeld, Frank

2012-08-06

Hybrid magnetic drug nanocarriers are prepared via a self-assembly process of poly(methacrylic acid)-graft-poly(ethyleneglycol methacrylate) (p(MAA-g-EGMA)) on growing iron oxide nanocrystallites. The nanocarriers successfully merge together bio-repellent properties, pronounced magnetic response, and high loading capacity for the potent anticancer drug doxorubicin (adriamicin), in a manner not observed before in such hybrid colloids. High magnetic responses are accomplished by engineering the size of the magnetic nanocrystallites (∼13.5 nm) following an aqueous single-ferrous precursor route, and through adjustment of the number of cores in each colloidal assembly. Complementing conventional magnetometry, the magnetic response of the nanocarriers is evaluated by magnetophoretic experiments providing insight into their internal organization and on their response to magnetic manipulation. The structural organization of the graft-copolymer, locked on the surface of the nanocrystallites, is further probed by small-angle neutron scattering on single-core colloids. Analysis showed that the MAA segments selectively populate the area around the magnetic nanocrystallites, while the poly(ethylene glycol)-grafted chains are arranged as protrusions, pointing towards the aqueous environment. These nanocarriers are screened at various pHs and in highly salted media by light scattering and electrokinetic measurements. According to the results, their stability is dramatically enhanced, as compared to uncoated nanocrystallites, owing to the presence of the external protective PEG canopy. The nanocarriers are also endowed with bio-repellent properties, as evidenced by stability assays using human blood plasma as the medium. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Propranolol blocks the stimulatory effects of naloxone on ventilation and oxygen consumption in hamsters.

PubMed

Schlenker, E H; Eikanger, J

1997-06-01

The purposes of these studies were: 1) to determine the effects of various doses of propranolol, a nonspecific beta-adrenergic antagonist, on ventilation, oxygen consumption, and body temperature in hamsters, and 2) to test the hypothesis that in hamsters the stimulatory effects of naloxone, an opioid receptor antagonist, on ventilation and oxygen consumption occur, at least in part, through the release of catecholamines that act via beta-adrenergic receptors. Propranolol, a non-specific beta adrenergic receptor antagonist, at a 20 mg/kg depressed body temperature, oxygen consumption, tidal volume, and ventilation relative to saline. The lower dose of 10 mg/kg had only transitory effects on tidal volume at 60 min and ventilation at 30 min post-injection-Naloxone (1 mg/kg) relative to saline stimulated ventilation and oxygen consumption. These effects were blocked by propranolol pretreatment. The results of these experiments demonstrate that in the hamster, 1) body temperature, oxygen consumption, and ventilation appear to be modulated by beta-adrenergic receptors, and 2) the stimulatory effects of naloxone on oxygen consumption and ventilation may occur through the interaction of endogenous opioids and beta-adrenergic receptor systems.

BioSentinel: Developing a Space Radiation Biosensor

NASA Technical Reports Server (NTRS)

Santa Maria, Sergio R.

2015-01-01

BioSentinel is an autonomous fully self-contained science mission that will conduct the first study of the biological response to space radiation outside low Earth orbit (LEO) in over 40 years. The 4-unit (4U) BioSentinel biosensor system, is housed within a 6-Unit (6U) spacecraft, and uses yeast cells in multiple independent microfluidic cards to detect and measure DNA damage that occurs in response to ambient space radiation. Cell growth and metabolic activity will be measured using a 3-color LED detection system and a metabolic indicator dye with a dedicated thermal control system per fluidic card.

Bio-prospecting of distillery yeasts as bio-control and bio-remediation agents.

PubMed

Ubeda, Juan F; Maldonado, María; Briones, Ana I; Francisco, J Fernández; González, Francisco J

2014-05-01

This work constitutes a preliminary study in which the capacity of non-Saccharomyces yeasts isolated from ancient distilleries as bio-control agents against moulds and in the treatment of waste waters contaminated by heavy metals-i.e. bio-remediation-is shown. In the first control assays, antagonist effect between non-Saccharomyces yeasts, their extracts and supernatants against some moulds, analysing the plausible (not exhaustive) involved factors were qualitatively verified. In addition, two enzymatic degrading properties of cell wall plant polymers, quitinolitic and pectinolitic, were screened. Finally, their use as agents of bio-remediation of three heavy metals (cadmium, chromium and lead) was analysed semi-quantitatively. The results showed that all isolates belonging to Pichia species effectively inhibited all moulds assayed. Moreover, P. kudriavzevii is a good candidate for both bio-control and bio-remediation because it inhibited moulds and accumulated the major proportion of the three tested metals.

Characterization of a Dopaminergic Stimulatory Factor Derived from Monoclonal Cell Lines of Striatal Origin

DTIC Science & Technology

2006-12-01

other substrates for its biosynthesis would be effective in raising MN9D dopamine content. The pyrimidine, cytidine triphosphate (CTP) reacts with...phosphatidylethanolamine or phosphatidylcholine. MN9D cells were treated for 48 hrs with 2 mM CTP, cytidine diphosphate (CDP) or cytidine monophosphate (CMP), in the...presence or absence of 25 µM ethanolamine or 25 µM phosphoethanolamine. Cytidine alone did not alter the dopaminergic stimulatory effect of

Evidence for Alterations in Stimulatory G proteins and Oxytocin Levels in Children with Autism

PubMed Central

Jacobson, Jill D.; Ellerbeck, Kathryn A.; Kelly, Kelsie A.; Fleming, Kandace K.; Jamison, T. Rene; Coffey, Charles W.; Smith, Catherine M.; Reese, R. Matthew; Sands, Scott A.

2014-01-01

The neurotransmitter oxytocin plays an important role in social affiliation. Low oxytocin levels and defects in the oxytocin receptor have been reported in childhood autism. However, little is known about oxytocin’s post-receptor signaling pathways in autism. Oxytocin signals via stimulatory and inhibitory G proteins. c-fos mRNA expression has been used as a marker of OT signaling as well as of G protein signaling. Herein, we hypothesized that oxytocin and its signaling pathways would be altered in children with autism. We measured plasma oxytocin levels by ELISA, G-protein and c-fos mRNA by PCR, and G proteins by immunoblot in cultured peripheral blood mononuclear cells (PBMCs) in children with autism and in age-matched controls. Males with autism displayed elevated oxytocin levels compared to controls (p<0.05). Children with autism displayed significantly higher mRNA for stimulatory G proteins compared to controls (p<0.05). Oxytocin levels correlated strongly positively with c-fos mRNA levels, but only in control participants (p<0.01). Oxytocin, G-protein, and c-fos mRNA levels correlated inversely with measures of social and emotional behaviors, but only in control participants. These data suggest that children with autism may exhibit a dysregulation in oxytocin and/or its signaling pathways. PMID:24485488

Nanotribological response of a plasma nitrided bio-steel.

PubMed

Samanta, Aniruddha; Chakraborty, Himel; Bhattacharya, Manjima; Ghosh, Jiten; Sreemany, Monjoy; Bysakh, Sandip; Rane, Ramkrishna; Joseph, Alphonsa; Jhala, Ghanshyam; Mukherjee, Subroto; Das, Mitun; Mukhopadhyay, Anoop K

2017-01-01

AISI 316L is a well known biocompatible, austenitic stainless steel (SS). It is thus a bio-steel. Considering its importance as a bio-prosthesis material here we report the plasma nitriding of AISI 316L (SS) followed by its microstructural and nanotribological characterization. Plasma nitriding of the SS samples was carried out in a plasma reactor with a hot wall vacuum chamber. For ease of comparison these plasma nitrided samples were termed as SSPN. The experimental results confirmed the formations of an embedded nitrided metal layer zone (ENMLZ) and an interface zone (IZ) between the ENMLZ and the unnitrided bulk metallic layer zone (BMLZ) in the SSPN sample. These ENMLZ and IZ in the SSPN sample were richer in iron nitride (FeN) chromium nitride (CrN) along with the austenite phase. The results from nanoindentation, microscratch, nanoscratch and sliding wear studies confirmed that the static contact deformation resistance, the microwear, nanowear and sliding wear resistance of the SSPN samples were much better than those of the SS samples. These results were explained in terms of structure-property correlations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Optical Properties of Plasmonic Nanostructures for Bio-Imaging and Bio-Sensing Applications

NASA Astrophysics Data System (ADS)

Kravets, Vira V.

Kravets, Vira V. (Ph.D., Physics). Optical properties of plasmonic nanostructures for bio-imaging and bio-sensing applications. Dissertation directed by Associate Professor Anatoliy Pinchuk. ABSTRACT. This dissertation explores the physics of free electron excitations in gold nanoparticle chains, silver nanoparticle colloids, and thin gold films. Electron excitations in nanostructures (surface plasmons, SP) are responsible for unique optical properties, which are applied in bio-sensing and bio-imaging applications. For gold nanoparticle chains, the effect of SP on resonance light absorption was studied experimentally and theoretically. Mainly, how the spectral position of the absorption peak depends on inter-particle distances. This dependence is used in “molecular rulers”, providing spatial resolution below the Rayleigh limit. The underlying theory is based on particle interaction via scattered dipole fields. Often in literature only the near-field component of the scattered field is considered. Here, I show that middle and far fields should not be neglected for calculation of extinction by particle chains. In silver nanoparticles, SP excitations produce two independent effects: (a) the intrinsic fluorescence of the particles, and (b) the enhancement of a molecule’s fluorescence by a particle’s surface. The mechanism of (a) is deduced by studying how fluorescence depends on particle size. For (b), I show that fluorescence of a dye molecule on the surface of a nanoparticle is enhanced, when compared to that of the free-standing dye. I demonstrate that the dye’s fluorescent quantum yield is dependent on the particle’s size, making labeled silver nanoparticles attractive candidates as bio-imaging agents. Labeled nanoparticles are applied to cell imaging, and their bio-compatibility with two cell lines is evaluated here. Finally, in gold films under attenuated total internal reflection (ATR) conditions, the SP create a propagating wave (SP-polariton, SPP

Piezoelectric materials as stimulatory biomedical materials and scaffolds for bone repair.

PubMed

Tandon, Biranche; Blaker, Jonny J; Cartmell, Sarah H

2018-04-16

The process of bone repair and regeneration requires multiple physiological cues including biochemical, electrical and mechanical - that act together to ensure functional recovery. Myriad materials have been explored as bioactive scaffolds to deliver these cues locally to the damage site, amongst these piezoelectric materials have demonstrated significant potential for tissue engineering and regeneration, especially for bone repair. Piezoelectric materials have been widely explored for power generation and harvesting, structural health monitoring, and use in biomedical devices. They have the ability to deform with physiological movements and consequently deliver electrical stimulation to cells or damaged tissue without the need of an external power source. Bone itself is piezoelectric and the charges/potentials it generates in response to mechanical activity are capable of enhancing bone growth. Piezoelectric materials are capable of stimulating the physiological electrical microenvironment, and can play a vital role to stimulate regeneration and repair. This review gives an overview of the association of piezoelectric effect with bone repair, and focuses on state-of-the-art piezoelectric materials (polymers, ceramics and their composites), the fabrication routes to produce piezoelectric scaffolds, and their application in bone repair. Important characteristics of these materials from the perspective of bone tissue engineering are highlighted. Promising upcoming strategies and new piezoelectric materials for this application are presented. Electrical stimulation/electrical microenvironment are known effect the process of bone regeneration by altering the cellular response and are crucial in maintaining tissue functionality. Piezoelectric materials, owing to their capability of generating charges/potentials in response to mechanical deformations, have displayed great potential for fabricating smart stimulatory scaffolds for bone tissue engineering. The growing

Determination of Carbonyl Functional Groups in Bio-oils by Potentiometric Titration: The Faix Method.

PubMed

Black, Stuart; Ferrell, Jack R

2017-02-07

Carbonyl compounds present in bio-oils are known to be responsible for bio-oil property changes upon storage and during upgrading. Specifically, carbonyls cause an increase in viscosity (often referred to as 'aging') during storage of bio-oils. As such, carbonyl content has previously been used as a method of tracking bio-oil aging and condensation reactions with less variability than viscosity measurements. Additionally, carbonyls are also responsible for coke formation in bio-oil upgrading processes. Given the importance of carbonyls in bio-oils, accurate analytical methods for their quantification are very important for the bio-oil community. Potentiometric titration methods based on carbonyl oximation have long been used for the determination of carbonyl content in pyrolysis bio-oils. Here, we present a modification of the traditional carbonyl oximation procedures that results in less reaction time, smaller sample size, higher precision, and more accurate carbonyl determinations. While traditional carbonyl oximation methods occur at room temperature, the Faix method presented here occurs at an elevated temperature of 80 °C.

Determination of Carbonyl Functional Groups in Bio-oils by Potentiometric Titration: The Faix Method

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

Black, Stuart; Ferrell, Jack R.

We know that carbonyl compounds, present in bio-oils, are responsible for bio-oil property changes upon storage and during upgrading. Specifically, carbonyls cause an increase in viscosity (often referred to as 'aging') during storage of bio-oils. As such, carbonyl content has previously been used as a method of tracking bio-oil aging and condensation reactions with less variability than viscosity measurements. In addition, carbonyls are also responsible for coke formation in bio-oil upgrading processes. Given the importance of carbonyls in bio-oils, accurate analytical methods for their quantification are very important for the bio-oil community. Potentiometric titration methods based on carbonyl oximation havemore » long been used for the determination of carbonyl content in pyrolysis bio-oils. Here, we present a modification of the traditional carbonyl oximation procedures that results in less reaction time, smaller sample size, higher precision, and more accurate carbonyl determinations. And while traditional carbonyl oximation methods occur at room temperature, the Faix method presented here occurs at an elevated temperature of 80 degrees C.« less

Determination of Carbonyl Functional Groups in Bio-oils by Potentiometric Titration: The Faix Method

DOE PAGES

Black, Stuart; Ferrell, Jack R.

2017-02-07

We know that carbonyl compounds, present in bio-oils, are responsible for bio-oil property changes upon storage and during upgrading. Specifically, carbonyls cause an increase in viscosity (often referred to as 'aging') during storage of bio-oils. As such, carbonyl content has previously been used as a method of tracking bio-oil aging and condensation reactions with less variability than viscosity measurements. In addition, carbonyls are also responsible for coke formation in bio-oil upgrading processes. Given the importance of carbonyls in bio-oils, accurate analytical methods for their quantification are very important for the bio-oil community. Potentiometric titration methods based on carbonyl oximation havemore » long been used for the determination of carbonyl content in pyrolysis bio-oils. Here, we present a modification of the traditional carbonyl oximation procedures that results in less reaction time, smaller sample size, higher precision, and more accurate carbonyl determinations. And while traditional carbonyl oximation methods occur at room temperature, the Faix method presented here occurs at an elevated temperature of 80 degrees C.« less

Treatment of Shwachman syndrome by Japanese herbal medicine (Juzen-taiho-to): stimulatory effects of its fatty acids on hemopoiesis in patients.

PubMed

Hisha, Hiroko; Kohdera, Urara; Hirayama, Masahiro; Yamada, Haruki; Iguchi-Uehira, Tomoko; Fan, Tian-Xue; Cui, Yun-Ze; Yang, Guo-Xiang; Li, Yongan; Sugiura, Kikuya; Inaba, Muneo; Kobayashi, Yohnosuke; Ikehara, Susumu

2002-01-01

Juzen-taiho-to (a Japanese herbal medicine) has been traditionally administered to patients with anemia, neutropenia, or wasting syndrome. We previously attempted to isolate and purify the hemopoiesis-stimulatory components in Juzen-taiho-to extracts using an in vitro hemopoietic stem cell (HSC) assay method in which mouse HSCs can proliferate on a stromal cell line (MS-5). We have found that fatty acids (particularly oleic acid and linolenic acid) actively promote the proliferation of HSCs, and that the effect is mediated by stromal cells, rather than by any direct action on the HSCs. In the present study, we show, using human normal bone marrow cells (BMCs) and umbilical cord blood cells, that similar stimulatory effects are due to the presence of oleic acid and linolenic acid, which stimulate the proliferation of HSCs in stroma-based culture systems. Furthermore, a marked stimulatory effect was noted on BMCs from patients with Shwachman syndrome, which shows pancreatic and bone marrow dysfunctions. We also show the data on hemopoietic recovery after the administration of Juzen-taiho-to to a patient with Shwachman syndrome. These findings suggest that decreased fatty acid levels in the blood, caused by exocrine pancreatic insufficiency, induce bone marrow dysfunction in Shwachman syndrome.

Mechanism insights into bio-floc bound water transformation based on synchrotron X-ray computed microtomography and viscoelastic acoustic response analysis.

PubMed

Wu, Boran; Zhou, Meng; Dai, Xiaohu; Chai, Xiaoli

2018-06-05

This study visually tracked the micro-spatial water distribution in bio-flocs of waste activated sludge through in situ synchrotron X-ray computed microtomography. Primarily, the two fractions of bound water, the vicinal water adhering to the surface of organic compositions and the interstitial water mechanically trapped in the net-like structure of bio-flocs, were proposed based on the cross-section imaging results. Furthermore, the determinants on bound water occurrences were explored in terms of viscoelastic acoustic responses of extracellular polymeric substances (EPS). The joint roles of hydrophilic substance removal, EPS aggregation compaction and colloidal instability of sludge flocs in bound water reduction were confirmed by the strong correlations (Pearson correlation coefficient, R p  > 0.95, p-value<0.04) among protein levels of EPS, EPS viscosity and bound water contents. Accordingly, providing adhering sites for vicinal water and forming bio-flocs with high viscosity for trapping interstitial water were proposed to be the contributions of EPS on bound water occurrences. Copyright © 2018 Elsevier Ltd. All rights reserved.

Dual-Responsive Metabolic Precursor and Light-Up AIEgen for Cancer Cell Bio-orthogonal Labeling and Precise Ablation.

PubMed

Hu, Fang; Yuan, Youyong; Wu, Wenbo; Mao, Duo; Liu, Bin

2018-06-05

Metabolic glycoengineering of unnatural glycans with bio-orthogonal chemical groups and a subsequent click reaction with fluorescent probes have been widely used in monitoring various bioprocesses. Herein, we developed a dual-responsive metabolic precursor that could specifically generate unnatural glycans with azide groups on the membrane of targeted cancer cells with high selectivity. Moreover, a water-soluble fluorescent light-up probe with aggregation-induced emission (AIE) was synthesized, which turned its fluorescence on upon a click reaction with azide groups on the cancer cell surface, enabling special cancer cell imaging with low background signal. Furthermore, the probe can generate 1 O 2 upon light irradiation, fulfilling its dual role as an imaging and therapeutic agent for cancer cells. Therefore, the concepts of the cancer-cell-specific metabolic precursor cRGD-S-Ac 3 ManNAz and the AIE light-up probe are promising in bio-orthogonal labeling and cancer-specific imaging and therapy.

Stimulatory versus suppressive effects of GM-CSF on tumor progression in multiple cancer types

PubMed Central

Hong, In-Sun

2016-01-01

Granulocyte-macrophage colony-stimulating factor (GM-CSF, also called CSF-2) is best known for its critical role in immune modulation and hematopoiesis. A large body of experimental evidence indicates that GM-CSF, which is frequently upregulated in multiple types of human cancers, effectively marks cancer cells with a ‘danger flag' for the immune system. In this context, most studies have focused on its function as an immunomodulator, namely its ability to stimulate dendritic cell (DC) maturation and monocyte/macrophage activity. However, recent studies have suggested that GM-CSF also promotes immune-independent tumor progression by supporting tumor microenvironments and stimulating tumor growth and metastasis. Although some studies have suggested that GM-CSF has inhibitory effects on tumor growth and metastasis, an even greater number of studies show that GM-CSF exerts stimulatory effects on tumor progression. In this review, we summarize a number of findings to provide the currently available information regarding the anticancer immune response of GM-CSG. We then discuss the potential roles of GM-CSF in the progression of multiple types of cancer to provide insights into some of the complexities of its clinical applications. PMID:27364892

[Progress in bio-based polyamides].

PubMed

Huang, Zhengqiang; Cui, Zhe; Zhang, Heming; Fu, Peng; Zhao, Qingxiang; Liu, Minying

2016-06-25

Bio-based polyamides are environment-friendly polymers. The precursors of bio-based polyamides come from bio-based materials such as castor oil, glucose and animal oil. Bio-based polyamides precursors include bio-based amino acids, bio-based lactams, bio-based diprotic acid and bio-based diamines. In this paper, we discussed the route of the precursors of bio-based polyamides that come from bio-based materials. We discussed the properties of bio-based polyamides. Bio-based PA11and bio-based PA1010 are well-known bio-based polyamides; we discussed the origin materials of the precursors, the route of manufacturing bio-based PA11 and PA1010, and their modifications status. The variety, classification and commercial production of bio-based polyamides were described in details, as well as bio-based polyamides development in China.

Using Autonomous Bio Nanosatellites for Deep Space Exploration

NASA Astrophysics Data System (ADS)

Santa Maria, S. R.; Liddell, L. C.; Tieze, S. M.; Ricco, A. J.; Hanel, R.; Bhattacharya, S.

2018-02-01

NASA's BioSentinel mission will conduct the first study of biological response to deep-space radiation in 45 years. It is an automated nanosatellite that will measure the DNA damage response to ambient space radiation in a model biological organism.

Cognitive bio-radar: The natural evolution of bio-signals measurement.

PubMed

Malafaia, Daniel; Oliveira, Beatriz; Ferreira, Pedro; Varum, Tiago; Vieira, José; Tomé, Ana

2016-10-01

In this article we discuss a novel approach to Bio-Radar, contactless measurement of bio-signals, called Cognitive Bio-Radar. This new approach implements the Bio-Radar in a Software Defined Radio (SDR) platform in order to obtain awareness of the environment where it operates. Due to this, the Cognitive Bio-Radar can adapt to its surroundings in order to have an intelligent usage of the radio frequency spectrum to improve its performance. In order to study the feasibility of such implementation, a SDR based Bio-Radar testbench was developed and evaluated. The prototype is shown to be able to acquire the heartbeat activity and the respiratory effort. The acquired data is compared with the acquisitions from a Biopac research data acquisition system, showing coherent results for both heartbeat and breathing rate.

BIOS Security Analysis and a Kind of Trusted BIOS

NASA Astrophysics Data System (ADS)

Zhou, Zhenliu; Xu, Rongsheng

The BIOS's security threats to computer system are analyzed and security requirements for firmware BIOS are summarized in this paper. Through discussion about TCG's trust transitivity, a new approach about CRTM implementation based on BIOS is developed. In this paper, we also put forward a new trusted BIOS architecture-UTBIOS which is built on Intel Framework for EFI/UEFI. The trustworthiness of UTBIOS is based on trusted hardware TPM. In UTBIOS, trust encapsulation and trust measurement are used to construct pre-OS trust chain. Performance of trust measurement is also analyzed in the end.

Stimulatory actions of bioflavenoids on tyrosine uptake into cultured bovine adrenal chromaffin cells

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

Morita, K.; Hamano, S.; Oka, M.

1990-09-28

The effects of flavenoids on L-({sup 14}C)tyrosine uptake into cultured adrenal chromaffin cells were examined. Flavone markedly stimulated tyrosine uptake into these cells in a manner dependent on its concentration. Apigenin also caused a moderate stimulatory action, but quercetin had no significant effect on the uptake. Flavone also stimulated the uptake of histidine, but did not affect the uptake of serine, lysine, or glutamic acid. These results are considered to propose the possibility that flavonoids may be able to stimulate the precursor uptake into the cells, resulting in an enhancement of the biogenic amine production.

Functional Tooth Restoration by Allogeneic Mesenchymal Stem Cell-Based Bio-Root Regeneration in Swine

PubMed Central

Wei, Fulan; Song, Tieli; Ding, Gang; Xu, Junji; Liu, Yi; Liu, Dayong; Fan, Zhipeng; Zhang, Chunmei

2013-01-01

Our previous proof-of-concept study showed the feasibility of regenerating the dental stem cell-based bioengineered tooth root (bio-root) structure in a large animal model. Here, we used allogeneic dental mesenchymal stem cells to regenerate bio-root, and then installed a crown on the bio-root to restore tooth function. A root shape hydroxyapatite tricalcium phosphate scaffold containing dental pulp stem cells was covered by a Vc-induced periodontal ligament stem cell sheet and implanted into a newly generated jaw bone implant socket. Six months after implantation, a prefabricated porcelain crown was cemented to the implant and subjected to tooth function. Clinical, radiological, histological, ultrastructural, systemic immunological evaluations and mechanical properties were analyzed for dynamic changes in the bio-root structure. The regenerated bio-root exhibited characteristics of a normal tooth after 6 months of use, including dentinal tubule-like and functional periodontal ligament-like structures. No immunological response to the bio-roots was observed. We developed a standard stem cell procedure for bio-root regeneration to restore adult tooth function. This study is the first to successfully regenerate a functional bio-root structure for artificial crown restoration by using allogeneic dental stem cells and Vc-induced cell sheet, and assess the recipient immune response in a preclinical model. PMID:23363023

Response of Human Osteoblast to n-HA/PEEK—Quantitative Proteomic Study of Bio-effects of Nano-Hydroxyapatite Composite

NASA Astrophysics Data System (ADS)

Zhao, Minzhi; Li, Haiyun; Liu, Xiaochen; Wei, Jie; Ji, Jianguo; Yang, Shu; Hu, Zhiyuan; Wei, Shicheng

2016-03-01

Nano-sized hydroxyapatite (n-HA) is considered as a bio-active material, which is often mixed into bone implant material, polyetheretherketone (PEEK). To reveal the global protein expression modulations of osteoblast in response to direct contact with the PEEK composite containing high level (40%) nano-sized hydroxyapatite (n-HA/PEEK) and explain its comprehensive bio-effects, quantitative proteomic analysis was conducted on human osteoblast-like cells MG-63 cultured on n-HA/PEEK in comparison with pure PEEK. Results from quantitative proteomic analysis showed that the most enriched categories in the up-regulated proteins were related to calcium ion processes and associated functions while the most enriched categories in the down-regulated proteins were related to RNA process. This enhanced our understanding to the molecular mechanism of the promotion of the cell adhesion and differentiation with the inhibition of the cell proliferation on n-HA/PEEK composite. It also exhibited that although the calcium ion level of incubate environment hadn’t increased, merely the calcium fixed on the surface of material had influence to intracellular calcium related processes, which was also reflect by the higher intracellular Ca2+ concentration of n-HA/PEEK. This study could lead to more comprehensive cognition to the versatile biocompatibility of composite materials. It further proves that proteomics is useful in new bio-effect discovery.

Response of Human Osteoblast to n-HA/PEEK--Quantitative Proteomic Study of Bio-effects of Nano-Hydroxyapatite Composite.

PubMed

Zhao, Minzhi; Li, Haiyun; Liu, Xiaochen; Wei, Jie; Ji, Jianguo; Yang, Shu; Hu, Zhiyuan; Wei, Shicheng

2016-03-09

Nano-sized hydroxyapatite (n-HA) is considered as a bio-active material, which is often mixed into bone implant material, polyetheretherketone (PEEK). To reveal the global protein expression modulations of osteoblast in response to direct contact with the PEEK composite containing high level (40%) nano-sized hydroxyapatite (n-HA/PEEK) and explain its comprehensive bio-effects, quantitative proteomic analysis was conducted on human osteoblast-like cells MG-63 cultured on n-HA/PEEK in comparison with pure PEEK. Results from quantitative proteomic analysis showed that the most enriched categories in the up-regulated proteins were related to calcium ion processes and associated functions while the most enriched categories in the down-regulated proteins were related to RNA process. This enhanced our understanding to the molecular mechanism of the promotion of the cell adhesion and differentiation with the inhibition of the cell proliferation on n-HA/PEEK composite. It also exhibited that although the calcium ion level of incubate environment hadn't increased, merely the calcium fixed on the surface of material had influence to intracellular calcium related processes, which was also reflect by the higher intracellular Ca(2+) concentration of n-HA/PEEK. This study could lead to more comprehensive cognition to the versatile biocompatibility of composite materials. It further proves that proteomics is useful in new bio-effect discovery.

The in vivo regulation of heart rate in the murine sinoatrial node by stimulatory and inhibitory heterotrimeric G proteins

PubMed Central

Sebastian, Sonia; Ang, Richard; Abramowitz, Joel; Weinstein, Lee S.; Chen, Min; Ludwig, Andreas; Birnbaumer, Lutz

2013-01-01

Reciprocal physiological modulation of heart rate is controlled by the sympathetic and parasympathetic systems acting on the sinoatrial (SA) node. However, there is little direct in vivo work examining the role of stimulatory and inhibitory G protein signaling in the SA node. Thus, we designed a study to examine the role of the stimulatory (Gαs) and inhibitory G protein (Gαi2) in in vivo heart rate regulation in the SA node in the mouse. We studied mice with conditional deletion of Gαs and Gαi2 in the conduction system using cre-loxP technology. We crossed mice in which cre recombinase expression was driven by a tamoxifen-inducible conduction system-specific construct with “Gαs floxed” and “Gαi2 floxed” mice. We studied the heart rate responses of adult mice compared with littermate controls by using radiotelemetry before and after administration of tamoxifen. The mice with conditional deletion of Gαs and Gαi2 had a loss of diurnal variation and were bradycardic or tachycardic, respectively, in the daytime. In mice with conditional deletion of Gαs, there was a selective loss of low-frequency power, while with deletion of Gαi2, there was a loss of high-frequency power in power spectral analysis of heart rate variability. There was no evidence of pathological arrhythmia. Pharmacological modulation of heart rate by isoprenaline was impaired in the Gαs mice, but a muscarinic agonist was still able to slow the heart rate in Gαi2 mice. We conclude that Gαs- and Gαi2-mediated signaling in the sinoatrial node is important in the reciprocal regulation of heart rate through the autonomic nervous system. PMID:23697798

The in vivo regulation of heart rate in the murine sinoatrial node by stimulatory and inhibitory heterotrimeric G proteins.

PubMed

Sebastian, Sonia; Ang, Richard; Abramowitz, Joel; Weinstein, Lee S; Chen, Min; Ludwig, Andreas; Birnbaumer, Lutz; Tinker, Andrew

2013-08-15

Reciprocal physiological modulation of heart rate is controlled by the sympathetic and parasympathetic systems acting on the sinoatrial (SA) node. However, there is little direct in vivo work examining the role of stimulatory and inhibitory G protein signaling in the SA node. Thus, we designed a study to examine the role of the stimulatory (Gαs) and inhibitory G protein (Gαi2) in in vivo heart rate regulation in the SA node in the mouse. We studied mice with conditional deletion of Gαs and Gαi2 in the conduction system using cre-loxP technology. We crossed mice in which cre recombinase expression was driven by a tamoxifen-inducible conduction system-specific construct with "Gαs floxed" and "Gαi2 floxed" mice. We studied the heart rate responses of adult mice compared with littermate controls by using radiotelemetry before and after administration of tamoxifen. The mice with conditional deletion of Gαs and Gαi2 had a loss of diurnal variation and were bradycardic or tachycardic, respectively, in the daytime. In mice with conditional deletion of Gαs, there was a selective loss of low-frequency power, while with deletion of Gαi2, there was a loss of high-frequency power in power spectral analysis of heart rate variability. There was no evidence of pathological arrhythmia. Pharmacological modulation of heart rate by isoprenaline was impaired in the Gαs mice, but a muscarinic agonist was still able to slow the heart rate in Gαi2 mice. We conclude that Gαs- and Gαi2-mediated signaling in the sinoatrial node is important in the reciprocal regulation of heart rate through the autonomic nervous system.

Bio-microfluidics: biomaterials and biomimetic designs.

PubMed

Domachuk, Peter; Tsioris, Konstantinos; Omenetto, Fiorenzo G; Kaplan, David L

2010-01-12

Bio-microfluidics applies biomaterials and biologically inspired structural designs (biomimetics) to microfluidic devices. Microfluidics, the techniques for constraining fluids on the micrometer and sub-micrometer scale, offer applications ranging from lab-on-a-chip to optofluidics. Despite this wealth of applications, the design of typical microfluidic devices imparts relatively simple, laminar behavior on fluids and is realized using materials and techniques from silicon planar fabrication. On the other hand, highly complex microfluidic behavior is commonplace in nature, where fluids with nonlinear rheology flow through chaotic vasculature composed from a range of biopolymers. In this Review, the current state of bio-microfluidic materials, designs and applications are examined. Biopolymers enable bio-microfluidic devices with versatile functionalization chemistries, flexibility in fabrication, and biocompatibility in vitro and in vivo. Polymeric materials such as alginate, collagen, chitosan, and silk are being explored as bulk and film materials for bio-microfluidics. Hydrogels offer options for mechanically functional devices for microfluidic systems such as self-regulating valves, microlens arrays and drug release systems, vital for integrated bio-microfluidic devices. These devices including growth factor gradients to study cell responses, blood analysis, biomimetic capillary designs, and blood vessel tissue culture systems, as some recent examples of inroads in the field that should lead the way in a new generation of microfluidic devices for bio-related needs and applications. Perhaps one of the most intriguing directions for the future will be fully implantable microfluidic devices that will also integrate with existing vasculature and slowly degrade to fully recapitulate native tissue structure and function, yet serve critical interim functions, such as tissue maintenance, drug release, mechanical support, and cell delivery.

Reverse engineering biological networks :applications in immune responses to bio-toxins.

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

Martino, Anthony A.; Sinclair, Michael B.; Davidson, George S.

Our aim is to determine the network of events, or the regulatory network, that defines an immune response to a bio-toxin. As a model system, we are studying T cell regulatory network triggered through tyrosine kinase receptor activation using a combination of pathway stimulation and time-series microarray experiments. Our approach is composed of five steps (1) microarray experiments and data error analysis, (2) data clustering, (3) data smoothing and discretization, (4) network reverse engineering, and (5) network dynamics analysis and fingerprint identification. The technological outcome of this study is a suite of experimental protocols and computational tools that reverse engineermore » regulatory networks provided gene expression data. The practical biological outcome of this work is an immune response fingerprint in terms of gene expression levels. Inferring regulatory networks from microarray data is a new field of investigation that is no more than five years old. To the best of our knowledge, this work is the first attempt that integrates experiments, error analyses, data clustering, inference, and network analysis to solve a practical problem. Our systematic approach of counting, enumeration, and sampling networks matching experimental data is new to the field of network reverse engineering. The resulting mathematical analyses and computational tools lead to new results on their own and should be useful to others who analyze and infer networks.« less

Stimulatory effects of calcium on respiration and NAD(P)H synthesis in intact rat heart mitochondria utilizing physiological substrates cannot explain respiratory control in vivo.

PubMed

Vinnakota, Kalyan C; Dash, Ranjan K; Beard, Daniel A

2011-09-02

Mitochondrial TCA cycle dehydrogenase enzymes have been shown to be stimulated by Ca(2+) under various substrate and ADP incubation conditions in an attempt to determine and understand the role of Ca(2+) in maintaining energy homeostasis in working hearts. In this study, we tested the hypothesis that, at physiological temperature and 1 mM extramitochondrial free magnesium, Ca(2+) can stimulate the overall mitochondrial NAD(P)H generation flux in rat heart mitochondria utilizing pyruvate and malate as substrates at both subsaturating and saturating concentrations. In both cases, we found that, in the physiological regime of mitochondrial oxygen consumption observed in the intact animal and in the physiological range of cytosolic Ca(2+) concentration averaged per beat, Ca(2+) had no observable stimulatory effect. A modest apparent stimulatory effect (22-27%) was observable at supraphysiological maximal ADP-stimulated respiration at 2.5 mM initial phosphate. The stimulatory effects observed over the physiological Ca(2+) range are not sufficient to make a significant contribution to the control of oxidative phosphorylation in the heart in vivo.

Stimulatory Effects of Calcium on Respiration and NAD(P)H Synthesis in Intact Rat Heart Mitochondria Utilizing Physiological Substrates Cannot Explain Respiratory Control in Vivo*

PubMed Central

Vinnakota, Kalyan C.; Dash, Ranjan K.; Beard, Daniel A.

2011-01-01

Mitochondrial TCA cycle dehydrogenase enzymes have been shown to be stimulated by Ca2+ under various substrate and ADP incubation conditions in an attempt to determine and understand the role of Ca2+ in maintaining energy homeostasis in working hearts. In this study, we tested the hypothesis that, at physiological temperature and 1 mm extramitochondrial free magnesium, Ca2+ can stimulate the overall mitochondrial NAD(P)H generation flux in rat heart mitochondria utilizing pyruvate and malate as substrates at both subsaturating and saturating concentrations. In both cases, we found that, in the physiological regime of mitochondrial oxygen consumption observed in the intact animal and in the physiological range of cytosolic Ca2+ concentration averaged per beat, Ca2+ had no observable stimulatory effect. A modest apparent stimulatory effect (22–27%) was observable at supraphysiological maximal ADP-stimulated respiration at 2.5 mm initial phosphate. The stimulatory effects observed over the physiological Ca2+ range are not sufficient to make a significant contribution to the control of oxidative phosphorylation in the heart in vivo. PMID:21757763

Bio-threat preparedness: Need for a paradigm shift.

PubMed

Jindal, A K; Roy, Kaushik

2014-04-01

India of late has been vulnerable to Chemical, Biological, Radiological and Nuclear (CBRN) threat, on account of its unique geographic position. Biological threat is an imminent threat in the hands of a terrorist. The public health system of our country is overburdened due to its present role and bio-attack response is not a priority area. This paper suggests that as the prime focus is on the CR and N threats in the integrated CBRN preparedness strategy and that specialized and technical forces are needed to deal with a bio-threat; hence there is a need for a paradigm shift in policy. The emerging field of bio-threat needs to be delinked from the joint family of 'CBRN', with consequent structural and functional changes. A separate specialized cadre needs to be formed for dealing with bio-threat, created from the pool of doctors and non-medical scientists from the AFMS and the DRDO. Structural changes are needed in the organization, to bring in the resources of NCDC, New Delhi for enhanced disease surveillance capacity and creation of a bio-threat mitigation node in the AFMC, Pune.

Effect of anthrax immune globulin on response to BioThrax (anthrax vaccine adsorbed) in New Zealand white rabbits.

PubMed

Malkevich, Nina V; Basu, Subhendu; Rudge, Thomas L; Clement, Kristin H; Chakrabarti, Ajoy C; Aimes, Ronald T; Nabors, Gary S; Skiadopoulos, Mario H; Ionin, Boris

2013-11-01

Development of anthrax countermeasures that may be used concomitantly in a postexposure setting requires an understanding of the interaction between these products. Anthrax immune globulin intravenous (AIGIV) is a candidate immunotherapeutic that contains neutralizing antibodies against protective antigen (PA), a component of anthrax toxins. We evaluated the interaction between AIGIV and BioThrax (anthrax vaccine adsorbed) in rabbits. While pharmacokinetics of AIGIV were not altered by vaccination, the vaccine-induced immune response was abrogated in AIGIV-treated animals.

'Fingerprints' of central stimulatory drug effects by means of quantitative radioelectroencephalography in the rat (tele-stereo-EEG).

PubMed

Dimpfel, W; Spüler, M; Nickel, B; Tibes, U

1986-01-01

The new electrophysiological model earlier described as stereo-EEG is extended now to allow recording from the freely moving rat by means of a telemetric device. Chronic implantation of 4 electrodes into the brain allows simultaneous transmission of field potentials from frontal cortex, hippocampus, striatum and reticular formation. Frequency analysis of these potentials results in a drug-specific 'fingerprint' which cannot only be used to compare different chemicals with each other but also to detect onset and time dependence of drug actions. Application of the model to the question if fenetylline has its own intrinsic mode of action or merely develops its stimulatory effect after metabolic separation into its molecular moieties amphetamine and theophylline (prodrug hypothesis) revealed that fenetylline indeed displays its own stimulatory effect to the same extent and at a similar time course as amphetamine and theophylline. The 'fingerprint' as obtained by the analysis of the action of fenetylline in the rat resembles closely that obtained after the application of theophylline with respect to decreased alpha activity, but resembles amphetamine with respect to beta 1 activity. Thus the applied method allows studying structure function relationships as the action of fenetylline seems to reflect both its molecular moieties.

Moisture variation associated with water input and evaporation during sewage sludge bio-drying.

PubMed

Cai, Lu; Gao, Ding; Chen, Tong-Bin; Liu, Hong-Tao; Zheng, Guo-Di; Yang, Qi-Wei

2012-08-01

The variation of moisture during sewage sludge bio-drying was investigated. In situ measurements were conducted to monitor the bulk moisture and water vapor, while the moisture content, water generation, water evaporation and aeration water input of the bio-drying bulk were calculated based on the water mass balance. The moisture in the sewage sludge bio-drying material decreased from 66% to 54% in response to control technology for bio-drying. During the temperature increasing and thermophilic phases of sewage sludge bio-drying, the moisture content, water generation and water evaporation of the bulk initially increased and then decreased. The peak water generation and evaporation occurred during the thermophilic phase. During the bio-drying, water evaporation was much greater than water generation, and aeration facilitated the water evaporation. Copyright © 2012. Published by Elsevier Ltd.

Israel Marine Bio-geographic Database (ISRAMAR-BIO)

NASA Astrophysics Data System (ADS)

Greengrass, Eyal; Krivenko, Yevgeniya; Ozer, Tal; Ben Yosef, Dafna; Tom, Moshe; Gertman, Isaac

2015-04-01

The knowledge of the space/time variations of species is the basis for any ecological investigations. While historical observations containing integral concentrations of biological parameters (chlorophyll, abundance, biomass…) are organized partly in ISRAMAR Cast Database, the taxon-specific data collected in Israel has not been sufficiently organized. This has been hindered by the lack of standards, variability of methods and complexity of biological data formalization. The ISRAMAR-BIO DB was developed to store various types of historical and future available information related to marine species observations and related metadata. Currently the DB allows to store biological data acquired by the following sampling devices such as: van veer grab, box corer, sampling bottles, nets (plankton, trawls and fish), quadrates, and cameras. The DB's logical unit is information regarding a specimen (taxa name, barcode, image), related attributes (abundance, size, age, contaminants…), habitat description, sampling device and method, time and space of sampling, responsible organization and scientist, source of information (cruise, project and publication). The following standardization of specimen and attributes naming were implemented: Taxonomy according to World Register of Marine Species (WoRMS: http://www.marinespecies.org). Habitat description according to Coastal and Marine Ecological Classification Standards (CMECS: http://www.cmecscatalog.org) Parameter name; Unit; Device name; Developmental stage; Institution name; Country name; Marine region according to SeaDataNet Vocabularies (http://www.seadatanet.org/Standards-Software/Common-Vocabularies). This system supports two types of data submission procedures, which support the above stated data structure. The first is a downloadable excel file with drop-down fields based on the ISRAMAR-BIO vocabularies. The file is filled and uploaded online by the data contributor. Alternatively, the same dataset can be assembled by

Biphasic dose responses in biology, toxicology and medicine: accounting for their generalizability and quantitative features.

PubMed

Calabrese, Edward J

2013-11-01

The most common quantitative feature of the hormetic-biphasic dose response is its modest stimulatory response which at maximum is only 30-60% greater than control values, an observation that is consistently independent of biological model, level of organization (i.e., cell, organ or individual), endpoint measured, chemical/physical agent studied, or mechanism. This quantitative feature suggests an underlying "upstream" mechanism common across biological systems, therefore basic and general. Hormetic dose response relationships represent an estimate of the peak performance of integrative biological processes that are allometrically based. Hormetic responses reflect both direct stimulatory or overcompensation responses to damage induced by relatively low doses of chemical or physical agents. The integration of the hormetic dose response within an allometric framework provides, for the first time, an explanation for both the generality and the quantitative features of the hormetic dose response. Copyright © 2013 Elsevier Ltd. All rights reserved.

The occurrence of hormetic dose responses in the toxicological literature, the hormesis database: an overview

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

Calabrese, Edward J.; Blain, Robyn

A relational retrieval database has been developed compiling toxicological studies assessing the occurrence of hormetic dose responses and their quantitative characteristics. This database permits an evaluation of these studies over numerous parameters, including study design and dose-response features and physical/chemical properties of the agents. The database contains approximately 5600 dose-response relationships satisfying evaluative criteria for hormesis across over approximately 900 agents from a broadly diversified spectrum of chemical classes and physical agents. The assessment reveals that hormetic dose-response relationships occur in males and females of numerous animal models in all principal age groups as well as across species displaying amore » broad range of differential susceptibilities to toxic agents. The biological models are extensive, including plants, viruses, bacteria, fungi, insects, fish, birds, rodents, and primates, including humans. The spectrum of endpoints displaying hormetic dose responses is also broad being inclusive of growth, longevity, numerous metabolic parameters, disease incidences (including cancer), various performance endpoints such as cognitive functions, immune responses among others. Quantitative features of the hormetic dose response reveal that the vast majority of cases display a maximum stimulatory response less than two-fold greater than the control while the width of the stimulatory response is typically less than 100-fold in dose range immediately contiguous with the toxicological NO(A)EL. The database also contains a quantitative evaluation component that differentiates among the various dose responses concerning the strength of the evidence supporting a hormetic conclusion based on study design features, magnitude of the stimulatory response, statistical significance, and reproducibility of findings.« less

The occurrence of hormetic dose responses in the toxicological literature, the hormesis database: an overview.

PubMed

Calabrese, Edward J; Blain, Robyn

2005-02-01

A relational retrieval database has been developed compiling toxicological studies assessing the occurrence of hormetic dose responses and their quantitative characteristics. This database permits an evaluation of these studies over numerous parameters, including study design and dose-response features and physical/chemical properties of the agents. The database contains approximately 5600 dose-response relationships satisfying evaluative criteria for hormesis across over approximately 900 agents from a broadly diversified spectrum of chemical classes and physical agents. The assessment reveals that hormetic dose-response relationships occur in males and females of numerous animal models in all principal age groups as well as across species displaying a broad range of differential susceptibilities to toxic agents. The biological models are extensive, including plants, viruses, bacteria, fungi, insects, fish, birds, rodents, and primates, including humans. The spectrum of endpoints displaying hormetic dose responses is also broad being inclusive of growth, longevity, numerous metabolic parameters, disease incidences (including cancer), various performance endpoints such as cognitive functions, immune responses among others. Quantitative features of the hormetic dose response reveal that the vast majority of cases display a maximum stimulatory response less than two-fold greater than the control while the width of the stimulatory response is typically less than 100-fold in dose range immediately contiguous with the toxicological NO(A)EL. The database also contains a quantitative evaluation component that differentiates among the various dose responses concerning the strength of the evidence supporting a hormetic conclusion based on study design features, magnitude of the stimulatory response, statistical significance, and reproducibility of findings.

Bio-oil fractionation and condensation

DOEpatents

Brown, Robert C; Jones, Samuel T; Pollard, Anthony

2013-07-02

A method of fractionating bio-oil vapors which involves providing bio-oil vapors comprising bio-oil constituents is described. The bio-oil vapors are cooled in a first stage which comprises a condenser having passages for the bio-oil separated by a heat conducting wall from passages for a coolant. The coolant in the condenser of the first stage is maintained at a substantially constant temperature, set at a temperature in the range of 75 to 100.degree. C., to condense a first liquid fraction of liquefied bio-oil constituents in the condenser of the first stage. The first liquid fraction of liquified bio-oil constituents from the condenser in the first stage is collected. Also described are steps for subsequently recovering further liquid fractions of liquefied bio-oil constituents. Particular compositions of bio-oil condensation products are also described.

Combinatorial Nano-Bio Interfaces.

PubMed

Cai, Pingqiang; Zhang, Xiaoqian; Wang, Ming; Wu, Yun-Long; Chen, Xiaodong

2018-06-08

Nano-bio interfaces are emerging from the convergence of engineered nanomaterials and biological entities. Despite rapid growth, clinical translation of biomedical nanomaterials is heavily compromised by the lack of comprehensive understanding of biophysicochemical interactions at nano-bio interfaces. In the past decade, a few investigations have adopted a combinatorial approach toward decoding nano-bio interfaces. Combinatorial nano-bio interfaces comprise the design of nanocombinatorial libraries and high-throughput bioevaluation. In this Perspective, we address challenges in combinatorial nano-bio interfaces and call for multiparametric nanocombinatorics (composition, morphology, mechanics, surface chemistry), multiscale bioevaluation (biomolecules, organelles, cells, tissues/organs), and the recruitment of computational modeling and artificial intelligence. Leveraging combinatorial nano-bio interfaces will shed light on precision nanomedicine and its potential applications.

Monocytes/macrophages infected with Toxoplasma gondii do not increase co-stimulatory molecules while maintaining their migratory ability.

PubMed

Seipel, Daniele; Ribeiro-Gomes, Flavia Lima; Barcelos, Michelle Willmen; Ramalho, André Villaça; Kanashiro, Milton M; Kipnis, Thereza Liberman; Arnholdt, Andrea Cristina Veto

2009-09-01

Toxoplasma gondii is an obligate intracellular parasite that is able to disseminate into deep tissues and cross biological barriers, reaching immunoprivileged sites such as the brain and retina. The parasite is able to infect macrophages and dendritic cells and use them for dispersal throughout the body, but the activation state of those cells is unknown. We investigated the ability of human and murine cells from monocytic/macrophage lineages that had not previously been exposed to inflammatory cytokines to up-regulate co-stimulatory and adhesion molecules upon infection. Toxoplasma gondii-infected human monocytes (freshly isolated and THP1 lineage) were unable to up-regulate CD86, CD83, CD40 or CD1a. CD80 expression increased in infected cells but expression of l-selectin and beta2 integrin was unaltered. We evaluated the ability of infected macrophages from wild type C57/BL/6 or CD14(-/-) mice to migrate in 8 mum transwells. Infected cells from CD14(-/-) mice were more likely to de-adhere than infected cells from wild type mice but they did not show any increase in migratory ability. The non-stimulatory profile of these infected cells may contribute to parasite spread throughout the lymphatic circulation in the initial phases of infection.

Bio-oil fractionation and condensation

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

Brown, Robert C.; Jones, Samuel T.; Pollard, Anthony

The present invention relates to a method of fractionating bio-oil vapors which involves providing bio-oil vapors comprising bio-oil constituents. The bio-oil vapors are cooled in a first stage which comprises a condenser having passages for the bio-oil separated by a heat conducting wall from passages for a coolant. The coolant in the condenser of the first stage is maintained at a substantially constant temperature, set at a temperature in the range of 75 to 100.degree. C., to condense a first liquid fraction of liquefied bio-oil constituents in the condenser of the first stage. The first liquid fraction of liquified bio-oilmore » constituents from the condenser in the first stage is collected. Also disclosed are steps for subsequently recovering further liquid fractions of liquefied bio-oil constituents. Particular compositions of bio-oil condensation products are also described.« less

Subcritical hydrothermal liquefaction of cattle manure to bio-oil: Effects of conversion parameters on bio-oil yield and characterization of bio-oil.

PubMed

Yin, Sudong; Dolan, Ryan; Harris, Matt; Tan, Zhongchao

2010-05-01

In this study, cattle manure was converted to bio-oil by subcritical hydrothermal liquefaction in the presence of NaOH. The effects of conversion temperature, process gas, initial conversion pressure, residence time and mass ratio of cattle manure to water on the bio-oil yield were studied. The bio-oil was characterized in terms of elemental composition, higher heating value, ultraviolet-visible (UV/Vis) spectroscopy, Fourier transform infrared spectroscopy (FTIR), gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS). Results showed that the bio-oil yield depended on the conversion temperature and the process gas. Higher initial conversion pressure, longer residence time and larger mass ratio of cattle manure to water, however, had negative impacts on the bio-oil yield. The higher heating value of bio-oil was 35.53MJ/kg on average. The major non-polar components of bio-oil were toluene, ethyl benzene and xylene, which are components of crude oil, gasoline and diesel. Copyright 2010 Elsevier Ltd. All rights reserved.

Simultaneous and Dose Dependent Melanoma Cytotoxic and Immune Stimulatory Activity of Betulin

PubMed Central

Arlt, Olga; Neske, Christina; Dehelean, Cristina; Pfeilschifter, Josef M.; Radeke, Heinfried H.

2015-01-01

Conventional cytostatic cancer treatments rarely result in the complete eradication of tumor cells. Therefore, new therapeutic strategies focus on antagonizing the immunosuppressive activity of established tumors. In particular, recent studies of antigen-loaded dendritic cells (DCs) eliciting a specific antitumor immune response has raised the hopes of achieving the complete elimination of tumor tissue. Genistein, fingolimod and betulin have already been described as active compounds in different types of cancer. Herein, we applied an integrated screening approach to characterize both their cytostatic and their immune-modulating properties side-by-side. As will be described in detail, our data confirmed that all three compounds exerted proapoptotic and antiproliferative activity in different B16 melanoma cell lines to a given extent, as revealed by an MTT assay, CFSE and DAPI staining. However, while genistein and fingolimod also affected the survival of primary bone marrow (BM) derived DCs of C57BL/6 mice, betulin exhibited a lower cytotoxicity for BMDCs in comparison to the melanoma cells. Moreover, we could show for the first time, that only betulin caused a simultaneous, highly specific immune-stimulating activity, as measured by the IL-12p70 release of Toll-like receptor 4-stimulated BMDCs by ELISA, which was due to increased IL-12p35 mRNA expression. Interestingly, the activation of DCs resulted in enhanced T lymphocyte stimulation, indicated by increased IL-2 and IFN-γ production of cytotoxic T cells in spleen cell co-culture assays which led to a decreased viability of B16 cells in an antigen specific model system. This may overcome the immunosuppressive environment of a tumor and destroy tumor cells more effectively in vivo if the immune response is specific targeted against the tumor tissue by antigen-loaded dendritic cells. In summary, cytostatic agents, such as betulin, that simultaneously exhibit immune stimulatory activity may serve as lead compounds

Triterpene glycosides with stimulatory activity on melanogenesis from the aerial parts of Weigela subsessilis.

PubMed

Won, Yu-Mi; Seong, Zuh-Kyung; Kim, Jae-Lim; Kim, Hui-Seong; Song, Hyuk-Hwan; Kim, Doo-Young; Kim, Jung-Hee; Oh, Sei-Ryang; Cho, Hyun-Woo; Cho, Jung-Hee; Lee, Hyeong-Kyu

2015-08-01

Three new triterpene glycosides (Lonicerosides K, L and M) and 11 known compounds were isolated from the aerial parts of Weigela subsessilis. Among the known isolated compounds, loniceroside A, sweroside, kaempferol-3-O-glucopyranoside 6″-(3-hydroxy-3-methylglutarate), kaempferol-3-O-acetylglucoside and grandifloroside were reported for the first time in a Weigela genus plant. Their chemical structures were identified using extensive spectroscopic analysis including two-dimensional (2D)-NMR experiments, HR-ESI-QTOF-MS and comparison with reported data. Among these compounds, lonicerosides A and L had potent melanogenesis stimulatory activity in murine B16F0 melanoma cells. The structural relationship of active compounds was discussed.

The preparations of novel cellulose/phenylboronic acid composite intelligent bio-hydrogel and its glucose, pH-responsive behaviors.

PubMed

Peng, Huafeng; Ning, Xiaoyu; Wei, Gang; Wang, Shaopeng; Dai, Guoliang; Ju, Anqi

2018-09-01

Novel intelligent cellulose/4-vinyl-phenylboronic acid (VPBA) composite bio-hydrogels with glucose and pH-responsiveness were successfully prepared via electron beam irradiation technology at room temperature. The composites were characterized by Fourier transform infrared spectrum (FT-IR) and X-ray photoelectron spectroscopy (XPS). The electron beam irradiation results in the appearance of carbonyl in the polymerization of 4-ethenyl-phenylboronic acid, grafting and cross linking reaction in composites, and a novel composite hydrogel was formed between the poly-4-ethenyl-phenylboronic acid and cellulose matrix. By means of the incorporation of phenylboronic acid groups, the composite hydrogels with pH and glucose responsive properties was produced, and glucose responsive properties were investigated by the self-regulation of insulin release of composite hydrogel through a serial glucose solution with different concentrations, which is having great potential applications in many fields. Copyright © 2018 Elsevier Ltd. All rights reserved.

Reliability and Validity of the Zephyr[TM] BioHarness[TM] to Measure Respiratory Responses to Exercise

ERIC Educational Resources Information Center

Hailstone, Jono; Kilding, Andrew E.

2011-01-01

The Zephyr[TM] BioHarness[TM] (Zephyr Technology, Auckland, New Zealand) is a wireless physiological monitoring system that has the ability to measure respiratory rate unobtrusively. However, the ability of the BioHarness[TM] to accurately and reproducibly determine respiratory rate across a range of intensities is currently unknown. The aim of…

A bio-molecular inspired electronic architecture: bio-based device concepts for enhanced sensing (Invited Paper)

NASA Astrophysics Data System (ADS)

Woolard, Dwight L.; Luo, Ying; Gelmont, Boris L.; Globus, Tatiana; Jensen, James O.

2005-05-01

A biological(bio)-molecular inspired electronic architecture is presented that offers the potential for defining nanoscale sensor platforms with enhanced capabilities for sensing terahertz (THz) frequency bio-signatures. This architecture makes strategic use of integrated biological elements to enable communication and high-level function within densely-packed nanoelectronic systems. In particular, this architecture introduces a new paradigm for establishing hybrid Electro-THz-Optical (ETO) communication channels where the THz-frequency spectral characteristics that are uniquely associated with the embedded bio-molecules are utilized directly. Since the functionality of this architecture is built upon the spectral characteristics of bio-molecules, this immediately allows for defining new methods for enhanced sensing of THz bio-signatures. First, this integrated sensor concept greatly facilitates the collection of THz bio-signatures associated with embedded bio-molecules via interactions with the time-dependent signals propagating through the nanoelectronic circuit. Second, it leads to a new Multi-State Spectral Sensing (MS3) approach where bio-signature information can be collected from multiple metastable state conformations. This paper will also introduce a new class of prototype devices that utilize THz-sensitive bio-molecules to achieve molecular-level sensing and functionality. Here, new simulation results are presented for a class of bio-molecular components that exhibit the prescribed type of ETO characteristics required for realizing integrated sensor platforms. Most noteworthy, this research derives THz spectral bio-signatures for organic molecules that are amenable to photo-induced metastable-state conformations and establishes an initial scientific foundation and design blueprint for an enhanced THz bio-signature sensing capability.

Mesenchymal Stromal Cell Secreted Sphingosine 1-Phosphate (S1P) Exerts a Stimulatory Effect on Skeletal Myoblast Proliferation

PubMed Central

Tani, Alessia; Anderloni, Giulia; Pierucci, Federica; Matteini, Francesca; Chellini, Flaminia; Zecchi Orlandini, Sandra; Meacci, Elisabetta

2014-01-01

Bone-marrow-derived mesenchymal stromal cells (MSCs) have the potential to significantly contribute to skeletal muscle healing through the secretion of paracrine factors that support proliferation and enhance participation of the endogenous muscle stem cells in the process of repair/regeneration. However, MSC-derived trophic molecules have been poorly characterized. The aim of this study was to investigate paracrine signaling effects of MSCs on skeletal myoblasts. It was found, using a biochemical and morphological approach that sphingosine 1-phosphate (S1P), a natural bioactive lipid exerting a broad range of muscle cell responses, is secreted by MSCs and represents an important factor by which these cells exert their stimulatory effects on C2C12 myoblast and satellite cell proliferation. Indeed, exposure to conditioned medium obtained from MSCs cultured in the presence of the selective sphingosine kinase inhibitor (iSK), blocked increased cell proliferation caused by the conditioned medium from untreated MSCs, and the addition of exogenous S1P in the conditioned medium from MSCs pre-treated with iSK further increased myoblast proliferation. Finally, we also demonstrated that the myoblast response to MSC-secreted vascular endothelial growth factor (VEGF) involves the release of S1P from C2C12 cells. Our data may have important implications in the optimization of cell-based strategies to promote skeletal muscle regeneration. PMID:25264785

Bio-chemo-mechanical models of vascular mechanics

PubMed Central

Kim, Jungsil; Wagenseil, Jessica E.

2014-01-01

Models of vascular mechanics are necessary to predict the response of an artery under a variety of loads, for complex geometries, and in pathological adaptation. Classic constitutive models for arteries are phenomenological and the fitted parameters are not associated with physical components of the wall. Recently, microstructurally-linked models have been developed that associate structural information about the wall components with tissue-level mechanics. Microstructurally-linked models are useful for correlating changes in specific components with pathological outcomes, so that targeted treatments may be developed to prevent or reverse the physical changes. However, most treatments, and many causes, of vascular disease have chemical components. Chemical signaling within cells, between cells, and between cells and matrix constituents affects the biology and mechanics of the arterial wall in the short- and long-term. Hence, bio-chemo-mechanical models that include chemical signaling are critical for robust models of vascular mechanics. This review summarizes bio-mechanical and bio-chemo-mechanical models with a focus on large elastic arteries. We provide applications of these models and challenges for future work. PMID:25465618

Bio-oil Stabilization by Hydrogenation over Reduced Metal Catalysts at Low Temperatures

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

Wang, Huamin; Lee, Suh-Jane; Olarte, Mariefel V.

Biomass fast pyrolysis integrated with bio-oil upgrading represents a very attractive approach for converting biomass to hydrocarbon transportation fuels. However, the thermal and chemical instability of bio-oils presents significant problems when they are being upgraded, and development of effective approaches for stabilizing bio-oils is critical to the success of the technology. Catalytic hydrogenation to remove reactive species in bio-oil has been considered as one of the most efficient ways to stabilize bio-oil. This paper provides a fundamental understanding of hydrogenation of actual bio-oils over a Ru/TiO2 catalyst under conditions relevant to practical bio-oil hydrotreating processes. Bio-oil feed stocks, bio-oils hydrogenatedmore » to different extents, and catalysts have been characterized to provide insights into the chemical and physical properties of these samples and to understand the correlation of the properties with the composition of the bio-oil and catalysts. The results indicated hydrogenation of various components of the bio-oil, including sugars, aldehydes, ketones, alkenes, aromatics, and carboxylic acids, over the Ru/TiO2 catalyst and 120 to 160oC. Hydrogenation of these species significantly changed the chemical and physical properties of the bio-oil and overall improved its thermal stability, especially by reducing the carbonyl content, which represented the content of the most reactive species (i.e., sugar, aldehydes, and ketones). The change of content of each component in response to increasing hydrogen additions suggests the following bio-oil hydrogenation reaction sequence: sugar conversion to sugar alcohols, followed by ketone and aldehyde conversion to alcohols, followed by alkene and aromatic hydrogenation, and then followed by carboxylic acid hydrogenation to alcohols. Hydrogenation of bio-oil samples with different sulfur contents or inorganic material contents suggested that sulfur poisoning of the reduced Ru metal catalysts

Determining the bio-based content of bio-plastics used in Thailand by radiocarbon analysis

NASA Astrophysics Data System (ADS)

Ploykrathok, T.; Chanyotha, S.

2017-06-01

Presently, there is an increased interest in the development of bio-plastic products from agricultural materials which are biodegradable in order to reduce the problem of waste disposal. Since the amount of modern carbon in bio-plastics can indicate how much the amount of agricultural materials are contained in the bio-plastic products, this research aims to determine the modern carbon in bio-plastic using the carbon dioxide absorption method. The radioactivity of carbon-14 contained in the sample is measured by liquid scintillation counter (Tri-carb 3110 TR, PerkinElmer). The percentages of bio-based content in the samples were determined by comparing the observed modern carbon content with the values contained in agricultural raw materials. The experimental results show that only poly(lactic acid) samples have the modern carbon content of 97.4%, which is close to the agricultural materials while other bio-plastics types are found to have less than 50% of the modern carbon content. In other words, most of these bio-plastic samples were mixed with other materials which are not agriculturally originated.

Pyrolysis of hornbeam (Carpinus betulus L.) sawdust: Characterization of bio-oil and bio-char.

PubMed

Moralı, Uğur; Yavuzel, Nazan; Şensöz, Sevgi

2016-12-01

Slow pyrolysis of hornbeam (Carpinus betulus L.) sawdust was performed to produce bio-oil and bio-char. The operational variables were as follows: pyrolysis temperature (400-600°C), heating rate (10-50°Cmin -1 ) and nitrogen flow rate (50-150cm 3 min -1 ). Physicochemical and thermogravimetric characterizations of hornbeam sawdust were performed. The characteristics of bio-oil and bio-char were analyzed on the basis of various spectroscopic and chromatographic techniques such as FTIR, GC-MS, 1H NMR, SEM, BET. Higher heating value, density and kinematic viscosity of the bio-oil with maximum yield of 35.28% were 23.22MJkg -1 , 1289kgm -3 and 0.6mm 2 s -1 , respectively. The bio-oil with relatively high fuel potential can be obtained from the pyrolysis of the hornbeam sawdust and the bio-char with a calorific value of 32.88MJkg -1 is a promising candidate for solid fuel applications that also contributes to the preservation of the environment. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dye@bio-MOF-1 Composite as a Dual-Emitting Platform for Enhanced Detection of a Wide Range of Explosive Molecules.

PubMed

Wang, Chen; Tian, Li; Zhu, Wei; Wang, Shiqiang; Wang, Peng; Liang, Yun; Zhang, Wanlin; Zhao, Hongwei; Li, Guangtao

2017-06-14

By incorporating a cationic dye within a metal-organic framework (MOF) through an ion-exchange process, a responsive dye@bio-MOF-1 composite has been synthesized, serving as a dual-emitting platform for enhanced detection of different kinds of nitro-explosives, especially nitroalkanes, nitramines, and nitrate esters. The dye@bio-MOF-1 composite was constructed with free amines on their well-defined cavities, which is essential for the capture of explosives into their confined nanospace. It was observed that the encapsulation of explosives into the constructed dye@bio-MOF-1 composite could dramatically alter the luminescent properties of the dyes as well as the MOF skeletons owing to the size exclusivity and confinement-induced effect. For nitroaromatics, the dye@bio-MOF-1 composite exhibits turn-off responses via fluorescence quenching. Unexpectedly, the composite shows unique turn-on responses for aliphatic nitro-organics via confinement-induced enhancement, demonstrating enhanced ability to detecting different kinds of explosives selectively in aqueous solution. Furthermore, the dye@bio-MOF-1 film was facilely fabricated, making the chemical sensing more convenient and easier to realize the discrimination of the targeted explosives. The dual tunable responses indicate that dye@bio-MOF-1 composites are favorable materials for molecular sensing. On the basis of the host-guest properties of the constructed dye@bio-MOF-1 composite, our work can be further extended to sensing specific analytes with remarkable turn-on sensing properties, in particular those difficult to recognize with conventional methods.

The problem of bio-concepts: biopolitics, bio-economy and the political economy of nothing

NASA Astrophysics Data System (ADS)

Birch, Kean

2017-12-01

Scholars in science and technology studies—and no doubt other fields—have increasingly drawn on Michel Foucault's concept of biopolitics to theorize a variety of new `bio-concepts'. While there might be some theoretical value in such exercises, many of these bio-concepts have simply replaced more rigorous—and therefore time-consuming—analytical work. This article provides a (sympathetic) critique of these various bio-concepts, especially as they are applied to the emerging `bio-economy'. In so doing, the article seeks to show that the analysis of the bio-economy could be better framed as a political economy of nothing. This has several implications for science education, which are raised in the article.

Method to upgrade bio-oils to fuel and bio-crude

DOEpatents

Steele, Philip H; Pittman, Jr., Charles U; Ingram, Jr., Leonard L; Gajjela, Sanjeev; Zhang, Zhijun; Bhattacharya, Priyanka

2013-12-10

This invention relates to a method and device to produce esterified, olefinated/esterified, or thermochemolytic reacted bio-oils as fuels. The olefinated/esterified product may be utilized as a biocrude for input to a refinery, either alone or in combination with petroleum crude oils. The bio-oil esterification reaction is catalyzed by addition of alcohol and acid catalyst. The olefination/esterification reaction is catalyzed by addition of resin acid or other heterogeneous catalyst to catalyze olefins added to previously etherified bio-oil; the olefins and alcohol may also be simultaneously combined and catalyzed by addition of resin acid or other heterogeneous catalyst to produce the olefinated/esterified product.

Ethical, social and public awareness issues in gene therapy EuropaBio.

PubMed

2002-01-01

EuropaBio, the European Association for Bio-industries, represents 40 corporate members operating world wide and 14 national associations (totaling up to 700 small- and medium-sized enterprises) involved in research, development, testing, manufacturing, sales, and distribution of biotechnology-derived products and services in the field of health cae, agriculture, food, and the environment. AGE is a group of researchers and university professors involved in high-level professional activities related to bioethics, and particularly interested in ethical issues related to the development and use of modern technology. It is essential that industry actively participates in, and contributes to, the social debate on emerging technologies. Therefore, EuropaBio presents herein its view on gene therapy and its responsible development and use.

Frameshifting in alphaviruses: a diversity of 3' stimulatory structures.

PubMed

Chung, Betty Y-W; Firth, Andrew E; Atkins, John F

2010-03-26

Programmed ribosomal frameshifting allows the synthesis of alternative, N-terminally coincident, C-terminally distinct proteins from the same RNA. Many viruses utilize frameshifting to optimize the coding potential of compact genomes, to circumvent the host cell's canonical rule of one functional protein per mRNA, or to express alternative proteins in a fixed ratio. Programmed frameshifting is also used in the decoding of a small number of cellular genes. Recently, specific ribosomal -1 frameshifting was discovered at a conserved U_UUU_UUA motif within the sequence encoding the alphavirus 6K protein. In this case, frameshifting results in the synthesis of an additional protein, termed TF (TransFrame). This new case of frameshifting is unusual in that the -1 frame ORF is very short and completely embedded within the sequence encoding the overlapping polyprotein. The present work shows that there is remarkable diversity in the 3' sequences that are functionally important for efficient frameshifting at the U_UUU_UUA motif. While many alphavirus species utilize a 3' RNA structure such as a hairpin or pseudoknot, some species (such as Semliki Forest virus) apparently lack any intra-mRNA stimulatory structure, yet just 20 nt 3'-adjacent to the shift site stimulates up to 10% frameshifting. The analysis, both experimental and bioinformatic, significantly expands the known repertoire of -1 frameshifting stimulators in mammalian and insect systems.

Biochemical gas sensor (bio-sniffer) for ultrahigh-sensitive gaseous formaldehyde monitoring.

PubMed

Kudo, Hiroyuki; Suzuki, Yuki; Gessei, Tomoko; Takahashi, Daishi; Arakawa, Takahiro; Mitsubayashi, Kohji

2010-10-15

An ultrahigh-sensitive fiber-optic biochemical gas sensor (bio-sniffer) for continuous monitoring of indoor formaldehyde was constructed and tested. The bio-sniffer measures gaseous formaldehyde as fluorescence of nicotinamide adenine dinucleotide (NADH), which is the product of formaldehyde dehydrogenase (FALDH) reaction. The bio-sniffer device was constructed by attaching a flow cell with a FALDH immobilized membrane onto a fiber-optic NADH measurement system. The NADH measurement system utilizes an ultraviolet-light emitting diode (UV-LED) with peak emission of 335 nm as an excitation light source. The excitation light was introduced to an optical fiber probe, and fluorescence emission of neighboring NADH, which was produced by applying formaldehyde vapor to the FALDH membrane, was concentrically measured with a photomultiplier tube. Assessment of the bio-sniffer was carried out using a standard gas generator. Response, calibration range and selectivity to other chemical substances were investigated. Circulating phosphate buffer, which contained NAD+, available for continuous monitoring of formaldehyde vapor. The calibration range of the bio-sniffer was 2.5 ppb to 10 ppm, which covers the guideline value of the World Health Organization (80 ppb). High selectivity to other gaseous substances due to specific activity of FALDH was also confirmed. Considering its high sensitivity, a possible application of the bio-sniffer is continuous indoor formaldehyde monitoring to provide healthy residential atmosphere. Copyright © 2010 Elsevier B.V. All rights reserved.

Stimulatory effect of cooling tower biocides on amoebae.

PubMed

Srikanth, S; Berk, S G

1993-10-01

Two species of amoebae were isolated from the cooling tower of an air-conditioning system and examined for effects of exposure to four cooling tower biocides, a thiocarbamate compound, tributyltin neodecanoate mixed with quaternary ammonium compounds, another quaternary ammonium compound alone, and an isothiazolin derivative. The amoebae isolated were Acanthamoeba hatchetti and a Cochliopodium species. Two other amoeba cultures, an A. hatchetti culture and Cochliopodium bilimbosum, were obtained from the American Type Culture Collection (ATCC) and were also tested. The cooling tower isolates were more resistant to most of the biocides than the ATCC isolates were. The isothiazolin derivative was the least inhibitory to all four amoeba isolates, and tributyltin neodecanoate mixed with quaternary ammonium compounds was the most inhibitory to three of the four isolates. After exposure to lower concentrations of the biocides, including for one strain the manufacturer's recommended concentration of one biocide, the cooling tower amoeba populations increased significantly compared with unexposed controls, whereas the ATCC isolates were not stimulated at any of the concentrations tested. In some cases, concentrations which stimulated cooling tower amoebae inhibited the growth of the ATCC isolates. These results suggest that cooling tower amoebae may adapt to biocides, underscoring the need to use freshly isolated cooling tower organisms rather than organisms from culture collections for testing the efficacy of such biocides. The stimulatory effect of biocides on amoeba populations is an alarming observation, since these organisms may be reservoirs for legionellae. Biocides used to control microbial growth may actually enhance populations of host organisms for pathogenic bacteria.

Three generation production biotechnology of biomass into bio-fuel

NASA Astrophysics Data System (ADS)

Zheng, Chaocheng

2017-08-01

The great change of climate change, depletion of natural resources, and scarcity of fossil fuel in the whole world nowadays have witnessed a sense of urgency home and abroad among scales of researchers, development practitioners, and industrialists to search for completely brand new sustainable solutions in the area of biomass transforming into bio-fuels attributing to our duty-that is, it is our responsibility to take up this challenge to secure our energy in the near future with the help of sustainable approaches and technological advancements to produce greener fuel from nature organic sources or biomass which comes generally from organic natural matters such as trees, woods, manure, sewage sludge, grass cuttings, and timber waste with a source of huge green energy called bio-fuel. Biomass includes most of the biological materials, livings or dead bodies. This energy source is ripely used industrially, or domestically for rather many years, but the recent trend is on the production of green fuel with different advance processing systems in a greener. More sustainable method. Biomass is becoming a booming industry currently on account of its cheaper cost and abundant resources all around, making it fairly more effective for the sustainable use of the bio-energy. In the past few years, the world has witnessed a remarkable development in the bio-fuel production technology, and three generations of bio-fuel have already existed in our society. The combination of membrane technology with the existing process line can play a vital role for the production of green fuel in a sustainable manner. In this paper, the science and technology for sustainable bio-fuel production will be introduced in detail for a cleaner world.

Isolation and Characterization of Lactoferrin Peptides with Stimulatory Effect on Osteoblast Proliferation.

PubMed

Fan, Fengjiao; Tu, Maolin; Liu, Meng; Shi, Pujie; Wang, Yun; Wu, Di; Du, Ming

2017-08-23

Lactoferrin is reported to be a potential food protein with osteogenic activity. However, the activity of lactoferrin peptides is questionable. In the present study, we isolated and characterized peptides from lactoferrin with stimulatory effect on osteoblast proliferation. Peptides from the lactoferrin pepsin hydrolysate were purified using cation-exchange and gel-filtration chromatography. Effects of different hydrolysates and peptides on the proliferation of osteoblast MC3T3-E1 cells were compared by MTT assay. Results showed that fraction P5-a from Superdex Peptide 10/300 GL gel chromatography showed better activity. Tricine-sodium dodecyl sulfate polyacrylamide gel electrophoresis and high-performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry confirmed that two peptides components of P5-a corresponded to fractions of 20-78 and 191-277 amino acids in Bos taurus lactoferrin molecule (GI: 221706349). These results will provide some theoretical and practical data for the preparation and application of osteogenic peptides in functional food industry.

Pyrolysis of waste animal fats in a fixed-bed reactor: Production and characterization of bio-oil and bio-char

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

Ben Hassen-Trabelsi, A., E-mail: aidabenhassen@yahoo.fr; Kraiem, T.; Département de Géologie, Université de Tunis, 2092, Tunis

Highlights: • Produced bio-fuels (bio-oil and bio-char) from some animal fatty wastes. • Investigated the effects of main parameters on pyrolysis products distribution. • Determined the suitable conditions for the production of the maximum of bio-oil. • Characterized bio-oils and bio-chars obtained from several animal fatty wastes. - Abstract: Several animal (lamb, poultry and swine) fatty wastes were pyrolyzed under nitrogen, in a laboratory scale fixed-bed reactor and the main products (liquid bio-oil, solid bio-char and syngas) were obtained. The purpose of this study is to produce and characterize bio-oil and bio-char obtained from pyrolysis of animal fatty wastes. Themore » maximum production of bio-oil was achieved at a pyrolysis temperature of 500 °C and a heating rate of 5 °C/min. The chemical (GC–MS analyses) and spectroscopic analyses (FTIR analyses) of bio-oil showed that it is a complex mixture consisting of different classes of organic compounds, i.e., hydrocarbons (alkanes, alkenes, cyclic compounds…etc.), carboxylic acids, aldehydes, ketones, esters,…etc. According to fuel properties, produced bio-oils showed good properties, suitable for its use as an engine fuel or as a potential source for synthetic fuels and chemical feedstock. Obtained bio-chars had low carbon content and high ash content which make them unattractive for as renewable source energy.« less

Fourier and non-Fourier bio-heat transfer models to predict ex vivo temperature response to focused ultrasound heating

NASA Astrophysics Data System (ADS)

Li, Chenghai; Miao, Jiaming; Yang, Kexin; Guo, Xiasheng; Tu, Juan; Huang, Pintong; Zhang, Dong

2018-05-01

Although predicting temperature variation is important for designing treatment plans for thermal therapies, research in this area is yet to investigate the applicability of prevalent thermal conduction models, such as the Pennes equation, the thermal wave model of bio-heat transfer, and the dual phase lag (DPL) model. To address this shortcoming, we heated a tissue phantom and ex vivo bovine liver tissues with focused ultrasound (FU), measured the temperature response, and compared the results with those predicted by these models. The findings show that, for a homogeneous-tissue phantom, the initial temperature increase is accurately predicted by the Pennes equation at the onset of FU irradiation, although the prediction deviates from the measured temperature with increasing FU irradiation time. For heterogeneous liver tissues, the predicted response is closer to the measured temperature for the non-Fourier models, especially the DPL model. Furthermore, the DPL model accurately predicts the temperature response in biological tissues because it increases the phase lag, which characterizes microstructural thermal interactions. These findings should help to establish more precise clinical treatment plans for thermal therapies.

Navigating the Bio-Politics of Childhood

ERIC Educational Resources Information Center

Lee, Nick; Motzkau, Johanna

2011-01-01

Childhood research has long shared a bio-political terrain with state agencies in which children figure primarily as "human futures". In the 20th century bio-social dualism helped to make that terrain navigable by researchers, but, as life processes increasingly become key sites of bio-political action, bio-social dualism is becoming…

Bio-Aerosol Testkamer: Ontwikkeling van Protocollen (Bio Aerosol Test Chamber: Development of Protocols)

DTIC Science & Technology

2007-07-01

testfaciliteit detector met de drie simulanten getest beschikbaar gekomen voor het testen van Beschrijving van de worden volgens gangbare internationale bio...2005 werd de Bio-Adrosol Testkamer (BAT-kamer) geplaatst door de firma Dycor Technologies Ltd., Canada. In de BAT-kamner kan een bio-ai5rosol...bestaande ruimte past. In beide gevallen bleek de firma Dycor Technologies Ltd in Canada (http://www.dycor.com) de beste leverancier te zijn, en voor beide

BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments

PubMed Central

Thomas, Brandon R.; Chylek, Lily A.; Colvin, Joshua; Sirimulla, Suman; Clayton, Andrew H.A.; Hlavacek, William S.; Posner, Richard G.

2016-01-01

Summary: Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here, we present BioNetFit, a general-purpose fitting tool that is compatible with BioNetGen and NFsim. BioNetFit is designed to take advantage of distributed computing resources. This feature facilitates fitting (i.e. optimization of parameter values for consistency with data) when simulations are computationally expensive. Availability and implementation: BioNetFit can be used on stand-alone Mac, Windows/Cygwin, and Linux platforms and on Linux-based clusters running SLURM, Torque/PBS, or SGE. The BioNetFit source code (Perl) is freely available (http://bionetfit.nau.edu). Supplementary information: Supplementary data are available at Bioinformatics online. Contact: bionetgen.help@gmail.com PMID:26556387

The BioC-BioGRID corpus: full text articles annotated for curation of protein–protein and genetic interactions

PubMed Central

Kim, Sun; Chatr-aryamontri, Andrew; Chang, Christie S.; Oughtred, Rose; Rust, Jennifer; Wilbur, W. John; Comeau, Donald C.; Dolinski, Kara; Tyers, Mike

2017-01-01

A great deal of information on the molecular genetics and biochemistry of model organisms has been reported in the scientific literature. However, this data is typically described in free text form and is not readily amenable to computational analyses. To this end, the BioGRID database systematically curates the biomedical literature for genetic and protein interaction data. This data is provided in a standardized computationally tractable format and includes structured annotation of experimental evidence. BioGRID curation necessarily involves substantial human effort by expert curators who must read each publication to extract the relevant information. Computational text-mining methods offer the potential to augment and accelerate manual curation. To facilitate the development of practical text-mining strategies, a new challenge was organized in BioCreative V for the BioC task, the collaborative Biocurator Assistant Task. This was a non-competitive, cooperative task in which the participants worked together to build BioC-compatible modules into an integrated pipeline to assist BioGRID curators. As an integral part of this task, a test collection of full text articles was developed that contained both biological entity annotations (gene/protein and organism/species) and molecular interaction annotations (protein–protein and genetic interactions (PPIs and GIs)). This collection, which we call the BioC-BioGRID corpus, was annotated by four BioGRID curators over three rounds of annotation and contains 120 full text articles curated in a dataset representing two major model organisms, namely budding yeast and human. The BioC-BioGRID corpus contains annotations for 6409 mentions of genes and their Entrez Gene IDs, 186 mentions of organism names and their NCBI Taxonomy IDs, 1867 mentions of PPIs and 701 annotations of PPI experimental evidence statements, 856 mentions of GIs and 399 annotations of GI evidence statements. The purpose, characteristics and possible future

Bangalore India Bio 2010.

PubMed

Thammanabhatla, Pratibha; Pailla, Mamatha

2010-08-01

The Bangalore India Bio 2010 conference, held in Bangalore, India, included topics covering new developments in the biopharma industry. This conference report highlights selected presentations on novel therapeutics for the treatment of cancer, including identification of novel benzimidazole, N-subsituted isatin and azetidine derivatives, and an Wnt antagonist. In addition, presentations from several biopharma companies and universities are highlighted, including Proteomics International Pty Ltd, Oxford BioMedica plc, AnaptysBio Inc, SIOGEN Biotech, RV College of Engineering and Indian Institute of Science.

Utilization of different waste proteins to create a novel PGPR-containing bio-organic fertilizer

NASA Astrophysics Data System (ADS)

Huang, Yan; Sun, Li; Zhao, Jianshu; Huang, Rong; Li, Rong; Shen, Qirong

2015-01-01

High-quality bio-organic fertilizers (BIOs) cannot be produced without the addition of some proteins, while many waste proteins are haphazardly disposed, causing serious environmental pollution. In this study, several waste proteins were used as additives to assist with the reproduction of the functional microbe (Bacillus amyloliquefaciens SQR9) inoculated into matured composts to produce BIOs. An optimized composition of solid-state fermentation (SSF) raw materials was predicted by response surface methodology and experimental validation. The results showed that 7.61% (w/w, DW, the same below) rapeseed meal, 8.85% expanded feather meal, 6.47% dewatered blue algal sludge and 77.07% chicken compost resulted in maximum biomass of strain SQR-9 and the maximum amount of lipopeptides 7 days after SSF. Spectroscopy experiments showed that the inner material structural changes in the novel SSF differed from the control and the novel BIO had higher dissolved organic matter. This study offers a high value-added utilization of waste proteins for producing economical but high-quality BIO.

Phase separation of bio-oil produced by co-pyrolysis of corn cobs and polypropylene

NASA Astrophysics Data System (ADS)

Supramono, D.; Julianto; Haqqyana; Setiadi, H.; Nasikin, M.

2017-11-01

In co-pyrolysis of biomass-plastics, bio-oil produced contains both oxygenated and non-oxygenated compounds. High oxygen composition is responsible for instability and low heating value of bio-oil and high acid content for corrosiveness. Aims of the present work are to evaluate possibilities of achieving phase separation between oxygenated and non-oxygenated compounds in bio-oil using a proposed stirred tank reactor and to achieve synergistic effects on bio-oil yield and non-oxygenated compound layer yield. Separation of bio-oil into two layers, i.e. that containing oxygenated compounds (polar phase) and non-oxygenated compounds (non-polar phase) is important to obtain pure non-polar phase ready for the next processing of hydrogenation and used directly as bio-fuel. There has been no research work on co-pyrolysis of biomass-plastic considering possibility of phase separation of bio-oil. The present work is proposing a stirred tank reactor for co-pyrolysis with nitrogen injection, which is capable of tailoring co-pyrolysis conditions leading to low viscosity and viscosity asymmetry, which induce phase separation between polar phase and non-polar phase. The proposed reactor is capable of generating synergistic effect on bio-oil and non-polar yields as the composition of PP in feed is more than 25% weight in which non-polar layers contain only alkanes, alkenes, cycloalkanes and cycloalkenes.

Clinical application of bio ceramics

NASA Astrophysics Data System (ADS)

Anu, Sharma; Gayatri, Sharma

2016-05-01

Ceramics are the inorganic crystalline material. These are used in various field such as biomedical, electrical, electronics, aerospace, automotive and optical etc. Bio ceramics are the one of the most active areas of research. Bio ceramics are the ceramics which are biocompatible. The unique properties of bio ceramics make them an attractive option for medical applications and offer some potential advantages over other materials. During the past three decades, a number of major advances have been made in the field of bio ceramics. This review focuses on the use of these materials in variety of clinical scenarios.

Clinical application of bio ceramics

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

Anu, Sharma, E-mail: issaranu@gmail.com; Gayatri, Sharma, E-mail: sharmagayatri@gmail.com

Ceramics are the inorganic crystalline material. These are used in various field such as biomedical, electrical, electronics, aerospace, automotive and optical etc. Bio ceramics are the one of the most active areas of research. Bio ceramics are the ceramics which are biocompatible. The unique properties of bio ceramics make them an attractive option for medical applications and offer some potential advantages over other materials. During the past three decades, a number of major advances have been made in the field of bio ceramics. This review focuses on the use of these materials in variety of clinical scenarios.

BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments

DOE PAGES

Thomas, Brandon R.; Chylek, Lily A.; Colvin, Joshua; ...

2015-11-09

Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here in this paper, we present BioNetFit, a general-purpose fitting tool that is compatible with BioNetGen and NFsim. BioNetFit is designed to take advantage of distributed computing resources. This feature facilitates fitting (i.e. optimization of parameter values for consistency with data) when simulations are computationally expensive.

BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments.

PubMed

Thomas, Brandon R; Chylek, Lily A; Colvin, Joshua; Sirimulla, Suman; Clayton, Andrew H A; Hlavacek, William S; Posner, Richard G

2016-03-01

Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here, we present BioNetFit, a general-purpose fitting tool that is compatible with BioNetGen and NFsim. BioNetFit is designed to take advantage of distributed computing resources. This feature facilitates fitting (i.e. optimization of parameter values for consistency with data) when simulations are computationally expensive. BioNetFit can be used on stand-alone Mac, Windows/Cygwin, and Linux platforms and on Linux-based clusters running SLURM, Torque/PBS, or SGE. The BioNetFit source code (Perl) is freely available (http://bionetfit.nau.edu). Supplementary data are available at Bioinformatics online. bionetgen.help@gmail.com. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Stimulatory effect of Eucalyptus essential oil on innate cell-mediated immune response

PubMed Central

Serafino, Annalucia; Vallebona, Paola Sinibaldi; Andreola, Federica; Zonfrillo, Manuela; Mercuri, Luana; Federici, Memmo; Rasi, Guido; Garaci, Enrico; Pierimarchi, Pasquale

2008-01-01

Background Besides few data concerning the antiseptic properties against a range of microbial agents and the anti-inflammatory potential both in vitro and in vivo, little is known about the influence of Eucalyptus oil (EO) extract on the monocytic/macrophagic system, one of the primary cellular effectors of the immune response against pathogen attacks. The activities of this natural extract have mainly been recognized through clinical experience, but there have been relatively little scientific studies on its biological actions. Here we investigated whether EO extract is able to affect the phagocytic ability of human monocyte derived macrophages (MDMs) in vitro and of rat peripheral blood monocytes/granulocytes in vivo in absence or in presence of immuno-suppression induced by the chemotherapeutic agent 5-fluorouracil (5-FU). Methods Morphological activation of human MDMs was analysed by scanning electron microscopy. Phagocytic activity was tested: i) in vitro in EO treated and untreated MDMs, by confocal microscopy after fluorescent beads administration; ii) in vivo in monocytes/granulocytes from peripheral blood of immuno-competent or 5-FU immuno-suppressed rats, after EO oral administration, by flow cytometry using fluorescein-labelled E. coli. Cytokine release by MDMs was determined using the BD Cytometric Bead Array human Th1/Th2 cytokine kit. Results EO is able to induce activation of MDMs, dramatically stimulating their phagocytic response. EO-stimulated internalization is coupled to low release of pro-inflammatory cytokines and requires integrity of the microtubule network, suggesting that EO may act by means of complement receptor-mediated phagocytosis. Implementation of innate cell-mediated immune response was also observed in vivo after EO administration, mainly involving the peripheral blood monocytes/granulocytes. The 5-FU/EO combined treatment inhibited the 5-FU induced myelotoxicity and raised the phagocytic activity of the granulocytic

Three-dimensional bio-printing.

PubMed

Gu, Qi; Hao, Jie; Lu, YangJie; Wang, Liu; Wallace, Gordon G; Zhou, Qi

2015-05-01

Three-dimensional (3D) printing technology has been widely used in various manufacturing operations including automotive, defence and space industries. 3D printing has the advantages of personalization, flexibility and high resolution, and is therefore becoming increasingly visible in the high-tech fields. Three-dimensional bio-printing technology also holds promise for future use in medical applications. At present 3D bio-printing is mainly used for simulating and reconstructing some hard tissues or for preparing drug-delivery systems in the medical area. The fabrication of 3D structures with living cells and bioactive moieties spatially distributed throughout will be realisable. Fabrication of complex tissues and organs is still at the exploratory stage. This review summarize the development of 3D bio-printing and its potential in medical applications, as well as discussing the current challenges faced by 3D bio-printing.

Optimizing Clinical Drug Product Performance: Applying Biopharmaceutics Risk Assessment Roadmap (BioRAM) and the BioRAM Scoring Grid.

PubMed

Dickinson, Paul A; Kesisoglou, Filippos; Flanagan, Talia; Martinez, Marilyn N; Mistry, Hitesh B; Crison, John R; Polli, James E; Cruañes, Maria T; Serajuddin, Abu T M; Müllertz, Anette; Cook, Jack A; Selen, Arzu

2016-11-01

The aim of Biopharmaceutics Risk Assessment Roadmap (BioRAM) and the BioRAM Scoring Grid is to facilitate optimization of clinical performance of drug products. BioRAM strategy relies on therapy-driven drug delivery and follows an integrated systems approach for formulating and addressing critical questions and decision-making (J Pharm Sci. 2014,103(11): 3777-97). In BioRAM, risk is defined as not achieving the intended in vivo drug product performance, and success is assessed by time to decision-making and action. Emphasis on time to decision-making and time to action highlights the value of well-formulated critical questions and well-designed and conducted integrated studies. This commentary describes and illustrates application of the BioRAM Scoring Grid, a companion to the BioRAM strategy, which guides implementation of such an integrated strategy encompassing 12 critical areas and 6 assessment stages. Application of the BioRAM Scoring Grid is illustrated using published literature. Organizational considerations for implementing BioRAM strategy, including the interactions, function, and skillsets of the BioRAM group members, are also reviewed. As a creative and innovative systems approach, we believe that BioRAM is going to have a broad-reaching impact, influencing drug development and leading to unique collaborations influencing how we learn, and leverage and share knowledge. Published by Elsevier Inc.

DSC studies to evaluate the impact of bio-oil on cold flow properties and oxidation stability of bio-diesel.

PubMed

Garcia-Perez, Manuel; Adams, Thomas T; Goodrum, John W; Das, K C; Geller, Daniel P

2010-08-01

This paper describes the use of Differential Scanning Calorimetry (DSC) to evaluate the impact of varying mix ratios of bio-oil (pyrolysis oil) and bio-diesel on the oxidation stability and on some cold flow properties of resulting blends. The bio-oils employed were produced from the semi-continuous Auger pyrolysis of pine pellets and the batch pyrolysis of pine chips. The bio-diesel studied was obtained from poultry fat. The conditions used to prepare the bio-oil/bio-diesel blends as well as some of the fuel properties of these blends are reported. The experimental results suggest that the addition of bio-oil improves the oxidation stability of the resulting blends and modifies the crystallization behavior of unsaturated compounds. Upon the addition of bio-oil an increase in the oxidation onset temperature, as determined by DSC, was observed. The increase in bio-diesel oxidation stability is likely to be due to the presence of hindered phenols abundant in bio-oils. A relatively small reduction in DSC characteristic temperatures which are associated with cold flow properties was also observed but can likely be explained by a dilution effect. (c) 2010 Elsevier Ltd. All rights reserved.

Bio-threat microparticle simulants

DOEpatents

Farquar, George Roy; Leif, Roald N

2012-10-23

A bio-threat simulant that includes a carrier and DNA encapsulated in the carrier. Also a method of making a simulant including the steps of providing a carrier and encapsulating DNA in the carrier to produce the bio-threat simulant.

Bio-threat microparticle simulants

DOEpatents

Farquar, George Roy; Leif, Roald

2014-09-16

A bio-threat simulant that includes a carrier and DNA encapsulated in the carrier. Also a method of making a simulant including the steps of providing a carrier and encapsulating DNA in the carrier to produce the bio-threat simulant.

Chitosan: An undisputed bio-fabrication material for tissue engineering and bio-sensing applications.

PubMed

Baranwal, Anupriya; Kumar, Ashutosh; Priyadharshini, A; Oggu, Gopi Suresh; Bhatnagar, Ira; Srivastava, Ananya; Chandra, Pranjal

2018-04-15

Biopolymers have been serving the mankind in various ways since long. Over the last few years, these polymers have found great demand in various domains which includes bio medicine, tissue engineering, bio sensor fabrications etc. because of their excellent bio compatibility. In this context, chitosan has found global attention due to its environmentally benign nature, biocompatibility, biodegradability, and ease of availability. In last one decade or so, extensive research in active biomaterials, like chitosan has led to the development of novel delivery systems for drugs, genes, and biomolecules; and regenerative medicine. Additionally, chitosan has also witnessed its usage in functionalization of biocompatible materials, nanoparticle (NP) synthesis, and immobilization of various bio-recognition elements (BREs) to form active bio-surfaces with great ease. Keeping these aspects in mind, we have written a comprehensive review which aims to acquaint its readers with the exceptional properties of chitosan and its usage in the domain of biomedicine, tissue engineering, and biosensor fabrication. Herein, we have briefly explained various aspects of direct utilization of chitosan and then presented vivid strategies towards formulation of chitosan based nanocomposites for biomedicine, tissue engineering, and biosensing applications. Copyright © 2018 Elsevier B.V. All rights reserved.

Stimulatory effects of Euphorbia cheiradenia on cell mediated immunity and humoral antibody synthesis.

PubMed

Amirghofran, Zahra; Azadmehr, Abbas; Bahmani, Masoud; Javidnia, Katayoun

2008-06-01

Studies have demonstrated that plant extracts possess various biological characteristics including immunomodulatory activity. Euphorbia cheiradenia Boiss et Hohen (Euphorbiaceae), a medicinal herb native to Iran was investigated for its immunomodulatory effects. The methanolic extract of the plant was prepared and added to mitogen-induced human peripheral blood lymphocyte cultures at different concentrations. Effect of E. cheiradenia on in vivo cell-mediated immunity was measured by delayed type hypersensitivity (DTH) reaction. The effect of the extract on humoral antibody synthesis was also measured in immunized mice treated with different extract concentrations. The stimulation index (SI) for cultures treated with 0.01 to 200 microg/ml of the extract ranged from 1.3+/-0.04 to 2.4+/-0.06, (p<0.01) showing a significant stimulatory effect of E. cheiradenia on the lymphocytes. IL-2 secreted from lymphocytes treated with the extract was significantly higher than that from the non-treated cells (p<0.001). Cell cycle analysis on mitogen-treated lymphocytes exposed to different concentrations of the extract showed an increase in the percentage of cells at G2M phase with increases in the concentration of the extract, but the results was not significant. In DTH skin test, the mean footpad thickness of all mice groups treated with 1, 50 and 100 mg/kg of the extract at 24 hours after immunization with antigen was 3.5+/-0.6 mm compared to 2.5+/-0.5 mm for the non-treated group (p=0.005). Moreover, an increase in production of specific antibody in mice immunized with different extract concentrations was also demonstrated. Results of this study showed the ability of the E. cheiradenia extract to induce proliferation of lymphocytes and enhance both cellular and humoral specific immune responses.

Negated bio-events: analysis and identification

PubMed Central

2013-01-01

Background Negation occurs frequently in scientific literature, especially in biomedical literature. It has previously been reported that around 13% of sentences found in biomedical research articles contain negation. Historically, the main motivation for identifying negated events has been to ensure their exclusion from lists of extracted interactions. However, recently, there has been a growing interest in negative results, which has resulted in negation detection being identified as a key challenge in biomedical relation extraction. In this article, we focus on the problem of identifying negated bio-events, given gold standard event annotations. Results We have conducted a detailed analysis of three open access bio-event corpora containing negation information (i.e., GENIA Event, BioInfer and BioNLP’09 ST), and have identified the main types of negated bio-events. We have analysed the key aspects of a machine learning solution to the problem of detecting negated events, including selection of negation cues, feature engineering and the choice of learning algorithm. Combining the best solutions for each aspect of the problem, we propose a novel framework for the identification of negated bio-events. We have evaluated our system on each of the three open access corpora mentioned above. The performance of the system significantly surpasses the best results previously reported on the BioNLP’09 ST corpus, and achieves even better results on the GENIA Event and BioInfer corpora, both of which contain more varied and complex events. Conclusions Recently, in the field of biomedical text mining, the development and enhancement of event-based systems has received significant interest. The ability to identify negated events is a key performance element for these systems. We have conducted the first detailed study on the analysis and identification of negated bio-events. Our proposed framework can be integrated with state-of-the-art event extraction systems. The

Bio-Liquid Morphological Analysis

PubMed Central

Shatokhina, S.N.; Shabalin, V.N.; Buzoverya, M.E.; Punin, V.T.

2004-01-01

Information is presented on the new scientific line in medicine and biology: bio-liquid morphology. The interdisciplinary character of the given research area is emphasized. The problems and prospects of bio-liquid morphological analysis development both in applied and fundamental aspects are discussed. PMID:15349509

BrisSynBio: a BBSRC/EPSRC-funded Synthetic Biology Research Centre.

PubMed

Sedgley, Kathleen R; Race, Paul R; Woolfson, Derek N

2016-06-15

BrisSynBio is the Bristol-based Biotechnology and Biological Sciences Research Council (BBSRC)/Engineering and Physical Sciences Research Council (EPSRC)-funded Synthetic Biology Research Centre. It is one of six such Centres in the U.K. BrisSynBio's emphasis is on rational and predictive bimolecular modelling, design and engineering in the context of synthetic biology. It trains the next generation of synthetic biologists in these approaches, to facilitate translation of fundamental synthetic biology research to industry and the clinic, and to do this within an innovative and responsible research framework. © 2016 The Author(s).

Bio-Oil Analysis Laboratory Procedures | Bioenergy | NREL

Science.gov Websites

Bio-Oil Analysis Laboratory Procedures Bio-Oil Analysis Laboratory Procedures NREL develops standard procedures have been validated and allow for reliable bio-oil analysis. Procedures Determination different hydroxyl groups (-OH) in pyrolysis bio-oil: aliphatic-OH, phenolic-OH, and carboxylic-OH. Download

BioASF: a framework for automatically generating executable pathway models specified in BioPAX.

PubMed

Haydarlou, Reza; Jacobsen, Annika; Bonzanni, Nicola; Feenstra, K Anton; Abeln, Sanne; Heringa, Jaap

2016-06-15

Biological pathways play a key role in most cellular functions. To better understand these functions, diverse computational and cell biology researchers use biological pathway data for various analysis and modeling purposes. For specifying these biological pathways, a community of researchers has defined BioPAX and provided various tools for creating, validating and visualizing BioPAX models. However, a generic software framework for simulating BioPAX models is missing. Here, we attempt to fill this gap by introducing a generic simulation framework for BioPAX. The framework explicitly separates the execution model from the model structure as provided by BioPAX, with the advantage that the modelling process becomes more reproducible and intrinsically more modular; this ensures natural biological constraints are satisfied upon execution. The framework is based on the principles of discrete event systems and multi-agent systems, and is capable of automatically generating a hierarchical multi-agent system for a given BioPAX model. To demonstrate the applicability of the framework, we simulated two types of biological network models: a gene regulatory network modeling the haematopoietic stem cell regulators and a signal transduction network modeling the Wnt/β-catenin signaling pathway. We observed that the results of the simulations performed using our framework were entirely consistent with the simulation results reported by the researchers who developed the original models in a proprietary language. The framework, implemented in Java, is open source and its source code, documentation and tutorial are available at http://www.ibi.vu.nl/programs/BioASF CONTACT: j.heringa@vu.nl. © The Author 2016. Published by Oxford University Press.

Utilization of different waste proteins to create a novel PGPR-containing bio-organic fertilizer

PubMed Central

Huang, Yan; Sun, Li; Zhao, Jianshu; Huang, Rong; Li, Rong; Shen, Qirong

2015-01-01

High-quality bio-organic fertilizers (BIOs) cannot be produced without the addition of some proteins, while many waste proteins are haphazardly disposed, causing serious environmental pollution. In this study, several waste proteins were used as additives to assist with the reproduction of the functional microbe (Bacillus amyloliquefaciens SQR9) inoculated into matured composts to produce BIOs. An optimized composition of solid-state fermentation (SSF) raw materials was predicted by response surface methodology and experimental validation. The results showed that 7.61% (w/w, DW, the same below) rapeseed meal, 8.85% expanded feather meal, 6.47% dewatered blue algal sludge and 77.07% chicken compost resulted in maximum biomass of strain SQR-9 and the maximum amount of lipopeptides 7 days after SSF. Spectroscopy experiments showed that the inner material structural changes in the novel SSF differed from the control and the novel BIO had higher dissolved organic matter. This study offers a high value-added utilization of waste proteins for producing economical but high-quality BIO. PMID:25586328

Clinical comparison between two hyaluronic acid-derived fillers in the treatment of nasolabial folds in Chinese subjects: BioHyalux versus Restylane.

PubMed

Wu, Yan; Sun, Nan; Xu, Yue; Liu, Huixian; Zhong, Shaomin; Chen, Liyang; Li, Dong

2016-04-01

Hyaluronic acid fillers are used to improve the appearance of nasolabial folds (NLF). This study aimed to compare the efficacy, safety, and durability of a new hyaluronic acid gel (BioHyalux) versus Restylane for the correction of NLF. This was a multicenter, double-blinded, randomized, controlled, non-inferiority clinical trial involving 88 subjects with moderate to severe NLF. Subjects were randomized to BioHyalux and Restylane on either sides of the NLF. NLF was assessed before and right after injection, and at 1 week, 1, 3, and 6 months. Patients were followed up for 13-15 months to evaluate the durability and long-term safety. A clinically meaningful response was predefined as at least one-point improvement on the Wrinkle Severity Rating Scale, which is a five-point scale. At 6 months, the response rate of BioHyalux was not inferior to that of Restylane (P < 0.05). At the 13-15 months follow-up, the response rate by investigators was 58.0 % on the BioHyalux side versus 63.8 % on the Restylane side. The response rate by subjects showed similar results, which was 56.5 % on the BioHyalux side versus 60.9 % on the Restylane side at 13-15 months. The subjects' Global Aesthetic Improvement Scale (GAIS) showed that most subjects felt improvements on both sides of NLF (P > 0.05) at all time points. At 6 months, 100 % reported improvements on both side; at 13-15 months, 60 % of subjects reported improvements with BioHyalux versus 64 % with Restylane. Adverse events were transient and predominantly mild or moderate in severity including injection site swelling, pain, itching, bruising, and tenderness. BioHyalux had reliable safety and tolerance, and could be an effective injectable filler for correcting NLF.

Finding abbreviations in biomedical literature: three BioC-compatible modules and four BioC-formatted corpora.

PubMed

Islamaj Doğan, Rezarta; Comeau, Donald C; Yeganova, Lana; Wilbur, W John

2014-01-01

BioC is a recently created XML format to share text data and annotations, and an accompanying input/output library to promote interoperability of data and tools for natural language processing of biomedical text. This article reports the use of BioC to address a common challenge in processing biomedical text information-that of frequent entity name abbreviation. We selected three different abbreviation definition identification modules, and used the publicly available BioC code to convert these independent modules into BioC-compatible components that interact seamlessly with BioC-formatted data, and other BioC-compatible modules. In addition, we consider four manually annotated corpora of abbreviations in biomedical text: the Ab3P corpus of 1250 PubMed abstracts, the BIOADI corpus of 1201 PubMed abstracts, the old MEDSTRACT corpus of 199 PubMed(®) citations and the Schwartz and Hearst corpus of 1000 PubMed abstracts. Annotations in these corpora have been re-evaluated by four annotators and their consistency and quality levels have been improved. We converted them to BioC-format and described the representation of the annotations. These corpora are used to measure the three abbreviation-finding algorithms and the results are given. The BioC-compatible modules, when compared with their original form, have no difference in their efficiency, running time or any other comparable aspects. They can be conveniently used as a common pre-processing step for larger multi-layered text-mining endeavors. Database URL: Code and data are available for download at the BioC site: http://bioc.sourceforge.net. Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

Bio-Terrorism Threat and Casualty Prevention

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

NOEL,WILLIAM P.

2000-01-01

The bio-terrorism threat has become the ''poor man's'' nuclear weapon. The ease of manufacture and dissemination has allowed an organization with only rudimentary skills and equipment to pose a significant threat with high consequences. This report will analyze some of the most likely agents that would be used, the ease of manufacture, the ease of dissemination and what characteristics of the public health response that are particularly important to the successful characterization of a high consequence event to prevent excessive causalities.

[Current status of bio-based materials industry in China].

PubMed

Diao, Xiaoqian; Weng, Yunxuan; Huang, Zhigang; Yang, Nan; Wang, Xiyuan; Zhang, Min; Jin, Yujuan

2016-06-25

In recent years, bio-based materials are becoming a new dominant industry leading the scientific and technological innovation, and economic development of the world. We reviewed the new development of bio-based materials industry in China, analyzed the entire market of bio-based materials products comprehensively, and also stated the industry status of bio-based chemicals, such as lactic acid, 1,3-propanediol, and succinic acid; biodegradable bio-based polymers, such as co-polyester of diacid and diol, polylactic acid, carbon dioxide based copolymer, polyhydroxyalknoates, polycaprolactone, and thermoplastic bio-based plastics; non-biodegradable bio-based polymers, such as bio-based polyamide, polytrimethylene terephthalate, bio-based polyurethane, and bio-based fibers.

Diamond bio electronics.

PubMed

Linares, Robert; Doering, Patrick; Linares, Bryant

2009-01-01

The use of diamond for advanced applications has been the dream of mankind for centuries. Until recently this dream has been realized only in the use of diamond for gemstones and abrasive applications where tons of diamonds are used on an annual basis. Diamond is the material system of choice for many applications, but its use has historically been limited due to the small size, high cost, and inconsistent (and typically poor) quality of available diamond materials until recently. The recent development of high quality, single crystal diamond crystal growth via the Chemical Vapor Deposition (CVD) process has allowed physcists and increasingly scientists in the life science area to think beyond these limitations and envision how diamond may be used in advanced applications ranging from quantum computing, to power generation and molecular imaging, and eventually even diamond nano-bots. Because of diamond's unique properties as a bio-compatible material, better understanding of diamond's quantum effects and a convergence of mass production, semiconductor-like fabrication process, diamond now promises a unique and powerful key to the realization of the bio-electronic devices being envisioned for the new era of medical science. The combination of robust in-the-body diamond based sensors, coupled with smart bio-functionalized diamond devices may lead to diamond being the platform of choice for bio-electronics. This generation of diamond based bio-electronic devices would contribute substantially to ushering in a paradigm shift for medical science, leading to vastly improved patient diagnosis, decrease of drug development costs and risks, and improved effectiveness of drug delivery and gene therapy programs through better timed and more customized solutions.

Assessing the Need for an On-Line Educational Module for Volunteer Leaders on Bio-Security in Washington State 4-H Livestock Projects

ERIC Educational Resources Information Center

Stevenson, Jill L.; Moore, Dale A.; Newman, Jerry; Schmidt, Janet L.; Smith, Sarah M.; Smith, Jean; Kerr, Susan; Wallace, Michael; BoyEs, Pat

2011-01-01

4-H livestock projects present disease transmission risks that can be reduced by the use of bio-security practices. The responsibility of teaching bio-security to youth belongs primarily to volunteer leaders, who may not be aware of the importance of these practices. A needs assessment for an online educational module about bio-security revealed…

Stimulatory effects of histamine on migration of nasal fibroblasts.

PubMed

Hong, Sung-Moon; Park, Il-Ho; Um, Ji-Young; Shin, Jae-Min; Lee, Heung-Man

2015-10-01

Fibroblast migration is crucial for normal wound repair after sinonasal surgery. Histamine is known to be involved in wound healing by its effects on cell proliferation and migration. This study aimed to determine whether histamine affects the migration of nasal fibroblasts and to investigate the mechanism of action of histamine on nasal fibroblasts. Primary cultures of nasal fibroblasts were established from inferior turbinate samples. Fibroblast migration was evaluated with scratch assays. Cells were treated with histamine and/or histamine receptor-selective antagonists. U-73122 and pertussis toxin, which are selective inhibitors of the lower signaling pathway of H1R and H4R, were used to confirm the modulation of nasal fibroblast migration by histamine. Fibroblast cytoskeletal structures were visualized with immunocytochemistry. Histamine significantly stimulated the migration of nasal fibroblasts. Antagonists selective for HR1 and HR4 significantly reduced nasal fibroblast migration. In immunocytochemical staining, histamine treatment increased membrane ruffling and pyrilamine, diphenhydramine, fexofenadine, and JNJ7777120 decreased histamine-induced membrane ruffling. U-73122 and pertussis toxin also decreased histamine-induced migration of fibroblasts. Histamine maintains its stimulatory effects on fibroblast migration in the presence of mitomycin C, which blocks proliferation of cells. We showed that histamine stimulates fibroblast migration in nasal fibroblasts. This effect appeared to be mediated by HR1 and HR4. However, because fibroblast migration also can be involved in scaring and fibrosis, more research is necessary to determine the effects of antihistamine on wound healing after sinus surgery. © 2015 ARS-AAOA, LLC.

Bio-objects and the media: the role of communication in bio-objectification processes.

PubMed

Maeseele, Pieter; Allgaier, Joachim; Martinelli, Lucia

2013-06-01

The representation of biological innovations in and through communication and media practices is vital for understanding the nature of "bio-objects" and the process we call "bio-objectification." This paper discusses two ideal-typical analytical approaches based on different underlying communication models, ie, the traditional (science- and media-centered) and media sociological (a multi-layered process involving various social actors in defining the meanings of scientific and technological developments) approach. In this analysis, the latter is not only found to be the most promising approach for understanding the circulation, (re)production, and (re)configuration of meanings of bio-objects, but also to interpret the relationship between media and science. On the basis of a few selected examples, this paper highlights how media function as a primary arena for the (re)production and (re)configuration of scientific and biomedical information with regards to bio-objects in the public sphere in general, and toward decision-makers, interest groups, and the public in specific.

Bio-objects and the media: the role of communication in bio-objectification processes

PubMed Central

Maeseele, Pieter; Allgaier, Joachim; Martinelli, Lucia

2013-01-01

The representation of biological innovations in and through communication and media practices is vital for understanding the nature of “bio-objects” and the process we call “bio-objectification.” This paper discusses two ideal-typical analytical approaches based on different underlying communication models, ie, the traditional (science- and media-centered) and media sociological (a multi-layered process involving various social actors in defining the meanings of scientific and technological developments) approach. In this analysis, the latter is not only found to be the most promising approach for understanding the circulation, (re)production, and (re)configuration of meanings of bio-objects, but also to interpret the relationship between media and science. On the basis of a few selected examples, this paper highlights how media function as a primary arena for the (re)production and (re)configuration of scientific and biomedical information with regards to bio-objects in the public sphere in general, and toward decision-makers, interest groups, and the public in specific. PMID:23771763

Valorization of algal waste via pyrolysis in a fixed-bed reactor: Production and characterization of bio-oil and bio-char.

PubMed

Aboulkas, A; Hammani, H; El Achaby, M; Bilal, E; Barakat, A; El Harfi, K

2017-11-01

The aim of the present work is to develop processes for the production of bio-oil and bio-char from algae waste using the pyrolysis at controlled conditions. The pyrolysis was carried out at different temperatures 400-600°C and different heating rates 5-50°C/min. The algal waste, bio-oil and bio-char were successfully characterized using Elemental analysis, Chemical composition, TGA, FTIR, 1 H NMR, GC-MS and SEM. At a temperature of 500°C and a heating rate of 10°C/min, the maximum yield of bio-oil and bio-char was found to be 24.10 and 44.01wt%, respectively, which was found to be strongly influenced by the temperature variation, and weakly affected by the heating rate variation. Results show that the bio-oil cannot be used as bio-fuel, but can be used as a source of value-added chemicals. On the other hand, the bio-char is a promising candidate for solid fuel applications and for the production of carbon materials. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bio-Organic Reaction Animations (BioORA): Student Performance, Student Perceptions, and Instructor Feedback

ERIC Educational Resources Information Center

Gunersel, Adalet Baris; Fleming, Steven

2014-01-01

Research shows that computer animations are especially helpful in fields such as chemistry and in this mixed-methods study, we investigate the educational effectiveness of Bio-Organic Reaction Animations (BioORA), a 3-D software, in four undergraduate biochemistry classes at different universities. Statistically significant findings indicate that…

Study on demetalization of sewage sludge by sequential extraction before liquefaction for the production of cleaner bio-oil and bio-char.

PubMed

Leng, Lijian; Yuan, Xingzhong; Shao, Jianguang; Huang, Huajun; Wang, Hou; Li, Hui; Chen, Xiaohong; Zeng, Guangming

2016-01-01

Demetalization of sewage sludge (SS) by sequential extraction before liquefaction was implemented to produce cleaner bio-char and bio-oil. Demetalization steps 1 and 2 did not cause much organic matter loss on SS, and thus the bio-oil and bio-char yields and the compositions of bio-oils were also not affected significantly. However, the demetalization procedures resulted in the production of cleaner bio-chars and bio-oils. The total concentrations and the acid soluble/exchangeable fraction (F1 fraction, the most toxic heavy metal fraction) of heavy metals (Cu, Cr, Pb, Zn, and Cd) in these products were significantly reduced and the environmental risks of these products were also relived considerably compared with those produced from raw SS, respectively. Additionally, these bio-oils had less heavy fractions. Demetalization processes with removal of F1 and F2 fractions of heavy metals would benefit the production of cleaner bio-char and bio-oil by liquefaction of heavy metal abundant biomass like SS. Copyright © 2015 Elsevier Ltd. All rights reserved.

Bio-functionalization of biomedical metals.

PubMed

Xiao, M; Chen, Y M; Biao, M N; Zhang, X D; Yang, B C

2017-01-01

Bio-functionalization means to endow biomaterials with bio-functions so as to make the materials or devices more suitable for biomedical applications. Traditionally, because of the excellent mechanical properties, the biomedical metals have been widely used in clinic. However, the utilized functions are basically supporting or fixation especially for the implantable devices. Nowadays, some new functions, including bioactivity, anti-tumor, anti-microbial, and so on, are introduced to biomedical metals. To realize those bio-functions on the metallic biomedical materials, surface modification is the most commonly used method. Surface modification, including physical and chemical methods, is an effective way to alter the surface morphology and composition of biomaterials. It can endow the biomedical metals with new surface properties while still retain the good mechanical properties of the bulk material. Having analyzed the ways of realizing the bio-functionalization, this article briefly summarized the bio-functionalization concepts of six hot spots in this field. They are bioactivity, bony tissue inducing, anti-microbial, anti-tumor, anticoagulation, and drug loading functions. Copyright © 2016. Published by Elsevier B.V.

Bio-Decontamination of Water and Surfaces by DC Discharges in Atmospheric Air

NASA Astrophysics Data System (ADS)

Machala, Zdenko; Tarabová, Barbora; Pelach, Michal; Šipoldová, Zuzana; Hensel, Karol; Janda, Mário; Šikurová, Libuša

Two types of DC-driven atmospheric air discharges, including a streamer corona and a transient spark with short high current pulses of limited energy, were employed for bio-decontamination of water and various surfaces (agar plates, plastic foils, human teeth) contaminated by bacteria or spores (Salmonella typhimurium, Bacillus cereus). Both discharges generate cold non-equilibrium plasma. The discharges combined with the electro-spraying of the treated water through the needle electrode lead to fast and efficient bio-decontamination. Experiments comparing direct and indirect plasma effects, oxidation stress measurements in the cell membranes, and chemical changes induced in the treated water enable assessment of the plasma agents being responsible for microbial inactivation. Radicals and reactive oxygen species seem to be dominant biocidal agents, although deeper understanding of the plasma-induced water chemistry and of the temporal evolution of the bio-inactivation processes is needed.

Retrofitting hetrotrophically cultivated algae biomass as pyrolytic feedstock for biogas, bio-char and bio-oil production encompassing biorefinery.

PubMed

Sarkar, Omprakash; Agarwal, Manu; Naresh Kumar, A; Venkata Mohan, S

2015-02-01

Algal biomass grown hetrotrophically in domestic wastewater was evaluated as pyrolytic feedstock for harnessing biogas, bio-oil and bio-char. Freshly harvested microalgae (MA) and lipid extracted microalgae (LEMA) were pyrolysed in packed bed reactor in the presence and absence of sand as additive. MA (without sand additive) depicted higher biogas (420 ml/g; 800 °C; 3 h) and bio-oil (0.70 ml/g; 500 °C; 3 h). Sand addition enhanced biogas production (210 ml/g; 600 °C; 2 h) in LEMA operation. The composition of bio-gas and bio-oil was found to depend on the nature of feedstock as well as the process conditions viz., pyrolytic-temperature, retention time and presence of additive. Sand additive improved the H2 composition while pyrolytic temperature increment caused a decline in CO2 fraction. Bio-char productivity increased with increasing temperature specifically with LEMA. Integration of thermo-chemical process with microalgae cultivation showed to yield multiple resources and accounts for environmental sustainability in the bio-refinery framework. Copyright © 2014 Elsevier Ltd. All rights reserved.

Testing the Utility of a Bio-Neuropsychosocial Model for Predicting Medical Adherence and Responsibility During Early Adolescence in Youth With Spina Bifida.

PubMed

Psihogios, Alexandra M; Murray, Caitlin; Zebracki, Kathy; Acevedo, Laura; Holmbeck, Grayson N

2017-10-01

The present longitudinal, multi-method, and multi-informant study examined biological, neuropsychological, and social predictors of medical adherence and responsibility among early adolescents with spina bifida (SB). Youth with SB (M age = 11.40 at Time 1) and their parents and teachers completed surveys, and families and peers completed observational assessments, at two biennial data collection time points (n = 112 for both time points). Multinomial logistic regressions tested predictors of group membership (adherent vs. nonadherent and child responsible vs. not responsible with SB medical tasks). Consistent with the bio-neuropsychosocial model, several risk factors emerged for SB management. Impaired gross motor classification and low IQ were barriers to obtaining medical responsibility, and high family stress and executive dysfunction were barriers to adherence and responsibility. This study offered intervention targets to promote self-management and adherence for youth with SB and their families, including parent stress-management and family problem-solving. © The Author 2016. Published by Oxford University Press on behalf of the Society of Pediatric Psychology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

[Bio-Resources and Database for Preemptive Medicine.

PubMed

Saito, Kuniaki

2016-05-01

Establishing a primary defense for the improvement of individual quality of life by epidemiology and various clinical studies applying bio-resources/database analysis is very important. Furthermore, recent studies on understanding the epigenetic regulatory mechanisms of developmental origins of health and diseases are attracting increasing interest. Therefore, the storing of not only bio-fluid (i.e., blood, urine) but also certain tissues (i.e., placenta, cord) is very important for research. The Resource Center for Health Science (RECHS) and Bio-databases Institute of Reproductive and Developmental Medicine (BIRD) have estab- lished Bio-bank and initiated a project based on the development and utilization of bio-resources/database, comprising personal health records (PHR), such as health/medical records including individual records of daily diet and exercise, physically consolidated with bio-resources, taken from the same individuals. These Bio-Resources/Database projects are very important for the establishment of preemptive medicine and un- derstanding the mechanisms of the developmental origins of health and diseases.

Bios-3: Siberian experiments in bioregenerative life support

NASA Technical Reports Server (NTRS)

Salisbury, F. B.; Gitelson, J. I.; Lisovsky, G. M.

1997-01-01

The Russian experience with the bioregenerative life support system Bios-3 at Krasnoyarsk, Siberia, is reviewed. A brief review of other bioregenerative systems examines Biosphere 2 in Oracle, Arizona, and the Bios-1 and Bios-2 systems that preceded Bios-3. Physical details of the Bios-3 facility are provided. The use of Chlorella and higher plants for gas exchange is examined. Long-term studies of human habitation are discussed. Other topics include microflora in Bios-3, the theory of closed systems, and problems for the future.

Dose-response behavior of the bacterium Vibrio fischeri exposed to pharmaceuticals and personal care products.

PubMed

Ortiz de García, Sheyla; García-Encina, Pedro A; Irusta-Mata, Rubén

2016-01-01

The presence of pharmaceuticals and personal care products (PPCPs) in the environment has become a real and widespread concern in recent years. Therefore, the primary goal of this study was to investigate 20 common and widely used PPCPs to assess their individual and combined effect on an important species in one trophic level, i.e., bacteria. The ecotoxicological effects of PPCPs at two different concentration ranges were determined in the bacterium Vibrio fischeri using Microtox(®) and were statistically analyzed using three models in the GraphPad Prism 6 program for Windows, v.6.03. A four-parameter model best fit the majority of the compounds. The half maximal effective concentration (EC50) of each PPCP was estimated using the best-fitting model and was compared with the results from a recent study. Comparative analysis indicated that most compounds showed the same level of toxicity. Moreover, the stimulatory effects of PPCPs at environmental concentrations (low doses) were assessed. These results indicated that certain compounds have traditional inverted U- or J-shaped dose-response curves, and 55% of them presented a stimulatory effect below the zero effect-concentration point. Effective concentrations of 0 (EC0), 5 (EC5) and 50% (EC50) were calculated for each PPCP as the ecotoxicological points. All compounds that presented narcosis as a mode of toxic action at high doses also exhibited stimulation at low concentrations. The maximum stimulatory effect of a mixture was higher than the highest stimulatory effect of each individually tested compound. Moreover, when the exposure time was increased, the hormetic effect decreased. Hormesis is being increasingly included in dose-response studies because this may have a harmful, beneficial or indifferent effect in an environment. Despite the results obtained in this research, further investigations need to be conducted to elucidate the behavior of PPCPs in aquatic environments.

BioImageXD: an open, general-purpose and high-throughput image-processing platform.

PubMed

Kankaanpää, Pasi; Paavolainen, Lassi; Tiitta, Silja; Karjalainen, Mikko; Päivärinne, Joacim; Nieminen, Jonna; Marjomäki, Varpu; Heino, Jyrki; White, Daniel J

2012-06-28

BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes. We demonstrate its performance in a study of integrin clustering in response to selected inhibitors.

Application of advanced techniques for the assessment of bio-stability of biowaste-derived residues: A minireview.

PubMed

Lü, Fan; Shao, Li-Ming; Zhang, Hua; Fu, Wen-Ding; Feng, Shi-Jin; Zhan, Liang-Tong; Chen, Yun-Min; He, Pin-Jing

2018-01-01

Bio-stability is a key feature for the utilization and final disposal of biowaste-derived residues, such as aerobic compost or vermicompost of food waste, bio-dried waste, anaerobic digestate or landfilled waste. The present paper reviews conventional methods and advanced techniques used for the assessment of bio-stability. The conventional methods are reclassified into two categories. Advanced techniques, including spectroscopic (fluorescent, ultraviolet-visible, infrared, Raman, nuclear magnetic resonance), thermogravimetric and thermochemolysis analysis, are emphasized for their application in bio-stability assessment in recent years. Their principles, pros and cons are critically discussed. These advanced techniques are found to be convenient in sample preparation and to supply diversified information. However, the viability of these techniques as potential indicators for bio-stability assessment ultimately lies in the establishment of the relationship of advanced ones with the conventional methods, especially with the methods based on biotic response. Furthermore, some misuses in data explanation should be noted. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bio-oil and bio-char from low temperature pyrolysis of spent grains using activated alumina.

PubMed

Sanna, Aimaro; Li, Sujing; Linforth, Rob; Smart, Katherine A; Andrésen, John M

2011-11-01

The pyrolysis of wheat and barley spent grains resulting from bio-ethanol and beer production respectively was investigated at temperatures between 460 and 540 °C using an activated alumina bed. The results showed that the bio-oil yield and quality depend principally on the applied temperature where pyrolysis at 460 °C leaves a bio-oil with lower nitrogen content in comparison with the original spent grains and low oxygen content. The viscosity profile of the spent grains indicated that activated alumina could promote liquefaction and prevent charring of the structure between 400 and 460 °C. The biochar contains about 10-12% of original carbon and 13-20% of starting nitrogen resulting very attractive as a soil amendment and for carbon sequestration. Overall, value can be added to the spent grains opening a new market in bio-fuel production without the needs of external energy. The bio-oil from spent grains could meet about 9% of the renewable obligation in the UK. Copyright © 2011 Elsevier Ltd. All rights reserved.

Growth performance and immunological and antioxidant status of Chinese shrimp, Fennerpenaeus chinensis reared in bio-floc culture system using probiotics.

PubMed

Kim, Min-Su; Min, EunYoung; Kim, Jun-Hwan; Koo, Ja-Keun; Kang, Ju-Chan

2015-11-01

Chinese shrimp Fennerpenaeus chinensis (mean length 1.86 ± 0.15 cm, and weight 137.4 ± 12.7 mg) were reared in the different concentrations of bio-floc (control, 60, 80, 100, 120, and 140%) for 90 days. The growth rate was significantly increased over 100% bio-floc concentrations. In the immunological parameters, the gene expression of proPO and lysozyme was considerably increased over 120% bio-floc concentrations. The gene expression of SP was notably elevated at 140% bio-floc concentration. In the antioxidant enzymes, the activity of SOD was considerably decreased over 80% bio-floc concentrations. A notable decline in the activity of CAT was observed over 120% bio-floc concentrations. The results indicate that rearing of Chinese shrimp in bio-floc system can induce the increase of growth performance, enhancement of immune responses, and reduction of oxidative stress. Copyright © 2015 Elsevier Ltd. All rights reserved.

A Systems Approach to Bio-Oil Stabilization - Final Technical Report

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

Brown, Robert C; Meyer, Terrence; Fox, Rodney

2011-12-23

products: condensable vapors, non-condensable gases, and liquid aerosols. Traditionally these are recovered by a spray quencher or a conventional shell and tube condenser. The spray quencher or condenser is typically followed by an electrostatic precipitator to yield 1 or 2 distinct fractions of bio-oil. The pyrolyzer system developed at Iowa State University incorporates a proprietary fractionating condenser train. The system collects the bio-oil into five unique fractions. For conditions typical of fluidized bed pyrolyzers, stage fractions have been collected that are carbohydrate-rich (anhydrosugars), lignin-rich, and an aqueous solution of carboxylic acids and aldehydes. One important feature is that most of the water normally found in bio-oil appears in the last stage fraction along with several water-soluble components that are thought to be responsible for bio-oil aging (low molecular weight carboxylic acids and aldehydes). Research work on laser diagnostics for hot-vapor filtration and bio-oil recovery centered on development of analytical techniques for in situ measurements during fast pyrolysis, hot-vapor filtration, and fractionation relative to bio-oil stabilization. The methods developed in this work include laser-induced breakdown spectroscopy (LIBS), laser-induced incandescence (LII), and laser scattering for elemental analysis (N, O, H, C), detection of particulates, and detection of aerosols, respectively. These techniques were utilized in simulated pyrolysis environments and applied to a small-scale pyrolysis unit. Stability of Bio-oils is adversely affected by the presence of particulates that are formed as a consequence of thermal pyrolysis, improving the CFD simulations of moving bed granular filter (MBGF) is useful for improving the design of MBGF for bio-oil production. The current work uses fully resolved direct numerical simulation (where the flow past each granule is accurately represented) to calculate the filter efficiency that is used in the

Timescale Separation of Positive and Negative Signaling Creates History-Dependent Responses to IgE Receptor Stimulation

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

Harmon, Brooke; Chylek, Lily A.; Liu, Yanli

The high-affinity receptor for IgE expressed on the surface of mast cells and basophils interacts with antigens, via bound IgE antibody, and triggers secretion of inflammatory mediators that contribute to allergic reactions. To understand how past inputs (memory) influence future inflammatory responses in mast cells, a microfluidic device was used to precisely control exposure of cells to alternating stimulatory and non-stimulatory inputs. We determined that the response to subsequent stimulation depends on the interval of signaling quiescence. For shorter intervals of signaling quiescence, the second response is blunted relative to the first response, whereas longer intervals of quiescence induce anmore » enhanced second response. Through an iterative process of computational modeling and experimental tests, we found that these memory-like phenomena arise from a confluence of rapid, short-lived positive signals driven by the protein tyrosine kinase Syk; slow, long-lived negative signals driven by the lipid phosphatase Ship1; and slower degradation of Ship1 co-factors. This work advances our understanding of mast cell signaling and represents a generalizable approach for investigating the dynamics of signaling systems.« less

Bio-removal of Nickel ions by Sporosarcina pasteurii and Bacillus megaterium, A Comparative Study

NASA Astrophysics Data System (ADS)

Gheethi, AA; Efaq, AN; Mohamed, RM; Abdel-Monem, MO; Halid Abdullah, Abd; Hashim, M. Amir

2017-08-01

The aim of this work was to study the potential of Sporosarcina pasteurii 586S and Bacillus megaterium 1295S isolated from sewage treatment plants (STPs) in removing of nickel ions from the aqueous solution. The bacterial cells were used as living and dead cell biomass. The efficiency of bio-removal process was investigated as a response for nickel and biomass concentrations, time, pH and temperature. The bio-removal capacity (Qmax) of both strains were compared. The highest bio-removal percentage was recorded by dead cells in comparison to living cells. Dead cell biomass of B. megaterium 1295S exhibited higher efficiency for bio-removing of Ni2+ than S. pasteurii 586S at196.4 and 200.2 mg Ni2+ g-1, respectively. It can be concluded that both bacterial strains have high potential to be applied in the biotechnology for removing of Ni2+ ions, however, dead cells of B. megaterium 1295S is the most potent.

The evolving clinical profile of abatacept (CTLA4–Ig): a novel co-stimulatory modulator for the treatment of rheumatoid arthritis

PubMed Central

2005-01-01

Abatacept (CTLA4–Ig) is a novel fusion protein designed to modulate the T cell co-stimulatory signal mediated through the CD28–CD80/86 pathway. Clinical trials have provided preliminary evidence of the efficacy of this compound in the treatment of rheumatoid arthritis. This review describes the molecular and biologic bases for the use of abatacept in rheumatoid arthritis and summarizes the current clinical data on its safety and effectiveness in this disease. PMID:15833145

[Ecological treatment of bacterial vaginosis and vaginitis with Bio-three].

PubMed

Chimura, T

1998-12-01

Ecological treatment of bacterial vaginosis and vaginitis with a Bio-three was studied, and the following results were obtained. 1. A total of 16 women with bacterial vaginosis and vaginitis were treated with intravaginal application of 2 g of Bio-three (E. faecalis T-110, C. butyricum TO-A, B. mesentericus TO-A, pH 6.9 +/- 0.3). The effect of the treatment was evaluated 3 days after administration by monitoring the vaginal discharge and bacteriological assessment. 2. The clinical improvement was evaluated and the decreases of vaginal discharge and vaginal redness were significant and vaginal pH was lowered significantly (5.29 +/- 0.24 vs. 4.31 +/- 0.37, p < 0.05). In the vaginal discharge 35 strains of bacteria were detected, but 3 days after administration, 16/30 strains of Gram-positive bacteria, and 2 strains of Gram-negative bacteria disappeared. As for the overall bacteriological effects, 7/16 cases were eradicated, 1 case was partly eradicated, 6 cases were replaced. These findings indicated that the Bio-three therapy was effective in both clinical and bacteriological responses.

Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks.

PubMed

Adalsteinsson, David; McMillen, David; Elston, Timothy C

2004-03-08

Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true for pathways that involve transcriptional regulation, where generally there are two copies of each gene and the number of messenger RNA (mRNA) molecules can be small. Therefore, there is a need for computational tools for developing and investigating stochastic models of biochemical networks. We have developed the software package Biochemical Network Stochastic Simulator (BioNetS) for efficiently and accurately simulating stochastic models of biochemical networks. BioNetS has a graphical user interface that allows models to be entered in a straightforward manner, and allows the user to specify the type of random variable (discrete or continuous) for each chemical species in the network. The discrete variables are simulated using an efficient implementation of the Gillespie algorithm. For the continuous random variables, BioNetS constructs and numerically solves the appropriate chemical Langevin equations. The software package has been developed to scale efficiently with network size, thereby allowing large systems to be studied. BioNetS runs as a BioSpice agent and can be downloaded from http://www.biospice.org. BioNetS also can be run as a stand alone package. All the required files are accessible from http://x.amath.unc.edu/BioNetS. We have developed BioNetS to be a reliable tool for studying the stochastic dynamics of large biochemical networks. Important features of BioNetS are its ability to handle hybrid models that consist of both continuous and discrete random variables and its ability to model cell growth and division. We have verified the accuracy and efficiency of the numerical methods by considering several test systems.

Examining porous bio-active glass as a potential osteo-odonto-keratoprosthetic skirt material.

PubMed

Huhtinen, Reeta; Sandeman, Susan; Rose, Susanna; Fok, Elsie; Howell, Carol; Fröberg, Linda; Moritz, Niko; Hupa, Leena; Lloyd, Andrew

2013-05-01

Bio-active glass has been developed for use as a bone substitute with strong osteo-inductive capacity and the ability to form strong bonds with soft and hard tissue. The ability of this material to enhance tissue in-growth suggests its potential use as a substitute for the dental laminate of an osteo-odonto-keratoprosthesis. A preliminary in vitro investigation of porous bio-active glass as an OOKP skirt material was carried out. Porous glass structures were manufactured from bio-active glasses 1-98 and 28-04 containing varying oxide formulation (1-98, 28-04) and particle size range (250-315 μm for 1-98 and 28-04a, 315-500 μm for 28-04b). Dissolution of the porous glass structure and its effect on pH was measured. Structural 2D and 3D analysis of porous structures were performed. Cell culture experiments were carried out to study keratocyte adhesion and the inflammatory response induced by the porous glass materials. The dissolution results suggested that the porous structure made out of 1-98 dissolves faster than the structures made from glass 28-04. pH experiments showed that the dissolution of the porous glass increased the pH of the surrounding solution. The cell culture results showed that keratocytes adhered onto the surface of each of the porous glass structures, but cell adhesion and spreading was greatest for the 98a bio-glass. Cytokine production by all porous glass samples was similar to that of the negative control indicating that the glasses do not induce a cytokine driven inflammatory response. Cell culture results support the potential use of synthetic porous bio-glass as an OOKP skirt material in terms of limited inflammatory potential and capacity to induce and support tissue ingrowth.

[Preface for special issue on bio-based materials (2016)].

PubMed

Weng, Yunxuan

2016-06-25

Bio-based materials are new materials or chemicals with renewable biomass as raw materials such as grain, legume, straw, bamboo and wood powder. This class of materials includes bio-based polymer, biobased fiber, glycotechnology products, biobased rubber and plastics produced by biomass thermoplastic processing and basic biobased chemicals, for instance, bio-alcohols, organic acids, alkanes, and alkenes, obtained by bio-synthesis, bio-processing and bio-refinery. Owing to its environmental friendly and resource conservation, bio-based materials are becoming a new dominant industry taking the lead in the world scientific and technological innovation and economic development. An overview of bio-based materials development is reported in this special issue, and the industrial status and research progress of the following aspects, including biobased fiber, polyhydroxyalkanoates, biodegradable mulching film, bio-based polyamide, protein based biomedical materials, bio-based polyurethane, and modification and processing of poly(lactic acid), are introduced.

PVA bio-nanocomposites: a new take-off using cellulose nanocrystals and PLGA nanoparticles.

PubMed

Rescignano, N; Fortunati, E; Montesano, S; Emiliani, C; Kenny, J M; Martino, S; Armentano, I

2014-01-01

The formation of a new generation of hybrid bio-nanocomposites is reported: these are intended at modulating the mechanical, thermal and biocompatibility properties of the poly(vinyl alcohol) (PVA) by the combination of cellulose nanocrystals (CNC) and poly (D,L-lactide-co-glycolide) (PLGA) nanoparticles (NPs) loaded with bovine serum albumin fluorescein isothiocynate conjugate (FITC-BSA). CNC were synthesized from microcrystalline cellulose by hydrolysis, while PLGA nanoparticles were produced by a double emulsion with subsequent solvent evaporation. Firstly, binary bio-nanocomposites with different CNC amounts were developed in order to select the right content of CNC. Next, ternary PVA/CNC/NPs bio-nanocomposites were developed. The addition of CNC increased the elongation properties without compromising the other mechanical responses. Thermal analysis underlined the nucleation effect of the synergic presence of cellulose and nanoparticles. Remarkably, bio-nanocomposite films are suitable to vehiculate biopolymeric nanoparticles to adult bone marrow mesenchymal stem cells successfully, thus representing a new tool for drug delivery strategies. Copyright © 2013 Elsevier Ltd. All rights reserved.

BioSearch: a semantic search engine for Bio2RDF

PubMed Central

Qiu, Honglei; Huang, Jiacheng

2017-01-01

Abstract Biomedical data are growing at an incredible pace and require substantial expertise to organize data in a manner that makes them easily findable, accessible, interoperable and reusable. Massive effort has been devoted to using Semantic Web standards and technologies to create a network of Linked Data for the life sciences, among others. However, while these data are accessible through programmatic means, effective user interfaces for non-experts to SPARQL endpoints are few and far between. Contributing to user frustrations is that data are not necessarily described using common vocabularies, thereby making it difficult to aggregate results, especially when distributed across multiple SPARQL endpoints. We propose BioSearch — a semantic search engine that uses ontologies to enhance federated query construction and organize search results. BioSearch also features a simplified query interface that allows users to optionally filter their keywords according to classes, properties and datasets. User evaluation demonstrated that BioSearch is more effective and usable than two state of the art search and browsing solutions. Database URL: http://ws.nju.edu.cn/biosearch/ PMID:29220451

Impact of bio-palladium nanoparticles (bio-Pd NPs) on the activity and structure of a marine microbial community.

PubMed

Nuzzo, Andrea; Hosseinkhani, Baharak; Boon, Nico; Zanaroli, Giulio; Fava, Fabio

2017-01-01

Biogenic palladium nanoparticles (bio-Pd NPs) represent a promising catalyst for organohalide remediation in water and sediments. However, the available information regarding their possible impact in case of release into the environment, particularly on the environmental microbiota, is limited. In this study the toxicity of bio-Pd NPs on the model marine bacterium V. fischeri was assessed. The impacts of different concentrations of bio-Pd NPs on the respiratory metabolisms (i.e. organohalide respiration, sulfate reduction and methanogenesis) and the structure of a PCB-dechlorinating microbial community enriched form a marine sediment were also investigated in microcosms mimicking the actual sampling site conditions. Bio-Pd NPs had no toxic effect on V. fischeri. In addition, they had no significant effects on PCB-dehalogenating activity, while showing a partial, dose-dependent inhibitory effect on sulfate reduction as well as on methanogenesis. No toxic effects by bio-Pd NPs could be also observed on the total bacterial community structure, as its biodiversity was increased compared to the not exposed community. In addition, resilience of the microbial community to bio-Pd NPs exposure was observed, being the final community organization (Gini coefficient) of samples exposed to bio-Pd NPs similar to that of the not exposed one. Considering all the factors evaluated, bio-Pd NPs could be deemed as non-toxic to the marine microbiota in the conditions tested. This is the first study in which the impact of bio-Pd NPs is extensively evaluated over a microbial community in relevant environmental conditions, providing important information for the assessment of their environmental safety. Copyright © 2016 Elsevier Ltd. All rights reserved.

76 FR 42130 - Agency Information Collection Activities: BioWatch Filter Holder Log

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-18

... DEPARTMENT OF HOMELAND SECURITY Agency Information Collection Activities: BioWatch Filter Holder...) assigned responsibility for installing and removing filters from aerosol collection devices and transportation to local laboratories for sample analysis. A standard filter log form is completed for each sample...

76 FR 24504 - Agency Information Collection Activities: BioWatch Filter Holder Log

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-02

... DEPARTMENT OF HOMELAND SECURITY Agency Information Collection Activities: BioWatch Filter Holder...) assigned responsibility for installing and removing filters from aerosol collection devices and transportation to local laboratories for sample analysis. A standard filter log form is completed for each sample...

BioLab: Using Yeast Fermentation as a Model for the Scientific Method.

ERIC Educational Resources Information Center

Pigage, Helen K.; Neilson, Milton C.; Greeder, Michele M.

This document presents a science experiment demonstrating the scientific method. The experiment consists of testing the fermentation capabilities of yeasts under different circumstances. The experiment is supported with computer software called BioLab which demonstrates yeast's response to different environments. (YDS)

Hydrolase BioH knockout in E. coli enables efficient fatty acid methyl ester bioprocessing.

PubMed

Kadisch, Marvin; Schmid, Andreas; Bühler, Bruno

2017-03-01

Fatty acid methyl esters (FAMEs) originating from plant oils are most interesting renewable feedstocks for biofuels and bio-based materials. FAMEs can also be produced and/or functionalized by engineered microbes to give access to, e.g., polymer building blocks. Yet, they are often subject to hydrolysis yielding free fatty acids, which typically are degraded by microbes. We identified BioH as the key enzyme responsible for the hydrolysis of medium-chain length FAME derivatives in different E. coli K-12 strains. E. coli ΔbioH strains showed up to 22-fold reduced FAME hydrolysis rates in comparison with respective wild-type strains. Knockout strains showed, beside the expected biotin auxotrophy, unchanged growth behavior and biocatalytic activity. Thus, high specific rates (~80 U g CDW -1 ) for terminal FAME oxyfunctionalization catalyzed by a recombinant alkane monooxygenase could be combined with reduced hydrolysis. Biotransformations in process-relevant two-liquid phase systems profited from reduced fatty acid accumulation and/or reduced substrate loss via free fatty acid metabolization. The BioH knockout strategy was beneficial in all tested strains, although its effect was found to differ according to specific strain properties, such as FAME hydrolysis and FFA degradation activities. BioH or functional analogs can be found in virtually all microorganisms, making bioH deletion a broadly applicable strategy for efficient microbial bioprocessing involving FAMEs.

Bio-Carbon Accounting for Bio-Oil Co-Processing: 14C and 13C/ 12C

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

Mora, Claudia I.; Li, Zhenghua; Vance, Zachary

This is a powerpoint presentation on bio-carbon accounting for bio-oil co-processing. Because of the overlapping range in the stable C isotope compositions of fossil oils and biooils from C3-type feedstocks, it is widely thought that stable isotopes are not useful to track renewable carbon during co-production. In contrast, our study demonstrates the utility of stable isotopes to: • capture a record of renewable carbon allocation between FCC products of co-processing • record changes in carbon apportionments due to changes in reactor or feed temperature Stable isotope trends as a function of percent bio-oil in the feed are more pronounced whenmore » the δ 13C of the bio-oil endmember differs greatly from the VGO (i.e., it has a C4 biomass source–corn stover, switch grass, Miscanthus, sugarcane– versus a C3 biomass source– pine, wheat, rice, potato), but trends on the latter case are significant for endmember differences of just a few permil. The correlation between measured 14C and δ 13C may be useful as an alternative to carbon accounting, but the relationship must first be established for different bio-oil sources.« less

Composition and parameters of household bio-waste in four seasons.

PubMed

Hanc, Ales; Novak, Pavel; Dvorak, Milan; Habart, Jan; Svehla, Pavel

2011-07-01

Bio-waste makes up almost half portion of municipal solid waste. The characterization of household bio-waste is important in determining the most appropriate treatment method. The differences in composition and parameters of bio-waste derived from urban settlement (U-bio-waste) and family houses (F-bio-waste) during the four climate seasons are described in this paper. Twelve components and 20 parameters for bio-waste were evaluated. The composition of U-bio-waste was almost steady over those seasons, unlike F-bio-waste. U-bio-waste was comprised mainly (58.2%) of fruit and vegetable debris. F-bio-waste was primarily made up of seasonal garden components. The amount of variation among seasons in both type of bio-waste increased in sequence: basic parametersbio-waste were found out. Results of this research could be utilized to support another composition and parameters of bio-waste and be suitable for establishing bio-waste processing. Copyright © 2011 Elsevier Ltd. All rights reserved.

Green bio-oil extraction for oil crops

NASA Astrophysics Data System (ADS)

Zainab, H.; Nurfatirah, N.; Norfaezah, A.; Othman, H.

2016-06-01

The move towards a green bio-oil extraction technique is highlighted in this paper. The commonly practised organic solvent oil extraction technique could be replaced with a modified microwave extraction. Jatropha seeds (Jatropha curcas) were used to extract bio-oil. Clean samples were heated in an oven at 110 ° C for 24 hours to remove moisture content and ground to obtain particle size smaller than 500μm. Extraction was carried out at different extraction times 15 min, 30 min, 45 min, 60 min and 120 min to determine oil yield. The biooil yield obtained from microwave assisted extraction system at 90 minutes was 36% while that from soxhlet extraction for 6 hours was 42%. Bio-oil extracted using the microwave assisted extraction (MAE) system could enhance yield of bio-oil compared to soxhlet extraction. The MAE extraction system is rapid using only water as solvent which is a nonhazardous, environment-friendly technique compared to soxhlet extraction (SE) method using hexane as solvent. Thus, this is a green technique of bio-oil extraction using only water as extractant. Bio-oil extraction from the pyrolysis of empty fruit bunch (EFB), a biomass waste from oil palm crop, was enhanced using a biocatalyst derived from seashell waste. Oil yield for non-catalytic extraction was 43.8% while addition of seashell based biocatalyst was 44.6%. Oil yield for non-catalytic extraction was 43.8% while with addition of seashell-based biocatalyst was 44.6%. The pH of bio-oil increased from 3.5 to 4.3. The viscosity of bio-oil obtained by catalytic means increased from 20.5 to 37.8 cP. A rapid and environment friendly extraction technique is preferable to enhance bio-oil yield. The microwave assisted approach is a green, rapid and environmental friendly extraction technique for the production of bio-oil bearing crops.

BIO::Phylo-phyloinformatic analysis using perl.

PubMed

Vos, Rutger A; Caravas, Jason; Hartmann, Klaas; Jensen, Mark A; Miller, Chase

2011-02-27

Phyloinformatic analyses involve large amounts of data and metadata of complex structure. Collecting, processing, analyzing, visualizing and summarizing these data and metadata should be done in steps that can be automated and reproduced. This requires flexible, modular toolkits that can represent, manipulate and persist phylogenetic data and metadata as objects with programmable interfaces. This paper presents Bio::Phylo, a Perl5 toolkit for phyloinformatic analysis. It implements classes and methods that are compatible with the well-known BioPerl toolkit, but is independent from it (making it easy to install) and features a richer API and a data model that is better able to manage the complex relationships between different fundamental data and metadata objects in phylogenetics. It supports commonly used file formats for phylogenetic data including the novel NeXML standard, which allows rich annotations of phylogenetic data to be stored and shared. Bio::Phylo can interact with BioPerl, thereby giving access to the file formats that BioPerl supports. Many methods for data simulation, transformation and manipulation, the analysis of tree shape, and tree visualization are provided. Bio::Phylo is composed of 59 richly documented Perl5 modules. It has been deployed successfully on a variety of computer architectures (including various Linux distributions, Mac OS X versions, Windows, Cygwin and UNIX-like systems). It is available as open source (GPL) software from http://search.cpan.org/dist/Bio-Phylo.

BIO::Phylo-phyloinformatic analysis using perl

PubMed Central

2011-01-01

Background Phyloinformatic analyses involve large amounts of data and metadata of complex structure. Collecting, processing, analyzing, visualizing and summarizing these data and metadata should be done in steps that can be automated and reproduced. This requires flexible, modular toolkits that can represent, manipulate and persist phylogenetic data and metadata as objects with programmable interfaces. Results This paper presents Bio::Phylo, a Perl5 toolkit for phyloinformatic analysis. It implements classes and methods that are compatible with the well-known BioPerl toolkit, but is independent from it (making it easy to install) and features a richer API and a data model that is better able to manage the complex relationships between different fundamental data and metadata objects in phylogenetics. It supports commonly used file formats for phylogenetic data including the novel NeXML standard, which allows rich annotations of phylogenetic data to be stored and shared. Bio::Phylo can interact with BioPerl, thereby giving access to the file formats that BioPerl supports. Many methods for data simulation, transformation and manipulation, the analysis of tree shape, and tree visualization are provided. Conclusions Bio::Phylo is composed of 59 richly documented Perl5 modules. It has been deployed successfully on a variety of computer architectures (including various Linux distributions, Mac OS X versions, Windows, Cygwin and UNIX-like systems). It is available as open source (GPL) software from http://search.cpan.org/dist/Bio-Phylo PMID:21352572

Bio-TDS: bioscience query tool discovery system.

PubMed

Gnimpieba, Etienne Z; VanDiermen, Menno S; Gustafson, Shayla M; Conn, Bill; Lushbough, Carol M

2017-01-04

Bioinformatics and computational biology play a critical role in bioscience and biomedical research. As researchers design their experimental projects, one major challenge is to find the most relevant bioinformatics toolkits that will lead to new knowledge discovery from their data. The Bio-TDS (Bioscience Query Tool Discovery Systems, http://biotds.org/) has been developed to assist researchers in retrieving the most applicable analytic tools by allowing them to formulate their questions as free text. The Bio-TDS is a flexible retrieval system that affords users from multiple bioscience domains (e.g. genomic, proteomic, bio-imaging) the ability to query over 12 000 analytic tool descriptions integrated from well-established, community repositories. One of the primary components of the Bio-TDS is the ontology and natural language processing workflow for annotation, curation, query processing, and evaluation. The Bio-TDS's scientific impact was evaluated using sample questions posed by researchers retrieved from Biostars, a site focusing on BIOLOGICAL DATA ANALYSIS: The Bio-TDS was compared to five similar bioscience analytic tool retrieval systems with the Bio-TDS outperforming the others in terms of relevance and completeness. The Bio-TDS offers researchers the capacity to associate their bioscience question with the most relevant computational toolsets required for the data analysis in their knowledge discovery process. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

A novel 3-dimensional culture system uncovers growth stimulatory actions by TGFβ in pancreatic cancer cells.

PubMed

Sempere, Lorenzo F; Gunn, Jason R; Korc, Murray

2011-08-01

Transforming Growth Factor-β (TGF-β) exerts cell type-specific and context-dependent effects. Understanding the intrinsic effects of TGF-β on cancer cells in pancreatic ductal adenocarcinoma (PDAC) is a prerequisite for rationalized clinical implementation of TGF-β targeting therapies. Since the tumor microenvironment can affect how cancer cell respond to TGF-β, we employed a novel three-dimensional (3D) culturing system to recapitulate stromal and extracellular matrix interactions. We show here that TGF-β stimulates growth of human and murine pancreatic cancer cell lines (PCCs) when embedded in a 3% collagen IV/laminin-rich gelatinous medium (Matrigel™) over a solidified layer of soft agar. Moreover, in this novel 3D model, concomitant treatment with TGF-β1 and epidermal growth factor (EGF) enhanced PCC growth to a greater extent than either growth factor alone, and conferred increased chemoresistance to cytotoxic compounds. These cooperative growth-stimulatory effects were blocked by pharmacological inhibition of TGF-β type I receptor with SB431542 or the EGF receptor with erlotinib. Co-incubation with SB431542 and erlotinib enhanced the efficacy of gemcitabine and cisplatin in PCCs and in primary cell cultures established from pancreata of genetically-engineered mouse models of PDAC. These findings suggest that concomitant inhibition of TGF-β and EGF signaling may represent an effective therapeutic strategy in PDAC, and that this 3D culturing system could be utilized to test ex vivo the therapeutic response of pancreatic tumor biopsies from PDAC patients, thereby providing a functional assay to facilitate personalized targeted therapies.

The Problem of Bio-Concepts: Biopolitics, Bio-Economy and the Political Economy of Nothing

ERIC Educational Resources Information Center

Birch, Kean

2017-01-01

Scholars in science and technology studies--and no doubt other fields--have increasingly drawn on Michel Foucault's concept of biopolitics to theorize a variety of new "bio-concepts." While there might be some theoretical value in such exercises, many of these bio-concepts have simply replaced more rigorous--and therefore…

The mechanism and properties of bio-photon emission and absorption in protein molecules in living systems

NASA Astrophysics Data System (ADS)

Pang, Xiao-feng

2012-05-01

The mechanism and properties of bio-photon emission and absorption in bio-tissues were studied using Pang's theory of bio-energy transport, in which the energy spectra of protein molecules are obtained from the discrete dynamic equation. From the energy spectra, it was determined that the protein molecules could both radiate and absorb bio-photons with wavelengths of <3 μm and 5-7 μm, consistent with the energy level transitions of the excitons. These results were consistent with the experimental data; this consisted of infrared absorption data from collagen, bovine serum albumin, the protein-like molecule acetanilide, plasma, and a person's finger, and the laser-Raman spectra of acidity I-type collagen in the lungs of a mouse, and metabolically active Escherichia coli. We further elucidated the mechanism responsible for the non-thermal biological effects produced by the infrared light absorbed by the bio-tissues, using the above results. No temperature rise was observed; instead, the absorbed infrared light promoted the vibrations of amides as well the transport of the bio-energy from one place to other in the protein molecules, which changed their conformations. These experimental results, therefore, not only confirmed the validity of the mechanism of bio-photon emission, and the newly developed theory of bio-energy transport mentioned above, but also explained the mechanism and properties of the non-thermal biological effects produced by the absorption of infrared light by the living systems.

3D Bio-Printing Review

NASA Astrophysics Data System (ADS)

Du, Xianbin

2018-01-01

Ultimate goal of tissue engineering is to replace pathological or necrotic body tissue or organ by artificial tissue or organ and tissue engineering is a very promising research field. 3D bio-printing is a kind of emerging technologies and a branch of tissue engineering. It has made significant progress in the past decade. 3D bio-printing can realize tissue and organ construction in vitro and has wide application in basic research and pharmacy. This paper is to make an analysis and review on 3D bio-printing from the perspectives of bioink, printing technology and technology application.

Source and Biological Response of Biochar Organic Compounds Released into Water; Relationships with Bio-Oil Composition and Carbonization Degree.

PubMed

Ghidotti, Michele; Fabbri, Daniele; Mašek, Ondřej; Mackay, Colin Logan; Montalti, Marco; Hornung, Andreas

2017-06-06

Water-soluble organic compounds (WSOCs) were extracted from corn stalk biochar produced at increasing pyrolysis temperatures (350-650 °C) and from the corresponding vapors, collected as bio-oil. WSOCs were characterized by gas chromatography (semivolatile fraction), negative electron spray ionization high resolution mass spectrometry (hydrophilic fraction) and fluorescence spectroscopy. The pattern of semivolatile WSOCs in bio-oil was dominated by aromatic products from lignocellulose, while in biochar was featured by saturated carboxylic acids from hemi/cellulose and lipids with concentrations decreasing with decreasing H/C ratios. Hydrophilic species in poorly carbonized biochar resembled those in bio-oil, but the increasing charring intensity caused a marked reduction in the molecular complexity and degree of aromaticity. Differences in the fluorescence spectra were attributed to the predominance of fulvic acid-like structures in biochar and lignin-like moieties in bio-oil. The divergence between pyrolysis vapors and biochar in the distribution of WSOCs with increasing carbonization was explained by the hydrophobic carbonaceous matrix acting like a filter favoring the release into water of carboxylic and fulvic acid-like components. The formation of these structures was confirmed in biochar produced by pilot plant pyrolysis units. Biochar affected differently shoot and root length of cress seedlings in germination tests highlighting its complex role on plant growth.

Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine.

PubMed

Chiu, Billy; Pyysalo, Sampo; Vulić, Ivan; Korhonen, Anna

2018-02-05

Word representations support a variety of Natural Language Processing (NLP) tasks. The quality of these representations is typically assessed by comparing the distances in the induced vector spaces against human similarity judgements. Whereas comprehensive evaluation resources have recently been developed for the general domain, similar resources for biomedicine currently suffer from the lack of coverage, both in terms of word types included and with respect to the semantic distinctions. Notably, verbs have been excluded, although they are essential for the interpretation of biomedical language. Further, current resources do not discern between semantic similarity and semantic relatedness, although this has been proven as an important predictor of the usefulness of word representations and their performance in downstream applications. We present two novel comprehensive resources targeting the evaluation of word representations in biomedicine. These resources, Bio-SimVerb and Bio-SimLex, address the previously mentioned problems, and can be used for evaluations of verb and noun representations respectively. In our experiments, we have computed the Pearson's correlation between performances on intrinsic and extrinsic tasks using twelve popular state-of-the-art representation models (e.g. word2vec models). The intrinsic-extrinsic correlations using our datasets are notably higher than with previous intrinsic evaluation benchmarks such as UMNSRS and MayoSRS. In addition, when evaluating representation models for their abilities to capture verb and noun semantics individually, we show a considerable variation between performances across all models. Bio-SimVerb and Bio-SimLex enable intrinsic evaluation of word representations. This evaluation can serve as a predictor of performance on various downstream tasks in the biomedical domain. The results on Bio-SimVerb and Bio-SimLex using standard word representation models highlight the importance of developing dedicated

Multivariable bio-inspired photonic sensors for non-condensable gases

NASA Astrophysics Data System (ADS)

Potyrailo, Radislav A.; Karker, Nicholas; Carpenter, Michael A.; Minnick, Andrew

2018-02-01

Existing gas sensors often lose their measurement accuracy in practical field applications. To mitigate this significant problem, here, we report a demonstration of fabricated multivariable photonic sensors inspired by a known nanostructure of Morpho butterfly scales for detection of exemplary non-condensable gases such as H2, CO, and CO2. We fabricated bio-inspired nanostructures using conventional photolithography and chemical etching and detected individual gases that were difficult or unrealistic to detect using natural Morpho nanostructures. Such bio-inspired gas sensors are the critical step in the development of new sensors with improved accuracy for diverse operational scenarios. While this report is our initial demonstration of responses of fabricated multivariable sensors to individual gases in pristine laboratory conditions, it is a significant milestone in understanding the next steps toward field tests and practical applications of these sensors.

Bio-effectors from waste materials as growth promoters for tomato plants, an agronomic and metabolomic study

NASA Astrophysics Data System (ADS)

Abou Chehade, Lara; Chami, Ziad Al; De Pascali, Sandra; Cavoski, Ivana; Fanizzi, Francesco Paolo

2015-04-01

In organic farming, where nutrient management is constrained and sustainability is claimed, bio-effectors pave their way. Considering selected bio-effectors, this study integrates metabolomics to agronomy in depicting induced relevant phenomena. Extracts of three agro-industrial wastes (Lemon processing residues, Fennel processing residues and Brewer's spent grain) are being investigated as sources of bio-effectors for the third trial consequently. Corresponding individual and mixture aqueous extracts are assessed for their synergistic and/or single agronomic and qualitative performances on soil-grown tomato, compared to both a control and humic acid treatments. A metabolomic profiling of tomato fruits via the Proton Nuclear Magnetic Resonance (NMR) spectroscopy, as holistic indicator of fruit quality and extract-induced responses, complements crop productivity and organoleptic/nutritional qualitative analyses. Results are expected to show mainly an enhancement of the fruit qualitative traits, and to confirm partly the previous results of better crop productivity and metabolism enhancement. Waste-derived bio-effectors could be, accordingly, demonstrated as potential candidates of plant-enhancing substances. Keywords: bio-effectors, organic farming, agro-industrial wastes, nuclear magnetic resonance (NMR), tomato.

The Bio-Community Perl toolkit for microbial ecology.

PubMed

Angly, Florent E; Fields, Christopher J; Tyson, Gene W

2014-07-01

The development of bioinformatic solutions for microbial ecology in Perl is limited by the lack of modules to represent and manipulate microbial community profiles from amplicon and meta-omics studies. Here we introduce Bio-Community, an open-source, collaborative toolkit that extends BioPerl. Bio-Community interfaces with commonly used programs using various file formats, including BIOM, and provides operations such as rarefaction and taxonomic summaries. Bio-Community will help bioinformaticians to quickly piece together custom analysis pipelines and develop novel software. Availability an implementation: Bio-Community is cross-platform Perl code available from http://search.cpan.org/dist/Bio-Community under the Perl license. A readme file describes software installation and how to contribute. © The Author 2014. Published by Oxford University Press.

Fast-responding bio-based shape memory thermoplastic polyurethanes

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

Petrovic, Zoran S.; Milic, Jelena; Zhang, Fan

Fast response shape-memory polyurethanes were prepared from bio-based polyols, diphenyl methane diisocyanate and butane diol. The bio-based polyester polyols were synthesized from 9-hydroxynonanoic acid, a product obtained by ozonolysis of fatty acids extracted from soy oil and castor oil. The morphology of polyurethanes was investigated by synchrotron ultra-small angle X-ray scattering, which revealed the inter-domain spacing between the hard and soft phases, the degree of phase separation, and the level of intermixing between the hard and soft phases. We also conducted thorough investigations of the thermal, mechanical, and dielectric properties of the polyurethanes, and found that high crystallization rate ofmore » the soft segment gives these polyurethanes unique properties suitable for shapememory applications, such as adjustable transition temperatures, high degree of elastic elongations, and good mechanical strength. In conclusion, these materials are also potentially biodegradable and biocompatible, therefore suitable for biomedical and environmental applications.« less

Fast-responding bio-based shape memory thermoplastic polyurethanes

DOE PAGES

Petrovic, Zoran S.; Milic, Jelena; Zhang, Fan; ...

2017-05-31

Fast response shape-memory polyurethanes were prepared from bio-based polyols, diphenyl methane diisocyanate and butane diol. The bio-based polyester polyols were synthesized from 9-hydroxynonanoic acid, a product obtained by ozonolysis of fatty acids extracted from soy oil and castor oil. The morphology of polyurethanes was investigated by synchrotron ultra-small angle X-ray scattering, which revealed the inter-domain spacing between the hard and soft phases, the degree of phase separation, and the level of intermixing between the hard and soft phases. We also conducted thorough investigations of the thermal, mechanical, and dielectric properties of the polyurethanes, and found that high crystallization rate ofmore » the soft segment gives these polyurethanes unique properties suitable for shapememory applications, such as adjustable transition temperatures, high degree of elastic elongations, and good mechanical strength. In conclusion, these materials are also potentially biodegradable and biocompatible, therefore suitable for biomedical and environmental applications.« less

Fast-Responding Bio-Based Shape Memory Thermoplastic Polyurethanes.

PubMed

Petrović, Zoran S; Milić, Jelena; Zhang, Fan; Ilavsky, Jan

2017-07-14

Novel fast response shape-memory polyurethanes were prepared from bio-based polyols, diphenyl methane diisocyanate and butane diol for the first time. The bio-based polyester polyols were synthesized from 9-hydroxynonanoic acid, a product obtained by ozonolysis of fatty acids extracted from soy oil and castor oil. The morphology of polyurethanes was investigated by synchrotron ultra-small angle X-ray scattering, which revealed the inter-domain spacing between the hard and soft phases, the degree of phase separation, and the level of intermixing between the hard and soft phases. We also conducted thorough investigations of the thermal, mechanical, and dielectric properties of the polyurethanes, and found that high crystallization rate of the soft segment gives these polyurethanes unique properties suitable for shape-memory applications, such as adjustable transition temperatures, high degree of elastic elongations, and good mechanical strength. These materials are also potentially biodegradable and biocompatible, therefore suitable for biomedical and environmental applications.

Querying and Computing with BioCyc Databases

PubMed Central

Krummenacker, Markus; Paley, Suzanne; Mueller, Lukas; Yan, Thomas; Karp, Peter D.

2006-01-01

Summary We describe multiple methods for accessing and querying the complex and integrated cellular data in the BioCyc family of databases: access through multiple file formats, access through Application Program Interfaces (APIs) for LISP, Perl and Java, and SQL access through the BioWarehouse relational database. Availability The Pathway Tools software and 20 BioCyc DBs in Tiers 1 and 2 are freely available to academic users; fees apply to some types of commercial use. For download instructions see http://BioCyc.org/download.shtml PMID:15961440

New Horizons in Enhancing the Proliferation and Differentiation of Neural Stem Cells Using Stimulatory Effects of the Short Time Exposure to Radiofrequency Radiation

PubMed Central

Eghlidospour, M.; Mortazavi, S. M. J.; Yousefi, F.; Mortazavi, S. A. R.

2015-01-01

Mobile phone use and wireless communication technology have grown explosively over the past decades. This rapid growth has caused widespread global concern about the potential detrimental effects of this technology on human health. Stem cells generate specialized cell types of the tissue in which they reside through normal differentiation pathways. Considering the undeniable importance of stem cells in modern medicine, numerous studies have been performed on the effects of ionizing and non-ionizing radiation on cellular processes such as: proliferation, differentiation, cell cycle and DNA repair processes. We have conducted extensive studies on beneficial (stimulatory) or detrimental biological effects of exposure to different sources of electromagnetic fields such as mobile phones, mobile phone base stations, mobile phone jammers, radar systems, magnetic resonance imaging (MRI) systems and dentistry cavitrons over the past years. In this article, recent studies on the biological effects of non-ionizing electromagnetic radiation in the range of radiofrequency (RF) on some important features of stem cells such as their proliferation and differentiation are reviewed. Studies reviewed in this paper indicate that the stimulatory or inhibitory effects of RF radiation on the proliferation and differentiation of stem cells depend on various factors such as the biological systems, experiment conditions, the frequency and intensity of RF and the duration of exposure. PMID:26396965

New Horizons in Enhancing the Proliferation and Differentiation of Neural Stem Cells Using Stimulatory Effects of the Short Time Exposure to Radiofrequency Radiation.

PubMed

Eghlidospour, M; Mortazavi, S M J; Yousefi, F; Mortazavi, S A R

2015-09-01

Mobile phone use and wireless communication technology have grown explosively over the past decades. This rapid growth has caused widespread global concern about the potential detrimental effects of this technology on human health. Stem cells generate specialized cell types of the tissue in which they reside through normal differentiation pathways. Considering the undeniable importance of stem cells in modern medicine, numerous studies have been performed on the effects of ionizing and non-ionizing radiation on cellular processes such as: proliferation, differentiation, cell cycle and DNA repair processes. We have conducted extensive studies on beneficial (stimulatory) or detrimental biological effects of exposure to different sources of electromagnetic fields such as mobile phones, mobile phone base stations, mobile phone jammers, radar systems, magnetic resonance imaging (MRI) systems and dentistry cavitrons over the past years. In this article, recent studies on the biological effects of non-ionizing electromagnetic radiation in the range of radiofrequency (RF) on some important features of stem cells such as their proliferation and differentiation are reviewed. Studies reviewed in this paper indicate that the stimulatory or inhibitory effects of RF radiation on the proliferation and differentiation of stem cells depend on various factors such as the biological systems, experiment conditions, the frequency and intensity of RF and the duration of exposure.

Evaluation of the skin sensitization potential of chemicals using expression of co-stimulatory molecules, CD54 and CD86, on the naive THP-1 cell line.

PubMed

Yoshida, Y; Sakaguchi, H; Ito, Y; Okuda, M; Suzuki, H

2003-04-01

It has been known that dendritic cells (DCs) including Langerhans cells (LCs) play a critical role in the skin sensitization process. Many attempts have been made to develop in vitro sensitization tests that employ DCs derived from peripheral blood mononuclear cells (PBMC-DC) or CD34+ hematopoietic progenitor cells (CD34+ HPC) purified from cord blood or bone marrow. However, the use of the DCs in in vitro methods has been difficult due to the nature of these cells such as low levels in the source and/or donor-to-donor variability. In our studies, we employed the human monocytic leukemia cell line, THP-1, in order to avoid some of these difficulties. At the start, we examined whether treatment of the cells with various cytokines could produce DCs from THP-1. Treatment of THP-1 cells with cytokines such as GM-CSF, IL-4, TNF-alpha, and/or PMA did induce some phenotypic changes in THP-1 cells that were characteristic of DCs. Subsequently, responses to a known sensitizer, dinitrochlorobenzene (DNCB), and a non-sensitizer, dimethyl sulfoxide (DMSO) or sodium lauryl sulfate (SLS), on the expression of co-stimulatory molecules, CD54 and CD86, were examined between the naive cells and the cytokine-treated cells. Interestingly, the naive THP-1 cells responded only to DNCB and the response to the sensitizer was more distinct than cytokine-treated THP-1 cells. Similar phenomena were also observed in the human myeloid leukemia cell line, KG-1. Furthermore, with treatment of DNCB, naive THP-1 cells showed augmented expression of HLA, CD80 and secretion of IL-1 beta. The response of THP-1 cells to a sensitizer was similar to that of LCs/DCs. Upon demonstrating the differentiation of monocyte cells in our system, we then evaluated a series of chemicals, including known sensitizers and non-sensitizers, for their potential to augment CD54 and CD86 expression on naive THP-1 cells. Indeed, known sensitizers such as PPD and 2-MBT significantly augmented CD54 and CD86 expression in a

Biological and mechanical evaluation of a Bio-Hybrid scaffold for autologous valve tissue engineering.

PubMed

Jahnavi, S; Saravanan, U; Arthi, N; Bhuvaneshwar, G S; Kumary, T V; Rajan, S; Verma, R S

2017-04-01

Major challenge in heart valve tissue engineering for paediatric patients is the development of an autologous valve with regenerative capacity. Hybrid tissue engineering approach is recently gaining popularity to design scaffolds with desired biological and mechanical properties that can remodel post implantation. In this study, we fabricated aligned nanofibrous Bio-Hybrid scaffold made of decellularized bovine pericardium: polycaprolactone-chitosan with optimized polymer thickness to yield the desired biological and mechanical properties. CD44 + , αSMA + , Vimentin + and CD105 - human valve interstitial cells were isolated and seeded on these Bio-Hybrid scaffolds. Subsequent biological evaluation revealed interstitial cell proliferation with dense extra cellular matrix deposition that indicated the viability for growth and proliferation of seeded cells on the scaffolds. Uniaxial mechanical tests along axial direction showed that the Bio-Hybrid scaffolds has at least 20 times the strength of the native valves and its stiffness is nearly 3 times more than that of native valves. Biaxial and uniaxial mechanical studies on valve interstitial cells cultured Bio-Hybrid scaffolds revealed that the response along the axial and circumferential direction was different, similar to native valves. Overall, our findings suggest that Bio-Hybrid scaffold is a promising material for future development of regenerative heart valve constructs in children. Copyright © 2016 Elsevier B.V. All rights reserved.

Targeted Metabolomics Identifies Pharmacodynamic Biomarkers for BIO 300 Mitigation of Radiation-Induced Lung Injury.

PubMed

Jones, Jace W; Jackson, Isabel L; Vujaskovic, Zeljko; Kaytor, Michael D; Kane, Maureen A

2017-12-01

Biomarkers serve a number of purposes during drug development including defining the natural history of injury/disease, serving as a secondary endpoint or trigger for intervention, and/or aiding in the selection of an effective dose in humans. BIO 300 is a patent-protected pharmaceutical formulation of nanoparticles of synthetic genistein being developed by Humanetics Corporation. The primary goal of this metabolomic discovery experiment was to identify biomarkers that correlate with radiation-induced lung injury and BIO 300 efficacy for mitigating tissue damage based upon the primary endpoint of survival. High-throughput targeted metabolomics of lung tissue from male C57L/J mice exposed to 12.5 Gy whole thorax lung irradiation, treated daily with 400 mg/kg BIO 300 for either 2 weeks or 6 weeks starting 24 h post radiation exposure, were assayed at 180 d post-radiation to identify potential biomarkers. A panel of lung metabolites that are responsive to radiation and able to distinguish an efficacious treatment schedule of BIO 300 from a non-efficacious treatment schedule in terms of 180 d survival were identified. These metabolites represent potential biomarkers that could be further validated for use in drug development of BIO 300 and in the translation of dose from animal to human.

Bio-mimetic Flow Control

NASA Astrophysics Data System (ADS)

Choi, Haecheon

2009-11-01

Bio-mimetic engineering or bio-mimetics is the application of biological methods and systems found in nature to the study and design of engineering systems and modern technology (from Wikipedia). The concept itself is old, but successful developments have been made recently, especially in the research field of flow control. The objective of flow control based on the bio-mimetic approach is to develop novel concepts for reducing drag, increasing lift and enhancing aerodynamic performance. For skin friction reduction, a few ideas have been suggested such as the riblet from shark, compliant surface from dolphin, microbubble injection and multiple front-body curvature from penguin, and V-shaped protrusion from sailfish. For form drag reduction, several new attempts have been also made recently. Examples include the V-shaped spanwise grooves from saguaro cactus, overall shape of box fish, longitudinal grooves on scallop shell, bill of swordfish, hooked comb on owl wing, trailing-edge protrusion on dragonfly wing, and fillet. For the enhancement of aerodynamic performance, focuses have been made on the birds, fish and insects: e.g., double layered feather of landing bird, leading-edge serration of humpback-whale flipper, pectoral fin of flying fish, long tail on swallowtail-butterfly wing, wing flapping motion of dragonfly, and alula in birds. Living animals adapt their bodies to better performance in multi purposes, but engineering requires single purpose in most cases. Therefore, bio-mimetic approaches often produce excellent results more than expected. However, they are sometimes based on people's wrong understanding of nature and produce unwanted results. Successes and failures from bio-mimetic approaches in flow control will be discussed in the presentation.

Radiation Effects on the Immune Response to Prostate Cancer

DTIC Science & Technology

2008-02-01

as an alternative treatment since the discovery of prostate tumor-associated antigens (TAA) and of corresponding tumor-specific T cells in prostate...class I and co-stimulatory molecules, which could promote T cell filtration into tumors and T cell activation. On the other hand, we recently showed...immunotherapy (IT) has gained in popularity by finding some patients have specific T cell response to prostate tumor-associated antigens such as

Determination of Carbonyl Groups in Pyrolysis Bio-oils Using Potentiometric Titration: Review and Comparison of Methods

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

Black, Stuart; Ferrell, Jack R.

Carbonyl compounds present in bio-oils are known to be responsible for bio-oil property changes upon storage and during upgrading. As such, carbonyl content has previously been used as a method of tracking bio-oil aging and condensation reactions with less variability than viscosity measurements. Given the importance of carbonyls in bio-oils, accurate analytical methods for their quantification are very important for the bio-oil community. Potentiometric titration methods based on carbonyl oximation have long been used for the determination of carbonyl content in pyrolysis bio-oils. Here in this study, we present a modification of the traditional carbonyl oximation procedures that results inmore » less reaction time, smaller sample size, higher precision, and more accurate carbonyl determinations. Some compounds such as carbohydrates are not measured by the traditional method (modified Nicolaides method), resulting in low estimations of the carbonyl content. Furthermore, we have shown that reaction completion for the traditional method can take up to 300 hours. The new method presented here (the modified Faix method) reduces the reaction time to 2 hours, uses triethanolamine (TEA) in the place of pyridine, and requires a smaller sample size for the analysis. Carbonyl contents determined using this new method are consistently higher than when using the traditional titration methods.« less

Determination of Carbonyl Groups in Pyrolysis Bio-oils Using Potentiometric Titration: Review and Comparison of Methods

DOE PAGES

Black, Stuart; Ferrell, Jack R.

2016-01-06

Carbonyl compounds present in bio-oils are known to be responsible for bio-oil property changes upon storage and during upgrading. As such, carbonyl content has previously been used as a method of tracking bio-oil aging and condensation reactions with less variability than viscosity measurements. Given the importance of carbonyls in bio-oils, accurate analytical methods for their quantification are very important for the bio-oil community. Potentiometric titration methods based on carbonyl oximation have long been used for the determination of carbonyl content in pyrolysis bio-oils. Here in this study, we present a modification of the traditional carbonyl oximation procedures that results inmore » less reaction time, smaller sample size, higher precision, and more accurate carbonyl determinations. Some compounds such as carbohydrates are not measured by the traditional method (modified Nicolaides method), resulting in low estimations of the carbonyl content. Furthermore, we have shown that reaction completion for the traditional method can take up to 300 hours. The new method presented here (the modified Faix method) reduces the reaction time to 2 hours, uses triethanolamine (TEA) in the place of pyridine, and requires a smaller sample size for the analysis. Carbonyl contents determined using this new method are consistently higher than when using the traditional titration methods.« less

Past, Present, and Future Production of Bio-oil

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

Steele, Philip; Yu, Fei; Gajjela, Sanjeev

Bio-oil is a liquid product produced by fast pyrol-ysis of biomass. The fast pyrolysis is performed by heating the biomass rapidly (2 sec) at temperatures ranging from 350 to 650 oC. The vapors produced by this rapid heating are then condensed to produce a dark brown water-based emulsion composed of frag-ments of the original hemicellulose, cellulose and lignin molecules contained in the biomass. Yields range from 60 to 75% based on the feedstock type and the pyrolysis reactor employed. The bio-oil pro-duced by this process has a number of negative prop-erties that are produced mainly by the high oxygen contentmore » (40 to 50%) contributed by that contained in water (25 to 30% of total mass) and oxygenated compounds. Each bio-oil contains hundreds of chemi-cal compounds. The chemical composition of bio-oil renders it a very recalcitrant chemical compound. To date, the difficulties in utilizing bio-oil have limited its commercial development to the production of liq-uid smoke as food flavoring. Practitioners have at-tempted to utilize raw bio-oil as a fuel; they have also applied many techniques to upgrade bio-oil to a fuel. Attempts to utilize raw bio-oil as a combustion engine fuel have resulted in engine or turbine dam-age; however, Stirling engines have been shown to successfully combust raw bio-oil without damage. Utilization of raw bio-oil as a boiler fuel has met with more success and an ASTM standard has recently been released describing bio-oil characteristics in relation to assigned fuel grades. However, commercialization has been slow to follow and no reports of distribution of these bio-oil boiler fuels have been reported. Co-feeding raw bio-oil with coal has been successfully performed but no current power generation facilities are following this practice. Upgrading of bio-oils to hydrocarbons via hydroprocessing is being performed by several organizations. Currently, limited catalyst life is the obstacle to commercialization of this tech

GPER, IGF-IR, and EGFR transduction signaling are involved in stimulatory effects of zinc in breast cancer cells and cancer-associated fibroblasts.

PubMed

Pisano, Assunta; Santolla, Maria Francesca; De Francesco, Ernestina Marianna; De Marco, Paola; Rigiracciolo, Damiano Cosimo; Perri, Maria Grazia; Vivacqua, Adele; Abonante, Sergio; Cappello, Anna Rita; Dolce, Vincenza; Belfiore, Antonino; Maggiolini, Marcello; Lappano, Rosamaria

2017-02-01

Zinc (Zn) is an essential trace mineral that contributes to the regulation of several cellular functions; however, it may be also implicated in the progression of breast cancer through different mechanisms. It has been largely reported that the classical estrogen receptor (ER), as well as the G protein estrogen receptor (GPER, previously known as GPR30) can exert a main role in the development of breast tumors. In the present study, we demonstrate that zinc chloride (ZnCl 2 ) involves GPER in the activation of insulin-like growth factor receptor I (IGF-IR)/epidermal growth factor receptor (EGFR)-mediated signaling, which in turn triggers downstream pathways like ERK and AKT in breast cancer cells, and main components of the tumor microenvironment namely cancer-associated fibroblasts (CAFs). Further corroborating these findings, ZnCl 2 stimulates a functional crosstalk of GPER with IGF-IR and EGFR toward the transcription of diverse GPER target genes. Then, we show that GPER contributes to the stimulatory effects induced by ZnCl 2 on cell-cycle progression, proliferation, and migration of breast cancer cells as well as migration of CAFs. Together, our data provide novel insights into the molecular mechanisms through which zinc may exert stimulatory effects in breast cancer cells and CAFs toward tumor progression. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

BioC implementations in Go, Perl, Python and Ruby

PubMed Central

Liu, Wanli; Islamaj Doğan, Rezarta; Kwon, Dongseop; Marques, Hernani; Rinaldi, Fabio; Wilbur, W. John; Comeau, Donald C.

2014-01-01

As part of a communitywide effort for evaluating text mining and information extraction systems applied to the biomedical domain, BioC is focused on the goal of interoperability, currently a major barrier to wide-scale adoption of text mining tools. BioC is a simple XML format, specified by DTD, for exchanging data for biomedical natural language processing. With initial implementations in C++ and Java, BioC provides libraries of code for reading and writing BioC text documents and annotations. We extend BioC to Perl, Python, Go and Ruby. We used SWIG to extend the C++ implementation for Perl and one Python implementation. A second Python implementation and the Ruby implementation use native data structures and libraries. BioC is also implemented in the Google language Go. BioC modules are functional in all of these languages, which can facilitate text mining tasks. BioC implementations are freely available through the BioC site: http://bioc.sourceforge.net. Database URL: http://bioc.sourceforge.net/ PMID:24961236

Sustainability, polysaccharide science, and bio-economy.

PubMed

ten Bos, René; van Dam, Jan E G

2013-03-01

At the opening of the 2nd EPNOE conference the role and responsibility of polysaccharide scientists was reflected upon and placed in the context of actual global issues like the transition process towards "sustainable bio-economy". Difficulties in the chain of communication between the different parties involved and towards the wider public was addressed. The need for change in the relations between science and the public and to go beyond the horizon of the specialization was discussed. It was stated that polysaccharide science is one of the key sciences in those transitions. Copyright © 2012 Elsevier Ltd. All rights reserved.

Recycling used palm oil and used engine oil to produce white bio oil, bio petroleum diesel and heavy fuel

NASA Astrophysics Data System (ADS)

Al-abbas, Mustafa Hamid; Ibrahim, Wan Aini Wan; Sanagi, Mohd. Marsin

2012-09-01

Recycling waste materials produced in our daily life is considered as an additional resource of a wide range of materials and it conserves the environment. Used engine oil and used cooking oil are two oils disposed off in large quantities as a by-product of our daily life. This study aims at providing white bio oil, bio petroleum diesel and heavy fuel from the disposed oils. Toxic organic materials suspected to be present in the used engine oil were separated using vacuum column chromatography to reduce the time needed for the separation process and to avoid solvent usage. The compounds separated were detected by gas chromatography-mass spectrometry (GC-MS) and found to contain toxic aromatic carboxylic acids. Used cooking oils (thermally cracked from usage) were collected and separated by vacuum column chromatography. White bio oil produced was examined by GC-MS. The white bio oil consists of non-toxic hydrocarbons and is found to be a good alternative to white mineral oil which is significantly used in food industry, cosmetics and drugs with the risk of containing polycyclic aromatic compounds which are carcinogenic and toxic. Different portions of the used cooking oil and used engine were mixed to produce several blends for use as heavy oil fuels. White bio oil was used to produce bio petroleum diesel by blending it with petroleum diesel and kerosene. The bio petroleum diesel produced passed the PETRONAS flash point and viscosity specification test. The heat of combustion of the two blends of heavy fuel produced was measured and one of the blends was burned to demonstrate its burning ability. Higher heat of combustion was obtained from the blend containing greater proportion of used engine oil. This study has provided a successful recycled alternative for white bio oil, bio petroleum fuel and diesel which can be an energy source.

Core ethical values: EuropaBio.

PubMed

2002-01-01

EuropaBio, the European Association for BioIndustries, represents 40 companies operating world wide and 14 national association (totaling around 600 small and medium-sized enterprises) involved in the research, development, testing, manufacturing, marketing, sales and distribution of biotechnology products and services in the fields of healthcare, agriculture, food and the environment.

Preliminary investigation on the production of fuels and bio-char from Chlamydomonas reinhardtii biomass residue after bio-hydrogen production.

PubMed

Torri, Cristian; Samorì, Chiara; Adamiano, Alessio; Fabbri, Daniele; Faraloni, Cecilia; Torzillo, Giuseppe

2011-09-01

The aim of this work was to investigate the potential conversion of Chlamydomonas reinhardtii biomass harvested after hydrogen production. The spent algal biomass was converted into nitrogen-rich bio-char, biodiesel and pyrolysis oil (bio-oil). The yield of lipids (algal oil), obtained by solvent extraction, was 15 ± 2% w/w(dry-biomass). This oil was converted into biodiesel with a 8.7 ± 1% w/w(dry-biomass) yield. The extraction residue was pyrolysed in a fixed bed reactor at 350 °C obtaining bio-char as the principal fraction (44 ± 1% w/w(dry-biomass)) and 28 ± 2% w/w(dry-biomass) of bio-oil. Pyrolysis fractions were characterized by elemental analysis, while the chemical composition of bio-oil was fully characterized by GC-MS, using various derivatization techniques. Energy outputs resulting from this approach were distributed in hydrogen (40%), biodiesel (12%) and pyrolysis fractions (48%), whereas bio-char was the largest fraction in terms of mass. Copyright © 2011 Elsevier Ltd. All rights reserved.

Biochemical responses of isolated lung CSCs after application of low intensity laser irradiation

NASA Astrophysics Data System (ADS)

Abrahamse, Heidi; Crous, Anine

2016-03-01

Studies have shown that using high fluences of Low Intensity Laser Irradiation (HF-LILI) produce apoptotic effects on normal and neoplastic cells. This study aimed to determine whether HF-LILI induce cell death in lung CSCs. Lung CSCs were isolated using the stem cell marker CD 133, characterized using flow cytometry, and applied in experiments which included treatment with LILI at wavelengths of 636, 825 and 1060 nm with fluences ranging from 5 J/cm2 to 40 J/cm2. Viability and proliferation studies, using Alamar blue assay and adenosine triphosphate luminescence (ATP), indicated an increase when treating lung CSCs with low fluences of 5 - 20 J/cm2 and a decrease in viability and proliferation as well as an increase in apoptosis when applying a fluence of 40 J/cm2 indicated by flow cytometry using Annexin V and propidium iodide (PI) dyes. Results indicate that LILI, when treating lung CSCs, can induce either a bio-stimulatory or bio-inhibitory effect depending on the wavelength and fluence used. This study indicated successful apoptotic induction of lung CSCs. Future experiments should be able to conclude the exact mechanism behind HF-LILI, which can be used in the targeted treatments of CSC elimination, implementing HF-LILI in the same manner as PDT in the absence of a photosensitizer.

Bio-stimuli-responsive multi-scale hyaluronic acid nanoparticles for deepened tumor penetration and enhanced therapy.

PubMed

Huo, Mengmeng; Li, Wenyan; Chaudhuri, Arka Sen; Fan, Yuchao; Han, Xiu; Yang, Chen; Wu, Zhenghong; Qi, Xiaole

2017-09-01

In this study, we developed bio-stimuli-responsive multi-scale hyaluronic acid (HA) nanoparticles encapsulated with polyamidoamine (PAMAM) dendrimers as the subunits. These HA/PAMAM nanoparticles of large scale (197.10±3.00nm) were stable during systematic circulation then enriched at the tumor sites; however, they were prone to be degraded by the high expressed hyaluronidase (HAase) to release inner PAMAM dendrimers and regained a small scale (5.77±0.25nm) with positive charge. After employing tumor spheroids penetration assay on A549 3D tumor spheroids for 8h, the fluorescein isothiocyanate (FITC) labeled multi-scale HA/PAMAM-FITC nanoparticles could penetrate deeply into these tumor spheroids with the degradation of HAase. Moreover, small animal imaging technology in male nude mice bearing H22 tumor showed HA/PAMAM-FITC nanoparticles possess higher prolonged systematic circulation compared with both PAMAM-FITC nanoparticles and free FITC. In addition, after intravenous administration in mice bearing H22 tumors, methotrexate (MTX) loaded multi-scale HA/PAMAM-MTX nanoparticles exhibited a 2.68-fold greater antitumor activity. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Development and perspective of bio-based chemical fiber industry].

PubMed

Li, Zengjun

2016-06-25

Bio-based fiber is environment friendly, reproducible, easily biodegradable. Therefore, rapid development of bio-based fiber industry is an obvious in progress to replace petrochemical resources, develop sustainable economy, build resource saving and environment friendly society. This article describes the current development of bio-based fiber industry, analyzes existing problems, indicates the trends and objectives of bio-based fiber materials technology innovation and recommends developing bio-based fibers industry of our country.

Promotion of hydrogen-rich gas and phenolic-rich bio-oil production from green macroalgae Cladophora glomerata via pyrolysis over its bio-char.

PubMed

Norouzi, Omid; Jafarian, Sajedeh; Safari, Farid; Tavasoli, Ahmad; Nejati, Behnam

2016-11-01

Conversion of Cladophora glomerata (C. glomerata) as a Caspian Sea's green macroalgae into gaseous, liquid and solid products was carried out via pyrolysis at different temperatures to determine its potential for bio-oil and hydrogen-rich gas production for further industrial utilization. Non-catalytic tests were performed to determine the optimum condition for bio-oil production. The highest portion of bio-oil was retrieved at 500°C. The catalytic test was performed using the bio-char derived at 500°C as a catalyst. Effect of the addition of the algal bio-char on the composition of the bio-oil and also gaseous products was investigated. Pyrolysis derived bio-char was characterized by BET, FESEM and ICP method to show its surface area, porosity, and presence of inorganic metals on its surface, respectively. Phenols were increased from 8.5 to 20.76area% by the addition of bio-char. Moreover, the hydrogen concentration and hydrogen selectivity were also enhanced by the factors of 1.37, 1.59 respectively. Copyright © 2016 Elsevier Ltd. All rights reserved.

The BioGRID interaction database: 2013 update.

PubMed

Chatr-Aryamontri, Andrew; Breitkreutz, Bobby-Joe; Heinicke, Sven; Boucher, Lorrie; Winter, Andrew; Stark, Chris; Nixon, Julie; Ramage, Lindsay; Kolas, Nadine; O'Donnell, Lara; Reguly, Teresa; Breitkreutz, Ashton; Sellam, Adnane; Chen, Daici; Chang, Christie; Rust, Jennifer; Livstone, Michael; Oughtred, Rose; Dolinski, Kara; Tyers, Mike

2013-01-01

The Biological General Repository for Interaction Datasets (BioGRID: http//thebiogrid.org) is an open access archive of genetic and protein interactions that are curated from the primary biomedical literature for all major model organism species. As of September 2012, BioGRID houses more than 500 000 manually annotated interactions from more than 30 model organisms. BioGRID maintains complete curation coverage of the literature for the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe and the model plant Arabidopsis thaliana. A number of themed curation projects in areas of biomedical importance are also supported. BioGRID has established collaborations and/or shares data records for the annotation of interactions and phenotypes with most major model organism databases, including Saccharomyces Genome Database, PomBase, WormBase, FlyBase and The Arabidopsis Information Resource. BioGRID also actively engages with the text-mining community to benchmark and deploy automated tools to expedite curation workflows. BioGRID data are freely accessible through both a user-defined interactive interface and in batch downloads in a wide variety of formats, including PSI-MI2.5 and tab-delimited files. BioGRID records can also be interrogated and analyzed with a series of new bioinformatics tools, which include a post-translational modification viewer, a graphical viewer, a REST service and a Cytoscape plugin.

Optical and electrical interfacing technologies for living cell bio-chips.

PubMed

Shacham-Diamand, Y; Belkin, S; Rishpon, J; Elad, T; Melamed, S; Biran, A; Yagur-Kroll, S; Almog, R; Daniel, R; Ben-Yoav, H; Rabner, A; Vernick, S; Elman, N; Popovtzer, R

2010-06-01

Whole-cell bio-chips for functional sensing integrate living cells on miniaturized platforms made by micro-system-technologies (MST). The cells are integrated, deposited or immersed in a media which is in contact with the chip. The cells behavior is monitored via electrical, electrochemical or optical methods. In this paper we describe such whole-cell biochips where the signal is generated due to the genetic response of the cells. The solid-state platform hosts the biological component, i.e. the living cells, and integrates all the required micro-system technologies, i.e. the micro-electronics, micro-electro optics, micro-electro or magneto mechanics and micro-fluidics. The genetic response of the cells expresses proteins that generate: a. light by photo-luminescence or bioluminescence, b. electrochemical signal by interaction with a substrate, or c. change in the cell impedance. The cell response is detected by a front end unit that converts it to current or voltage amplifies and filters it. The resultant signal is analyzed and stored for further processing. In this paper we describe three examples of whole-cell bio chips, photo-luminescent, bioluminescent and electrochemical, which are based on the genetic response of genetically modified E. coli microbes integrated on a micro-fluidics MEMS platform. We describe the chip outline as well as the basic modeling scheme of such sensors. We discuss the highlights and problems of such system, from the point of view of micro-system-technology.

An In vitro Study of Bio-Control and Plant Growth Promotion Potential of Salicaceae Endophytes.

PubMed

Kandel, Shyam L; Firrincieli, Andrea; Joubert, Pierre M; Okubara, Patricia A; Leston, Natalie D; McGeorge, Kendra M; Mugnozza, Giuseppe S; Harfouche, Antoine; Kim, Soo-Hyung; Doty, Sharon L

2017-01-01

Microbial communities in the endosphere of Salicaceae plants, poplar ( Populus trichocarpa ) and willow ( Salix sitchensis ), have been demonstrated to be important for plant growth promotion, protection from biotic and abiotic stresses, and degradation of toxic compounds. Our study aimed to investigate bio-control activities of Salicaceae endophytes against various soil borne plant pathogens including Rhizoctonia solani AG-8, Fusarium culmorum, Gaeumannomyces graminis var. tritici , and Pythium ultimum . Additionally, different plant growth promoting traits such as biological nitrogen fixation (BNF), indole-3-acetic acid (IAA) biosynthesis, phosphate solubilization, and siderophore production were assessed in all bio-control positive strains. Burkholderia, Rahnella, Pseudomonas , and Curtobacterium were major endophyte genera that showed bio-control activities in the in-vitro assays. The bio-control activities of Burkholderia strains were stronger across all tested plant pathogens as compared to other stains. Genomes of sequenced Burkholderia strains WP40 and WP42 were surveyed to identify the putative genes involved in the bio-control activities. The ocf and hcnABC gene clusters responsible for biosynthesis of the anti-fungal metabolites, occidiofungin and hydrogen cyanide, are present in the genomes of WP40 and WP42. Nearly all endophyte strains showing the bio-control activities produced IAA, solubilized tricalcium phosphate, and synthesized siderophores in the culture medium. Moreover, some strains reduced acetylene into ethylene in the acetylene reduction assay, a common assay used for BNF. Salicaceae endophytes could be useful for bio-control of various plant pathogens, and plant growth promotion possibly through the mechanisms of BNF, IAA production, and nutrient acquisition.

BioNet Digital Communications Framework

NASA Technical Reports Server (NTRS)

Gifford, Kevin; Kuzminsky, Sebastian; Williams, Shea

2010-01-01

BioNet v2 is a peer-to-peer middleware that enables digital communication devices to talk to each other. It provides a software development framework, standardized application, network-transparent device integration services, a flexible messaging model, and network communications for distributed applications. BioNet is an implementation of the Constellation Program Command, Control, Communications and Information (C3I) Interoperability specification, given in CxP 70022-01. The system architecture provides the necessary infrastructure for the integration of heterogeneous wired and wireless sensing and control devices into a unified data system with a standardized application interface, providing plug-and-play operation for hardware and software systems. BioNet v2 features a naming schema for mobility and coarse-grained localization information, data normalization within a network-transparent device driver framework, enabling of network communications to non-IP devices, and fine-grained application control of data subscription band width usage. BioNet directly integrates Disruption Tolerant Networking (DTN) as a communications technology, enabling networked communications with assets that are only intermittently connected including orbiting relay satellites and planetary rover vehicles.

Bio-based Hydraulic Fluids

DTIC Science & Technology

2008-04-17

DEHULL, FLAKE HEXANE EXTRACTION PRESS HEXANE DISTILLATION CRUDE OIL 0.1-3% phosphatides 1% fatty acids 1 ppm chlorophyll DEGUM (H2 O, H3 PO4...program www.bfrl.nist.gov/oae/bees.html 617 April 2008 Seed Oils and Their Fatty Acid and Genetic Varieties Source: Leissner, O. et al (1989) Vegetable...Oils and Fats, Karlshammn, Sweden 717 April 2008 Bio-based Oil Process Volatile impurities: odor (aldehydes & ketones) fatty acids Bio-based Oil CRACK

Upgrading biomass pyrolysis bio-oil to renewable fuels.

DOT National Transportation Integrated Search

2015-01-01

Fast pyrolysis is a process that can convert woody biomass to a crude bio-oil (pyrolysis oil). However, some of these compounds : contribute to bio-oil shelf life instability and difficulty in refining. Catalytic hydrodeoxygenation (HDO) of the bio-o...

Dry electrode bio-potential recordings.

PubMed

Gargiulo, Gaetano; Bifulco, Paolo; McEwan, Alistair; Nasehi Tehrani, Joubin; Calvo, Rafael A; Romano, Maria; Ruffo, Mariano; Shephard, Richard; Cesarelli, Mario; Jin, Craig; Mohamed, Armin; van Schaik, André

2010-01-01

As wireless bio-medical long term monitoring moves towards personal monitoring it demands very high input impedance systems capable to extend the reading of bio-signal during the daily activities offering a kind of "stress free", convenient connection, with no need for skin preparation. In particular we highlight the development and broad applications of our own circuits for wearable bio-potential sensor systems enabled by the use of an FET based amplifier circuit with sufficiently high impedance to allow the use of passive dry electrodes which overcome the significant barrier of gel based contacts. In this paper we present the ability of dry electrodes in long term monitoring of ECG, EEG and fetal ECG.

BioC implementations in Go, Perl, Python and Ruby.

PubMed

Liu, Wanli; Islamaj Doğan, Rezarta; Kwon, Dongseop; Marques, Hernani; Rinaldi, Fabio; Wilbur, W John; Comeau, Donald C

2014-01-01

As part of a communitywide effort for evaluating text mining and information extraction systems applied to the biomedical domain, BioC is focused on the goal of interoperability, currently a major barrier to wide-scale adoption of text mining tools. BioC is a simple XML format, specified by DTD, for exchanging data for biomedical natural language processing. With initial implementations in C++ and Java, BioC provides libraries of code for reading and writing BioC text documents and annotations. We extend BioC to Perl, Python, Go and Ruby. We used SWIG to extend the C++ implementation for Perl and one Python implementation. A second Python implementation and the Ruby implementation use native data structures and libraries. BioC is also implemented in the Google language Go. BioC modules are functional in all of these languages, which can facilitate text mining tasks. BioC implementations are freely available through the BioC site: http://bioc.sourceforge.net. Database URL: http://bioc.sourceforge.net/ Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

[Bio-oil production from biomass pyrolysis in molten salt].

PubMed

Ji, Dengxiang; Cai, Tengyue; Ai, Ning; Yu, Fengwen; Jiang, Hongtao; Ji, Jianbing

2011-03-01

In order to investigate the effects of pyrolysis conditions on bio-oil production from biomass in molten salt, experiments of biomass pyrolysis were carried out in a self-designed reactor in which the molten salt ZnCl2-KCl (with mole ratio 7/6) was selected as heat carrier, catalyst and dispersion agent. The effects of metal salt added into ZnCl2-KCl and biomass material on biomass pyrolysis were discussed, and the main compositions of bio-oil were determined by GC-MS. Metal salt added into molten salt could affect pyrolysis production yields remarkably. Lanthanon salt could enhance bio-oil yield and decrease water content in bio-oil, when mole fraction of 5.0% LaCl3 was added, bio-oil yield could reach up to 32.0%, and water content of bio-oil could reduce to 61.5%. The bio-oil and char yields were higher when rice straw was pyrolysed, while gas yield was higher when rice husk was used. Metal salts showed great selectivity on compositions of bio-oil. LiCl and FeCl2 promoted biomass to pyrolyse into smaller molecular weight compounds. CrCl3, CaCl2 and LaCl3 could restrain second pyrolysis of bio-oil. The research provided a scientific reference for production of bio-oil from biomass pyrolysis in molten salt.

A Bio-Realistic Analog CMOS Cochlea Filter With High Tunability and Ultra-Steep Roll-Off.

PubMed

Wang, Shiwei; Koickal, Thomas Jacob; Hamilton, Alister; Cheung, Rebecca; Smith, Leslie S

2015-06-01

This paper presents the design and experimental results of a cochlea filter in analog very large scale integration (VLSI) which highly resembles physiologically measured response of the mammalian cochlea. The filter consists of three specialized sub-filter stages which respectively provide passive response in low frequencies, actively tunable response in mid-band frequencies and ultra-steep roll-off at transition frequencies from pass-band to stop-band. The sub-filters are implemented in balanced ladder topology using floating active inductors. Measured results from the fabricated chip show that wide range of mid-band tuning including gain tuning of over 20 dB, Q factor tuning from 2 to 19 as well as the bio-realistic center frequency shift are achieved by adjusting only one circuit parameter. Besides, the filter has an ultra-steep roll-off reaching over 300 dB/dec. By changing biasing currents, the filter can be configured to operate with center frequencies from 31 Hz to 8 kHz. The filter is 9th order, consumes 59.5 ∼ 90.0 μW power and occupies 0.9 mm2 chip area. A parallel bank of the proposed filter can be used as the front-end in hearing prosthesis devices, speech processors as well as other bio-inspired auditory systems owing to its bio-realistic behavior, low power consumption and small size.

PubChem BioAssay: 2017 update

PubMed Central

Wang, Yanli; Bryant, Stephen H.; Cheng, Tiejun; Wang, Jiyao; Gindulyte, Asta; Shoemaker, Benjamin A.; Thiessen, Paul A.; He, Siqian; Zhang, Jian

2017-01-01

PubChem's BioAssay database (https://pubchem.ncbi.nlm.nih.gov) has served as a public repository for small-molecule and RNAi screening data since 2004 providing open access of its data content to the community. PubChem accepts data submission from worldwide researchers at academia, industry and government agencies. PubChem also collaborates with other chemical biology database stakeholders with data exchange. With over a decade's development effort, it becomes an important information resource supporting drug discovery and chemical biology research. To facilitate data discovery, PubChem is integrated with all other databases at NCBI. In this work, we provide an update for the PubChem BioAssay database describing several recent development including added sources of research data, redesigned BioAssay record page, new BioAssay classification browser and new features in the Upload system facilitating data sharing. PMID:27899599

Design of pyrolysis reactor for production of bio-oil and bio-char simultaneously

NASA Astrophysics Data System (ADS)

Aladin, Andi; Alwi, Ratna Surya; Syarif, Takdir

2017-05-01

The residues from the wood industry are the main contributors to biomass waste in Indonesia. The conventional pyrolysis process, which needs a large energy as well as to produce various toxic chemical to the environment. Therefore, a pyrolysis unit on the laboratory scale was designed that can be a good alternative to achieve zero-waste and low energy cost. In this paper attempts to discuss design and system of pyrolysis reactor to produce bio-oil and bio-char simultaneously.

Canine Distemper Virus Infection Leads to an Inhibitory Phenotype of Monocyte-Derived Dendritic Cells In Vitro with Reduced Expression of Co-Stimulatory Molecules and Increased Interleukin-10 Transcription

PubMed Central

Herder, Vanessa; Stein, Veronika M.; Tipold, Andrea; Urhausen, Carola; Günzel-Apel, Anne-Rose; Rohn, Karl; Baumgärtner, Wolfgang; Beineke, Andreas

2014-01-01

Canine distemper virus (CDV) exhibits a profound lymphotropism that causes immunosuppression and increased susceptibility of affected dogs to opportunistic infections. Similar to human measles virus, CDV is supposed to inhibit terminal differentiation of dendritic cells (DCs), responsible for disturbed repopulation of lymphoid tissues and diminished antigen presenting function in dogs. In order to testify the hypothesis that CDV-infection leads to an impairment of professional antigen presenting cells, canine DCs have been generated from peripheral blood monocytes in vitro and infected with CDV. Virus infection was confirmed and quantified by transmission electron microscopy, CDV-specific immunofluorescence, and virus titration. Flow cytometric analyses revealed a significant down-regulation of the major histocompatibility complex class II and co-stimulatory molecules CD80 and CD86 in CDV-infected DCs, indicative of disturbed antigen presenting capacity. Molecular analyses revealed an increased expression of the immune inhibitory cytokine interleukin-10 in DCs following infection. Results of the present study demonstrate that CDV causes phenotypical changes and altered cytokine expression of DCs, which represent potential mechanisms to evade host immune responses and might contribute to immune dysfunction and virus persistence in canine distemper. PMID:24769532

Canine distemper virus infection leads to an inhibitory phenotype of monocyte-derived dendritic cells in vitro with reduced expression of co-stimulatory molecules and increased interleukin-10 transcription.

PubMed

Qeska, Visar; Barthel, Yvonne; Herder, Vanessa; Stein, Veronika M; Tipold, Andrea; Urhausen, Carola; Günzel-Apel, Anne-Rose; Rohn, Karl; Baumgärtner, Wolfgang; Beineke, Andreas

2014-01-01

Canine distemper virus (CDV) exhibits a profound lymphotropism that causes immunosuppression and increased susceptibility of affected dogs to opportunistic infections. Similar to human measles virus, CDV is supposed to inhibit terminal differentiation of dendritic cells (DCs), responsible for disturbed repopulation of lymphoid tissues and diminished antigen presenting function in dogs. In order to testify the hypothesis that CDV-infection leads to an impairment of professional antigen presenting cells, canine DCs have been generated from peripheral blood monocytes in vitro and infected with CDV. Virus infection was confirmed and quantified by transmission electron microscopy, CDV-specific immunofluorescence, and virus titration. Flow cytometric analyses revealed a significant down-regulation of the major histocompatibility complex class II and co-stimulatory molecules CD80 and CD86 in CDV-infected DCs, indicative of disturbed antigen presenting capacity. Molecular analyses revealed an increased expression of the immune inhibitory cytokine interleukin-10 in DCs following infection. Results of the present study demonstrate that CDV causes phenotypical changes and altered cytokine expression of DCs, which represent potential mechanisms to evade host immune responses and might contribute to immune dysfunction and virus persistence in canine distemper.

Stinging plants: as future bio-weapon.

PubMed

Gupta, Sanjay Mohan; Kumar, Kamal

2016-09-01

In the present opinion paper, we have been introducing for the first time the stinging plants and/or their biological toxins as novel bio-threat agents that may be used for the development of bio-weapons for self-defence purpose. The selected studied stinging plants are having dual role as nutraceutical and ethno-pharmacological uses apart from their less explored stinging property. However, future detailed work is required for identification and characterization of the precise stinging chemical components that will be used for the formulation of novel bio-warfare agents for self-defence purpose.

BioBlend.objects: metacomputing with Galaxy.

PubMed

Leo, Simone; Pireddu, Luca; Cuccuru, Gianmauro; Lianas, Luca; Soranzo, Nicola; Afgan, Enis; Zanetti, Gianluigi

2014-10-01

BioBlend.objects is a new component of the BioBlend package, adding an object-oriented interface for the Galaxy REST-based application programming interface. It improves support for metacomputing on Galaxy entities by providing higher-level functionality and allowing users to more easily create programs to explore, query and create Galaxy datasets and workflows. BioBlend.objects is available online at https://github.com/afgane/bioblend. The new object-oriented API is implemented by the galaxy/objects subpackage. © The Author 2014. Published by Oxford University Press.

Stimulatory Effects of Arsenic-Tolerant Soil Fungi on Plant Growth Promotion and Soil Properties

PubMed Central

Srivastava, Pankaj Kumar; Shenoy, Belle Damodara; Gupta, Manjul; Vaish, Aradhana; Mannan, Shivee; Singh, Nandita; Tewari, Shri Krishna; Tripathi, Rudra Deo

2012-01-01

Fifteen fungi were obtained from arsenic-contaminated agricultural fields in West Bengal, India and examined for their arsenic tolerance and removal ability in our previous study. Of these, the four best arsenic-remediating isolates were tested for plant growth promotion effects on rice and pea in the present study. A greenhouse-based pot experiment was conducted using soil inocula of individual fungi. The results indicated a significant (P<0.05) increase in plant growth and improvement of soil properties in inoculated soils compared to the control. A significant increase in plant growth was recorded in treated soils and varied from 16–293%. Soil chemical and enzymatic properties varied from 20–222% and 34–760%, respectively, in inoculated soil. Plants inoculated with inocula of Westerdykella and Trichoderma showed better stimulatory effects on plant growth and soil nutrient availability than Rhizopus and Lasiodiplodia. These fungi improved soil nutrient content and enhanced plant growth. These fungi may be used as bioinoculants for plant growth promotion and improved soil properties in arsenic-contaminated agricultural soils. PMID:23047145

Stimulatory effects of arsenic-tolerant soil fungi on plant growth promotion and soil properties.

PubMed

Srivastava, Pankaj Kumar; Shenoy, Belle Damodara; Gupta, Manjul; Vaish, Aradhana; Mannan, Shivee; Singh, Nandita; Tewari, Shri Krishna; Tripathi, Rudra Deo

2012-01-01

Fifteen fungi were obtained from arsenic-contaminated agricultural fields in West Bengal, India and examined for their arsenic tolerance and removal ability in our previous study. Of these, the four best arsenic-remediating isolates were tested for plant growth promotion effects on rice and pea in the present study. A greenhouse-based pot experiment was conducted using soil inocula of individual fungi. The results indicated a significant (P<0.05) increase in plant growth and improvement of soil properties in inoculated soils compared to the control. A significant increase in plant growth was recorded in treated soils and varied from 16-293%. Soil chemical and enzymatic properties varied from 20-222% and 34-760%, respectively, in inoculated soil. Plants inoculated with inocula of Westerdykella and Trichoderma showed better stimulatory effects on plant growth and soil nutrient availability than Rhizopus and Lasiodiplodia. These fungi improved soil nutrient content and enhanced plant growth. These fungi may be used as bioinoculants for plant growth promotion and improved soil properties in arsenic-contaminated agricultural soils.

Stimulatory action of itopride hydrochloride on colonic motor activity in vitro and in vivo.

PubMed

Tsubouchi, Tadashi; Saito, Takaharu; Mizutani, Fujie; Yamauchi, Toshie; Iwanaga, Yuji

2003-08-01

We investigated the effects of itopride hydrochloride (itopride, N-[4-[2-(dimethylamino)ethoxy]benzyl]-3,4-dimethoxybenzamide hydrochloride), a gastroprokinetic agent, on the colonic motor activity in vitro and in vivo, in comparison with benzamides, cisapride hydrate (cisapride), and mosapride citrate (mosapride). Itopride stimulated both peristaltic and segmental motility induced by applying intraluminal pressure to the isolated guinea pig colon. Although cisapride and mosapride enhanced the segmental motility, they markedly reduced the peristaltic motility. In conscious dogs with implanted strain gauge force transducers, itopride stimulated contractile activity in the gastrointestinal tract from the stomach to the colon. Cisapride stimulated contractile activity in the gastric antrum, ileum, and ascending colon. Mosapride stimulated contractile activity only in the gastric antrum and ileum. In guinea pigs and rats, itopride accelerated colonic luminal transit. On the other hand, cisapride and mosapride failed to enhance colonic transit. These results demonstrate that itopride has a stimulatory action on colonic peristalsis, propelling colonic luminal contents, different from that of cisapride and mosapride. Therefore, itopride may be a useful drug for the treatment of functional bowel disorders such as functional constipation.

The BioGRID Interaction Database: 2011 update

PubMed Central

Stark, Chris; Breitkreutz, Bobby-Joe; Chatr-aryamontri, Andrew; Boucher, Lorrie; Oughtred, Rose; Livstone, Michael S.; Nixon, Julie; Van Auken, Kimberly; Wang, Xiaodong; Shi, Xiaoqi; Reguly, Teresa; Rust, Jennifer M.; Winter, Andrew; Dolinski, Kara; Tyers, Mike

2011-01-01

The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans (http://www.thebiogrid.org). BioGRID currently holds 347 966 interactions (170 162 genetic, 177 804 protein) curated from both high-throughput data sets and individual focused studies, as derived from over 23 000 publications in the primary literature. Complete coverage of the entire literature is maintained for budding yeast (Saccharomyces cerevisiae), fission yeast (Schizosaccharomyces pombe) and thale cress (Arabidopsis thaliana), and efforts to expand curation across multiple metazoan species are underway. The BioGRID houses 48 831 human protein interactions that have been curated from 10 247 publications. Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health. The BioGRID 3.0 web interface contains new search and display features that enable rapid queries across multiple data types and sources. An automated Interaction Management System (IMS) is used to prioritize, coordinate and track curation across international sites and projects. BioGRID provides interaction data to several model organism databases, resources such as Entrez-Gene and other interaction meta-databases. The entire BioGRID 3.0 data collection may be downloaded in multiple file formats, including PSI MI XML. Source code for BioGRID 3.0 is freely available without any restrictions. PMID:21071413

Development of Bio-Based Foams Prepared from Pbat/Pla Reinforced with Bio-Calcium Carbonate Compatibilized by Electron-Beam Radiation

NASA Astrophysics Data System (ADS)

Cardoso, Elizabeth Carvalho L.; Seixas, Marcus Vinicius S.; Wiebeck, Helio; Oliveira, René R.; Machado, Glauson Aparecido F.; Moura, Esperidiana A. B.

In Brazil, the food industry generates every year huge amounts of avian eggshell waste, an industrial byproduct containing 95% of calcium carbonate, and its disposal constitutes a serious environmental hazard. This study aims to the development of bio-foams from PBAT/PLA blends reinforced with bio-calcium carbonate from eggshells. Composites were obtained by melting extrusion process, blending PBAT/PLA (50/50) with 25% of bio-calcium carbonate, PBAT/PLA (50/45) with 25% of bio-calcium carbonate and 5 % of pre-irradiated PLA and PBAT/PLA (50/40) with 25% of bio-calcium carbonate and 10 % of pre-irradiated PLA. PLA was previously e-beam irradiated at 150kGy in air and used as compatibilizer agent. The composites were then extruded in a Rheomex 332p single special screw for foaming. Samples were submitted to Tensile and Compression tests, MFI, DSC, TGA, XRD and FEG/SEM, analyses.

OX62+OX6+OX35+ rat dendritic cells are unable to prime CD4+ T cells for an effective immune response following acute burn injury.

PubMed

Fazal, Nadeem

2013-01-01

Co-stimulatory molecules expressed on Dendritic Cells (DCs) function to coordinate an efficient immune response by T cells in the peripheral lymph nodes. We hypothesized that CD4+ T cell-mediated immune suppression following burn injury may be related to dysfunctional DCs residing in gut associated lymphoid tissues (GALT), such as Mesenteric Lymph Nodes (MLN). Therefore, we studied co-stimulatory molecules expressed on burn rat MLN DCs as an index of functional DCs that would mount an effective normal CD4+ T cell immune response. In a rat model of 30% Total Body Surface Area (TBSA) scald burn, OX62+OX6+OX35+ DCs and CD4+ T cells were isolated from MLN of day 3 post-burn and sham control rats. DCs were tested for their expression of co-stimulatory molecules, and prime CD4+ T cell (DC:CD4+T cell co-culture assays) to determine an effector immune response such as CD4+ T cell proliferation. The surface receptor expressions of MLN DCs co-stimulatory molecules, i.e., MHC-II, CD40, CD80 (B7-1), and CD86 (B7-2) were determined by Flow cytometry (quantitatively) and confocal microscopy (qualitatively). Tritiated thymidine and CFDA-SE determined CD4+ T cell proliferation following co-incubation with DCs. Cytokine milieu of MLN (IL-12 and IL-10) was assessed by mRNA determination by RT-PCR. The results showed down-regulated expressions of co-stimulatory markers (CD80, CD86, CD40 and MHC-II) of MLN DCs obtained from burn-injured rats, as well as lack of ability of these burn-induced DCs to stimulate CD4+ T cell proliferation in co-culture assays, as compared to the sham rats. Moreover, anti-CD40 stimulation of affected burn MLN DCs did not reverse this alteration. Furthermore, a marked up-regulation of mRNA IL-10 and down-regulation of mRNA IL-12 in burn MLN as compared to sham animals was also observed. To surmise, the data indicated that dysfunctional OX62+OX6+OX35+ rat MLN DCs may contribute to CD4+ T-cell-mediated immune suppression observed following acute burn injury.

OX62+OX6+OX35+ rat dendritic cells are unable to prime CD4+ T cells for an effective immune response following acute burn injury☆

PubMed Central

Fazal, Nadeem

2013-01-01

Co-stimulatory molecules expressed on Dendritic Cells (DCs) function to coordinate an efficient immune response by T cells in the peripheral lymph nodes. We hypothesized that CD4+ T cell-mediated immune suppression following burn injury may be related to dysfunctional DCs residing in gut associated lymphoid tissues (GALT), such as Mesenteric Lymph Nodes (MLN). Therefore, we studied co-stimulatory molecules expressed on burn rat MLN DCs as an index of functional DCs that would mount an effective normal CD4+ T cell immune response. In a rat model of 30% Total Body Surface Area (TBSA) scald burn, OX62+OX6+OX35+ DCs and CD4+ T cells were isolated from MLN of day 3 post-burn and sham control rats. DCs were tested for their expression of co-stimulatory molecules, and prime CD4+ T cell (DC:CD4+T cell co-culture assays) to determine an effector immune response such as CD4+ T cell proliferation. The surface receptor expressions of MLN DCs co-stimulatory molecules, i.e., MHC-II, CD40, CD80 (B7-1), and CD86 (B7-2) were determined by Flow cytometry (quantitatively) and confocal microscopy (qualitatively). Tritiated thymidine and CFDA-SE determined CD4+ T cell proliferation following co-incubation with DCs. Cytokine milieu of MLN (IL-12 and IL-10) was assessed by mRNA determination by RT-PCR. The results showed down-regulated expressions of co-stimulatory markers (CD80, CD86, CD40 and MHC-II) of MLN DCs obtained from burn-injured rats, as well as lack of ability of these burn-induced DCs to stimulate CD4+ T cell proliferation in co-culture assays, as compared to the sham rats. Moreover, anti-CD40 stimulation of affected burn MLN DCs did not reverse this alteration. Furthermore, a marked up-regulation of mRNA IL-10 and down-regulation of mRNA IL-12 in burn MLN as compared to sham animals was also observed. To surmise, the data indicated that dysfunctional OX62+OX6+OX35+ rat MLN DCs may contribute to CD4+ T-cell-mediated immune suppression observed following acute burn injury

Acidity of biomass fast pyrolysis bio-oils

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

Oasmaa, Anja; Elliott, Douglas C.; Korhonen, Jaana

2010-12-17

The use of the TAN method for measuring the acidity of biomass fast pyrolysis bio-oil was evaluated. Suggestions for carrying out the analysis have been made. The TAN method by ASTM D664 or D3339 can be used for measuring the acidity of fast pyrolysis bio-oils and their hydrotreating products. The main difference between the methods is that ASTM D664 is specified for higher TAN values than ASTM D3339. Special focus should be placed on the interpretation of the TAN curves because they differ significantly from those of mineral oils. The curve for bio-oils is so gentle that the automatic detectionmore » may not observe the end point properly and derivatization should be used. The acidity of fast pyrolysis bio-oils is mainly derived (60-70%) from volatile acids. Other groups of compounds in fast pyrolysis bio-oils that influence acidity include phenolics, fatty and resin acids, and hydroxy acids.« less

Comparative Ethanol-Induced Potentiation of Stimulatory Responses to Dexmethylphenidate Versus Methylphenidate.

PubMed

Patrick, Kennerly S; Straughn, Arthur B; Reeves, Owen T; Bernstein, Hilary; Malcolm, Robert

2015-08-01

The potentiation of positive subjective responses to immediate-release dexmethylphenidate (d-MPH) or dl-methylphenidate (dl-MPH) by ethanol was investigated over the time course of maximal drug exposure after a single dose. In a 4-way, randomized, crossover study design, 12 men and 12 women normal volunteers received d-MPH (0.15 mg/kg) or dl-MPH (0.3 mg/kg) with or without ethanol (0.6 g/kg). Serial visual analog scales were used as surrogates for drug abuse liability ("high," "good," "like," "stimulated," and "any drug effect"). Combining pure d-MPH with ethanol significantly (P < 0.005) increased the area under the effect curves (AUC(0-5.25h)) of all 5 subscales. The dl-MPH-ethanol combination significantly (P < 0.05) increased these AUCs with the exception of like (P = 0.08). Effects of the pure d-MPH-ethanol combination exhibited delayed potentiation relative to dl-MPH-ethanol. A pharmacokinetic interaction between the l-isomer of dl-MPH and ethanol has previously been shown to increase early exposure to d-MPH. Administration of the pure isomer d-MPH precludes this absorption phase pharmacokinetic interaction with ethanol. This notwithstanding, the pure d-MPH-ethanol combination resulted in comparable, if not greater, cumulative stimulant potentiation than the dl-MPH-ethanol combination. These findings provide evidence of a pharmacodynamic component to d-MPH-ethanol synergistic interactions and carry implications for the rational drug individualization in the treatment of attention-deficit/hyperactivity disorder.

A Response to "BIO 2010: Transforming Undergraduate Education for Future Research Biologists," from the Perspective of the Biochemistry and Molecular Biology Major Program at Kenyon College

ERIC Educational Resources Information Center

Slonczewski, Joan L.; Marusak, Rosemary

2004-01-01

The National Research Council completed a major study of undergraduate biology education, "BIO 2010-Transforming Undergraduate Education For Future Research Biologists (BIO 2010)," funded by the Howard Hughes Medical Institute and the National Institutes of Health. The "BIO 2010" report recommends that biology pedagogy should use an…

STABILIZATION OF BIO-OIL TO ENABLE ITS HYDROTREATING TO PRODUCE BIOFUELS

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

Wang, Huamin

Fast pyrolysis is considered to be the simplest and most cost-effective approach to produce liquid oil (bio-oil) from biomass. Bio-oil is not suitable to substitute for petroleum as high-quality fuels and significant upgrading such as hydrotreating is required to remove oxygen, add hydrogen, and rearrange carbon backbone of bio-oil. However, the grand challenge in bio-oil hydrotreating technology is bio-oil instability, which limits the lifetime of catalyst and operation. To enable a sustainable and economically viable process for bio-oil hydrotreating, it is vital to develop effective technologies for stabilizing bio-oils. This chapter will be devoted to bio-oil stabilization. The current understatingmore » of the major cause of bio-oil instability, condensation of reactive species such as sugar, aldehydes, ketones, and phenolics, is elucidated. The reported physical and chemical methods for bio-oil stabilization are summarized in detail, with a specific focus on bio-oil catalytic hydrogenation for stabilization. The impact of stabilization on bio-oil hydrotreating is discussed as well.« less

Beclometasone oral--DOR BioPharma.

PubMed

2007-01-01

orBec is an oral enteric-coated tablet formulation of the corticosteroid beclometasone, which has been developed by Enteron Pharmaceuticals, a subsidiary of Corporate Technology Development (now DOR BioPharma). orBec is being developed for the treatment of gastrointestinal graft-versus-host disease (GVHD) and an NDA has been filed in the US. DOR BioPharma has also filed an MAA in Europe for the same indication.orBec is designed to reduce the need for systemic immunosuppressive drugs, thereby improving the outcome of bone marrow and stem cell transplantation.DOR BioPharma may seek a marketing partner in the US and elsewhere for orBec in GVHD and will seek a partner for other potential indications of the drug.In December 2001, Corporate Technology Development was acquired by Endorex Corporation (now DOR BioPharma). In October 1998, Enteron Pharmaceuticals (DOR BioPharma) entered into an exclusive, worldwide, royalty bearing license agreement with George B. McDonald, MD, including the right to grant sublicenses, for the rights to the intellectual property and know-how relating to orBec. In January 2007, DOR BioPharma received $US3 million under a non-binding letter of intent from Sigma-Tau Pharmaceuticals. The agreement grants Sigma-Tau an exclusive right to negotiate terms and conditions for a possible business transaction or strategic alliance regarding orBec and potentially other DOR pipeline compounds until 1 March 2007. Under the terms of the agreement, Sigma-Tau purchased $US1 million of DOR's common stock, with an additional $US2 million paid in cash. If no agreement is reached by 1 March 2007, DOR will return the $US2 million to Sigma-Tau within 60 days. DOR BioPharma received an unsolicited proposal from Cell Therapeutics, Inc. to acquire DOR BioPharma in January 2007. Because of the non-binding agreement already signed with Sigma-Tau, DOR BioPharma's board of directors cannot consider Cell Therapeutics' merger proposal at this time. orBec has been filed for

Helicos BioSciences.

PubMed

Milos, Patrice

2008-04-01

Helicos BioSciences Corporation is a life sciences company developing revolutionary new single molecule sequencing technology to provide the path to the US$1000 genome. True Single Molecule Sequencing (tSMS) will drive advancements in pharmacogenomics that can enable a better understanding of an individual's susceptibility to disease, develop more effective disease diagnoses and differentiate response to disease therapies. During 2007, genome-wide disease-association studies, the encylopedia of DNA elements (ENCODE) and the published genome sequence of two individuals have revealed human genome variation far more extensive than originally believed. These also demonstrated that common variations explain only a fraction of the genetic basis of disease. Therefore, the capability to understand an individual genome is critical in setting the foundation for the next great revolution in healthcare. Helicos is committed to this vision and will provide cost-effective genome sequencing and comprehensive analysis of the transcribed genome that can unlock the era of personalized healthcare.

The BioGRID interaction database: 2017 update

PubMed Central

Chatr-aryamontri, Andrew; Oughtred, Rose; Boucher, Lorrie; Rust, Jennifer; Chang, Christie; Kolas, Nadine K.; O'Donnell, Lara; Oster, Sara; Theesfeld, Chandra; Sellam, Adnane; Stark, Chris; Breitkreutz, Bobby-Joe; Dolinski, Kara; Tyers, Mike

2017-01-01

The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the annotation and archival of protein, genetic and chemical interactions for all major model organism species and humans. As of September 2016 (build 3.4.140), the BioGRID contains 1 072 173 genetic and protein interactions, and 38 559 post-translational modifications, as manually annotated from 48 114 publications. This dataset represents interaction records for 66 model organisms and represents a 30% increase compared to the previous 2015 BioGRID update. BioGRID curates the biomedical literature for major model organism species, including humans, with a recent emphasis on central biological processes and specific human diseases. To facilitate network-based approaches to drug discovery, BioGRID now incorporates 27 501 chemical–protein interactions for human drug targets, as drawn from the DrugBank database. A new dynamic interaction network viewer allows the easy navigation and filtering of all genetic and protein interaction data, as well as for bioactive compounds and their established targets. BioGRID data are directly downloadable without restriction in a variety of standardized formats and are freely distributed through partner model organism databases and meta-databases. PMID:27980099

Direct Bio-printing with Heterogeneous Topology Design.

PubMed

Ahsan, Amm Nazmul; Xie, Ruinan; Khoda, Bashir

2017-01-01

Bio-additive manufacturing is a promising tool to fabricate porous scaffold structures for expediting the tissue regeneration processes. Unlike the most traditional bulk material objects, the microstructures of tissue and organs are mostly highly anisotropic, heterogeneous, and porous in nature. However, modelling the internal heterogeneity of tissues/organs structures in the traditional CAD environment is difficult and oftentimes inaccurate. Besides, the de facto STL conversion of bio-models introduces loss of information and piles up more errors in each subsequent step (build orientation, slicing, tool-path planning) of the bio-printing process plan. We are proposing a topology based scaffold design methodology to accurately represent the heterogeneous internal architecture of tissues/organs. An image analysis technique is used that digitizes the topology information contained in medical images of tissues/organs. A weighted topology reconstruction algorithm is implemented to represent the heterogeneity with parametric functions. The parametric functions are then used to map the spatial material distribution. The generated information is directly transferred to the 3D bio-printer and heterogeneous porous tissue scaffold structure is manufactured without STL file. The proposed methodology is implemented to verify the effectiveness of the approach and the designed example structure is bio-fabricated with a deposition based bio-additive manufacturing system.

Boron brings big benefits to bio-based blends

USDA-ARS?s Scientific Manuscript database

The solution to the problems with bio-based lubrication can be approached by a combination of blending and additive strategies. However, many additives do not show efficacy when used in bio-based lubricants. Additive addition also lowers the bio-based content of the blend, which in turn limits the a...

Spider Silk: Mother Nature's Bio-Superlens

NASA Astrophysics Data System (ADS)

Monks, James N.; Yan, Bing; Hawkins, Nicholas; Vollrath, Fritz; Wang, Zengbo

2016-09-01

This paper demonstrates a possible new microfiber bio near field lens that uses minor ampullate spider silk,spun from the Nephila edulis spider, to create a real time image of a surface using near field optical techniques. The microfiber bio lens is the world's first natural superlens created by exploring biological materials. The resolution of the surface image overcomes the diffraction limit, with the ability to resolve patterns at 100 nm under a standard white light source in reflection mode. This resolution offers further developments in superlens technology and paves the way for new bio optics.

Branding the bio/biomedical engineering degree.

PubMed

Voigt, Herbert F

2011-01-01

The future challenges to medical and biological engineering, sometimes referred to as biomedical engineering or simply bioengineering, are many. Some of these are identifiable now and others will emerge from time to time as new technologies are introduced and harnessed. There is a fundamental issue regarding "Branding the bio/biomedical engineering degree" that requires a common understanding of what is meant by a B.S. degree in Biomedical Engineering, Bioengineering, or Biological Engineering. In this paper we address some of the issues involved in branding the Bio/Biomedical Engineering degree, with the aim of clarifying the Bio/Biomedical Engineering brand.

The concept of bio-corona in modulating the toxicity of engineered nanomaterials (ENM)

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

Westmeier, Dana; Stauber, Roland H.; Docter, Dominic, E-mail: docter@uni-mainz.de

Besides the wide use of engineered nanomaterials (ENM) in technical products, their application spectrum in biotechnology and biomedicine is steadily increasing. In complex physiological environments the physico-chemical properties and the behavior of nanoparticles (NPs) are challenging to characterize. Biomolecules rapidly adsorb to the nanomaterial, leading to the formation of the protein/biomolecule corona, which critically affects the nanomaterials' (patho)biological and technical identities. This formation can trigger an immune response and affect nanoparticles' toxicity and targeting capabilities. In this review, we provide a survey of recent findings on the (protein)corona-nanoparticle interaction and discuss how the corona modulates both cytotoxicity and the immunemore » response as well as to improve the efficacy of targeted delivery of nanocarriers. - Highlights: • “Nanotoxicology” has emerged an autonomous field with an explosive growth. • Nanomaterials adsorb (bio)molecules forming the so-called (bio)molecule corona. • (Fine-)tune of the corona composition could enable new possibilities in nanomedicine.« less

Quercetin as natural stabilizing agent for bio-polymer

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

Morici, Elisabetta; Arrigo, Rossella; Dintcheva, Nadka Tzankova

The introduction of antioxidants in polymers is the main way to prevent or delay the degradation process. In particular natural antioxidants receive attention in the food industry also because of their presumed safety. In this work bio-polymers, i.e. a commercial starch-based polymer (Mater-Bi®) and a bio-polyester (PLA), and a bio-polyether (PEO) were additivated with quercetin, a natural flavonoid antioxidants, in order to formulate bio-based films for ecosustainable packaging and outdoor applications. The photo-oxidation behavior of unstabilized and quercetin stabilized films was analyzed and compared with the behavior of films additivated with a commercial synthetic light stabilizer. The quercetin is ablemore » to slow down the photo-degradation rate of all bio-polymeric films investigated in similar way to the synthetic stabilizer.« less

Quercetin as natural stabilizing agent for bio-polymer

NASA Astrophysics Data System (ADS)

Morici, Elisabetta; Arrigo, Rossella; Dintcheva, Nadka Tzankova

2014-05-01

The introduction of antioxidants in polymers is the main way to prevent or delay the degradation process. In particular natural antioxidants receive attention in the food industry also because of their presumed safety. In this work bio-polymers, i.e. a commercial starch-based polymer (Mater-Bi®) and a bio-polyester (PLA), and a bio-polyether (PEO) were additivated with quercetin, a natural flavonoid antioxidants, in order to formulate bio-based films for ecosustainable packaging and outdoor applications. The photo-oxidation behavior of unstabilized and quercetin stabilized films was analyzed and compared with the behavior of films additivated with a commercial synthetic light stabilizer. The quercetin is able to slow down the photo-degradation rate of all bio-polymeric films investigated in similar way to the synthetic stabilizer.

A Survey of Business Trends at BioOne Publishing Partners and its Implications for BioOne

ERIC Educational Resources Information Center

Carpenter, Todd A.; Joseph, Heather; Waltham, Mary

2004-01-01

This paper describes a survey of BioOne participating publishers that was conducted during the fall of 2003. In that survey, BioOne collected data from 18 not-for-profit publishers on circulation levels, scholarly output in terms of pages and articles produced, revenues, and expenditures. From eight of the publishers, complete profit, loss, and…

Bio and health informatics meets cloud : BioVLab as an example.

PubMed

Chae, Heejoon; Jung, Inuk; Lee, Hyungro; Marru, Suresh; Lee, Seong-Whan; Kim, Sun

2013-01-01

The exponential increase of genomic data brought by the advent of the next or the third generation sequencing (NGS) technologies and the dramatic drop in sequencing cost have driven biological and medical sciences to data-driven sciences. This revolutionary paradigm shift comes with challenges in terms of data transfer, storage, computation, and analysis of big bio/medical data. Cloud computing is a service model sharing a pool of configurable resources, which is a suitable workbench to address these challenges. From the medical or biological perspective, providing computing power and storage is the most attractive feature of cloud computing in handling the ever increasing biological data. As data increases in size, many research organizations start to experience the lack of computing power, which becomes a major hurdle in achieving research goals. In this paper, we review the features of publically available bio and health cloud systems in terms of graphical user interface, external data integration, security and extensibility of features. We then discuss about issues and limitations of current cloud systems and conclude with suggestion of a biological cloud environment concept, which can be defined as a total workbench environment assembling computational tools and databases for analyzing bio/medical big data in particular application domains.

Bio-oil transport by pipeline: a techno-economic assessment.

PubMed

Pootakham, Thanyakarn; Kumar, Amit

2010-09-01

Bio-oil, produced by fast pyrolysis of biomass, has high energy density compared to 'as received' biomass. The study assesses and compares the cost of transportation ($/liter of bio-oil) of bio-oil by pipeline and truck. The fixed and variable cost components of transportation of bio-oil at a pipeline capacity of 560 m(3)/day and to a distance of 100 km are 0.0423$/m(3) and 0.1201$/m(3)/km, respectively. Pipeline transportation of bio-oil costs less than transportation by liquid tank truck (load capacity 30 m(3)) and super B-train trailer (load capacity 60 m(3)) above pipeline capacities of 1000 and 1700 m(3)/day, respectively. When transportation distance is greater than 100 km, bio-oil must be heated at booster stations. When transporting bio-oil by pipeline to a distance of 400 km, minimum pipeline capacities of 1150 and 2000 m(3)/day are required to compete economically with liquid tank trucks and super B-train tank trailers, respectively. Copyright 2010 Elsevier Ltd. All rights reserved.

Bio-objects’ political capacity: a research agenda

PubMed Central

Maeseele, Pieter; Hendrickx, Kim; Pavone, Vincenzo; Van Hoyweghen, Ine

2013-01-01

This article explores the merits of foregrounding the dichotomy of politicization vs de-politicization for our understanding of bio-objects in order to study their production, circulation, and governance in European societies. By asking how bio-objects are configured in science, policy, public, and media discourses and practices, we focus on the role of socio-technical configurations in generating political relations. The bio-object thereby serves as an entry point to approach and conceptualize “the political” in an innovative way. PMID:23630150

Bio-tribology.

PubMed

Dowson, Duncan

2012-01-01

It is now forty six years since the separate topics of friction, lubrication, wear and bearing design were integrated under the title 'Tribology' [Department of Education and Science, Lubrication (Tribology) Education and Research. A Report on the Present Position and Industry's Needs, HMSO, London, 1966]. Significant developments have been reported in many established and new aspects of tribology during this period. The subject has contributed to improved performance of much familiar equipment, such as reciprocating engines, where there have been vast improvements in engine reliability and efficiency. Nano-tribology has been central to remarkable advances in information processing and digital equipment. Shortly after widespread introduction of the term tribology, integration with biology and medicine prompted rapid and extensive interest in the fascinating sub-field now known as Bio-tribology [D. Dowson and V. Wright, Bio-tribology, in The Rheology of Lubricants, ed. T. C. Davenport, Applied Science Publishers, Barking, 1973, pp. 81-88]. An outline will be given of some of the developments in the latter field.

Xenogeneic Bio-Root Prompts the Constructive Process Characterized by Macrophage Phenotype Polarization in Rodents and Nonhuman Primates.

PubMed

Li, Hui; Sun, Jingjing; Li, Jie; Yang, Hefeng; Luo, Xiangyou; Chen, Jinlong; Xie, Li; Huo, Fangjun; Zhu, Tian; Guo, Weihua; Tian, Weidong

2017-03-01

Tissue or organ regeneration using xenogeneic matrices is a promising approach to address the shortage of donor matrices for allotransplantation. Success of such approach has been demonstrated to correlate with macrophage-mediated fibrotic homeostasis and tissue remodeling. The previous studies have demonstrated that treated dentin matrix (TDM) could be a suitable bioactive substrate for allogeneic tooth root regeneration. This study constructed xenogeneic bioengineered tooth root (bio-root) via a combination of porcine TDM (pTDM) with allogeneic dental follicle cells (DFCs). Macrophage phenotypes are used to evaluate the remodeling process of xenogeneic bio-roots in vitro and in vivo. pTDM can facilitate odontoblast differentiation of human derived DFCs. Xenogeneic bio-roots in rat subcutaneous tissue prompt constructive response via M1 macrophage infiltration during early postimplantation stages and increase restorative M2 phenotype at later stages. After implantation of bio-roots into jaws of rhesus monkeys for six months, periodontal ligament-like fibers accompanied by macrophage polarization are observed, which are positive for COL-1, Periostin, βIII-tubulin and display such structures as fibroblasts and blood vessels. The reconstructed bio-root possesses biomechanical properties for the dissipation of masticatory forces. These results support that xenogeneic bio-root could maintain fibrotic homeostasis during remodeling process and highlight the potential application of xenogeneic matrices in regenerative medicine. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Lateral ridge augmentation with Bio-Oss alone or Bio-Oss mixed with particulate autogenous bone graft: a systematic review.

PubMed

Aludden, H C; Mordenfeld, A; Hallman, M; Dahlin, C; Jensen, T

2017-08-01

The objective of this systematic review was to test the hypothesis of no difference in implant treatment outcomes when using Bio-Oss alone or Bio-Oss mixed with particulate autogenous bone grafts for lateral ridge augmentation. A search of the MEDLINE, Cochrane Library, and Embase databases in combination with a hand-search of relevant journals was conducted. Human studies published in English from 1 January 1990 to 1 May 2016 were included. The search provided 337 titles and six studies fulfilled the inclusion criteria. Considerable variation prevented a meta-analysis from being performed. The two treatment modalities have never been compared within the same study. Non-comparative studies demonstrated a 3-year implant survival of 96% with 50% Bio-Oss mixed with 50% autogenous bone graft. Moreover, Bio-Oss alone or Bio-Oss mixed with autogenous bone graft seems to increase the amount of newly formed bone as well as the width of the alveolar process. Within the limitations of this systematic review, lateral ridge augmentation with Bio-Oss alone or in combination with autogenous bone graft seems to induce newly formed bone and increase the width of the alveolar process, with high short-term implant survival. However, long-term studies comparing the two treatment modalities are needed before final conclusions can be drawn. Copyright © 2017 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Computing with motile bio-agents

NASA Astrophysics Data System (ADS)

Nicolau, Dan V., Jr.; Burrage, Kevin; Nicolau, Dan V.

2007-12-01

We describe a model of computation of the parallel type, which we call 'computing with bio-agents', based on the concept that motions of biological objects such as bacteria or protein molecular motors in confined spaces can be regarded as computations. We begin with the observation that the geometric nature of the physical structures in which model biological objects move modulates the motions of the latter. Consequently, by changing the geometry, one can control the characteristic trajectories of the objects; on the basis of this, we argue that such systems are computing devices. We investigate the computing power of mobile bio-agent systems and show that they are computationally universal in the sense that they are capable of computing any Boolean function in parallel. We argue also that using appropriate conditions, bio-agent systems can solve NP-complete problems in probabilistic polynomial time.

Use of Bio-Amp, a commercial bio-additive for the treatment of grease trap wastewater containing fat, oil, and grease.

PubMed

Tang, Hao L; Xie, Yuefeng F; Chen, Yen-Chih

2012-11-01

This research investigated the application of Bio-Amp, a commercial bio-additive for the treatment of fat, oil, and grease (FOG) in a grease trap, and evaluated potential impacts of treated effluent on downstream collection system and treatment processes. Results show that after Bio-Amp treatment, FOG deposit formation was reduced by 40%, implicating a potential reduction of sewer line blockages. Chemical oxygen demand (COD), total nitrogen (TN), total phosphorus (TP) and total fatty acids were reduced by 39%, 33%, 56%, and 59%, respectively, which represents an overall loading reduction of 9% COD, 5% TN and 40% TP received by the treatment plant from all the dining halls. On the other hand, readily biodegradable COD fractions significantly increased, which implies a potential improvement on Bio-P removal. Overall, the results showed that application of Bio-Amp in grease trap provides potential reduction of sewer line blockages, and can also alleviate downstream treatment burden. Copyright © 2012 Elsevier Ltd. All rights reserved.

BioBrick assembly standards and techniques and associated software tools.

PubMed

Røkke, Gunvor; Korvald, Eirin; Pahr, Jarle; Oyås, Ove; Lale, Rahmi

2014-01-01

The BioBrick idea was developed to introduce the engineering principles of abstraction and standardization into synthetic biology. BioBricks are DNA sequences that serve a defined biological function and can be readily assembled with any other BioBrick parts to create new BioBricks with novel properties. In order to achieve this, several assembly standards can be used. Which assembly standards a BioBrick is compatible with, depends on the prefix and suffix sequences surrounding the part. In this chapter, five of the most common assembly standards will be described, as well as some of the most used assembly techniques, cloning procedures, and a presentation of the available software tools that can be used for deciding on the best method for assembling of different BioBricks, and searching for BioBrick parts in the Registry of Standard Biological Parts database.

Alkaline hydrothermal liquefaction of swine carcasses to bio-oil

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

Zheng, Ji-Lu, E-mail: triace@163.com; Zhu, Ming-Qiang; Wu, Hai-tang

Highlights: • Swine carcasses can be converted to bio-oil by alkaline hydrothermal liquefaction. • It seems that the use of the bio-oil for heat or CHP is technically suitable. • Some valuable chemicals were found in the bio-oils. • The bio-oil and the solid residue constituted an energy efficiency of 93.63% for the feedstock. • The solid residue can be used as a soil amendment, to sequester C and for preparing activated carbon. - Abstract: It is imperative that swine carcasses are disposed of safely, practically and economically. Alkaline hydrothermal liquefaction of swine carcasses to bio-oil was performed. Firstly, themore » effects of temperature, reaction time and pH value on the yield of each liquefaction product were determined. Secondly, liquefaction products, including bio-oil and solid residue, were characterized. Finally, the energy recovery ratio (ERR), which was defined as the energy of the resultant products compared to the energy input of the material, was investigated. Our experiment shows that reaction time had certain influence on the yield of liquefaction products, but temperature and pH value had bigger influence on the yield of liquefaction products. Yields of 62.2 wt% bio-oil, having a high heating value of 32.35 MJ/kg and a viscosity of 305cp, and 22 wt% solid residue were realized at a liquefaction temperature of 250 °C, a reaction time of 60 min and a pH value of 9.0. The bio-oil contained up to hundreds of different chemical components that may be classified according to functional groups. Typical compound classes in the bio-oil were hydrocarbons, organic acids, esters, ketones and heterocyclics. The energy recovery ratio (ERR) reached 93.63%. The bio-oil is expected to contribute to fossil fuel replacement in stationary applications, including boilers and furnaces, and upgrading processes for the bio-oil may be used to obtain liquid transport fuels.« less

BioRuby: bioinformatics software for the Ruby programming language.

PubMed

Goto, Naohisa; Prins, Pjotr; Nakao, Mitsuteru; Bonnal, Raoul; Aerts, Jan; Katayama, Toshiaki

2010-10-15

The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser. BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/. katayama@bioruby.org

Security enhanced BioEncoding for protecting iris codes

NASA Astrophysics Data System (ADS)

Ouda, Osama; Tsumura, Norimichi; Nakaguchi, Toshiya

2011-06-01

Improving the security of biometric template protection techniques is a key prerequisite for the widespread deployment of biometric technologies. BioEncoding is a recently proposed template protection scheme, based on the concept of cancelable biometrics, for protecting biometric templates represented as binary strings such as iris codes. The main advantage of BioEncoding over other template protection schemes is that it does not require user-specific keys and/or tokens during verification. Besides, it satisfies all the requirements of the cancelable biometrics construct without deteriorating the matching accuracy. However, although it has been shown that BioEncoding is secure enough against simple brute-force search attacks, the security of BioEncoded templates against more smart attacks, such as record multiplicity attacks, has not been sufficiently investigated. In this paper, a rigorous security analysis of BioEncoding is presented. Firstly, resistance of BioEncoded templates against brute-force attacks is revisited thoroughly. Secondly, we show that although the cancelable transformation employed in BioEncoding might be non-invertible for a single protected template, the original iris code could be inverted by correlating several templates used in different applications but created from the same iris. Accordingly, we propose an important modification to the BioEncoding transformation process in order to hinder attackers from exploiting this type of attacks. The effectiveness of adopting the suggested modification is validated and its impact on the matching accuracy is investigated empirically using CASIA-IrisV3-Interval dataset. Experimental results confirm the efficacy of the proposed approach and show that it preserves the matching accuracy of the unprotected iris recognition system.

The frequency of U-shaped dose responses in the toxicological literature.

PubMed

Calabrese, E J; Baldwin, L A

2001-08-01

Hormesis has been defined as a dose-response relationship in which there is a stimulatory response at low doses, but an inhibitory response at high doses, resulting in a U- or inverted U-shaped dose response. To assess the proportion of studies satisfying criteria for evidence of hormesis, a database was created from published toxicological literature using rigorous a priori entry and evaluative criteria. One percent (195 out of 20,285) of the published articles contained 668 dose-response relationships that met the entry criteria. Subsequent application of evaluative criteria revealed that 245 (37% of 668) dose-response relationships from 86 articles (0.4% of 20,285) satisfied requirements for evidence of hormesis. Quantitative evaluation of false-positive and false-negative responses indicated that the data were not very susceptible to such influences. A complementary analysis of all dose responses assessed by hypothesis testing or distributional analyses, where the units of comparison were treatment doses below the NOAEL, revealed that of 1089 doses below the NOAEL, 213 (19.5%) satisfied statistical significance or distributional data evaluative criteria for hormesis, 869 (80%) did not differ from the control, and 7 (0.6%) displayed evidence of false-positive values. The 32.5-fold (19.5% vs 0.6%) greater occurrence of hormetic responses than a response of similar magnitude in the opposite (negative) direction strongly supports the nonrandom nature of hormetic responses. This study, which provides the first documentation of a data-derived frequency of hormetic responses in the toxicologically oriented literature, indicates that when the study design satisfies a priori criteria (i.e., a well-defined NOAEL, > or = 2 doses below the NOAEL, and the end point measured has the capacity to display either stimulatory or inhibitory responses), hormesis is frequently encountered and is broadly represented according to agent, model, and end point. These findings have broad

Bio-robots automatic navigation with electrical reward stimulation.

PubMed

Sun, Chao; Zhang, Xinlu; Zheng, Nenggan; Chen, Weidong; Zheng, Xiaoxiang

2012-01-01

Bio-robots that controlled by outer stimulation through brain computer interface (BCI) suffer from the dependence on realtime guidance of human operators. Current automatic navigation methods for bio-robots focus on the controlling rules to force animals to obey man-made commands, with animals' intelligence ignored. This paper proposes a new method to realize the automatic navigation for bio-robots with electrical micro-stimulation as real-time rewards. Due to the reward-seeking instinct and trial-and-error capability, bio-robot can be steered to keep walking along the right route with rewards and correct its direction spontaneously when rewards are deprived. In navigation experiments, rat-robots learn the controlling methods in short time. The results show that our method simplifies the controlling logic and realizes the automatic navigation for rat-robots successfully. Our work might have significant implication for the further development of bio-robots with hybrid intelligence.

Protein bio-corona: critical issue in immune nanotoxicology.

PubMed

Neagu, Monica; Piperigkou, Zoi; Karamanou, Konstantina; Engin, Ayse Basak; Docea, Anca Oana; Constantin, Carolina; Negrei, Carolina; Nikitovic, Dragana; Tsatsakis, Aristidis

2017-03-01

With the expansion of the nanomedicine field, the knowledge focusing on the behavior of nanoparticles in the biological milieu has rapidly escalated. Upon introduction to a complex biological system, nanomaterials dynamically interact with all the encountered biomolecules and form the protein "bio-corona." The decoration with these surface biomolecules endows nanoparticles with new properties. The present review will address updates of the protein bio-corona characteristics as influenced by nanoparticle's physicochemical properties and by the particularities of the encountered biological milieu. Undeniably, bio-corona generation influences the efficacy of the nanodrug and guides the actions of innate and adaptive immunity. Exploiting the dynamic process of protein bio-corona development in combination with the new engineered horizons of drugs linked to nanoparticles could lead to innovative functional nanotherapies. Therefore, bio-medical nanotechnologies should focus on the interactions of nanoparticles with the immune system for both safety and efficacy reasons.

BioSig-Air-Force

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

2011-07-15

1) Configured servers: In coordination with the INSIGHT team, a hardware configuration was selected. Two nodes were purchased, configured, and shipped with compatible OS and database installation. The servers have been stress tested for reliability as they use leading edge technologies. Each node has two CPUs and 12 cores per CPU with maximum onboard memory for high performance. 2) LIM and Experimental module: The original BioSig system was developed for cancer research. Accordingly, the LIM system its corresponding web pages are being modified to facilitate (i) pathogene-donor interactions, (ii) media composition, (iii) chemical and siRNA plate configurations. The LIM systemmore » has been redesigned. The revised system allows design of new media and tracking it from lot-to-lot so that variations in the phenotypic responses can be tracked to a specific media and lot number. Similar associations are also possible with other experimental factors (e.g., donor-pathoge, siRNA, and chemical). Furthermore, the design of the experimental variables has also been revised to (i) interact with the newly developed LIM system, (ii) simplify experimental specifications, and (iii) test for potential operator's error during the data entry. Part of the complication has been due to the handshake between multiple teams that provide the small molecule plates and the team that creates assay plates. Our efforts have focused to harmonize these interactions (e.g., various data formats) so that each assay plate can be mapped to its source so that a correct set of experimental variables can be associated with each image. For example, depending upon the source of the chemical plates, they may have different formats. We have developed a canonical representation that registers SMILES code, for each chemical compound, along with its physiochemical properties. The schema for LIM conjunction with customized Web pages. 3) Import of Images and computed descriptors module: In coordination with the

A stimulatory effect of Artemisia leaf extract on the proliferation of cultured endothelial cells.

PubMed

Kaji, T; Kaga, K; Miezi, N; Ejiri, N; Sakuragawa, N

1990-02-01

To investigate the effect of the hot water extract from Artemisia leaf (Artemisia princeps Panpanini) (AFE) on the proliferation of endothelial cells, the cells from bovine aorta were cultured for up to 96 h in the presence of 1, 5, 10 or 50 micrograms/ml AFE in RPMI1640 medium supplemented with 10% fetal bovine serum. After a 72 h culture, the cell number was significantly increased by AFE at 1, 5 and 10 micrograms/ml. An increase in the cell number by 5 micrograms/ml AFE observed after a 72 or 96 h treatment. The incorporations of both [3H]thymidine and [14C]leucine by the growing cells were significantly increased by 5 micrograms/ml AFE after a 72 h treatment. In addition, the incorporation of [3H]thymidine by either growing or confluent cells was significantly increased by 50 micrograms/ml AFE after a 72 h treatment. The stimulatory activity of AFE was recognized in the low-molecular-weight fraction (molecular weight less than or equal to 10000 dalton). These results clearly indicated that AFE contained some low-molecular-weight component(s) which stimulates the proliferation of vascular endothelial cells in vitro.

Brucella BioR regulator defines a complex regulatory mechanism for bacterial biotin metabolism.

PubMed

Feng, Youjun; Xu, Jie; Zhang, Huimin; Chen, Zeliang; Srinivas, Swaminath

2013-08-01

The enzyme cofactor biotin (vitamin H or B7) is an energetically expensive molecule whose de novo biosynthesis requires 20 ATP equivalents. It seems quite likely that diverse mechanisms have evolved to tightly regulate its biosynthesis. Unlike the model regulator BirA, a bifunctional biotin protein ligase with the capability of repressing the biotin biosynthetic pathway, BioR has been recently reported by us as an alternative machinery and a new type of GntR family transcriptional factor that can repress the expression of the bioBFDAZ operon in the plant pathogen Agrobacterium tumefaciens. However, quite unusually, a closely related human pathogen, Brucella melitensis, has four putative BioR-binding sites (both bioR and bioY possess one site in the promoter region, whereas the bioBFDAZ [bio] operon contains two tandem BioR boxes). This raised the question of whether BioR mediates the complex regulatory network of biotin metabolism. Here, we report that this is the case. The B. melitensis BioR ortholog was overexpressed and purified to homogeneity, and its solution structure was found to be dimeric. Functional complementation in a bioR isogenic mutant of A. tumefaciens elucidated that Brucella BioR is a functional repressor. Electrophoretic mobility shift assays demonstrated that the four predicted BioR sites of Brucella plus the BioR site of A. tumefaciens can all interact with the Brucella BioR protein. In a reporter strain that we developed on the basis of a double mutant of A. tumefaciens (the ΔbioR ΔbioBFDA mutant), the β-galactosidase (β-Gal) activity of three plasmid-borne transcriptional fusions (bioBbme-lacZ, bioYbme-lacZ, and bioRbme-lacZ) was dramatically decreased upon overexpression of Brucella bioR. Real-time quantitative PCR analyses showed that the expression of bioBFDA and bioY is significantly elevated upon removal of bioR from B. melitensis. Together, we conclude that Brucella BioR is not only a negative autoregulator but also a repressor of

Brucella BioR Regulator Defines a Complex Regulatory Mechanism for Bacterial Biotin Metabolism

PubMed Central

Xu, Jie; Zhang, Huimin; Srinivas, Swaminath

2013-01-01

The enzyme cofactor biotin (vitamin H or B7) is an energetically expensive molecule whose de novo biosynthesis requires 20 ATP equivalents. It seems quite likely that diverse mechanisms have evolved to tightly regulate its biosynthesis. Unlike the model regulator BirA, a bifunctional biotin protein ligase with the capability of repressing the biotin biosynthetic pathway, BioR has been recently reported by us as an alternative machinery and a new type of GntR family transcriptional factor that can repress the expression of the bioBFDAZ operon in the plant pathogen Agrobacterium tumefaciens. However, quite unusually, a closely related human pathogen, Brucella melitensis, has four putative BioR-binding sites (both bioR and bioY possess one site in the promoter region, whereas the bioBFDAZ [bio] operon contains two tandem BioR boxes). This raised the question of whether BioR mediates the complex regulatory network of biotin metabolism. Here, we report that this is the case. The B. melitensis BioR ortholog was overexpressed and purified to homogeneity, and its solution structure was found to be dimeric. Functional complementation in a bioR isogenic mutant of A. tumefaciens elucidated that Brucella BioR is a functional repressor. Electrophoretic mobility shift assays demonstrated that the four predicted BioR sites of Brucella plus the BioR site of A. tumefaciens can all interact with the Brucella BioR protein. In a reporter strain that we developed on the basis of a double mutant of A. tumefaciens (the ΔbioR ΔbioBFDA mutant), the β-galactosidase (β-Gal) activity of three plasmid-borne transcriptional fusions (bioBbme-lacZ, bioYbme-lacZ, and bioRbme-lacZ) was dramatically decreased upon overexpression of Brucella bioR. Real-time quantitative PCR analyses showed that the expression of bioBFDA and bioY is significantly elevated upon removal of bioR from B. melitensis. Together, we conclude that Brucella BioR is not only a negative autoregulator but also a repressor of

A brief review of extrusion-based tissue scaffold bio-printing.

PubMed

Ning, Liqun; Chen, Xiongbiao

2017-08-01

Extrusion-based bio-printing has great potential as a technique for manipulating biomaterials and living cells to create three-dimensional (3D) scaffolds for damaged tissue repair and function restoration. Over the last two decades, advances in both engineering techniques and life sciences have evolved extrusion-based bio-printing from a simple technique to one able to create diverse tissue scaffolds from a wide range of biomaterials and cell types. However, the complexities associated with synthesis of materials for bio-printing and manipulation of multiple materials and cells in bio-printing pose many challenges for scaffold fabrication. This paper presents an overview of extrusion-based bio-printing for scaffold fabrication, focusing on the prior-printing considerations (such as scaffold design and materials/cell synthesis), working principles, comparison to other techniques, and to-date achievements. This paper also briefly reviews the recent development of strategies with regard to hydrogel synthesis, multi-materials/cells manipulation, and process-induced cell damage in extrusion-based bio-printing. The key issue and challenges for extrusion-based bio-printing are also identified and discussed along with recommendations for future, aimed at developing novel biomaterials and bio-printing systems, creating patterned vascular networks within scaffolds, and preserving the cell viability and functions in scaffold bio-printing. The address of these challenges will significantly enhance the capability of extrusion-based bio-printing. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The NCBI BioSystems database.

PubMed

Geer, Lewis Y; Marchler-Bauer, Aron; Geer, Renata C; Han, Lianyi; He, Jane; He, Siqian; Liu, Chunlei; Shi, Wenyao; Bryant, Stephen H

2010-01-01

The NCBI BioSystems database, found at http://www.ncbi.nlm.nih.gov/biosystems/, centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI's Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type, without requiring time-consuming inference of biological relationships from the literature or multiple experimental datasets.

Production of bio-based phenolic resin and activated carbon from bio-oil and biochar derived from fast pyrolysis of palm kernel shells.

PubMed

Choi, Gyung-Goo; Oh, Seung-Jin; Lee, Soon-Jang; Kim, Joo-Sik

2015-02-01

A fraction of palm kernel shells (PKS) was pyrolyzed in a fluidized bed reactor. The experiments were performed in a temperature range of 479-555 °C to produce bio-oil, biochar, and gas. All the bio-oils were analyzed quantitatively and qualitatively by GC-FID and GC-MS. The maximum content of phenolic compounds in the bio-oil was 24.8 wt.% at ∼500 °C. The maximum phenol content in the bio-oil, as determined by the external standard method, was 8.1 wt.%. A bio-oil derived from the pyrolysis of PKS was used in the synthesis of phenolic resin, showing that the bio-oil could substitute for fossil phenol up to 25 wt.%. The biochar was activated using CO2 at a final activation temperature of 900 °C with different activation time (1-3 h) to produce activated carbon. Activated carbons produced were microporous, and the maximum surface area of the activated carbons produced was 807 m(2)/g. Copyright © 2014 Elsevier Ltd. All rights reserved.

Nano-catalysts for upgrading bio-oil: Catalytic decarboxylation and hydrodeoxygenation

NASA Astrophysics Data System (ADS)

Uemura, Yoshimitsu; Tran, Nga T. T.; Naqvi, Salman Raza; Nishiyama, Norikazu

2017-09-01

Bio-oil is a mixture of oxygenated chemicals produced by fast pyrolysis of lignocellulose, and has attracted much attention recently because the raw material is renewable. Primarily, bio-oil can be used as a replacement of heavy oil. But it is not highly recommended due to bio-oil's inferior properties: high acidity and short shelf life. Upgrading of bio-oil is therefore one of the important technologies nowadays, and is categorized into the two: (A) decrarboxylation/decarbonylation by solid acid catalysts and (B) hydrodeoxygenation (HDO) by metallic catalysts. In our research group, decarboxylation of bio-oil by zeolites and HDO of guaiacol (a model compound of bio-oil) have been investigated. In this paper, recent developments of these upgrading reactions in our research group will be introduced.

Bio-functionalization of conductive textile materials with redox enzymes

NASA Astrophysics Data System (ADS)

Kahoush, M.; Behary, N.; Cayla, A.; Nierstrasz, V.

2017-10-01

In recent years, immobilization of oxidoreductase enzymes on electrically conductive materials has played an important role in the development of sustainable bio-technologies. Immobilization process allows the re-use of these bio-catalysts in their final applications. In this study, different methods of immobilizing redox enzymes on conductive textile materials were used to produce bio-functionalized electrodes. These electrodes can be used for bio-processes and bio-sensing in eco-designed applications in domains such as medicine and pollution control. However, the main challenge facing the stability and durability of these electrodes is the maintenance of the enzymatic activity after the immobilization. Hence, preventing the enzyme’s denaturation and leaching is a critical factor for the success of the immobilization processes.

Performance Analysis of the Enhanced Bio-Inspired Planning Algorithm for Rapid Situation Awareness Response

DTIC Science & Technology

2013-10-18

low cost robot testbed. 15. SUBJECT TERMS Bio-inspired trajectory generation, in-situ obstacle avoidance, low-cost LEGO robots, vision- based...will not affect the solution optimality and thus will be regarded as zero. Following the LP motion strategy Eq. (1), the position vector of the Lego ...Lobatto (LGL) method [14], the position of Lego robot can be further represented as ’ 1 ,( )j p jD   ζ ζ (6) in which ,0 ,,..., T j j j

BioNSi: A Discrete Biological Network Simulator Tool.

PubMed

Rubinstein, Amir; Bracha, Noga; Rudner, Liat; Zucker, Noga; Sloin, Hadas E; Chor, Benny

2016-08-05

Modeling and simulation of biological networks is an effective and widely used research methodology. The Biological Network Simulator (BioNSi) is a tool for modeling biological networks and simulating their discrete-time dynamics, implemented as a Cytoscape App. BioNSi includes a visual representation of the network that enables researchers to construct, set the parameters, and observe network behavior under various conditions. To construct a network instance in BioNSi, only partial, qualitative biological data suffices. The tool is aimed for use by experimental biologists and requires no prior computational or mathematical expertise. BioNSi is freely available at http://bionsi.wix.com/bionsi , where a complete user guide and a step-by-step manual can also be found.

BioData: a national aquatic bioassessment database

USGS Publications Warehouse

MacCoy, Dorene

2011-01-01

BioData is a U.S. Geological Survey (USGS) web-enabled database that for the first time provides for the capture, curation, integration, and delivery of bioassessment data collected by local, regional, and national USGS projects. BioData offers field biologists advanced capabilities for entering, editing, and reviewing the macroinvertebrate, algae, fish, and supporting habitat data from rivers and streams. It offers data archival and curation capabilities that protect and maintain data for the long term. BioData provides the Federal, State, and local governments, as well as the scientific community, resource managers, the private sector, and the public with easy access to tens of thousands of samples collected nationwide from thousands of stream and river sites. BioData also provides the USGS with centralized data storage for delivering data to other systems and applications through automated web services. BioData allows users to combine data sets of known quality from different projects in various locations over time. It provides a nationally aggregated database for users to leverage data from many independent projects that, until now, was not feasible at this scale. For example, from 1991 to 2011, the USGS Idaho Water Science Center collected more than 816 bioassessment samples from 63 sites for the National Water Quality Assessment (NAWQA) Program and more than 477 samples from 39 sites for a cooperative USGS and State of Idaho Statewide Water Quality Network (fig. 1). Using BioData, 20 years of samples collected for both of these projects can be combined for analysis. BioData delivers all of the data using current taxonomic nomenclature, thus relieving users of the difficult and time-consuming task of harmonizing taxonomy among samples collected during different time periods. Fish data are reported using the Integrated Taxonomic Information Service (ITIS) Taxonomic Serial Numbers (TSN's). A simple web-data input interface and self-guided, public data

Bio-Mimetic Sensors Based on Molecularly Imprinted Membranes

PubMed Central

Algieri, Catia; Drioli, Enrico; Guzzo, Laura; Donato, Laura

2014-01-01

An important challenge for scientific research is the production of artificial systems able to mimic the recognition mechanisms occurring at the molecular level in living systems. A valid contribution in this direction resulted from the development of molecular imprinting. By means of this technology, selective molecular recognition sites are introduced in a polymer, thus conferring it bio-mimetic properties. The potential applications of these systems include affinity separations, medical diagnostics, drug delivery, catalysis, etc. Recently, bio-sensing systems using molecularly imprinted membranes, a special form of imprinted polymers, have received the attention of scientists in various fields. In these systems imprinted membranes are used as bio-mimetic recognition elements which are integrated with a transducer component. The direct and rapid determination of an interaction between the recognition element and the target analyte (template) was an encouraging factor for the development of such systems as alternatives to traditional bio-assay methods. Due to their high stability, sensitivity and specificity, bio-mimetic sensors-based membranes are used for environmental, food, and clinical uses. This review deals with the development of molecularly imprinted polymers and their different preparation methods. Referring to the last decades, the application of these membranes as bio-mimetic sensor devices will be also reported. PMID:25196110

A Nascent Peptide Signal Responsive to Endogenous Levels of Polyamines Acts to Stimulate Regulatory Frameshifting on Antizyme mRNA.

PubMed

Yordanova, Martina M; Wu, Cheng; Andreev, Dmitry E; Sachs, Matthew S; Atkins, John F

2015-07-17

The protein antizyme is a negative regulator of cellular polyamine concentrations from yeast to mammals. Synthesis of functional antizyme requires programmed +1 ribosomal frameshifting at the 3' end of the first of two partially overlapping ORFs. The frameshift is the sensor and effector in an autoregulatory circuit. Except for Saccharomyces cerevisiae antizyme mRNA, the frameshift site alone only supports low levels of frameshifting. The high levels usually observed depend on the presence of cis-acting stimulatory elements located 5' and 3' of the frameshift site. Antizyme genes from different evolutionary branches have evolved different stimulatory elements. Prior and new multiple alignments of fungal antizyme mRNA sequences from the Agaricomycetes class of Basidiomycota show a distinct pattern of conservation 5' of the frameshift site consistent with a function at the amino acid level. As shown here when tested in Schizosaccharomyces pombe and mammalian HEK293T cells, the 5' part of this conserved sequence acts at the nascent peptide level to stimulate the frameshifting, without involving stalling detectable by toe-printing. However, the peptide is only part of the signal. The 3' part of the stimulator functions largely independently and acts at least mostly at the nucleotide level. When polyamine levels were varied, the stimulatory effect was seen to be especially responsive in the endogenous polyamine concentration range, and this effect may be more general. A conserved RNA secondary structure 3' of the frameshift site has weaker stimulatory and polyamine sensitizing effects on frameshifting. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

The NCBI BioSystems database

PubMed Central

Geer, Lewis Y.; Marchler-Bauer, Aron; Geer, Renata C.; Han, Lianyi; He, Jane; He, Siqian; Liu, Chunlei; Shi, Wenyao; Bryant, Stephen H.

2010-01-01

The NCBI BioSystems database, found at http://www.ncbi.nlm.nih.gov/biosystems/, centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI’s Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type, without requiring time-consuming inference of biological relationships from the literature or multiple experimental datasets. PMID:19854944

Bio-Manufacturing to market pilot project

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

Dressen, Tiffaney

The Bio-Manufacturing to Market pilot project was a part of the AMJIAC, the Advanced Manufacturing Jobs and Innovation Accelerator Challenge grant. This internship program set out to further define and enhance the talent pipeline from the University and local Community Colleges to startup culture in East Bay Area, provide undergraduate STEM students with opportunities outside academia, and provide startup companies with much needed talent. Over the 4 year period of performance, the Bio-Manufacturing to Market internship program sponsored 75 undergraduate STEM students who were able to spend anywhere from one to six semesters working with local Bay Area startup companiesmore » and DOE sponsored facilities/programs in the biotech, bio-manufacturing, and biomedical device fields.« less

Characterization of Deactivated Bio-oil Hydrotreating Catalysts

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

Wang, Huamin; Wang, Yong

Deactivation of bio-oil hydrotreating catalysts remains a significant challenge because of the poor quality of pyrolysis bio-oil input for hydrotreating and understanding their deactivation mode is critical to developing improved catalysts and processes. In this research, we developed an understanding of the deactivation of two-step bio-oil hydrotreating catalysts (sulfided Ru/C and sulfided CoMo/C) through detailed characterization of the catalysts using various complimentary analytical techniques. Severe fouling of both catalysts by carbonaceous species was the major form of deactivation, which is consistent with the significant loss of surface area and pore volume of both deactivated catalysts and the significant increase ofmore » the bulk density. Further analysis of the carbonaceous species by thermogravimetric analysis and x-ray photoelectron spectroscopy indicated that the carbonaceous species was formed by condensation reaction of active species such as sugars and sugar derivatives (aldehydes and ketones) in bio-oil feedstock during bio-oil hydrotreating under the conditions and catalysts used. Microscopy results did not show metal sintering of the Ru/C catalyst. However, X-ray diffraction indicated a probable transformation of the highly-active CoMoS phase in the sulfided CoMo/C catalyst to Co8S9 and MoS2 phase with low activity. Loss of the active site by transport of inorganic elements from the bio-oil and the reactor construction material onto the catalyst surface also might be a cause of deactivation as indicated by elemental analysis of spent catalysts.« less

BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling.

PubMed

Feng, Song; Ollivier, Julien F; Swain, Peter S; Soyer, Orkun S

2015-10-30

Systems biologists aim to decipher the structure and dynamics of signaling and regulatory networks underpinning cellular responses; synthetic biologists can use this insight to alter existing networks or engineer de novo ones. Both tasks will benefit from an understanding of which structural and dynamic features of networks can emerge from evolutionary processes, through which intermediary steps these arise, and whether they embody general design principles. As natural evolution at the level of network dynamics is difficult to study, in silico evolution of network models can provide important insights. However, current tools used for in silico evolution of network dynamics are limited to ad hoc computer simulations and models. Here we introduce BioJazz, an extendable, user-friendly tool for simulating the evolution of dynamic biochemical networks. Unlike previous tools for in silico evolution, BioJazz allows for the evolution of cellular networks with unbounded complexity by combining rule-based modeling with an encoding of networks that is akin to a genome. We show that BioJazz can be used to implement biologically realistic selective pressures and allows exploration of the space of network architectures and dynamics that implement prescribed physiological functions. BioJazz is provided as an open-source tool to facilitate its further development and use. Source code and user manuals are available at: http://oss-lab.github.io/biojazz and http://osslab.lifesci.warwick.ac.uk/BioJazz.aspx. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Identification and molecular characterization of oat peptides implicated on coeliac immune response

PubMed Central

Comino, Isabel; Bernardo, David; Bancel, Emmanuelle; Moreno, María de Lourdes; Sánchez, Borja; Barro, Francisco; Šuligoj, Tanja; Ciclitira, Paul J.; Cebolla, Ángel; Knight, Stella C.; Branlard, Gérard; Sousa, Carolina

2016-01-01

Background Oats provide important nutritional and pharmacological properties, although their safety in coeliac patients remains controversial. Previous studies have confirmed that the reactivity of the anti-33-mer monoclonal antibody with different oat varieties is proportional to the immune responses in terms of T-cell proliferation. Although the impact of these varieties on the adaptive response has been studied, the role of the dendritic cells (DC) is still poorly understood. The aim of this study is to characterize different oat fractions and to study their effect on DC from coeliac patients. Methods and results Protein fractions were isolated from oat grains and analyzed by SDS–PAGE. Several proteins were characterized in the prolamin fraction using immunological and proteomic tools, and by Nano-LC-MS/MS. These proteins, analogous to α- and γ-gliadin-like, showed reactive sequences to anti-33-mer antibody suggesting their immunogenic potential. That was further confirmed as some of the newly identified oat peptides had a differential stimulatory capacity on circulating DC from coeliac patients compared with healthy controls. Conclusions This is the first time, to our knowledge, where newly identified oat peptides have been shown to elicit a differential stimulatory capacity on circulating DC obtained from coeliac patients, potentially identifying immunogenic properties of these oat peptides. PMID:26853779

Bio-printing cell-laden Matrigel–agarose constructs

PubMed Central

Fan, Rong; Piou, Marine; Darling, Evan; Cormier, Denis; Sun, Jun; Wan, Jiandi

2017-01-01

3D printing of biological architectures that mimic the structural and functional features of in vivo tissues is of great interest in tissue engineering and the development of transplantable organ constructs. Printable bio-inks that are compatible with cellular activities play critical roles in the process of 3D bio-printing. Although a variety of hydrogels have been used as bio-inks for 3D bio-printing, they inherit poor mechanical properties and/or the lack of essential protein components that compromise their performance. Here, a hybrid Matrigel–agarose hydrogel system has been demonstrated that possesses both desired rheological properties for bio-printing and biocompatibility for long-term (11 days) cell culture. The agarose component in the hybrid hydrogel system enables the maintenance of 3D-printed structures, whereas Matrigel provides essential microenvironments for cell growth. When human intestinal epithelial HCT116 cells are encapsulated in the printed Matrigel–agarose constructs, high cell viability and proper cell spreading morphology are observed. Given that Matrigel is used extensively for 3D cell culturing, the developed 3D-printable Matrigel–agarose system will open a new way to construct Matrigel-based 3D constructs for cell culture and tissue engineering. PMID:27638155

Influence of dynamic coupled hydro-bio-mechanical processes on response of municipal solid waste and liner system in bioreactor landfills.

PubMed

Reddy, Krishna R; Kumar, Girish; Giri, Rajiv K

2017-05-01

A two-dimensional (2-D) mathematical model is presented to predict the response of municipal solid waste (MSW) of conventional as well as bioreactor landfills undergoing coupled hydro-bio-mechanical processes. The newly developed and validated 2-D coupled mathematical modeling framework combines and simultaneously solves a two-phase flow model based on the unsaturated Richard's equation, a plain-strain formulation of Mohr-Coulomb mechanical model and first-order decay kinetics biodegradation model. The performance of both conventional and bioreactor landfill was investigated holistically, by evaluating the mechanical settlement, extent of waste degradation with subsequent changes in geotechnical properties, landfill slope stability, and in-plane shear behavior (shear stress-displacement) of composite liner system and final cover system. It is concluded that for the given specific conditions considered, bioreactor landfill attained an overall stabilization after a continuous leachate injection of 16years, whereas the stabilization was observed after around 50years of post-closure in conventional landfills, with a total vertical strain of 36% and 37% for bioreactor and conventional landfills, respectively. The significant changes in landfill settlement, the extent of MSW degradation, MSW geotechnical properties, along with their influence on the in-plane shear response of composite liner and final cover system, between the conventional and bioreactor landfills, observed using the mathematical model proposed in this study, corroborates the importance of considering coupled hydro-bio-mechanical processes while designing and predicting the performance of engineered bioreactor landfills. The study underscores the importance of considering the effect of coupled processes while examining the stability and integrity of the liner and cover systems, which form the integral components of a landfill. Moreover, the spatial and temporal variations in the landfill settlement, the

The soil-water balance simulations of a grassland in response to CO2, rainfall, and biodiversity manipulations at BioCON

NASA Astrophysics Data System (ADS)

Flinker, R. H.; Cardenas, M.; Caldwell, T. G.; Rich, R.; Reich, P.

2013-12-01

The BioCON (Biodiversity, CO2 and N) experiment has been continuously running since 1997. Operated by the University of Minnesota and located within the Cedar Creek Ecosystem Science Reserve in Minnesota, USA, BioCON is a Free-Air CO2 Enrichment (FACE) experiment that investigates plant community response to three key environmental variables: nitrogen, atmospheric CO2 and biodiversity. More recently rainfall exclusion and temperature manipulation were added to the experiment which amounts to 371 plots. The site attempts to replicate predicted average temperature increases and a northern shift of plant species and any associated consequences. FACE experiments have been conducted for a number of years in different countries, but the focus has generally been on how plant communities, soil respiration and microbes respond. Minimal work has been focused on the hydrologic aspects of these experiments which are potentially valuable for investigating global warming effects on local and plot-scale ecohydrology. Thus, the objective of this work is to characterize and model unsaturated flow for different CO2 and rainfall treatments in order to see how they affect soil moisture dynamics and groundwater recharge on grasslands of central Minnesota. Our study focuses on simulating soil moisture dynamics in eighteen of the BioCON plots: six bare plots with regular rainfall regimes (zero plant species, three plots with elevated atmospheric CO2 levels), six regular rainfall regimes (nine plant species, three plots with elevated atmospheric CO2 levels) and six reduced rainfall regimes (nine plant species, three plots with elevated atmospheric CO2 levels). The Simultaneous Heat and Water (SHAW) model, which solves the Richards equation for unsaturated zone water flow coupled to a comprehensive energy balance model, was parameterized with a combination of field and lab estimates of soil properties. Field estimates of saturated hydraulic conductivity using tension infiltrometers ranged

Potency of bio-charcoal briquette from leather cassava tubers and industrial sludge

NASA Astrophysics Data System (ADS)

Citrasari, Nita; Pinatih, Tety A.; Kuncoro, Eko P.; Soegianto, Agoes; Salamun, Irawan, Bambang

2017-06-01

The purpose of this study was to determine the quality of the bio-charcoal briquette with materials from leather cassava tubers and sludge of wastewater treatment plant. The first, bio-charcoal briquette analized stability test and compressive strength. Then, bio-charcoal briquette with best value analyzed for parameter including moisture content, ash content, calorific content, and burned test. The result briquette quality based on compressive strength for bio-charcoal briquettes carbonated water content between 3.8%-4.5% and non-carbonated bio-charcoal briquettes between 5.2%-7.6%. Bio-charcoal carbonation briquette ash content was between 5.30%-7.40% and non-carbonated bio-charcoal briquettes was between 6.86%-7.46%. Bio-charcoal carbonation levels briquettes heated between 578.2 calories/g-1837.7 calories/g and non carbonatedbio-charcoal briquettes between 858.1 calories/g-891.1 calories/g. Carbonated bio-charcoal burned test was between 48-63 minutes and non-carbonated bio-charcoal was between 22-42 minutes. Emissions resulted from the bio-charcoal briquettes for carbonated and non carbonated composition according to the government regulations ESDM No. 047 of 2006 which, at 128 mg/Nm3 and 139 mg/Nm3.

Bio-oil based biorefinery strategy for the production of succinic acid.

PubMed

Wang, Caixia; Thygesen, Anders; Liu, Yilan; Li, Qiang; Yang, Maohua; Dang, Dan; Wang, Ze; Wan, Yinhua; Lin, Weigang; Xing, Jianmin

2013-01-01

Succinic acid is one of the key platform chemicals which can be produced via biotechnology process instead of petrochemical process. Biomass derived bio-oil have been investigated intensively as an alternative of diesel and gasoline fuels. Bio-oil could be fractionized into organic phase and aqueous phase parts. The organic phase bio-oil can be easily upgraded to transport fuel. The aqueous phase bio-oil (AP-bio-oil) is of low value. There is no report for its usage or upgrading via biological methods. In this paper, the use of AP-bio-oil for the production of succinic acid was investigated. The transgenic E. coli strain could grow in modified M9 medium containing 20 v/v% AP-bio-oil with an increase in OD from 0.25 to 1.09. And 0.38 g/L succinic acid was produced. With the presence of 4 g/L glucose in the medium, succinic acid concentration increased from 1.4 to 2.4 g/L by addition of 20 v/v% AP-bio-oil. When enzymatic hydrolysate of corn stover was used as carbon source, 10.3 g/L succinic acid was produced. The obtained succinic acid concentration increased to 11.5 g/L when 12.5 v/v% AP-bio-oil was added. However, it decreased to 8 g/L when 50 v/v% AP-bio-oil was added. GC-MS analysis revealed that some low molecular carbon compounds in the AP-bio-oil were utilized by E. coli. The results indicate that AP-bio-oil can be used by E. coli for cell growth and succinic acid production.

Smart surface coating of drug nanoparticles with cross-linkable polyethylene glycol for bio-responsive and highly efficient drug delivery

NASA Astrophysics Data System (ADS)

Wei, Weijia; Zhang, Xiujuan; Chen, Xianfeng; Zhou, Mengjiao; Xu, Ruirui; Zhang, Xiaohong

2016-04-01

Many drug molecules can be directly used as nanomedicine without the requirement of any inorganic or organic carriers such as silica and liposome nanostructures. This new type of carrier-free drug nanoparticles (NPs) has great potential in clinical treatment because of its ultra-high drug loading capacity and biodegradability. For practical applications, it is essential for such nanomedicine to possess robust stability and minimal premature release of therapeutic molecules during circulation in the blood stream. To meet this requirement, herein, we develop GSH-responsive and crosslinkable amphiphilic polyethylene glycol (PEG) molecules to modify carrier-free drug NPs. These PEG molecules can be cross-linked on the surface of the NPs to endow them with greater stability and the cross-link is sensitive to intracellular environment for bio-responsive drug release. With this elegant design, our experimental results show that the liberation of DOX from DOX-cross-linked PEG NPs is dramatically slower than that from DOX-non-cross-linked PEG NPs, and the DOX release profile can be controlled by tuning the concentration of the reducing agent to break the cross-link between PEG molecules. More importantly, in vivo studies reveal that the DOX-cross-linked PEG NPs exhibit favorable blood circulation half-life (>4 h) and intense accumulation in tumor areas, enabling effective anti-cancer therapy. We expect this work will provide a powerful strategy for stabilizing carrier-free nanomedicines and pave the way to their successful clinical applications in the future.Many drug molecules can be directly used as nanomedicine without the requirement of any inorganic or organic carriers such as silica and liposome nanostructures. This new type of carrier-free drug nanoparticles (NPs) has great potential in clinical treatment because of its ultra-high drug loading capacity and biodegradability. For practical applications, it is essential for such nanomedicine to possess robust stability

Fast Pyrolysis Oil Stabilization: An Integrated Catalytic and Membrane Approach for Improved Bio-oils. Final Report

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

George W. Huber; Upadhye, Aniruddha A.; Ford, David M.

. Experiments with model AFBO excluding guaiacol were also conducted. NF membranes showed retention factors of glucose greater than 80% and of acetic acid less than 15% when operated at transmembrane pressures near 60 bar. Task 3.0 Acid Removal by Catalytic Processing It was found that the TAN reduction in bio-oil was very difficult using low temperature hydrogenation in flow and batch reactors. Acetic acid is very resilient to hydrogenation and we could only achieve about 16% conversion for acetic acid. Although it was observed that acetic acid was not responsible for instability of aqueous fraction of bio-oil during ageing studies (described in task 5). The bimetallic catalyst PtRe/ceria-zirconia was found to be best catalyst because its ability to convert the acid functionality with low conversion to gas phase carbon. Hydrogenation of the whole bio-oil was carried out at 125°C, 1450 psi over Ru/C catalyst in a flow reactor. Again, negligible acetic acid conversion was obtained in low temperature hydrogenation. Hydrogenation experiments with whole bio-oil were difficult to perform because of difficulty to pumping the high viscosity oil and reactor clogging. Task 4.0 Acid Removal using Ion Exchange Resins DOWEX M43 resin was used to carry out the neutralization of bio-oil using a packed bed column. The pH of the bio-oil increased from 2.43 to 3.7. The GC analysis of the samples showed that acetic acid was removed from the bio-oil during the neutralization and recovered in the methanol washing. But it was concluded that process would not be economical at large scale as it is extremely difficult to regenerate the resin once the bio-oil is passed over it. Task 5.0 Characterization of Upgraded Bio-oils We investigated the viscosity, microstructure, and chemical composition of bio-oils prepared by a fast pyrolysis approach, upon aging these fuels at 90ºC for periods of several days. Our results suggest that the viscosity increase is not correlated with the acids or char present

Bioelectronic platforms for optimal bio-anode of bio-electrochemical systems: From nano- to macro scopes.

PubMed

Kim, Bongkyu; An, Junyeong; Fapyane, Deby; Chang, In Seop

2015-11-01

The current trend of bio-electrochemical systems is to improve strategies related to their applicability and potential for scaling-up. To date, literature has suggested strategies, but the proposal of correlations between each research field remains insufficient. This review paper provides a correlation based on platform techniques, referred to as bio-electronics platforms (BEPs). These BEPs consist of three platforms divided by scope scale: nano-, micro-, and macro-BEPs. In the nano-BEP, several types of electron transfer mechanisms used by electrochemically active bacteria are discussed. In the micro-BEP, factors affecting the formation of conductive biofilms and transport of electrons in the conductive biofilm are investigated. In the macro-BEP, electrodes and separators in bio-anode are debated in terms of real applications, and a scale-up strategy is discussed. Overall, the challenges of each BEP are highlighted, and potential solutions are suggested. In addition, future research directions are provided and research ideas proposed to develop research interest. Copyright © 2015 Elsevier Ltd. All rights reserved.

Amphiphilic Bio-molecules/ZnO Interface: Enhancement of Bio-affinity and Dispersibility

NASA Astrophysics Data System (ADS)

Meng, Xiu-Qing; Fang, Yun-Zhang; Wu, Feng-Min

2012-01-01

The dispersibility of bio-molecules such as lecithins on the surface of ZnO nanowires are investigated for biosensor applications. Lecithins can be absorbed on an as-synthesized ZnO nanowire surface in the form of sub-micro sized clusters, while scattering well on those annealed under oxygen atmosphere. Wettability analysis reveals that the as-synthesized ZnO nanowires bear a super-hydrophobic surface, which convents to superhydrophilic after oxygen annealing. First-principles calculations indicate that the adsorption energy of ZnO with water is about 0.2 eV at a distance of 2 Å when it is superhydrophilic, suggesting that lecithin can be absorbed on the hydrophilic surface stably at this distance and the bio-affinity can be enhanced under this condition.

Neurite outgrowth stimulatory effects of culinary-medicinal mushrooms and their toxicity assessment using differentiating Neuro-2a and embryonic fibroblast BALB/3T3.

PubMed

Phan, Chia-Wei; David, Pamela; Naidu, Murali; Wong, Kah-Hui; Sabaratnam, Vikineswary

2013-10-11

Mushrooms are not only regarded as gourmet cuisine but also as therapeutic agent to promote cognition health. However, little toxicological information is available regarding their safety. Therefore, the aim of this study was to screen selected ethno-pharmacologically important mushrooms for stimulatory effects on neurite outgrowth and to test for any cytotoxicity. The stimulatory effect of mushrooms on neurite outgrowth was assessed in differentiating mouse neuroblastoma (N2a) cells. Neurite length was measured using Image-Pro Insight processor system. Neuritogenesis activity was further validated by fluorescence immunocytochemical staining of neurofilaments. In vitro cytotoxicity was investigated by using mouse embryonic fibroblast (BALB/3T3) and N2a cells for any embryo- and neuro-toxic effects; respectively. Aqueous extracts of Ganoderma lucidum, Lignosus rhinocerotis, Pleurotus giganteus and Grifola frondosa; as well as an ethanol extract of Cordyceps militaris significantly (p < 0.05) promoted the neurite outgrowth in N2a cells by 38.4 ± 4.2%, 38.1 ± 2.6%, 33.4 ± 4.6%, 33.7 ± 1.5%, and 35.8 ± 3.4%; respectively. The IC50 values obtained from tetrazolium (MTT), neutral red uptake (NRU) and lactate dehydrogenase (LDH) release assays showed no toxic effects following 24 h exposure of N2a and 3T3 cells to mushroom extracts. Our results indicate that G. lucidum, L. rhinocerotis, P. giganteus, G. frondosa and C. militaris may be developed as safe and healthy dietary supplements for brain and cognitive health.

Technical and technological solution for vegetal bio-stimulants obtaining

NASA Astrophysics Data System (ADS)

Anghelache, D. G.; Diaconescu, I.; Pătraşcu, R.

2017-08-01

The paper presents a modern technology for bio fertilizers resulted from waste plant mass after harvesting crops Experimental products were obtained rich in nutrients, but unstable in terms of existing microorganisms. Therefore, they conducted further studies to obtaining bio fungicide herb, so in all investigations undertaken so far in the laboratory, were able to conclude that the introduction of medicinal plant extracts with fungicidal effect into the bio fertilizers obtained by degradation of plant material post-harvest can get various bio-stimulants with nourishing effect upon the plants. Following this technology the paper’s objective is to identify a flux scheme for experimental equipment which can produce as final outcome this type of bio-stimulant. Also, in this work, this equipment will be chosen and will be designed following and obeying to the request of every step of the above technology.

Bio-composites from mycelium reinforced agricultural substrates

USDA-ARS?s Scientific Manuscript database

There is a need for biodegradable alternatives to the inert plastics and expanded foams currently used in in manufacturing processes and device components. The material focused on in this report is a bio-composite patented by Ecovative Design, LLC. The bio-composite utilizes the fungus mycelium to i...

BioWarehouse: a bioinformatics database warehouse toolkit.

PubMed

Lee, Thomas J; Pouliot, Yannick; Wagner, Valerie; Gupta, Priyanka; Stringer-Calvert, David W J; Tenenbaum, Jessica D; Karp, Peter D

2006-03-23

This article addresses the problem of interoperation of heterogeneous bioinformatics databases. We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. BioWarehouse embodies significant progress on the database integration problem for bioinformatics.

BioCartilage Improves Cartilage Repair Compared With Microfracture Alone in an Equine Model of Full-Thickness Cartilage Loss.

PubMed

Fortier, Lisa A; Chapman, Hannah S; Pownder, Sarah L; Roller, Brandon L; Cross, Jessica A; Cook, James L; Cole, Brian J

2016-09-01

Microfracture (MFx) remains a dominant treatment strategy for symptomatic articular cartilage defects. Biologic scaffold adjuncts, such as particulated allograft articular cartilage (BioCartilage) combined with platelet-rich plasma (PRP), offer promise in improving clinical outcomes as an adjunct to MFx. To evaluate the safety, biocompatibility, and efficacy of BioCartilage and PRP for cartilage repair in a preclinical equine model of full-thickness articular cartilage loss. Controlled laboratory study. Two 10-mm-diameter full-thickness cartilage defects were created in 5 horses in the trochlear ridge of both knees: one proximal (high load) and another distal (low load). Complete blood counts were performed on each peripheral blood and resultant PRP sample. In each horse, one knee received MFx with BioCartilage + PRP, and the other knee received MFx alone. Horses were euthanized at 13 months. Outcomes were assessed with serial arthroscopy, magnetic resonance imaging (MRI), micro-computed tomography (micro-CT), and histology. Statistics were performed using a mixed-effects model with response variable contrasts. No complications occurred. PRP generated in all subjects yielded an increase in platelet fold of 3.8 ± 4.7. Leukocyte concentration decreased in PRP samples by an average fold change of 5 ± 0.1. The overall International Cartilage Repair Society repair score in both the proximal and distal defects was significantly higher (better) in the BioCartilage group compared with MFx (proximal BioCartilage: 7.4 ± 0.51, MFx 4.8 ± 0.1, P = .041; distal BioCartilage: 5.6 ± 0.98, MFx 2.6 ± 1.5, P = .022). BioCartilage-treated proximal defects demonstrated improved histologic scores for repair-host integration (BioCartilage, 96 ± 9; MFx, 68 ± 18; P = .02), base integration (BioCartilage, 100 ± 0; MFx, 70 ± 37; P = .04), and formation of collagen type II (BioCartilage, 82 ± 8; MFx, 58 ± 11; P = .05) compared with the positive control. On MRI, T2 relaxation time

Characterization of bio char derived from tapioca skin

NASA Astrophysics Data System (ADS)

Hasnan, F. I.; Iamail, K. N.; Musa, M.; Jaapar, J.; Alwi, H.; Hamid, K. K. K.

2018-03-01

Pyrolysis of tapioca skin was conducted to produce bio chars in the range between 500°C–800°C. Surface modification treatment were performed on bio chars by using chemicals within 24 hours at 30°C and hot water within 1 hour to enhance the bio char’s adsorption properties according to surface area, pore volume, pore size, crystallinity structure and functional groups. The samples were characterized by using BET, XRD, FTIR and Methylene Blue adsorption. Based on BET result, it showed the surface area increased as the pyrolysis temperature increased followed by pore volume and pore size for S0. The optimum temperature for SNaOH, SHW and SMeOH was at 600°C, 700°C and 800°C with the surface area of 75.9874, 274.5066 and 351.5531 m2/g respectively compared to S0 while SP3HO4 has the worst result since it felt on macroporous structure. The percentage of MB adsorption was followed the size of bio chars surface area. Based on FTIR result, at temperature 500°C to 700°C, the bio chars still have functional groups while at 800°C, many functional groups were diminished due to high temperature struck on them. XRD result showed all the bio chars were amorphous. In conclusion, the best surface modification treatment was by Methanol followed by hot water and Sodium Hydroxide at temperature of 700°C and 800°C while Ortho-Phosphoric acid was the worst one and was not suitable for bio char’s surface modification for adsorption purpose.

Bio-oil based biorefinery strategy for the production of succinic acid

PubMed Central

2013-01-01

Background Succinic acid is one of the key platform chemicals which can be produced via biotechnology process instead of petrochemical process. Biomass derived bio-oil have been investigated intensively as an alternative of diesel and gasoline fuels. Bio-oil could be fractionized into organic phase and aqueous phase parts. The organic phase bio-oil can be easily upgraded to transport fuel. The aqueous phase bio-oil (AP-bio-oil) is of low value. There is no report for its usage or upgrading via biological methods. In this paper, the use of AP-bio-oil for the production of succinic acid was investigated. Results The transgenic E. coli strain could grow in modified M9 medium containing 20 v/v% AP-bio-oil with an increase in OD from 0.25 to 1.09. And 0.38 g/L succinic acid was produced. With the presence of 4 g/L glucose in the medium, succinic acid concentration increased from 1.4 to 2.4 g/L by addition of 20 v/v% AP-bio-oil. When enzymatic hydrolysate of corn stover was used as carbon source, 10.3 g/L succinic acid was produced. The obtained succinic acid concentration increased to 11.5 g/L when 12.5 v/v% AP-bio-oil was added. However, it decreased to 8 g/L when 50 v/v% AP-bio-oil was added. GC-MS analysis revealed that some low molecular carbon compounds in the AP-bio-oil were utilized by E. coli. Conclusions The results indicate that AP-bio-oil can be used by E. coli for cell growth and succinic acid production. PMID:23657107

BioGraph: unsupervised biomedical knowledge discovery via automated hypothesis generation

PubMed Central

2011-01-01

We present BioGraph, a data integration and data mining platform for the exploration and discovery of biomedical information. The platform offers prioritizations of putative disease genes, supported by functional hypotheses. We show that BioGraph can retrospectively confirm recently discovered disease genes and identify potential susceptibility genes, outperforming existing technologies, without requiring prior domain knowledge. Additionally, BioGraph allows for generic biomedical applications beyond gene discovery. BioGraph is accessible at http://www.biograph.be. PMID:21696594

[Characteristics and operation of enhanced continuous bio-hydrogen production reactor using support carrier].

PubMed

Ren, Nan-qi; Tang, Jing; Gong, Man-li

2006-06-01

A kind of granular activated carbon, whose granular size is no more than 2mm and specific gravity is 1.54g/cm3, was used as the support carrier to allow retention of activated sludge within a continuous stirred-tank reactor (CSTR) using molasses wastewater as substrate for bio-hydrogen production. Continuous operation characteristics and operational controlling strategy of the enhanced continuous bio-hydrogen production system were investigated. It was indicated that, support carriers could expand the activity scope of hydrogen production bacteria, make the system fairly stable in response to organic load impact and low pH value (pH <3.8), and maintain high biomass concentration in the reactor at low HRT. The reactor with ethanol-type fermentation achieved an optimal hydrogen production rate of 0.37L/(g x d), while the pH value ranged from 3.8 to 4.4, and the hydrogen content was approximately 40% approximately 57% of biogas. It is effective to inhibit the methanogens by reducing the pH value of the bio-hydrogen production system, consequently accelerate the start-up of the reactor.

Bio-Nanobattery Development and Characterization

NASA Technical Reports Server (NTRS)

King, Glen C.; Choi, Sang H.; Chu, Sang-Hyon; Kim, Jae-Woo; Watt, Gerald D.; Lillehei, Peter T.; Park, Yeonjoon; Elliott, James R.

2005-01-01

A bio-nanobattery is an electrical energy storage device that utilizes organic materials and processes on an atomic, or nanometer-scale. The bio-nanobattery under development at NASA s Langley Research Center provides new capabilities for electrical power generation, storage, and distribution as compared to conventional power storage systems. Most currently available electronic systems and devices rely on a single, centralized power source to supply electrical power to a specified location in the circuit. As electronic devices and associated components continue to shrink in size towards the nanometer-scale, a single centralized power source becomes impractical. Small systems, such as these, will require distributed power elements to reduce Joule heating, to minimize wiring quantities, and to allow autonomous operation of the various functions performed by the circuit. Our research involves the development and characterization of a bio-nanobattery using ferritins reconstituted with both an iron core (Fe-ferritin) and a cobalt core (Co-ferritin). Synthesis and characterization of the Co-ferritin and Fe-ferritin electrodes were performed, including reducing capability and the half-cell electrical potentials. Electrical output of nearly 0.5 V for the battery cell was measured. Ferritin utilizing other metallic cores were also considered to increase the overall electrical output. Two dimensional ferritin arrays were produced on various substrates to demonstrate the feasibility of a thin-film nano-scaled power storage system for distributed power storage applications. The bio-nanobattery will be ideal for nanometerscaled electronic applications, due to the small size, high energy density, and flexible thin-film structure. A five-cell demonstration article was produced for concept verification and bio-nanobattery characterization. Challenges to be addressed include the development of a multi-layered thin-film, increasing the energy density, dry-cell bionanobattery

Bio-oils from biomass slow pyrolysis: a chemical and toxicological screening.

PubMed

Cordella, Mauro; Torri, Cristian; Adamiano, Alessio; Fabbri, Daniele; Barontini, Federica; Cozzani, Valerio

2012-09-15

Bio-oils were produced from bench-scale slow-pyrolysis of three different biomass samples (corn stalks, poplar and switchgrass). Experimental protocols were developed and applied in order to screen their chemical composition. Several hazardous compounds were detected in the bio-oil samples analysed, including phenols, furans and polycyclic aromatic hydrocarbons. A procedure was outlined and applied to the assessment of toxicological and carcinogenic hazards of the bio-oils. The following hazardous properties were considered: acute toxicity; ecotoxicity; chronic toxicity; carcinogenicity. Parameters related to these properties were quantified for each component identified in the bio-oils and overall values were estimated for the bio-oils. The hazard screening carried out for the three bio-oils considered suggested that: (i) hazards to human health could be associated with chronic exposures to the bio-oils; (ii) acute toxic effects on humans and eco-toxic effects on aquatic ecosystems could also be possible in the case of loss of containment; and (iii) bio-oils may present a marginal potential carcinogenicity. The approach outlined allows the collection of screening information on the potential hazards posed by the bio-oils. This can be particularly useful when limited time and analytical resources reduce the possibility to obtain detailed specific experimental data. Copyright © 2012 Elsevier B.V. All rights reserved.

Stabilization of Bio-Oil Fractions for Insertion into Petroleum Refineries

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

Brown, Robert C.; Smith, Ryan; Wright, Mark

This project is part of a collaboration effort between Iowa State University (ISU), University of Oklahoma (OK) and Pacific Northwest National Laboratory (PNNL). The purpose of this project is to stabilize bio-oil fractions and improve their suitability for insertion into petroleum refineries. Bio-oil from fast pyrolysis of biomass is a complex mixture of unstable organic compounds. These organic compounds react under standard room conditions resulting in increases in bio-oil viscosity and water content – both detrimental for bio-oil storage and transportation. This study employed fractionation and upgrading systems to improve the stability of bio-oil. The fractionation system consists of amore » series of condensers, and electrostatic precipitators designed to separate bio-oil into five fractions: soluble carbohydrates (SF1&2), clean phenolic oligomers (CPO) and middle fraction (SF3&4), light oxygenates (SF5). A two-stage upgrading process was designed to process bio-oil stage fractions into stable products that can be inserted into a refinery. In the upgrading system, heavy and middle bio-oil fractions were upgraded into stable oil via cracking and subsequent hydrodeoxygenation. The light oxygenate fraction was steam reformed to provide a portion of requisite hydrogen for hydroprocessing. Hydrotreating and hydrocracking employed hydrogen from natural gas, fuel gas and light oxygenates reforming. The finished products from this study consist of gasoline- and diesel-blend stock fuels.« less

The Evolution of Psychology as a Basic Bio-behavioral Science in Healthcare Education.

PubMed

Carr, John E

2017-12-01

For over a century, researchers and educators have called for the integration of psychological science into medical school curricula, but such efforts have been impeded by barriers within medicine and psychology. In addressing these barriers, Psychology has re-examined its relationship to Medicine, incorporated psychological practices into health care, and redefined its parameters as a science. In response to interdisciplinary research into the mechanisms of bio-behavioral interaction, Psychology evolved from an ancillary social science to a bio-behavioral science that is fundamental to medicine and health care. However, in recent medical school curriculum innovations, psychological science is being reduced to a set of "clinical skills," and once again viewed as an ancillary social science. These developments warrant concern and consideration of new approaches to integrating psychological science in medical education.

An ex situ evaluation of TBA- and MTBE-baited bio-traps.

PubMed

North, Katharine P; Mackay, Douglas M; Annable, Michael D; Sublette, Kerry L; Davis, Greg; Holland, Reef B; Petersen, Daniel; Scow, Kate M

2012-08-01

Aquifer microbial communities can be investigated using Bio-traps(®) ("bio-traps"), passive samplers containing Bio-Sep(®) beads ("bio-beads") that are deployed in monitoring wells to be colonized by bacteria delivered via groundwater flow through the well. When bio-beads are "baited" with organic contaminants enriched in (13)C, stable isotope probing allows assessment of the composition and activity of the microbial community. This study used an ex situ system fed by groundwater continuously extracted from an adjacent monitoring well within an experimentally-created aerobic zone treating a tert-butyl alcohol (TBA) plume. The goal was to evaluate aspects of bio-trap performance that cannot be studied quantitatively in situ. The measured groundwater flow through a bio-trap housing suggests that such traps might typically "sample" about 1.8 L per month. The desorption of TBA or methyl tert-butyl ether (MTBE) bait from bio-traps during a typical deployment duration of 6 weeks was approximately 90% and 45%, respectively, of the total initial bait load, with initially high rate of mass loss that decreased markedly after a few days. The concentration of TBA in groundwater flowing by the TBA-baited bio-beads was estimated to be as high as 3400 mg/L during the first few days, which would be expected to inhibit growth of TBA-degrading microbes. Initial inhibition was also implied for the MTBE-baited bio-trap, but at lower concentrations and for a shorter time. After a few days, concentrations in groundwater flowing through the bio-traps dropped below inhibitory concentrations but remained 4-5 orders of magnitude higher than TBA or MTBE concentrations within the aquifer at the experimental site. Desorption from the bio-beads during ex situ deployment occurred at first as predicted by prior sorption analyses of bio-beads but with apparent hysteresis thereafter, possibly due to mass transfer limitations caused by colonizing microbes. These results suggest that TBA- or MTBE

An ex situ evaluation of TBA- and MTBE-baited bio-traps

PubMed Central

North, Katharine P.; Mackay, Douglas M.; Annable, Michael D.; Sublette, Kerry L.; Davis, Greg; Holland, Reef B.; Petersen, Daniel; Scow, Kate M.

2013-01-01

Aquifer microbial communities can be investigated using Bio-traps® (“bio-traps”), passive samplers containing Bio-Sep® beads (“bio-beads”) that are deployed in monitoring wells to be colonized by bacteria delivered via groundwater flow through the well. When bio-beads are “baited” with organic contaminants enriched in 13C, stable isotope probing allows assessment of the composition and activity of the microbial community. This study used an ex situ system fed by groundwater continuously extracted from an adjacent monitoring well within an experimentally-created aerobic zone treating a tert-butyl alcohol (TBA) plume. The goal was to evaluate aspects of bio-trap performance that cannot be studied quantitatively in situ. The measured groundwater flow through a bio-trap housing suggests that such traps might typically “sample” about 1.8 L per month. The desorption of TBA or methyl tert-butyl ether (MTBE) bait from bio-traps during a typical deployment duration of 6 weeks was approximately 90% and 45%, respectively, of the total initial bait load, with initially high rate of mass loss that decreased markedly after a few days. The concentration of TBA in groundwater flowing by the TBA-baited bio-beads was estimated to be as high as 3400 mg/L during the first few days, which would be expected to inhibit growth of TBA-degrading microbes. Initial inhibition was also implied for the MTBE-baited bio-trap, but at lower concentrations and for a shorter time. After a few days, concentrations in groundwater flowing through the bio-traps dropped below inhibitory concentrations but remained 4–5 orders of magnitude higher than TBA or MTBE concentrations within the aquifer at the experimental site. Desorption from the bio-beads during ex situ deployment occurred at first as predicted by prior sorption analyses of bio-beads but with apparent hysteresis thereafter, possibly due to mass transfer limitations caused by colonizing microbes. These results suggest that

Cyanobacteria: A Precious Bio-resource in Agriculture, Ecosystem, and Environmental Sustainability

PubMed Central

Singh, Jay Shankar; Kumar, Arun; Rai, Amar N.; Singh, Devendra P.

2016-01-01

Keeping in view, the challenges concerning agro-ecosystem and environment, the recent developments in biotechnology offers a more reliable approach to address the food security for future generations and also resolve the complex environmental problems. Several unique features of cyanobacteria such as oxygenic photosynthesis, high biomass yield, growth on non-arable lands and a wide variety of water sources (contaminated and polluted waters), generation of useful by-products and bio-fuels, enhancing the soil fertility and reducing green house gas emissions, have collectively offered these bio-agents as the precious bio-resource for sustainable development. Cyanobacterial biomass is the effective bio-fertilizer source to improve soil physico-chemical characteristics such as water-holding capacity and mineral nutrient status of the degraded lands. The unique characteristics of cyanobacteria include their ubiquity presence, short generation time and capability to fix the atmospheric N2. Similar to other prokaryotic bacteria, the cyanobacteria are increasingly applied as bio-inoculants for improving soil fertility and environmental quality. Genetically engineered cyanobacteria have been devised with the novel genes for the production of a number of bio-fuels such as bio-diesel, bio-hydrogen, bio-methane, synga, and therefore, open new avenues for the generation of bio-fuels in the economically sustainable manner. This review is an effort to enlist the valuable information about the qualities of cyanobacteria and their potential role in solving the agricultural and environmental problems for the future welfare of the planet. PMID:27148218

Cyanobacteria: A Precious Bio-resource in Agriculture, Ecosystem, and Environmental Sustainability.

PubMed

Singh, Jay Shankar; Kumar, Arun; Rai, Amar N; Singh, Devendra P

2016-01-01

Keeping in view, the challenges concerning agro-ecosystem and environment, the recent developments in biotechnology offers a more reliable approach to address the food security for future generations and also resolve the complex environmental problems. Several unique features of cyanobacteria such as oxygenic photosynthesis, high biomass yield, growth on non-arable lands and a wide variety of water sources (contaminated and polluted waters), generation of useful by-products and bio-fuels, enhancing the soil fertility and reducing green house gas emissions, have collectively offered these bio-agents as the precious bio-resource for sustainable development. Cyanobacterial biomass is the effective bio-fertilizer source to improve soil physico-chemical characteristics such as water-holding capacity and mineral nutrient status of the degraded lands. The unique characteristics of cyanobacteria include their ubiquity presence, short generation time and capability to fix the atmospheric N2. Similar to other prokaryotic bacteria, the cyanobacteria are increasingly applied as bio-inoculants for improving soil fertility and environmental quality. Genetically engineered cyanobacteria have been devised with the novel genes for the production of a number of bio-fuels such as bio-diesel, bio-hydrogen, bio-methane, synga, and therefore, open new avenues for the generation of bio-fuels in the economically sustainable manner. This review is an effort to enlist the valuable information about the qualities of cyanobacteria and their potential role in solving the agricultural and environmental problems for the future welfare of the planet.

The BioCyc collection of microbial genomes and metabolic pathways.

PubMed

Karp, Peter D; Billington, Richard; Caspi, Ron; Fulcher, Carol A; Latendresse, Mario; Kothari, Anamika; Keseler, Ingrid M; Krummenacker, Markus; Midford, Peter E; Ong, Quang; Ong, Wai Kit; Paley, Suzanne M; Subhraveti, Pallavi

2017-08-17

BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by biologist curators. BioCyc also provides an extensive range of query tools, visualization services and analysis software. Recent advances in BioCyc include an expansion in the content of BioCyc in terms of both the number of genomes and the types of information available for each genome; an expansion in the amount of curated content within BioCyc; and new developments in the BioCyc software tools including redesigned gene/protein pages and metabolite pages; new search tools; a new sequence-alignment tool; a new tool for visualizing groups of related metabolic pathways; and a facility called SmartTables, which enables biologists to perform analyses that previously would have required a programmer's assistance. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Alkaline hydrothermal liquefaction of swine carcasses to bio-oil.

PubMed

Zheng, Ji-Lu; Zhu, Ming-Qiang; Wu, Hai-tang

2015-09-01

It is imperative that swine carcasses are disposed of safely, practically and economically. Alkaline hydrothermal liquefaction of swine carcasses to bio-oil was performed. Firstly, the effects of temperature, reaction time and pH value on the yield of each liquefaction product were determined. Secondly, liquefaction products, including bio-oil and solid residue, were characterized. Finally, the energy recovery ratio (ERR), which was defined as the energy of the resultant products compared to the energy input of the material, was investigated. Our experiment shows that reaction time had certain influence on the yield of liquefaction products, but temperature and pH value had bigger influence on the yield of liquefaction products. Yields of 62.2wt% bio-oil, having a high heating value of 32.35MJ/kg and a viscosity of 305cp, and 22wt% solid residue were realized at a liquefaction temperature of 250°C, a reaction time of 60min and a pH value of 9.0. The bio-oil contained up to hundreds of different chemical components that may be classified according to functional groups. Typical compound classes in the bio-oil were hydrocarbons, organic acids, esters, ketones and heterocyclics. The energy recovery ratio (ERR) reached 93.63%. The bio-oil is expected to contribute to fossil fuel replacement in stationary applications, including boilers and furnaces, and upgrading processes for the bio-oil may be used to obtain liquid transport fuels. Copyright © 2015 Elsevier Ltd. All rights reserved.

Investigation of the Optimum Farming Temperature for Grifola frondosa and Growth Promotion using the Bio-Electric Potential as an Index

NASA Astrophysics Data System (ADS)

Yanagibashi, Hideyuki; Hirama, Junji; Matsuda, Masato; Miyamoto, Toshio

The purpose of this study was to investigate the optimum farming conditions for mushrooms from the view point of engineering field. As the bio-electric potential of mushrooms is considered to be closely related to the activation of mushroom cells, this relationship has been used to analyze the dependence of the morphogenetic characteristics of Grifola frondosa on farming temperatures (from 16 to 22 degree C). The experimental results indicated that a maximum response was exhibited, with correspondingly favorable morphogenesis obtained at 18 degree C. Based on the experimental results, including those in a previous study, it was assumed that the larger the bio-electric potential becomes, the higher the growth yield reaches. In order to support this assumption, growth promotion was conducted by intentionally activating the bio-electric potential within the mushrooms by stimulating them with short bursts of illumination. The resulting observation of growth promotion permitted the conclusion that the bio-electric potential can, indeed, be regarded as an index of growth.

BioWarehouse: a bioinformatics database warehouse toolkit

PubMed Central

Lee, Thomas J; Pouliot, Yannick; Wagner, Valerie; Gupta, Priyanka; Stringer-Calvert, David WJ; Tenenbaum, Jessica D; Karp, Peter D

2006-01-01

Background This article addresses the problem of interoperation of heterogeneous bioinformatics databases. Results We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. Conclusion BioWarehouse embodies significant progress on the database integration problem for

Pro-stimulatory role of methemoglobin in inflammation through hemin oxidation and polymerization.

PubMed

Deshmukh, Rohitas; Trivedi, Vishal

2013-02-01

Inflammation or vascular occlusion by parasitized red blood cell contributes to the pathogenesis of cerebral malaria. The current study aimed to characterize the role of major pro-oxidant factor methemoglobin present in the malaria culture supernatant contributing in inflammation during malaria. Heme and heme polymer stimulate macrophage to secrete large amount of reactive oxygen species into the external micro-environment. The addition of methemoglobin along with heme or heme polymer amplifies production of ROS from macrophages several folds. Methemoglobin mediated stimulatory effect is not due to release of iron, enhanced production of H2O2 or mutual interaction of reaction components. Spectroscopic studies show that methemoglobin accepts heme as a substrate and oxidizes it through a single electron transfer mechanism. Heme oxidation product is a heme polymer with similar chemical and structural properties to synthetic β-hematin. Phenyl N-t-butylnitrone inhibits heme polymerization (IC50=30 nM) and indicates the absolute necessity of heme oxidation and heme free radical generation for heme polymerization. Methemoglobin produced heme polymer is a potent pro-inflammatory factor to release ROS into external microenvironment. Interestingly, methemoglobin not only produces pro-inflammatory heme polymer, but it also amplifies the potential of heme or preformed heme polymer (haemozoin or β-hematin) to produce several folds high ROS production from macrophages. This study illustrates the pro-inflammatory effect of methemoglobin, the underlying novel mechanism by which this occurs and a possible clinical intervention. Based on the results, we recommend methemoglobin directed peroxidase inhibitors as an adjuvant therapy during malaria.

cap alpha. /sub i/-3 cDNA encodes the. cap alpha. subunit of G/sub k/, the stimulatory G protein of receptor-regulated K/sup +/ channels

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

Codina, J.; Olate, J.; Abramowitz, J.

1988-05-15

cDNA cloning has identified the presence in the human genome of three genes encoding ..cap alpha.. subunits of pertussis toxin substrates, generically called G/sub i/. They are named ..cap alpha../sub i/-1, ..cap alpha../sub i/-2 and ..cap alpha../sub i/-3. However, none of these genes has been functionally identified with any of the ..cap alpha.. subunits of several possible G proteins, including pertussis toxin-sensitive G/sub p/'s, stimulatory to phospholipase C or A/sub 2/, G/sub i/, inhibitory to adenylyl cyclase, or G/sub k/, stimulatory to a type of K/sup +/ channels. The authors now report the nucleotide sequence and the complete predicted aminomore » acid sequence of human liver ..cap alpha../sub i/-3 and the partial amino acid sequence of proteolytic fragments of the ..cap alpha.. subunit of human erythrocyte G/sub k/. The amino acid sequence of the proteolytic fragment is uniquely encoded by the cDNA of ..cap alpha../sub i/-3, thus identifying it as ..cap alpha../sub k/. The probable identity of ..cap alpha../sub i/-1 with ..cap alpha../sub p/ and possible roles for ..cap alpha../sub i/-2, as well as additional roles for ..cap alpha../sub i/-1 and ..cap alpha../sub i/-3 (..cap alpha../sub k/) are discussed.« less

Creating a Bio-Inspired Solution to Prevent Erosion

NASA Astrophysics Data System (ADS)

Reher, R.; Martinez, A.; Cola, J.; Frost, D.

2016-12-01

Through the study of geophysical sciences, lessons can be developed which allow for the introduction of bio-inspired design and art concepts to K-5 elementary students. Students are placed into an engineering mindset in which they must apply the concepts of bio-geotechnics to observe how we can use nature to prevent and abate erosion. Problems are staged for students using realistic engineering scenarios such as erosion prevention through biomimicry and the study of anchorage characteristics of root structures in regard to stability of soil. Specifically, a lesson is introduced where students research, learn, and present information about bio-inspired designs to understand these concepts. They lean how plant roots differ in size and shape to stabilize soil. In addition, students perform a series of hands-on experiments which demonstrate how bio-cements and roots can slow erosion.

Tim-3 directly enhances CD8 T cell responses to acute Listeria monocytogenes infection

PubMed Central

Gorman, Jacob V.; Starbeck-Miller, Gabriel; Pham, Nhat-Long L.; Traver, Geri L.; Rothman, Paul B.; Harty, John T.; Colgan, John D.

2014-01-01

Tim-3 is a surface molecule expressed throughout the immune system that can mediate both stimulatory and inhibitory effects. Previous studies have provided evidence that Tim-3 functions to enforce CD8 T cell exhaustion, a dysfunctional state associated with chronic stimulation. In contrast, the role of Tim-3 in the regulation of CD8 T cell responses to acute and transient stimulation remains undefined. To address this knowledge gap, we examined how Tim-3 affects CD8 T cell responses to acute Listeria monocytogenes (LM) infection. Analysis of wild-type (WT) mice infected with LM revealed that Tim-3 was transiently expressed by activated CD8 T cells and was associated primarily with acquisition of an effector phenotype. Comparison of responses to LM by WT and Tim-3 KO mice showed that the absence of Tim-3 significantly reduced the magnitudes of both primary and secondary CD8 T cell responses, which correlated with decreased IFN-γ production and degranulation by Tim-3 KO cells stimulated with peptide antigen ex vivo. To address the T cell-intrinsic role of Tim-3, we analyzed responses to LM infection by WT and Tim-3 KO TCR-transgenic CD8 T cells following adoptive transfer into a shared WT host. In this setting, the accumulation of CD8 T cells and the generation of cytokine-producing cells were significantly reduced by the lack of Tim-3, demonstrating that this molecule has a direct effect on CD8 T cell function. Combined, our results suggest that Tim-3 can mediate a stimulatory effect on CD8 T cell responses to an acute infection. PMID:24567532

Heterogeneous Deformable Modeling of Bio-Tissues and Haptic Force Rendering for Bio-Object Modeling

NASA Astrophysics Data System (ADS)

Lin, Shiyong; Lee, Yuan-Shin; Narayan, Roger J.

This paper presents a novel technique for modeling soft biological tissues as well as the development of an innovative interface for bio-manufacturing and medical applications. Heterogeneous deformable models may be used to represent the actual internal structures of deformable biological objects, which possess multiple components and nonuniform material properties. Both heterogeneous deformable object modeling and accurate haptic rendering can greatly enhance the realism and fidelity of virtual reality environments. In this paper, a tri-ray node snapping algorithm is proposed to generate a volumetric heterogeneous deformable model from a set of object interface surfaces between different materials. A constrained local static integration method is presented for simulating deformation and accurate force feedback based on the material properties of a heterogeneous structure. Biological soft tissue modeling is used as an example to demonstrate the proposed techniques. By integrating the heterogeneous deformable model into a virtual environment, users can both observe different materials inside a deformable object as well as interact with it by touching the deformable object using a haptic device. The presented techniques can be used for surgical simulation, bio-product design, bio-manufacturing, and medical applications.

Lessons learned from U.S. Department of Defense 911-Bio Advanced Concept Technology Demonstrations.

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

Baldwin, T.; Gasper, W.; Lacher, L.

1999-07-06

The US Department of Defense (DoD), in cooperation with other federal agencies, has taken many initiatives to improve its ability to support civilian response to a domestic biological terrorism incident. This paper discusses one initiative, the 911-Bio Advanced Concept Technology Demonstrations (ACTDs), conducted by the Office of the Secretary of Defense during 1997 to better understand: (1) the capability of newly developed chemical and biological collection and identification technologies in a field environment; (2) the ability of specialized DoD response teams to use these new technologies within the structure of cooperating DoD and civilian consequence management organizations; and (3) themore » adequacy of current modeling tools for predicting the dispersal of biological hazards. This paper discusses the experience of the ACTDs from the civilian community support perspective. The 911-Bio ACTD project provided a valuable opportunity for DoD and civilian officials to learn how they should use their combined capabilities to manage the aftermath of a domestic biological terrorism incident.« less

Tarsal taste neuron activity and proboscis extension reflex in response to sugars and amino acids in Helicoverpa armigera (Hubner).

PubMed

Zhang, Yun-Feng; van Loon, Joop J A; Wang, Chen-Zhu

2010-08-15

In adult female Helicoverpa armigera (Hübner), the fifth tarsomere of the prothoracic legs bears 14 gustatory trichoid chemosensilla. These chemosensilla were characterized through electrophysiological experiments by stimulating with sucrose, glucose, fructose, maltose, myo-inositol and 20 common amino acids. In electrophysiological recordings from nine sensilla, responses were obtained to certain compounds tested at 100 mmol l(-1), and the response spectra differed from broad to narrow. The four sugars excited the same receptor neuron in sensillum a and sensillum b; sucrose and myo-inositol, sucrose and lysine, myo-inositol and lysine excited two different receptor neurons respectively in sensillum a; fructose and lysine excited two different receptor neurons in sensillum n. Furthermore, the four sugars, myo-inositol and lysine all elicited concentration-dependent electrophysiological responses. These six compounds also induced the proboscis extension reflex (PER) followed by ingestion of the solution when they were applied on the tarsi. Lysine and sucrose caused the strongest electrophysiological responses. However, sucrose had the strongest stimulatory effect on the PER whereas lysine had the weakest. Mixtures of sucrose with the other sugars or with lysine had a similar stimulatory effect on the PER as sucrose alone. The electrophysiological and behavioural responses caused by a range of sucrose concentrations were positively correlated. We conclude that the tarsal gustatory sensilla play an essential role in perceiving sugars available in floral nectar and provide chemosensory information determining feeding behaviour. Tarsal taste-receptor-neuron responses to lysine are implicated in oviposition behaviour.

Bio-Security Proficiencies Project for Beginning Producers in 4-H

ERIC Educational Resources Information Center

Smith, Martin H.; Meehan, Cheryl L.; Borba, John A.

2014-01-01

Improving bio-security practices among 4-H members who raise and show project animals is important. Bio-security measures can reduce the risk of disease spread and mitigate potential health and economic risks of disease outbreaks involving animal and zoonotic pathogens. Survey data provided statistical evidence that the Bio-Security Proficiencies…

Bio-Monitoring of Ozone by Young Students

ERIC Educational Resources Information Center

Lorenzini, Giacomo; Nali, Cristina

2004-01-01

An educational pilot project on the bio-monitoring of air quality was carried out in the Umbria Region of Central Italy. It involved about 1000 young students (ages 4 to 16) from 42 schools of 16 municipalities in active biomonitoring of tropospheric ozone with bio-indicator sensitive tobacco seedlings. Some 6500 raw biological readings were used…

Constitutive stimulatory G protein activity in limb mesenchyme impairs bone growth.

PubMed

Karaca, Anara; Malladi, Vijayram Reddy; Zhu, Yan; Tafaj, Olta; Paltrinieri, Elena; Wu, Joy Y; He, Qing; Bastepe, Murat

2018-05-01

GNAS mutations leading to constitutively active stimulatory G protein alpha-subunit (Gsα) cause different tumors, fibrous dysplasia of bone, and McCune-Albright syndrome, which are typically not associated with short stature. Enhanced signaling of the parathyroid hormone/parathyroid hormone-related peptide receptor, which couples to multiple G proteins including Gsα, leads to short bones with delayed endochondral ossification. It has remained unknown whether constitutive Gsα activity also impairs bone growth. Here we generated mice expressing a constitutively active Gsα mutant (Gsα-R201H) conditionally upon Cre recombinase (cGsα R201H mice). Gsα-R201H was expressed in cultured bone marrow stromal cells from cGsα R201H mice upon adenoviral-Cre transduction. When crossed with mice in which Cre is expressed in a tamoxifen-regulatable fashion (CAGGCre-ER™), tamoxifen injection resulted in mosaic expression of the transgene in double mutant offspring. We then crossed the cGsα R201H mice with Prx1-Cre mice, in which Cre is expressed in early limb-bud mesenchyme. The double mutant offspring displayed short limbs at birth, with narrow hypertrophic chondrocyte zones in growth plates and delayed formation of secondary ossification center. Consistent with enhanced Gsα signaling, bone marrow stromal cells from these mice demonstrated increased levels of c-fos mRNA. Our findings indicate that constitutive Gsα activity during limb development disrupts endochondral ossification and bone growth. Given that Gsα haploinsufficiency also leads to short bones, as in patients with Albright's hereditary osteodystrophy, these results suggest that a tight control of Gsα activity is essential for normal growth plate physiology. Copyright © 2018 Elsevier Inc. All rights reserved.

Recent progress in making protein microarray through BioLP

NASA Astrophysics Data System (ADS)

Yang, Rusong; Wei, Lian; Feng, Ying; Li, Xiujian; Zhou, Quan

2017-02-01

Biological laser printing (BioLP) is a promising biomaterial printing technique. It has the advantage of high resolution, high bioactivity, high printing frequency and small transported liquid amount. In this paper, a set of BioLP device is design and made, and protein microarrays are printed by this device. It's found that both laser intensity and fluid layer thickness have an influence on the microarrays acquired. Besides, two kinds of the fluid layer coating methods are compared, and the results show that blade coating method is better than well-coating method in BioLP. A microarray of 0.76pL protein microarray and a "NUDT" patterned microarray are printed to testify the printing ability of BioLP.

Advancing sustainable forestry by using engineered wood or bio-composites

Treesearch

Jerrold E. Winandy

2005-01-01

As worldwide demand for timber and bio-fiber resources grows, sustainable resource management and industrial utilization must collaborate to develop a shared vision for both long-term sustainable management of forest and bio-resources and sustainable economic development. Engineered wood- and bio-composites offer a tool that can both achieve resource sustainability and...

Response to bio-terrorism directed against animals.

PubMed

Williams, J L; Sheesley, D

2000-01-01

The Animal and Plant Health Inspection Service (APHIS) has a long history of rapid direction, control, and eradication of devastating diseases. Our immediate response mechanisms to diseases such as avian influenza, Venezuelan equine encephalomyelitis, and Newcastle disease, have long been recognized by the global emergency response community as models of control and eradication. APHIS and the U.S. livestock industries, in partnership with the Animal Agriculture Coalition, re-evaluated the Nation's animal health emergency preparedness and response systems. The group identified areas that negatively impact, biologically and/or economically, the Nation's animal and food production industries. To counter the increased risks including bioterrorism, APHIS plans to establish a world-class "Center of Excellence for Animal Health Emergency Management." APHIS, Intelligence agencies, other Federal departments, State governments, and industries are working together to provide accurate information on the foreign and domestic threats posed to the U.S. agricultural sector by biological weapons. Additionally, the same agencies and organizations are evaluating, updating, and improving the coordination and training mechanisms necessary to respond in the even of a widespread pest or disease outbreak.

[Research progress on the technique and materials for three-dimensional bio-printing].

PubMed

Yang, Runhuai; Chen, Yueming; Ma, Changwang; Wang, Huiqin; Wang, Shuyue

2017-04-01

Three-dimensional (3D) bio-printing is a novel engineering technique by which the cells and support materials can be manufactured to a complex 3D structure. Compared with other 3D printing methods, 3D bio-printing should pay more attention to the biocompatible environment of the printing methods and the materials. Aimed at studying the feature of the 3D bio-printing, this paper mainly focuses on the current research state of 3D bio-printing, with the techniques and materials of the bio-printing especially emphasized. To introduce current printing methods, the inkjet method, extrusion method, stereolithography skill and laser-assisted technique are described. The printing precision, process, requirements and influence of all the techniques on cell status are compared. For introduction of the printing materials, the cross-link, biocompatibility and applications of common bio-printing materials are reviewed and compared. Most of the 3D bio-printing studies are being remained at the experimental stage up to now, so the review of 3D bio-printing could improve this technique for practical use, and it could also contribute to the further development of 3D bio-printing.

EcAMSat and BioSentinel: Autonomous Bio Nanosatellites Addressing Strategic Knowledge Gaps for Manned Spaceflight Beyond LEO

NASA Technical Reports Server (NTRS)

Padgen, Michael R.

2017-01-01

Manned missions beyond low Earth orbit (LEO) require that several strategic knowledge gaps about the effects of space travel on the human body be addressed. NASA Ames Research Center has been the leader in developing autonomous bio nanosatellites, including past successful missions for GeneSat, PharmaSat, and O/OREOS, that tackled some of these issues. These nanosatellites provide in situ measurements, which deliver insight into the dynamic changes in cell behavior in microgravity. In this talk, two upcoming bio nanosatellites developed at Ames, the E. coli Antimicrobial Satellite (EcAMSat) and BioSentinel, will be discussed. Both satellites contain microfluidic systems that precisely deliver nutrients to the microorganisms stored within wells of fluidic cards. Each well, in turn, has its own 3-color LED and detector system which is used to monitor changes in metabolic activity with alamarBlue, a redox indicator, and the optical density of the cells. EcAMSat investigates the effects of microgravity on bacterial resistance to antimicrobial drugs, vital knowledge for understanding how to maintain the health of astronauts in long-term and beyond LEO spaceflight. The behavior of wild type and mutant uropathic E. coli will be compared in microgravity and with ground data to help understand the molecular mechanisms behind antibiotic resistance and how these phenotypes might change in space. BioSentinel seeks to directly measure the effects of space radiation on budding yeast S. cerevisiae, particularly double strand breaks (DSB). While hitching a ride on the SLS EM-1 mission (Orion's first unmanned mission to the moon) in 2018, BioSentinel will be kicked off and enter into a heliocentric orbit, becoming the first study of the effects of radiation on living organisms outside LEO since the Apollo program. The yeast are stored in eighteen independent 16-well microfluidic cards, which will be individually activated over the 12 month mission duration. In addition to the wild

EcAMSat and BioSentinel: Autonomous Bio Nanosatellites Addressing Strategic Knowledge Gaps for Manned Spaceflight Beyond LEO

NASA Technical Reports Server (NTRS)

Padgen, Mike

2017-01-01

Manned missions beyond low Earth orbit (LEO) require that several strategic knowledge gaps about the effects of space travel on the human body be addressed. NASA Ames Research Center has been the leader in developing autonomous bio nanosatellites, including past successful missions for GeneSat, PharmaSat, and OOREOS, that tackled some of these issues. These nanosatellites provide in situ measurements, which deliver insight into the dynamic changes in cell behavior in microgravity. In this talk, two upcoming bio nanosatellites developed at Ames, the E. coli Antimicrobial Satellite (EcAMSat) and BioSentinel, will be discussed. Both satellites contain microfluidic systems that precisely deliver nutrients to the microorganisms stored within wells of fluidic cards. Each well, in turn, has its own 3-color LED and detector system which is used to monitor changes in metabolic activity with alamarBlue, a redox indicator, and the optical density of the cells. EcAMSat investigates the effects of microgravity on bacterial resistance to antimicrobial drugs, vital knowledge for understanding how to maintain the health of astronauts in long-term and beyond LEO spaceflight. The behavior of wild type and mutant uropathic E. coli will be compared in microgravity and with ground data to help understand the molecular mechanisms behind antibiotic resistance and how these phenotypes might change in space. BioSentinel seeks to directly measure the effects of space radiation on budding yeast S. cerevisiae, particularly double strand breaks (DSB). While hitching a ride on the SLS EM-1 mission (Orions first unmanned mission to the moon) in 2018, BioSentinel will be kicked off and enter into a heliocentric orbit, becoming the first study of the effects of radiation on living organisms outside LEO since the Apollo program. The yeast are stored in eighteen independent 16-well microfluidic cards, which will be individually activated over the 12 month mission duration. In addition to the wild

Computing through Scientific Abstractions in SysBioPS

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

Chin, George; Stephan, Eric G.; Gracio, Deborah K.

2004-10-13

Today, biologists and bioinformaticists have a tremendous amount of computational power at their disposal. With the availability of supercomputers, burgeoning scientific databases and digital libraries such as GenBank and PubMed, and pervasive computational environments such as the Grid, biologists have access to a wealth of computational capabilities and scientific data at hand. Yet, the rapid development of computational technologies has far exceeded the typical biologist’s ability to effectively apply the technology in their research. Computational sciences research and development efforts such as the Biology Workbench, BioSPICE (Biological Simulation Program for Intra-Cellular Evaluation), and BioCoRE (Biological Collaborative Research Environment) are importantmore » in connecting biologists and their scientific problems to computational infrastructures. On the Computational Cell Environment and Heuristic Entity-Relationship Building Environment projects at the Pacific Northwest National Laboratory, we are jointly developing a new breed of scientific problem solving environment called SysBioPSE that will allow biologists to access and apply computational resources in the scientific research context. In contrast to other computational science environments, SysBioPSE operates as an abstraction layer above a computational infrastructure. The goal of SysBioPSE is to allow biologists to apply computational resources in the context of the scientific problems they are addressing and the scientific perspectives from which they conduct their research. More specifically, SysBioPSE allows biologists to capture and represent scientific concepts and theories and experimental processes, and to link these views to scientific applications, data repositories, and computer systems.« less

Optical bio-sniffer for methyl mercaptan in halitosis.

PubMed

Mitsubayashi, Kohji; Minamide, Takeshi; Otsuka, Kimio; Kudo, Hiroyuki; Saito, Hirokazu

2006-07-28

An optical bio-sniffer for methyl mercaptan (MM) one of major odorous chemicals in halitosis (bad breath) was constructed by immobilizing monoamine oxidase type A (MAO-A) onto a tip of a fiber optic oxygen sensor (od: 1.59 mm) with an oxygen sensitive ruthenium organic complex (excitation: 470 nm, fluorescent: 600 nm). A flow cell for circulating buffer solution was applied to rinse and clean the tip of the device like nasal mucosa. In order to amplify the bio-sniffer output, a substrate regeneration cycle caused by coupling MAO-A with l-ascorbic acid (AsA) as reducing reaction with reagent system was applied to the sensor system. After evaluating the sensor characteristics using a gas flow measurement system with a gas generator, the optical bio-sniffer was applied to expired gases from healthy male volunteers for halitosis analysis as a physiological application. The optical bio-sniffer was applied to detect the oxygen consumption induced by MAO-A enzymatic reaction (and AsA chemical reduction) with gaseous MM application. The bio-sniffer was calibrated against MM vapor from 8.7 to 11500 ppb with correlation coefficient of 0.977, including a MM threshold (200 ppb) of pathologic halitosis and the human sense of smell level 3.5 (10.0 ppb), with good gas-selectivity based on the MAO-A substrate specificity. As the result of the physiological application, the optical bio-sniffer could successfully monitor the MM level change in breath samples during daytime, which is consistent with the previously reported results.

The electromagnetic bio-field: clinical experiments and interferences.

PubMed

Burnei, G; Hodorogea, D; Georgescu, I; Gavriliu, Ş; Drăghici, I; Dan, D; Vlad, C; Drăghici, L

2012-06-12

One of the most important factors is the technical and scientifically rapid development that is continually modifying the world we live in and polluting it with electromagnetic radiations. A functional and structural influence of magnetic and electromagnetic field on living organisms is presented in the literature by many performed experiments. The notion of bio-field represents the electromagnetic field generated by the bio-structures, not only in their normal physiological activities but also in their pathological states. There is a tight interdependency between the bio-field and the bio-structure, which respects the primary notion of an electromagnetic field given by the Maxwell-Faraday laws, in which, the electromagnetic phenomena are simplified to the field variations. These variations can be expressed in a coherent differential equation system that bounds the field vectors to different space points at different time moments. The living organisms cannot contain electrostatic and magneto-static fields due to the intense activity of the bio-structures. The biochemical reactions that have high rhythms and speeds always impose the electrodynamics character of the biologic field that also corresponds to the stability of the protein molecule that can be explained only through a dynamic way. The existent energy is not considered an exciting agent, and it does not lead to any effects. The parameters of these elementary bio-fields cannot yet be fully known due to technical reasons. The biological structures are very complex ones and undergo continuous dynamical activity. That is why the calculus model should be related to the constant dynamics, nowadays being very difficult to express.

Starch-based bio-elastomers functionalized with red beetroot natural antioxidant.

PubMed

Tran, Thi Nga; Athanassiou, Athanassia; Basit, Abdul; Bayer, Ilker S

2017-02-01

Red beetroot (RB) powder was incorporated into starch-based bio-elastomers to obtain flexible biocomposites with tunable antioxidant properties. Starch granules within the bio-elastomers affected the release of the antioxidant molecule betanin in the RB powder. The bio-elastomers were hydrophobic and resisted dissolution in water, hence the release of betanin was due to diffusion rather than polymer matrix disintegration. Hydrophobicity was maintained even after water immersion. Released betanin demonstrated highly efficient antioxidant scavenging activity against 2,2-diphenyl-1-picrylhydrazyl free radical (DPPH) and 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) radical cation (ABTS(+)). RB powder was also found to increase the Young's modulus of the bio-elastomers without compromising their elongation ability. Infrared spectral analysis indicated weak interactions through hydrogen bonding among starch granules, RB powder and PDMS polymer within the bio-elastomers. Hence, as a simple but intelligent biomaterial consisting of mainly edible starch and RB powder the present bio-elastomers can be used in active packaging for a variety of pharmaceutical, medical, and food applications. Copyright © 2016 Elsevier Ltd. All rights reserved.

Neurite outgrowth stimulatory effects of culinary-medicinal mushrooms and their toxicity assessment using differentiating Neuro-2a and embryonic fibroblast BALB/3T3

PubMed Central

2013-01-01

Background Mushrooms are not only regarded as gourmet cuisine but also as therapeutic agent to promote cognition health. However, little toxicological information is available regarding their safety. Therefore, the aim of this study was to screen selected ethno-pharmacologically important mushrooms for stimulatory effects on neurite outgrowth and to test for any cytotoxicity. Methods The stimulatory effect of mushrooms on neurite outgrowth was assessed in differentiating mouse neuroblastoma (N2a) cells. Neurite length was measured using Image-Pro Insight processor system. Neuritogenesis activity was further validated by fluorescence immunocytochemical staining of neurofilaments. In vitro cytotoxicity was investigated by using mouse embryonic fibroblast (BALB/3T3) and N2a cells for any embryo- and neuro-toxic effects; respectively. Results Aqueous extracts of Ganoderma lucidum, Lignosus rhinocerotis, Pleurotus giganteus and Grifola frondosa; as well as an ethanol extract of Cordyceps militaris significantly (p < 0.05) promoted the neurite outgrowth in N2a cells by 38.4 ± 4.2%, 38.1 ± 2.6%, 33.4 ± 4.6%, 33.7 ± 1.5%, and 35.8 ± 3.4%; respectively. The IC50 values obtained from tetrazolium (MTT), neutral red uptake (NRU) and lactate dehydrogenase (LDH) release assays showed no toxic effects following 24 h exposure of N2a and 3T3 cells to mushroom extracts. Conclusion Our results indicate that G. lucidum, L. rhinocerotis, P. giganteus, G. frondosa and C. militaris may be developed as safe and healthy dietary supplements for brain and cognitive health. PMID:24119256

Opportunity and development of bio-based composites

Treesearch

Zhiyong Cai; Jerrold E. Winandy

2005-01-01

Our forests are a naturally renewable resource that has been used as a principal source of bio-energy and building materials for centuries. The rapid growth of world population has now resulted in substantial increases in demand and in consumption of all raw materials. This now provides a unique opportunity of developing new bio-based composites. The 100-year history...

Bio-phobias/techno-philias: virtual reality exposure as treatment for phobias of 'nature'.

PubMed

Davidson, Joyce; Smith, Mick

2003-09-01

In modern society natural objects like spiders or snakes have a primary role as the loci of specific phobias. Drawing on interviews with members of the UK National Phobics Society (NPS) and associated service providers, this paper explores the implications of the increasingly significant role played by new media, particularly Virtual Reality technologies, in the treatment of these 'bio-phobias'. While advanced technological approaches provide new possibilities for individual sufferers to experiment with and control their phobic responses they also exemplify certain aspects of those specifically modern social relations that are the media within which bio-phobic behaviours develop. From a critical sociological perspective the techno-philic move to the medium of cyber-space may actually exaggerate characteristically modern social relations that seek (but never convincingly manage) to assert complete 'cultural' control over the unpredictable 'natural' elements threatening our cultural integrity.

Utilization of acetic acid-rich pyrolytic bio-oil by microalga Chlamydomonas reinhardtii: reducing bio-oil toxicity and enhancing algal toxicity tolerance.

PubMed

Liang, Yi; Zhao, Xuefei; Chi, Zhanyou; Rover, Marjorie; Johnston, Patrick; Brown, Robert; Jarboe, Laura; Wen, Zhiyou

2013-04-01

This work was to utilize acetic acid contained in bio-oil for growth and lipid production of the microalga Chlamydomonas reinhardtii. The acetic acid-rich bio-oil fraction derived from fast pyrolysis of softwood contained 26% (w/w) acetic acid, formic acid, methanol, furfural, acetol, and phenolics as identified compounds, and 13% (w/w) unidentified compounds. Among those identified compounds, phenolics were most inhibitory to algal growth, followed by furfural and acetol. To enhance the fermentability of the bio-oil fraction, activated carbon was used to reduce the toxicity of the bio-oil, while metabolic evolution was used to enhance the toxicity tolerance of the microalgae. Combining activated carbon treatment and using evolved algal strain resulted in significant algal growth improvement. The results collectively showed that fast pyrolysis-fermentation process was a viable approach for converting biomass into fuels and chemicals. Copyright © 2013 Elsevier Ltd. All rights reserved.

What can law do for the development of bio-economy?

PubMed

Chang-Qiu, Liu

2012-03-01

Bio-technology has become a new impeller to the development of the world economy since the 1970's. The development of bio-economy has two sides for mankind which calls for intervention by law. During the legislation of bioeconomy, some special principles should be esteemed and observed by legislators. It is necessary for the healthy development of bio-economy.

Bio-methane from an-aerobic digestion using activated carbon adsorption.

PubMed

Farooq, Muhammad; Bell, Alexandra H; Almustapha, M N; Andresen, John M

2017-08-01

There is an increasing global demand for carbon-neutral bio-methane from an-aerobic digestion (AD) to be injected into national gas grids. Bio-gas, a methane -rich energy gas, is produced by microbial decomposition of organic matter through an-aerobic conditions where the presence of carbon dioxide and hydrogen sulphide affects its performance. Although the microbiological process in the AD can be tailored to enhance the bio-gas composition, physical treatment is needed to convert the bio-gas into bio-methane. Water washing is the most common method for upgrading bio-gas for bio-methane production, but its large use of water is challenging towards industrial scale-up. Hence, the present study focuses on scale-up comparison of water washing with activated-carbon adsorption using HYSYS and Aspen Process Economic Analyzer. The models show that for plants processing less than 500 m 3 /h water scrubbing was cost effective compared with activated carbon. However, against current fossil natural-gas cost of about 1 p/kWh in the UK both relied heavily on governmental subsidies to become economically feasible. For plants operating at 1000 m 3 /hr, the treatment costs were reduced to below 1.5 p/kWh for water scrubbing and 0.9 p/kWh for activated carbon where the main benefits of activated carbon were lower capital and operating costs and virtually no water losses. It is envisioned that this method can significantly aid the production of sustainable bio-methane. Copyright © 2017 Elsevier Ltd. All rights reserved.

Paracoccus denitrificans possesses two BioR homologs having a role in regulation of biotin metabolism.

PubMed

Feng, Youjun; Kumar, Ritesh; Ravcheev, Dmitry A; Zhang, Huimin

2015-08-01

Recently, we determined that BioR, the GntR family of transcription factor, acts as a repressor for biotin metabolism exclusively distributed in certain species of α-proteobacteria, including the zoonotic agent Brucella melitensis and the plant pathogen Agrobacterium tumefaciens. However, the scenario is unusual in Paracoccus denitrificans, another closely related member of the same phylum α-proteobacteria featuring with denitrification. Not only does it encode two BioR homologs Pden_1431 and Pden_2922 (designated as BioR1 and BioR2, respectively), but also has six predictive BioR-recognizable sites (the two bioR homolog each has one site, whereas the two bio operons (bioBFDAGC and bioYB) each contains two tandem BioR boxes). It raised the possibility that unexpected complexity is present in BioR-mediated biotin regulation. Here we report that this is the case. The identity of the purified BioR proteins (BioR1 and BioR2) was confirmed with LC-QToF-MS. Phylogenetic analyses combined with GC percentage raised a possibility that the bioR2 gene might be acquired by horizontal gene transfer. Gel shift assays revealed that the predicted BioR-binding sites are functional for the two BioR homologs, in much similarity to the scenario seen with the BioR site of A. tumefaciens bioBFDAZ. Using the A. tumefaciens reporter system carrying a plasmid-borne LacZ fusion, we revealed that the two homologs of P. denitrificans BioR are functional repressors for biotin metabolism. As anticipated, not only does the addition of exogenous biotin stimulate efficiently the expression of bioYB operon encoding biotin transport/uptake system BioY, but also inhibits the transcription of the bioBFDAGC operon resembling the de novo biotin synthetic pathway. EMSA-based screening failed to demonstrate that the biotin-related metabolite is involved in BioR-DNA interplay, which is consistent with our former observation with Brucella BioR. Our finding defined a complex regulatory network for biotin

Paracoccus denitrificans possesses two BioR homologs having a role in regulation of biotin metabolism

PubMed Central

Feng, Youjun; Kumar, Ritesh; Ravcheev, Dmitry A; Zhang, Huimin

2015-01-01

Recently, we determined that BioR, the GntR family of transcription factor, acts as a repressor for biotin metabolism exclusively distributed in certain species of α-proteobacteria, including the zoonotic agent Brucella melitensis and the plant pathogen Agrobacterium tumefaciens. However, the scenario is unusual in Paracoccus denitrificans, another closely related member of the same phylum α-proteobacteria featuring with denitrification. Not only does it encode two BioR homologs Pden_1431 and Pden_2922 (designated as BioR1 and BioR2, respectively), but also has six predictive BioR-recognizable sites (the two bioR homolog each has one site, whereas the two bio operons (bioBFDAGC and bioYB) each contains two tandem BioR boxes). It raised the possibility that unexpected complexity is present in BioR-mediated biotin regulation. Here we report that this is the case. The identity of the purified BioR proteins (BioR1 and BioR2) was confirmed with LC-QToF-MS. Phylogenetic analyses combined with GC percentage raised a possibility that the bioR2 gene might be acquired by horizontal gene transfer. Gel shift assays revealed that the predicted BioR-binding sites are functional for the two BioR homologs, in much similarity to the scenario seen with the BioR site of A. tumefaciens bioBFDAZ. Using the A. tumefaciens reporter system carrying a plasmid-borne LacZ fusion, we revealed that the two homologs of P. denitrificans BioR are functional repressors for biotin metabolism. As anticipated, not only does the addition of exogenous biotin stimulate efficiently the expression of bioYB operon encoding biotin transport/uptake system BioY, but also inhibits the transcription of the bioBFDAGC operon resembling the de novo biotin synthetic pathway. EMSA-based screening failed to demonstrate that the biotin-related metabolite is involved in BioR-DNA interplay, which is consistent with our former observation with Brucella BioR. Our finding defined a complex regulatory network for biotin

[Effects of bio-fertilizer on organically cultured cucumber growth and soil biological characteristics].

PubMed

Cao, Dan; Zong, Liang-gang; Xiao, Jun; Zhang, Qian; Zhao, Yan

2010-10-01

Field trials of organic farming were conducted to examine the effects of different bio-fertilizers on the organically cultured cucumber growth, soil enzyme activities, and soil microbial biomass. Four treatments were installed, i. e., organic fertilizer only (CK), bio-fertilizer "Zhonghe" combined with organic fertilizer (ZHH), bio-fertilizer "NST" combined with organic fertilizer (NST), and bio-fertilizer "Bio" combined with organic fertilizer (BIO). Bio-fertilizers combined with organic fertilizer increased the cucumber yield significantly, and improved the root growth and leaf chlorophyll content. Comparing with that in CK, the cucumber yield in treatments ZHH, NST, and BIO was increased by 10.4%, 12.4%, and 29.2%, respectively. At the seedling stage, early flowering stage, and picking time of cucumber, the soil microbial biomass C and N in treatments ZHH, NST, and BIO were significantly higher than that in CK, and the activities of soil urease, acid phosphatase, and catalase were also higher.

Cyclin D1 and Cyclin E as Markers of Therapeutic Responsiveness in Breast Cancer

DTIC Science & Technology

2002-05-01

address whether cyclin D1 and cyclin E were predictive markers for therapeutic responsiveness in breast cancer. Both estrogen and progesterone ...although whether progesterone is tion of p 18 N K4c and increased association of the CDK stimulatory or inhibitory for normal breast epithelium remains...steroid progesterone and its synthetic ana- p2 7Ki pl and p21 ip 1 available to bind other proteins (8). Thus, logues, progestins, have complex effects

BioPCD - A Language for GUI Development Requiring a Minimal Skill Set.

PubMed

Alvare, Graham Gm; Roche-Lima, Abiel; Fristensky, Brian

2012-11-01

BioPCD is a new language whose purpose is to simplify the creation of Graphical User Interfaces (GUIs) by biologists with minimal programming skills. The first step in developing BioPCD was to create a minimal superset of the language referred to as PCD (Pythonesque Command Description). PCD defines the core of terminals and high-level nonterminals required to describe data of almost any type. BioPCD adds to PCD the constructs necessary to describe GUI components and the syntax for executing system commands. BioPCD is implemented using JavaCC to convert the grammar into code. BioPCD is designed to be terse and readable and simple enough to be learned by copying and modifying existing BioPCD files. We demonstrate that BioPCD can easily be used to generate GUIs for existing command line programs. Although BioPCD was designed to make it easier to run bioinformatics programs, it could be used in any domain in which many useful command line programs exist that do not have GUI interfaces.

BioPCD - A Language for GUI Development Requiring a Minimal Skill Set

PubMed Central

Alvare, Graham GM; Roche-Lima, Abiel; Fristensky, Brian

2016-01-01

BioPCD is a new language whose purpose is to simplify the creation of Graphical User Interfaces (GUIs) by biologists with minimal programming skills. The first step in developing BioPCD was to create a minimal superset of the language referred to as PCD (Pythonesque Command Description). PCD defines the core of terminals and high-level nonterminals required to describe data of almost any type. BioPCD adds to PCD the constructs necessary to describe GUI components and the syntax for executing system commands. BioPCD is implemented using JavaCC to convert the grammar into code. BioPCD is designed to be terse and readable and simple enough to be learned by copying and modifying existing BioPCD files. We demonstrate that BioPCD can easily be used to generate GUIs for existing command line programs. Although BioPCD was designed to make it easier to run bioinformatics programs, it could be used in any domain in which many useful command line programs exist that do not have GUI interfaces. PMID:27818582

Microbial conversion of biomass into bio-based polymers.

PubMed

Kawaguchi, Hideo; Ogino, Chiaki; Kondo, Akihiko

2017-12-01

The worldwide market for plastics is rapidly growing, and plastics polymers are typically produced from petroleum-based chemicals. The overdependence on petroleum-based chemicals for polymer production raises economic and environmental sustainability concerns. Recent progress in metabolic engineering has expanded fermentation products from existing aliphatic acids or alcohols to include aromatic compounds. This diversity provides an opportunity to expand the development and industrial uses of high-performance bio-based polymers. However, most of the biomonomers are produced from edible sugars or starches that compete directly with food and feed uses. The present review focuses on recent progress in the microbial conversion of biomass into bio-based polymers, in which fermentative products from renewable feedstocks serve as biomonomers for the synthesis of bio-based polymers. In particular, the production of biomonomers from inedible lignocellulosic feedstocks by metabolically engineered microorganisms and the synthesis of bio-based engineered plastics from the biological resources are discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Kinetic Modeling using BioPAX ontology

PubMed Central

Ruebenacker, Oliver; Moraru, Ion. I.; Schaff, James C.; Blinov, Michael L.

2010-01-01

Thousands of biochemical interactions are available for download from curated databases such as Reactome, Pathway Interaction Database and other sources in the Biological Pathways Exchange (BioPAX) format. However, the BioPAX ontology does not encode the necessary information for kinetic modeling and simulation. The current standard for kinetic modeling is the System Biology Markup Language (SBML), but only a small number of models are available in SBML format in public repositories. Additionally, reusing and merging SBML models presents a significant challenge, because often each element has a value only in the context of the given model, and information encoding biological meaning is absent. We describe a software system that enables a variety of operations facilitating the use of BioPAX data to create kinetic models that can be visualized, edited, and simulated using the Virtual Cell (VCell), including improved conversion to SBML (for use with other simulation tools that support this format). PMID:20862270

C-MEMS for bio-sensing applications

NASA Astrophysics Data System (ADS)

Song, Yin; Agrawal, Richa; Wang, Chunlei

2015-05-01

Developing highly sensitive, selective, and reproducible miniaturized bio-sensing platforms require reliable biointerface which should be compatible with microfabrication techniques. In this study, we have fabricated pyrolyzed carbon arrays with high surface area as a bio-sensing electrode, and developed the surface functionalization methods to increase biomolecules immobilization efficiency and further understand electrochemical phenomena at biointerfaces. The carbon microelectrode arrays with high aspect ratio have been fabricated by carbon microelectromechanical systems (C-MEMS) and nanomaterials such as graphene have been integrated to further increase surface area. To achieve the efficient covalent immobilization of biomolecules, various oxidation and reduction functionalization methods have been investigated. The oxidation treatment in this study includes vacuum ultraviolet, electrochemical activation, UV/Ozone and oxygen RIE. The reduction treatment includes direct amination and diazonium grafting. The developed bio-sensing platform was then applied for several applications, such as: DNA sensor; H2O2 sensor; aptamer sensor and HIV sensor.

Rare Disease Biospecimens and Patient Registries: Interoperability for Research Promotion, a European Example: EuroBioBank and SpainRDR-BioNER.

PubMed

Rubinstein, Yaffa R; Posada de la Paz, Manuel; Mora, Marina

2017-01-01

Well-annotated and properly preserved specimens are crucial both for diagnostic purposes and for use in basic and pre-clinical research, and are especially important for rare disease (RD) studies. Several consortia have been established in the recent years in order to facilitate research and to maximise access to rare biological samples and data stored in rare disease biobanks and registries, among them the EuroBioBank network and the Spain National Rare Disease Registry (RDR) and Biobank (BioNER).EuroBioBank, established in 2001, was the first network of RD biobanks to operate in Europe as a service distributing human DNA, cells, and tissue to the scientific community conducting research on rare diseases.The Spanish RDR and BioNER were created for facilitating rare disease research and health-related matters. The coordination of these two bodies represents an example of great scientific value as biological samples donated by patients at BioNER are linked to clinical information collected in the RDR.Rare disease biobanks and registries will need for the future to increase their effort to improve interconnection so to enable investigators to better locate samples and associated data, while protecting security of the data and privacy of the participants and adhering to international ethical and legal requirements.

Mastering multi-depth bio-chip patterns with DVD LBRs

NASA Astrophysics Data System (ADS)

Carson, Doug

2017-08-01

Bio chip and bio disc are rapidly growing technologies used in medical, health and other industries. While there are numerous unique designs and features, these products all rely on precise three-dimensional micro-fluidic channels or arrays to move, separate and combine samples under test. These bio chip and bio disc consumables are typically manufactured by molding these parts to a precise three-dimensional pattern on a negative metal stamper, or they can be made in smaller quantities using an appropriate curable resin and a negative mold/stamper. Stampers required for bio chips have been traditionally made using either micro machining or XY stepping lithography. Both of these technologies have their advantages as well as limitations when it comes to creating micro-fluidic patterns. Significant breakthroughs in continuous maskless lithography have enabled accurate and efficient manufacturing of micro-fluidic masters using LBRs (Laser Beam Recorders) and DRIE (Deep Reactive Ion Etching). The important advantages of LBR continuous lithography vs. XY stepping lithography and micro machining are speed and cost. LBR based continuous lithography is >100x faster than XY stepping lithography and more accurate than micro machining. Several innovations were required in order to create multi-depth patterns with sub micron accuracy. By combining proven industrial LBRs with DCA's G3-VIA pattern generator and DRIE, three-dimensional bio chip masters and stampers are being manufactured efficiently and accurately.

Properties of piezoresistive silicon nano-scale cantilevers with applications to BioNEMS

NASA Astrophysics Data System (ADS)

Arlett, Jessica Lynn

Over the last decade a great deal of interest has been raised in applications of Microelectromechanical Sensors [MEMS] for the detection of biological molecules and to the study of their forces of interaction. Experiments in these areas have included Force Spectroscopy (Chemical Force Microscopy), MEMS patch clamp technology, and surface stress sensors. All of these technologies suffer from limitations on temporal response and involve devices with active surface areas that are large compared to molecular dimensions. Biofunctionalized nanoelectromechanical systems (BioNEMS) have the potential to overcome both of these hurdles, offering important new prospects for single-molecule force assays that are amenable to large scale integration. Results are presented here on the characterization of piezoresistive silicon cantilevers with applications to BioNEMS devices. The cantilevers were characterized by studying their response in gaseous ambients under a number of drive conditions including magnetic, piezoelectric, and thermal actuation, in addition to passive detection of the thermomechanical response. The measurements were performed at liquid helium temperature, at room temperature, and over a range of pressures (atmospheric pressure to 30mT). Theoretical studies have been performed on the response of these devices to Brownian fluctuations in fluid, on the feasibility of these devices as surface stress sensors, and on improvements in device design as compared to piezoresistive surface stress sensors currently discussed in the literature. The devices were encapsulated in microfluidics and measurements were performed to show the noise floor in fluid. The piezoresistive response of the device in fluid was shown through the use of pulsatory fluidic drive. As a proof of concept, biodetection experiments are presented for biotin labeled beads. The biofunctionalization for the latter experiment was performed entirely within the microfluidics. A discussion of how these

Palladium catalyzed hydrogenation of bio-oils and organic compounds

DOEpatents

Elliott, Douglas C [Kennewick, WA; Hu, Jianli [Richland, WA; Hart,; Todd, R [Kennewick, WA; Neuenschwander, Gary G [Burbank, WA

2011-06-07

The invention provides palladium-catalyzed hydrogenations of bio-oils and certain organic compounds. Experimental results have shown unexpected and superior results for palladium-catalyzed hydrogenations of organic compounds typically found in bio-oils.

Palladium catalyzed hydrogenation of bio-oils and organic compounds

DOEpatents

Elliott, Douglas C [Richland, WA; Hu, Jianli [Kennewick, WA; Hart, Todd R [Kennewick, WA; Neuenschwander, Gary G [Burbank, WA

2008-09-16

The invention provides palladium-catalyzed hydrogenations of bio-oils and certain organic compounds. Experimental results have shown unexpected and superior results for palladium-catalyzed hydrogenations of organic compounds typically found in bio-oils.

Mechanism of bio molecule stabilized selenium nanoparticles against oxidation process and Clostridium Botulinum.

PubMed

Tareq, Foysal Kabir; Fayzunnesa, Mst; Kabir, Md Shahariar; Nuzat, Musrat

2018-02-01

The bio molecules from plant leaf extract utilized in the preparation of selenium material at the nano scale. The selenium ion was reduced to selenium nanoparticles in the presence of molecule residue of the plant leaf extract. The bio molecule stabilized selenium nanoparticles were grown gradually in the reaction mixture. The selenium nanoparticles were characterized using atomic absorption spectroscopy, fourier transform inferred spectroscopy, X-ray diffraction, scanning electronic microscope and transmission electronic microscope. The selenium nanoparticles were synthesized successfully as the nano-crystalline pure hexagonal phase and the size range of 26-41 nm with spherical in shape. The activity and mechanism of nanoparticles suggested that the selenium nanoparticles are causes of leakage of reducing sugars and protein of pathogens membrane cell. The selenium nano are responsible for death and fully inhibited the microbial growth of pathogen. The bio molecule stabilized selenium nanoparticles were also investigated for the antioxidant agent. Selenium nanoparticles showed scavenging activity up to 94.48%. These results recommended that the advantages of using this method for synthesis of selenium nanoparticles with excellent antioxidant and antimicrobial mechanism and activity, which can be used as the antioxidant and antibiotic agent. Copyright © 2017 Elsevier Ltd. All rights reserved.

The BioHub Knowledge Base: Ontology and Repository for Sustainable Biosourcing.

PubMed

Read, Warren J; Demetriou, George; Nenadic, Goran; Ruddock, Noel; Stevens, Robert; Winter, Jerry

2016-06-01

The motivation for the BioHub project is to create an Integrated Knowledge Management System (IKMS) that will enable chemists to source ingredients from bio-renewables, rather than from non-sustainable sources such as fossil oil and its derivatives. The BioHubKB is the data repository of the IKMS; it employs Semantic Web technologies, especially OWL, to host data about chemical transformations, bio-renewable feedstocks, co-product streams and their chemical components. Access to this knowledge base is provided to other modules within the IKMS through a set of RESTful web services, driven by SPARQL queries to a Sesame back-end. The BioHubKB re-uses several bio-ontologies and bespoke extensions, primarily for chemical feedstocks and products, to form its knowledge organisation schema. Parts of plants form feedstocks, while various processes generate co-product streams that contain certain chemicals. Both chemicals and transformations are associated with certain qualities, which the BioHubKB also attempts to capture. Of immediate commercial and industrial importance is to estimate the cost of particular sets of chemical transformations (leading to candidate surfactants) performed in sequence, and these costs too are captured. Data are sourced from companies' internal knowledge and document stores, and from the publicly available literature. Both text analytics and manual curation play their part in populating the ontology. We describe the prototype IKMS, the BioHubKB and the services that it supports for the IKMS. The BioHubKB can be found via http://biohub.cs.manchester.ac.uk/ontology/biohub-kb.owl .

BioCreative Workshops for DOE Genome Sciences: Text Mining for Metagenomics

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

Wu, Cathy H.; Hirschman, Lynette

The objective of this project was to host BioCreative workshops to define and develop text mining tasks to meet the needs of the Genome Sciences community, focusing on metadata information extraction in metagenomics. Following the successful introduction of metagenomics at the BioCreative IV workshop, members of the metagenomics community and BioCreative communities continued discussion to identify candidate topics for a BioCreative metagenomics track for BioCreative V. Of particular interest was the capture of environmental and isolation source information from text. The outcome was to form a “community of interest” around work on the interactive EXTRACT system, which supported interactive taggingmore » of environmental and species data. This experiment is included in the BioCreative V virtual issue of Database. In addition, there was broad participation by members of the metagenomics community in the panels held at BioCreative V, leading to valuable exchanges between the text mining developers and members of the metagenomics research community. These exchanges are reflected in a number of the overview and perspective pieces also being captured in the BioCreative V virtual issue. Overall, this conversation has exposed the metagenomics researchers to the possibilities of text mining, and educated the text mining developers to the specific needs of the metagenomics community.« less

Bio-based Industries Joint Undertaking: The catalyst for sustainable bio-based economic growth in Europe.

PubMed

Mengal, Philippe; Wubbolts, Marcel; Zika, Eleni; Ruiz, Ana; Brigitta, Dieter; Pieniadz, Agata; Black, Sarah

2018-01-25

This article discusses the preparation, structure and objectives of the Bio-based Industries Joint Undertaking (BBI JU). BBI JU is a public-private partnership (PPP) between the European Commission (EC) and the Bio-based Industries Consortium (BIC), the industry-led private not-for-profit organisation representing the private sectors across the bio-based industries. The model of the public-private partnership has been successful as a new approach to supporting research and innovation and de-risking investment in Europe. The BBI JU became a reality in 2014 and represents the largest industrial and economic cooperation endeavour financially ever undertaken in Europe in the area of industrial biotechnologies. It is considered to be one of the most forward-looking initiatives under Horizon 2020 and demonstrates the circular economy in action. The BBI JU will be the catalyst for this strategy to mobilise actors across Europe including large industry, small and medium-sized enterprises (SMEs), all types of research organisations, networks and universities. It will support regions and in doing so, the European Union Member States and associated countries in the implementation of their bioeconomy strategies. Copyright © 2017 Elsevier B.V. All rights reserved.

Promoting Bio-Ethanol in the United States by Incorporating Lessons from Brazil's National Alcohol Program

ERIC Educational Resources Information Center

Du, Yangbo

2007-01-01

Current U.S. energy policy supports increasing the use of bio-ethanol as a gasoline substitute, which Brazil first produced on a large scale in response to the 1970s energy crises. Brazil's National Alcohol Program stood out among its contemporaries regarding its success at displacing a third of Brazil's gasoline requirements, primarily due to…

The water footprint of sweeteners and bio-ethanol.

PubMed

Gerbens-Leenes, Winnie; Hoekstra, Arjen Y

2012-04-01

An increasing demand for food together with a growing demand for energy crops result in an increasing demand for and competition over water. Sugar cane, sugar beet and maize are not only essential food crops, but also important feedstock for bio-ethanol. Crop growth requires water, a scarce resource. This study aims to assess the green, blue and grey water footprint (WF) of sweeteners and bio-ethanol from sugar cane, sugar beet and maize in the main producing countries. The WFs of sweeteners and bio-ethanol are mainly determined by the crop type that is used as a source and by agricultural practise and agro-climatic conditions; process water footprints are relatively small. The weighted global average WF of sugar cane is 209 m(3)/tonne; for sugar beet this is 133 m(3)/tonne and for maize 1222 m(3)/tonne. Large regional differences in WFs indicate that WFs of crops for sweeteners and bio-ethanol can be improved. It is more favourable to use maize as a feedstock for sweeteners or bio-ethanol than sugar beet or sugar cane. The WF of sugar cane contributes to water stress in the Indus and Ganges basins. In the Ukraine, the large grey WF of sugar beet contributes to water pollution. In some western European countries, blue WFs of sugar beet and maize need a large amount of available blue water for agriculture. The allocation of the limited global water resources to bio-energy on a large scale will be at the cost of water allocation to food and nature. Copyright © 2011 Elsevier Ltd. All rights reserved.

The electromagnetic bio-field: clinical experiments and interferences

PubMed Central

Burnei, G; Hodorogea, D; Georgescu, I; Gavriliu, Ş; Drăghici, I; Dan, D; Vlad, C; Drăghici, L

2012-01-01

Introduction: One of the most important factors is the technical and scientifically rapid development that is continually modifying the world we live in and polluting it with electromagnetic radiations. A functional and structural influence of magnetic and electromagnetic field on living organisms is presented in the literature by many performed experiments. Material and methods: The notion of bio-field represents the electromagnetic field generated by the bio-structures, not only in their normal physiological activities but also in their pathological states. There is a tight interdependency between the bio-field and the bio-structure, which respects the primary notion of an electromagnetic field given by the Maxwell-Faraday laws, in which, the electromagnetic phenomena are simplified to the field variations. These variations can be expressed in a coherent differential equation system that bounds the field vectors to different space points at different time moments. Results: The living organisms cannot contain electrostatic and magneto-static fields due to the intense activity of the bio-structures. The biochemical reactions that have high rhythms and speeds always impose the electrodynamics character of the biologic field that also corresponds to the stability of the protein molecule that can be explained only through a dynamic way. The existent energy is not considered an exciting agent, and it does not lead to any effects. Conclusions: The parameters of these elementary bio-fields cannot yet be fully known due to technical reasons. The biological structures are very complex ones and undergo continuous dynamical activity. That is why the calculus model should be related to the constant dynamics, nowadays being very difficult to express. PMID:22802878

BioSPICE: access to the most current computational tools for biologists.

PubMed

Garvey, Thomas D; Lincoln, Patrick; Pedersen, Charles John; Martin, David; Johnson, Mark

2003-01-01

The goal of the BioSPICE program is to create a framework that provides biologists access to the most current computational tools. At the program midpoint, the BioSPICE member community has produced a software system that comprises contributions from approximately 20 participating laboratories integrated under the BioSPICE Dashboard and a methodology for continued software integration. These contributed software modules are the BioSPICE Dashboard, a graphical environment that combines Open Agent Architecture and NetBeans software technologies in a coherent, biologist-friendly user interface. The current Dashboard permits data sources, models, simulation engines, and output displays provided by different investigators and running on different machines to work together across a distributed, heterogeneous network. Among several other features, the Dashboard enables users to create graphical workflows by configuring and connecting available BioSPICE components. Anticipated future enhancements to BioSPICE include a notebook capability that will permit researchers to browse and compile data to support model building, a biological model repository, and tools to support the development, control, and data reduction of wet-lab experiments. In addition to the BioSPICE software products, a project website supports information exchange and community building.

Bio-nano interactions detected by nanochannel electrophoresis.

PubMed

Luan, Binquan

2016-08-01

Engineered nanoparticles have been widely used in industry and are present in many consumer products. However, their bio-safeties especially in a long term are largely unknown. Here, a nanochannel-electrophoresis-based method is proposed for detecting the potential bio-nano interactions that may further lead to damages to human health and/or biological environment. Through proof-of-concept molecular dynamics simulations, it was demonstrated that the transport of a protein-nanoparticle complex is very different from that of a protein along. By monitoring the change of ionic currents induced by a transported analyte as well as the transport velocities of the analyte, the complex (with bio-nano interaction) can be clearly distinguished from the protein alone (with no interaction with tested nanoparticles). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Current and emerging challenges of field effect transistor based bio-sensing

NASA Astrophysics Data System (ADS)

Matsumoto, Akira; Miyahara, Yuji

2013-10-01

Field-effect-transistor (FET) based electrical signal transduction is an increasingly prevalent strategy for bio-sensing. This technique, often termed ``Bio-FETs'', provides an essentially label-free and real-time based bio-sensing platform effective for a variety of targets. This review highlights recent progress and challenges in the field. A special focus is on the comprehension of emerging nanotechnology-based approaches to facilitate signal-transduction and amplification. Some new targets of Bio-FETs and the future perspectives are also discussed.

Current and emerging challenges of field effect transistor based bio-sensing.

PubMed

Matsumoto, Akira; Miyahara, Yuji

2013-11-21

Field-effect-transistor (FET) based electrical signal transduction is an increasingly prevalent strategy for bio-sensing. This technique, often termed "Bio-FETs", provides an essentially label-free and real-time based bio-sensing platform effective for a variety of targets. This review highlights recent progress and challenges in the field. A special focus is on the comprehension of emerging nanotechnology-based approaches to facilitate signal-transduction and amplification. Some new targets of Bio-FETs and the future perspectives are also discussed.

75 FR 12492 - Departmental Management; Public Meeting on BioPreferredSM

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-16

...; Public Meeting on BioPreferred\\SM\\ Intermediate Material and Feedstock Product Designation AGENCY... after registering. FOR FURTHER INFORMATION CONTACT: Ron Buckhalt, BioPreferred Manager, U.S. Department... program together as the BioPreferred\\SM\\ Program. Due to the changes mandated by the 2008 Farm Bill, and...

Inhibitors removal from bio-oil aqueous fraction for increased ethanol production.

PubMed

Sukhbaatar, Badamkhand; Li, Qi; Wan, Caixia; Yu, Fei; Hassan, El-Barbary; Steele, Philip

2014-06-01

Utilization of 1,6-anhydro-β-d-glucopyranose (levoglucosan) present (11% w/v) in the water fraction of bio-oil for ethanol production will facilitate improvement in comprehensive utilization of total carbon in biomass. One of the major challenges for conversion of anhydrous sugars from the bio-oil water fraction to bio-ethanol is the presence of inhibitory compounds that slow or impede the microbial fermentation process. Removal of inhibitory compounds was first approached by n-butanol extraction. Optimal ratio of n-butanol and bio-oil water fraction was 1.8:1. Removal of dissolved n-butanol was completed by evaporation. Concentration of sugars in the bio-oil water fraction was performed by membrane filtration and freeze drying. Fermentability of the pyrolytic sugars was tested by fermentation of hydrolyzed sugars with Saccharomyces pastorianus lager yeast. The yield of ethanol produced from pyrolytic sugars in the bio-oil water fraction reached a maximum of 98% of the theoretical yield. Copyright © 2014 Elsevier Ltd. All rights reserved.

Changes of parameters during composting of bio-waste collected over four seasons.

PubMed

Hanc, Ales; Ochecova, Pavla; Vasak, Filip

2017-07-01

This study investigated the evolution of several main parameters during the composting of separately collected household bio-waste originating from urban settlements (U-bio-waste) and family houses (F-bio-waste) from four climate seasons. When comparing both types of composts, U-bio-waste compost contained a higher amount of nutrients, however F-bio-waste compost was characterized by greater yield, greater availability of phosphorus and magnesium, and faster stability. In terms of seasons, compost from bio-waste collected in spring contained the highest amount of nutrients, reflecting the high content of nutrients in plant feedstock. Dissolved organic carbon and pH in U- and F-bio-waste compost, respectively, frequently showed close relationships with other parameters. The seasonal variations of most of the parameters in the composts were found to be lower compared to the variations observed in the feedstocks. The greatest seasonal variation was found in nitrate nitrogen, which is the reason for the more frequent analysis of this parameter.

Smart surface coating of drug nanoparticles with cross-linkable polyethylene glycol for bio-responsive and highly efficient drug delivery.

PubMed

Wei, Weijia; Zhang, Xiujuan; Chen, Xianfeng; Zhou, Mengjiao; Xu, Ruirui; Zhang, Xiaohong

2016-04-21

Many drug molecules can be directly used as nanomedicine without the requirement of any inorganic or organic carriers such as silica and liposome nanostructures. This new type of carrier-free drug nanoparticles (NPs) has great potential in clinical treatment because of its ultra-high drug loading capacity and biodegradability. For practical applications, it is essential for such nanomedicine to possess robust stability and minimal premature release of therapeutic molecules during circulation in the blood stream. To meet this requirement, herein, we develop GSH-responsive and crosslinkable amphiphilic polyethylene glycol (PEG) molecules to modify carrier-free drug NPs. These PEG molecules can be cross-linked on the surface of the NPs to endow them with greater stability and the cross-link is sensitive to intracellular environment for bio-responsive drug release. With this elegant design, our experimental results show that the liberation of DOX from DOX-cross-linked PEG NPs is dramatically slower than that from DOX-non-cross-linked PEG NPs, and the DOX release profile can be controlled by tuning the concentration of the reducing agent to break the cross-link between PEG molecules. More importantly, in vivo studies reveal that the DOX-cross-linked PEG NPs exhibit favorable blood circulation half-life (>4 h) and intense accumulation in tumor areas, enabling effective anti-cancer therapy. We expect this work will provide a powerful strategy for stabilizing carrier-free nanomedicines and pave the way to their successful clinical applications in the future.

Catalytic upgrading of bio-oil produced from hydrothermal liquefaction of Nannochloropsis sp.

PubMed

Shakya, Rajdeep; Adhikari, Sushil; Mahadevan, Ravishankar; Hassan, El Barbary; Dempster, Thomas A

2018-03-01

Upgrading of bio-oil obtained from hydrothermal liquefaction (HTL) of algae is necessary for it to be used as a fuel. In this study, bio-oil obtained from HTL of Nannochloropsis sp. was upgraded using five different catalysts (Ni/C, ZSM-5, Ni/ZSM-5, Ru/C and Pt/C) at 300 °C and 350 °C. The upgraded bio-oil yields were higher at 300 °C; however, higher quality upgraded bio-oils were obtained at 350 °C. Ni/C gave the maximum upgraded bio-oil yield (61 wt%) at 350 °C. However, noble metal catalysts (Ru/C and Pt/C) gave the better upgraded bio-oils in terms of acidity, heating values, and nitrogen values. The higher heating value of the upgraded bio-oils ranged from 40 to 44 MJ/kg, and the nitrogen content decreased from 5.37 to 1.29 wt%. Most of the upgraded bio-oils (35-40 wt%) were in the diesel range. The major components present in the gaseous products were CH 4 , CO, CO 2 and lower alkanes. Copyright © 2017 Elsevier Ltd. All rights reserved.

75 FR 5033 - Departmental Management; Public meeting on BioPreferredSM

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-01

...; Public meeting on BioPreferred\\SM\\ Complex Products and Assemblies Designation and Industry Training on... include: 1. Using BioPreferred tools to position your business to sell or increase sales to the Federal...: Ron Buckhalt, BioPreferred Manager, U.S. Department of Agriculture, Office of Procurement and Property...

Multitip scanning bio-Kelvin probe

NASA Astrophysics Data System (ADS)

Baikie, I. D.; Smith, P. J. S.; Porterfield, D. M.; Estrup, P. J.

1999-03-01

We have developed a novel multitip scanning Kelvin probe which can measure changes in biological surface potential ΔVs to within 2 mV and, quasisimultaneously monitor displacement to <1 μm. The control and measurement subcomponents are PC based and incorporate a flexible user interface permitting software control of each individual tip, measurement, and scan parameters. We review the mode of operation and design features of the scanning bio-Kelvin probe including tip steering, signal processing, tip calibration, and novel tip tracking/dithering routines. This system uniquely offers both tip-to-sample spacing control (which is essential to avoid spurious changes in ΔVs due to variations in mean spacing) and a dithering routine to maintain tip orientation to the biological specimen, irrespective of the latter's movement. These features permit long term (>48 h) "active" tracking of the displacement and biopotentials developed along and around a plant shoot in response to an environmental stimulus, e.g., differential illumination (phototropism) or changes in orientation (gravitropism).

Molecular dynamics investigations of BioH protein substrate specificity for biotin synthesis.

PubMed

Xue, Qiao; Cui, Ying-Lu; Zheng, Qing-Chuan; Zhang, Hong-Xing

2016-05-01

BioH, an enzyme of biotin synthesis, plays an important role in fatty acid synthesis which assembles the pimelate moiety. Pimeloyl-acyl carrier protein (ACP) methyl ester, which is long known to be a biotin precursor, is the physiological substrate of BioH. Azelayl methyl ester, which has a longer chain than pimeloyl methyl ester, conjugated to ACP is also indeed accepted by BioH with very low rate of hydrolysis. To date, the substrate specificity for BioH and the molecular origin for the experimentally observed rate changes of hydrolysis by the chain elongation have remained elusive. To this end, we have investigated chain elongation effects on the structures by using the fully atomistic molecular dynamics simulations combined with binding free energy calculations. The results indicate that the substrate specificity is determined by BioH together with ACP. The added two methylenes would increase the structural flexibility by protein motions at the interface of ACP and BioH, instead of making steric clashes with the side chains of the BioH hydrophobic cavity. On the other hand, the slower hydrolysis of azelayl substrate is suggested to be associated with the loose of contacts between BioH and ACP, and with the lost electrostatic interactions of two ionic/hydrogen bonding networks at the interface of the two proteins. The present study provides important insights into the structure-function relationships of the complex of BioH with pimeloyl-ACP methyl ester, which could contribute to further understanding about the mechanism of the biotin synthetic pathway, including the catalytic role of BioH.

[Determination of lead in microemulsified rapeseed oil and bio-diesel oil by GFAAS].

PubMed

Li, Sheng-qing; He, Xiao-min; Du, Ping; Wang, Min; Chen, Hao; Wu, Mou-cheng

2008-10-01

Bio-diesel oil has attracted much attention as a substitutable energy sources for its renewable and eco-friendly property. However, problems of lead contamination in fuel are also emphasized increasingly at present. So it was of quite significance to determine the contents of lead in bio-diesel oil and its raw material rapeseed oil. An effective method was developed for the rapid determination of lead in rapeseed oil and bio-diesel oil by graphite furnace atomic absorption spectrometry (GFAAS) after their stabilization as microemulsions. In this research work, polyethyleneglycol octyl phenyl ether and n-butanol were used for emulsifier and auxiliary emulsifying agent, respectively. For Pb, efficient thermal stabilization was obtained using NH4H2PO4 as matrix modifier. Sample stabilization was necessary because of evident analyte losses that occurred immediately after sampling. Excellent long-term sample stabilization and the influence of the microemulsion composition on the GFAAS response were observed by mixing different organic solvents. The ashing and atomization temperature and ramp rate influenced the sensitivity obtained for Ph. Take this into account, the optimum conditions of the graphite furnace atomic absorption spectrometric determination of Pb in rapeseed oil and bio-diesel oil samples were investigated. The results showed that the microemulsion was quite stable when the value of V(20% polyethyleneglycol octyl phenyl ether), V(n-butanol), V(oil) and V(water) was 0.1: 8.9: 0.5: 0.5, without matrix interference effect. The determination limit of the proposed method was 126.2 microg x L(-1) for Pb, comfortably below the values found in the analyzed samples. The recoveries were from 81.8% to 109.0%, which performed using the addition of different concentrations of lead to bio-diesel oil, rapeseed oil and petrochemical diesel samples. The relative standard deviation of determination was 5.84%. This work showed the great efficiency of the microemulsion

Bio-inspired Edible Superhydrophobic Interface for Reducing Residual Liquid Food.

PubMed

Li, Yao; Bi, Jingran; Wang, Siqi; Zhang, Tan; Xu, Xiaomeng; Wang, Haitao; Cheng, Shasha; Zhu, Bei-Wei; Tan, Mingqian

2018-03-07

Significant wastage of residual liquid food, such as milk, yogurt, and honey, in food containers has attracted great attention. In this work, a bio-inspired edible superhydrophobic interface was fabricated using U.S. Food and Drug Administration-approved and edible honeycomb wax, arabic gum, and gelatin by a simple and low-cost method. The bio-inspired edible superhydrophobic interface showed multiscale structures, which were similar to that of a lotus leaf surface. This bio-inspired edible superhydrophobic interface displayed high contact angles for a variety of liquid foods, and the residue of liquid foods could be effectively reduced using the bio-inspired interface. To improve the adhesive force of the superhydrophobic interface, a flexible edible elastic film was fabricated between the interface and substrate material. After repeated folding and flushing for a long time, the interface still maintained excellent superhydrophobic property. The bio-inspired edible superhydrophobic interface showed good biocompatibility, which may have potential applications as a functional packaging interface material.

BioPAX – A community standard for pathway data sharing

PubMed Central

Demir, Emek; Cary, Michael P.; Paley, Suzanne; Fukuda, Ken; Lemer, Christian; Vastrik, Imre; Wu, Guanming; D’Eustachio, Peter; Schaefer, Carl; Luciano, Joanne; Schacherer, Frank; Martinez-Flores, Irma; Hu, Zhenjun; Jimenez-Jacinto, Veronica; Joshi-Tope, Geeta; Kandasamy, Kumaran; Lopez-Fuentes, Alejandra C.; Mi, Huaiyu; Pichler, Elgar; Rodchenkov, Igor; Splendiani, Andrea; Tkachev, Sasha; Zucker, Jeremy; Gopinath, Gopal; Rajasimha, Harsha; Ramakrishnan, Ranjani; Shah, Imran; Syed, Mustafa; Anwar, Nadia; Babur, Ozgun; Blinov, Michael; Brauner, Erik; Corwin, Dan; Donaldson, Sylva; Gibbons, Frank; Goldberg, Robert; Hornbeck, Peter; Luna, Augustin; Murray-Rust, Peter; Neumann, Eric; Reubenacker, Oliver; Samwald, Matthias; van Iersel, Martijn; Wimalaratne, Sarala; Allen, Keith; Braun, Burk; Whirl-Carrillo, Michelle; Dahlquist, Kam; Finney, Andrew; Gillespie, Marc; Glass, Elizabeth; Gong, Li; Haw, Robin; Honig, Michael; Hubaut, Olivier; Kane, David; Krupa, Shiva; Kutmon, Martina; Leonard, Julie; Marks, Debbie; Merberg, David; Petri, Victoria; Pico, Alex; Ravenscroft, Dean; Ren, Liya; Shah, Nigam; Sunshine, Margot; Tang, Rebecca; Whaley, Ryan; Letovksy, Stan; Buetow, Kenneth H.; Rzhetsky, Andrey; Schachter, Vincent; Sobral, Bruno S.; Dogrusoz, Ugur; McWeeney, Shannon; Aladjem, Mirit; Birney, Ewan; Collado-Vides, Julio; Goto, Susumu; Hucka, Michael; Le Novère, Nicolas; Maltsev, Natalia; Pandey, Akhilesh; Thomas, Paul; Wingender, Edgar; Karp, Peter D.; Sander, Chris; Bader, Gary D.

2010-01-01

BioPAX (Biological Pathway Exchange) is a standard language to represent biological pathways at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data (http://www.biopax.org). Pathway data captures our understanding of biological processes, but its rapid growth necessitates development of databases and computational tools to aid interpretation. However, the current fragmentation of pathway information across many databases with incompatible formats presents barriers to its effective use. BioPAX solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. BioPAX was created through a community process. Through BioPAX, millions of interactions organized into thousands of pathways across many organisms, from a growing number of sources, are available. Thus, large amounts of pathway data are available in a computable form to support visualization, analysis and biological discovery. PMID:20829833

BioCIDER: a Contextualisation InDEx for biological Resources discovery

PubMed Central

Horro, Carlos; Cook, Martin; Attwood, Teresa K.; Brazas, Michelle D.; Hancock, John M.; Palagi, Patricia; Corpas, Manuel; Jimenez, Rafael

2017-01-01

Abstract Summary The vast, uncoordinated proliferation of bioinformatics resources (databases, software tools, training materials etc.) makes it difficult for users to find them. To facilitate their discovery, various services are being developed to collect such resources into registries. We have developed BioCIDER, which, rather like online shopping ‘recommendations’, provides a contextualization index to help identify biological resources relevant to the content of the sites in which it is embedded. Availability and Implementation BioCIDER (www.biocider.org) is an open-source platform. Documentation is available online (https://goo.gl/Klc51G), and source code is freely available via GitHub (https://github.com/BioCIDER). The BioJS widget that enables websites to embed contextualization is available from the BioJS registry (http://biojs.io/). All code is released under an MIT licence. Contact carlos.horro@earlham.ac.uk or rafael.jimenez@elixir-europe.org or manuel@repositive.io PMID:28407033

SynBioSS-aided design of synthetic biological constructs.

PubMed

Kaznessis, Yiannis N

2011-01-01

We present walkthrough examples of using SynBioSS to design, model, and simulate synthetic gene regulatory networks. SynBioSS stands for Synthetic Biology Software Suite, a platform that is publicly available with Open Licenses at www.synbioss.org. An important aim of computational synthetic biology is the development of a mathematical modeling formalism that is applicable to a wide variety of simple synthetic biological constructs. SynBioSS-based modeling of biomolecular ensembles that interact away from the thermodynamic limit and not necessarily at steady state affords for a theoretical framework that is generally applicable to known synthetic biological systems, such as bistable switches, AND gates, and oscillators. Here, we discuss how SynBioSS creates links between DNA sequences and targeted dynamic phenotypes of these simple systems. Copyright © 2011 Elsevier Inc. All rights reserved.

Vapor-fed bio-hybrid fuel cell.

PubMed

Benyamin, Marcus S; Jahnke, Justin P; Mackie, David M

2017-01-01

Concentration and purification of ethanol and other biofuels from fermentations are energy-intensive processes, with amplified costs at smaller scales. To circumvent the need for these processes, and to potentially reduce transportation costs as well, we have previously investigated bio-hybrid fuel cells (FCs), in which a fermentation and FC are closely coupled. However, long-term operation requires strictly preventing the fermentation and FC from harming each other. We introduce here the concept of the vapor-fed bio-hybrid FC as a means of continuously extracting power from ongoing fermentations at ambient conditions. By bubbling a carrier gas (N 2 ) through a yeast fermentation and then through a direct ethanol FC, we protect the FC anode from the catalyst poisons in the fermentation (which are non-volatile), and also protect the yeast from harmful FC products (notably acetic acid) and from build-up of ethanol. Since vapor-fed direct ethanol FCs at ambient conditions have never been systematically characterized (in contrast to vapor-fed direct methanol FCs), we first assess the effects on output power and conversion efficiency of ethanol concentration, vapor flow rate, and FC voltage. The results fit a continuous stirred-tank reactor model. Over a wide range of ethanol partial pressures (2-8 mmHg), power densities are comparable to those for liquid-fed direct ethanol FCs at the same temperature, with power densities >2 mW/cm 2 obtained. We then demonstrate the continuous operation of a vapor-fed bio-hybrid FC with fermentation for 5 months, with no indication of performance degradation due to poisoning (of either the FC or the fermentation). It is further shown that the system is stable, recovering quickly from disturbances or from interruptions in maintenance. The vapor-fed bio-hybrid FC enables extraction of power from dilute bio-ethanol streams without costly concentration and purification steps. The concept should be scalable to both large and small

Nano-Bio Quantum Technology for Device-Specific Materials

NASA Technical Reports Server (NTRS)

Choi, Sang H.

2009-01-01

The areas discussed are still under development: I. Nano structured materials for TE applications a) SiGe and Be.Te; b) Nano particles and nanoshells. II. Quantum technology for optical devices: a) Quantum apertures; b) Smart optical materials; c) Micro spectrometer. III. Bio-template oriented materials: a) Bionanobattery; b) Bio-fuel cells; c) Energetic materials.

A Novel Bio-carrier Fabricated Using 3D Printing Technique for Wastewater Treatment

PubMed Central

Dong, Yang; Fan, Shu-Qian; Shen, Yu; Yang, Ji-Xiang; Yan, Peng; Chen, You-Peng; Li, Jing; Guo, Jin-Song; Duan, Xuan-Ming; Fang, Fang; Liu, Shao-Yang

2015-01-01

The structure of bio-carriers is one of the key operational characteristics of a biofilm reactor. The goal of this study is to develop a series of novel fullerene-type bio-carriers using the three-dimensional printing (3DP) technique. 3DP can fabricate bio-carriers with more specialized structures compared with traditional fabrication processes. In this research, three types of fullerene-type bio-carriers were fabricated using the 3DP technique and then compared with bio-carrier K3 (from AnoxKaldnes) in the areas of physicochemical properties and biofilm growth. Images acquired by 3D profiling and SEM indicated that the surface roughness of the 3DP bio-carrier was greater than that of K3. Furthermore, contact angle data indicated that the 3DP bio-carriers were more hydrophilic than K3. The biofilm on the 3DP bio-carriers exhibited higher microbial activity and stronger adhesion ability. These findings were attributed to excellent mass transfer of the substrate (and oxygen) between the vapour-liquid-solid tri-phase system and to the surface characteristics. It is concluded that the novel 3DP fullerene-type bio-carriers are ideal carriers for biofilm adherence and growth. PMID:26202477

A Novel Bio-carrier Fabricated Using 3D Printing Technique for Wastewater Treatment.

PubMed

Dong, Yang; Fan, Shu-Qian; Shen, Yu; Yang, Ji-Xiang; Yan, Peng; Chen, You-Peng; Li, Jing; Guo, Jin-Song; Duan, Xuan-Ming; Fang, Fang; Liu, Shao-Yang

2015-07-23

The structure of bio-carriers is one of the key operational characteristics of a biofilm reactor. The goal of this study is to develop a series of novel fullerene-type bio-carriers using the three-dimensional printing (3DP) technique. 3DP can fabricate bio-carriers with more specialized structures compared with traditional fabrication processes. In this research, three types of fullerene-type bio-carriers were fabricated using the 3DP technique and then compared with bio-carrier K3 (from AnoxKaldnes) in the areas of physicochemical properties and biofilm growth. Images acquired by 3D profiling and SEM indicated that the surface roughness of the 3DP bio-carrier was greater than that of K3. Furthermore, contact angle data indicated that the 3DP bio-carriers were more hydrophilic than K3. The biofilm on the 3DP bio-carriers exhibited higher microbial activity and stronger adhesion ability. These findings were attributed to excellent mass transfer of the substrate (and oxygen) between the vapour-liquid-solid tri-phase system and to the surface characteristics. It is concluded that the novel 3DP fullerene-type bio-carriers are ideal carriers for biofilm adherence and growth.

A histologic, histomorphometric, and radiographic comparison between two complexes of CenoBoen/CenoMembrane and Bio-Oss/Bio-Gide in lateral ridge augmentation: A clinical trial.

PubMed

Amoian, Babak; Moudi, Ehsan; Majidi, Maryam Seyed; Ali Tabatabaei, S M

2016-09-01

Several grafting materials have been used for alveolar ridge augmentation. The literature lacks researches to compare CenoBone to other grafting materials. The aim of this study was to compare CenoBone/CenoMembrane complex to Bio-Oss/Bio-Gide complex in lateral alveolar bone augmentation in terms of radiographic, histologic, and histomorphometric parameters. In this randomized controlled trial, ten patients who needed lateral ridge augmentation were selected and augmentations were done using either of CenoBone/CenoMembrane or Bio-Oss/Bio-Gide complexes. In the re-entry surgery in 6 months following augmentation, core biopsies were taken and clinical, radiographic, histologic, and histomorphometric evaluations were performed. No statistically significant difference was seen between groups except for the number of blood vessels and percentage of residual graft materials. CenoBone seems to present a comparable lateral ridge augmentation to Bio-Oss in.

Programmable Nano-Bio Interfaces for Functional Biointegrated Devices.

PubMed

Cai, Pingqiang; Leow, Wan Ru; Wang, Xiaoyuan; Wu, Yun-Long; Chen, Xiaodong

2017-07-01

A large amount of evidence has demonstrated the revolutionary role of nanosystems in the screening and shielding of biological systems. The explosive development of interfacing bioentities with programmable nanomaterials has conveyed the intriguing concept of nano-bio interfaces. Here, recent advances in functional biointegrated devices through the precise programming of nano-bio interactions are outlined, especially with regard to the rational assembly of constituent nanomaterials on multiple dimension scales (e.g., nanoparticles, nanowires, layered nanomaterials, and 3D-architectured nanomaterials), in order to leverage their respective intrinsic merits for different functions. Emerging nanotechnological strategies at nano-bio interfaces are also highlighted, such as multimodal diagnosis or "theragnostics", synergistic and sequential therapeutics delivery, and stretchable and flexible nanoelectronic devices, and their implementation into a broad range of biointegrated devices (e.g., implantable, minimally invasive, and wearable devices). When utilized as functional modules of biointegrated devices, these programmable nano-bio interfaces will open up a new chapter for precision nanomedicine. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enrichment of bio-oil after hydrothermal liquefaction (HTL) of microalgae C. vulgaris grown in wastewater: Bio-char and post HTL wastewater utilization studies.

PubMed

Arun, Jayaseelan; Varshini, Padmanabhan; Prithvinath, P Kamath; Priyadarshini, Venkataramani; Gopinath, Kannappan Panchamoorthy

2018-08-01

In this study, bio-oil was produced through hydrothermal liquefaction (HTL) of C. vulgaris biomass cultivated in wastewater and was enriched into transportation fuels. Bio-oil yield was 29.37% wt at 300 °C, 60 min, at 15 g/200 mL biomass loading rate with 3% wt nano ZnO catalyst loading. Applying catalyst reduced oxygen and nitrogen content in bio-oil and increased its calorific value (19.6 ± 0.8 MJ/Kg). Bio-oil was enriched through liquid-liquid extraction (LLE) and higher yield was obtained at 30 °C for dichloromethane solvent (18.2% wt). Compounds of enriched oil were within the petro-diesel range (C 8 -C 21 ). Bio-char after HTL process was activated and used as adsorbent in wastewater treatment process to remove organic pollutants (COD, NO 3 , NH 3 and PO 4 ). Treated wastewater can be supplied as growth medium for microalgae cultivation in further experiments. Nearly 3-4 times the nanocatalyst can be reused in the HTL process. Copyright © 2018 Elsevier Ltd. All rights reserved.

Using Bio-Optics to Reveal Phytoplankton Physiology from a Wirewalker Autonomous Platform

NASA Technical Reports Server (NTRS)

Omand, M. M.; Cetinic, I.; Lucas, A. J.

2017-01-01

Rapid, wave-powered profiling of bio-optical properties from an autonomous Wirewalker platform provides useful insights into phytoplankton physiology, including the patterns of diel growth, phytoplankton mortality, nonphotochemical quenching of chlorophyll a fluorescence, and natural (sun-induced) fluorescence of mixed communities. Methods are proposed to quantify each of these processes. Such autonomous measurements of phytoplankton physiological rates and responses open up new possibilities for studying phytoplankton in situ, over longer periods, and under a broader range of environmental conditions.

Bio-Photonic Detection of Various Cellular Cultures

NASA Astrophysics Data System (ADS)

Hann, Patrick; Garzon, Maria; Pfeiffer, Erik; Lofland, Samuel; Knoesel, Ernst

2008-03-01

Since it is non-invasive, there has been increased research in the field of bio-optics. Many biological systems display an unusual phenomenon, delayed luminescence, produced by what is known as bio-photons. We present an apparatus and procedure for the detection of these ultra-weak photonic emissions using a single photon detection device. The results of bread yeast, saccramyces, and algae will be presented and compared to other reports in the literature

Sublethal Exposure to Clove and Cinnamon Essential Oils Induces Hormetic-Like Responses and Disturbs Behavioral and Respiratory Responses in Sitophilus zeamais (Coleoptera: Curculionidae).

PubMed

Haddi, Khalid; Oliveira, Eugênio E; Faroni, Lêda R A; Guedes, Daniela C; Miranda, Natalie N S

2015-12-01

Essential oils have been suggested as suitable alternatives for controlling insect pests. However, the potential adaptive responses elicited in insects for mitigating the actions of these compounds have not received adequate attention. Furthermore, as is widely reported with traditional insecticides, sublethal exposure to essential oils might induce stimulatory responses or contribute to the development of resistance strategies that can compromise the management of insect pests. The current study evaluated the locomotory and respiratory responses as well as the number of larvae per grain produced by the maize weevil, Sitophilus zeamais Motschulsky, after being sublethally exposed to the essential oils of clove, Syzygium aromaticum L., and cinnamon, Cinnamomum zeylanicum L. The essential oils showed similar insecticidal toxicity (exposure route: contact with dried residues; Clove LC95 = 3.96 [2.78-6.75] µl/cm(2); Cinnamon LC95 = 3.47 [2.75-4.73] µl/cm(2)). A stimulatory effect on the median survival time (TL50) was observed when insects were exposed to low concentrations of each oil. Moreover, a higher number of larvae per grain was produced under sublethal exposure to clove essential oil. S. zeamais avoided the treated areas (in free-choice experiments) and altered their mobility when sublethally exposed to both essential oils. The respiratory rates of S. zeamais (i.e., CO2 production) were significantly reduced under low concentrations of the essential oils. We recommend the consideration of the potential sublethal effects elicited by botanical pesticides during the development of integrated pest management programs aiming to control S. zeamais. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

BIO-PRECIPITATES PRODUCED BY TWO AUTOCHTHONOUS BORON TOLERANT STREPTOMYCES STRAINS.

PubMed

Moraga, Norma Beatriz; Irazusta, Verónica; Amoroso, María Julia; Rajal, Verónica Beatriz

2017-08-01

Boron is widespread in the environment. Although contaminated soils are hard to recover different strategies have been investigated in the recent years. Bioremediation is one of the most studied because it is eco-friendly and less costly than other techniques. The aim of this research was to evaluate whether two Streptomyces strains isolated from boron contaminated soils in Salta, Argentina, may help remove boron from such soils. For this, they were grown in different liquid media with two boric acid concentrations and their specific growth rate and specific boric acid consumption rate were determined. Both strains showed great capacity to remove boron from the media. Increasing boric acid concentrations affected negatively the specific growth rate, however the specific boric acid consumption rate was superior. Boron bio-precipitates were observed when the strains grew in the presence of boric acid, probably due to an adaptive response developed by the cells to the exposure, for which many proteins were differentially synthetized. This strategy to tolerate high concentrations of boron by immobilizing it in bio-precipitates has not been previously described, to the best of our knowledge, and may have a great potential application in remediating soils contaminated with boron compounds.

Bio-antioxidants - a chemical base of their antioxidant activity and beneficial effect on human health.

PubMed

Kancheva, V D; Kasaikina, O T

2013-01-01

The paradox of aerobic life is that higher eukaryotic organisms cannot exist without oxygen, yet oxygen is inherently dangerous to their existence. Autoxidation of organic substances frequently occurs via free radical mechanism which generates different active radicals and peroxides OH(•), O2 (•-), LO2 (•), HOOH, LOOH, so called reactive oxygen species (ROS), which appear to be responsible for oxygen toxicity. To survive in such an unfriendly oxygen environment, living organisms generate - or obtain from food - a variety of water- and lipid-soluble antioxidant compounds. Biologically active compounds with antioxidant potential, i.e. bio-antioxidants (natural and their synthetic analogues) have a wide range of applications. They are important drugs, antibiotics, agrochemical substitutes, and food preservatives. Many of the drugs today are synthetic modifications of naturally obtained substances. This review presents information about the chemical base of antioxidant activities and beneficial effects on human health of known and new bio-antioxidants. There is abundant literature on the phenolic antioxidants and tocopherols in particular. In this review the following bio-antioxidants are considered: A) Carotenoids, B) Cathecholamines, C) Phospholipids, D) Chalcones, E) Coumarins, F) Phenolic acids, G) Flavonoids, H) Lignans, and I) Tannins.

A comparison of pipeline versus truck transport of bio-oil.

PubMed

Pootakham, Thanyakarn; Kumar, Amit

2010-01-01

Biomass-based energy and fuels are receiving attention because they are considered carbon neutral; i.e. the amount of CO(2) released during combustion of this biomass is nearly the same as that taken up by the plants during their growth. Bio-oil is a dark viscous liquid consisting of hydrocarbons. These are produced by fast pyrolysis of biomass. "As-is" biomass material has a low energy density (MJ m(-3)), hence, the cost of transporting this energy is high. Bio-oil has a high energy density as compared to "as-is" biomass material, consequently it helps in reducing the cost of energy transport. This study compares the life cycle assessment of transportation of bio-oil by pipeline with that by truck. The scope of the work includes the transportation of bio-oil by truck or pipeline from a centralized plant (supplied with forest biomass) to an end-user. Two cases are studied for pipeline transport of bio-oil: the first case considers a coal-based electricity supply for pumping the bio-oil through a pipeline; the second case considers an electricity supply from a renewable resource. The two cases of pipeline transport are compared to two cases of truck transport (truck trailer and super B-train truck). The life cycle greenhouse gas (GHG) emissions from the pipeline transport of bio-oil for the two cases of electricity supply are 345 and 17 g of CO(2) m(-3) km(-1), respectively. Similar values for transport by trailer (capacity - 30 m(3)) and super B-train truck (capacity - 60 m(3)) are 89 and 60 g of CO(2) m(-3) km(-1), respectively. Energy input for bio-oil transport is 3.95 MJ m(-3) km(-1) by pipeline, 2.59 MJ m(-3) km(-1) by truck and 1.66 MJ m(-3) km(-1) by super B-train truck. The results show that GHG emissions in pipeline transport are largely dependent on the source of electricity (higher for coal-based electricity). Substituting 250 m(3) day(-1) of pipeline-transported bio-oil for coal-based electricity can mitigate about 5.1 million tonnes of CO(2) per year

BioPig: a Hadoop-based analytic toolkit for large-scale sequence data.

PubMed

Nordberg, Henrik; Bhatia, Karan; Wang, Kai; Wang, Zhong

2013-12-01

The recent revolution in sequencing technologies has led to an exponential growth of sequence data. As a result, most of the current bioinformatics tools become obsolete as they fail to scale with data. To tackle this 'data deluge', here we introduce the BioPig sequence analysis toolkit as one of the solutions that scale to data and computation. We built BioPig on the Apache's Hadoop MapReduce system and the Pig data flow language. Compared with traditional serial and MPI-based algorithms, BioPig has three major advantages: first, BioPig's programmability greatly reduces development time for parallel bioinformatics applications; second, testing BioPig with up to 500 Gb sequences demonstrates that it scales automatically with size of data; and finally, BioPig can be ported without modification on many Hadoop infrastructures, as tested with Magellan system at National Energy Research Scientific Computing Center and the Amazon Elastic Compute Cloud. In summary, BioPig represents a novel program framework with the potential to greatly accelerate data-intensive bioinformatics analysis.

Preparation and characterization of bio-diesels from various bio-oils.

PubMed

Lang, X; Dalai, A K; Bakhshi, N N; Reaney, M J; Hertz, P B

2001-10-01

Methyl, ethyl, 2-propyl and butyl esters were prepared from canola and linseed oils through transesterification using KOH and/ or sodium alkoxides as catalysts. In addition, methyl and ethyl esters were prepared from rapeseed and sunflower oils using the same catalysts. Chemical composition of the esters was determined by HPLC for the class of lipids and by GC for fatty acid compositions. The bio-diesel esters were characterized for their physical and fuel properties including density, viscosity, iodine value, acid value, cloud point, pure point, gross heat of combustion and volatility. Methyl and ethyl esters prepared from a particular vegetable oil had similar viscosities, cloud points and pour points, whereas methyl, ethyl, 2-propyl and butyl esters derived from a particular vegetable oil had similar gross heating values. However, their densities, which were 2 7% higher than those of diesel fuels, statistically decreased in the order of methyl approximately 2-propyl > ethyl > butyl esters. Butyl esters showed reduced cloud points (-6 degrees C to -10 degrees C) and pour points (-13 degrees C to -16 degrees C) similar to those of summer diesel fuel having cloud and pour points of -8 degrees C and -15 degrees C, respectively. The viscosities of bio-diesels (3.3-7.6 x 10(-4) Pa s at 40 degrees C) were much less than those of pure oils (22.4-45.1 x 10(-4) Pa s at 40 degrees C) and were twice those of summer and winter diesel fuels (3.50 and 1.72 x 10(-4) Pa s at 40 degrees C), and their gross heat contents of approximately 40 MJ/kg were 11% less than those of diesel fuels (approximately 45 MJ/kg). For different esters from the same vegetable oil, methyl esters were the most volatile, and the volatility decreased as the alkyl group grew bulkier. However, the bio-diesels were considerably less volatile than the conventional diesel fuels.

Test-retest reliability and smallest detectable change of the Bristol Impact of Hypermobility (BIoH) questionnaire.

PubMed

Palmer, S; Manns, S; Cramp, F; Lewis, R; Clark, E M

2017-12-01

The Bristol Impact of Hypermobility (BIoH) questionnaire is a patient-reported outcome measure developed in conjunction with adults with Joint Hypermobility Syndrome (JHS). It has demonstrated strong concurrent validity with the Short Form-36 (SF-36) physical component score but other psychometric properties have yet to be established. This study aimed to determine its test-retest reliability and smallest detectable change (SDC). A test-retest reliability study. Participants were recruited from the Hypermobility Syndromes Association, a patient organisation in the United Kingdom. Recruitment packs were sent to 1080 adults who had given permission to be contacted about research. BIoH and SF-36 questionnaires were administered at baseline and repeated two weeks later. An 11-point global rating of change scale (-5 to +5) was also administered at two weeks. Test-retest analysis and calculation of the SDC was conducted on 'stable' patients (defined as global rating of change -1 to +1). 462 responses were received. 233 patients reported a 'stable' condition and were included in analysis (95% women; mean (SD) age 44.5 (13.9) years; BIoH score 223.6 (54.0)). The BIoH questionnaire demonstrated excellent test-retest reliability (ICC 0.923, 95% CI 0.900-0.940). The SDC was 42 points (equivalent to 19% of the mean baseline score). The SF-36 physical and mental component scores demonstrated poorer test-retest reliability and larger SDCs (as a proportion of the mean baseline scores). The results provide further evidence of the potential of the BIoH questionnaire to underpin research and clinical practice for people with JHS. Copyright © 2017 Elsevier Ltd. All rights reserved.

On the relationship between satellite-estimated bio-optical and thermal properties in the Gulf of Mexico

NASA Astrophysics Data System (ADS)

Jolliff, Jason K.; Kindle, John C.; Penta, Bradley; Helber, Robert; Lee, Zhongping; Shulman, Igor; Arnone, Robert; Rowley, Clark D.

2008-03-01

Three years of Sea-viewing Wide Field-of-view Sensor (SeaWiFS) ocean color data were combined with three-dimensional thermal fields generated by the U.S. Navy's Modular Ocean Data Assimilation System (MODAS) in order to examine the interdependencies between bio-optical fields and their relationship to seasonal and mesoscale changes in upper ocean thermal structure. The combined data set suggests that the oceanic boundary layer within the Gulf of Mexico may be broadly defined by two seasonally occurring bio-thermal periods. A winter mixing period, characterized by net heat losses to the atmosphere, deepening of the isothermal layer depth, and annual maxima of satellite-estimated colored detrital matter (CDM) absorption coefficients and surface pigment concentration, was followed by a thermally stratified period characterized by net surface ocean heating, reduced isothermal layer depths, and annual minima in surface bio-optical fields. Variability in the interdependencies of ocean color products was used to diagnose an attendant shift in the size-structure of surface phytoplankton communities as well as identify CDM as the constituent responsible for the majority of blue-light absorption in Gulf of Mexico surface waters. The mesoscale circulation, as resolved by MODAS thermal fields into cold and warm-core eddies, appears to significantly modulate the seasonal bio-optical cycle of CDM absorption and surface pigment concentration. An empirical model was developed to describe CDM absorption as a function of upper ocean thermal energy. The model accounted for nearly half the variance in the satellite-estimate of this bio-optical variable. Large mismatches between the model and satellite data implied episodes of shelf water export to the deep Gulf of Mexico.

BIO-ETHANOL FUELS: SHORT-TERM SOLUTIONS, LONG-TERM DISASTERS

EPA Science Inventory

Ethanol derived from bio-mass is often advocated as a significant contributor to possible solutions to our need for a sustainable transportation fuel. Substituting bio-ethanol for conventional fuel immediately addresses the issue of reducing our use of non-renewable resources (f...

Nano-Electronics and Bio-Electronics

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Kwak, Dochan (Technical Monitor)

2001-01-01

Viewgraph presentation on Nano-Electronics and Bio-Electronics is discussed. Topics discussed include: NASA Ames nanotechnology program, Potential Carbon Nanotube (CNT) application, CNT synthesis,Computational Nanotechnology, and protein nanotubes.

Results of the International Energy Agency Round Robin on Fast Pyrolysis Bio-oil Production

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

Elliott, Douglas C.; Meier, Dietrich; Oasmaa, Anja

An international round robin study of the production of fast pyrolysis bio-oil was undertaken. Fifteen institutions in six countries contributed. Three biomass samples were distributed to the laboratories for processing in fast pyrolysis reactors. Samples of the bio-oil produced were transported to a central analytical laboratory for analysis. The round robin was focused on validating the pyrolysis community understanding of production of fast pyrolysis bio-oil by providing a common feedstock for bio-oil preparation. The round robin included: •distribution of 3 feedstock samples from a common source to each participating laboratory; •preparation of fast pyrolysis bio-oil in each laboratory with themore » 3 feedstocks provided; •return of the 3 bio-oil products (minimum 500 ml) with operational description to a central analytical laboratory for bio-oil property determination. The analyses of interest were: density, viscosity, dissolved water, filterable solids, CHN, S, trace element analysis, ash, total acid number, pyrolytic lignin, and accelerated aging of bio-oil. In addition, an effort was made to compare the bio-oil components to the products of analytical pyrolysis through GC/MS analysis. The results showed that clear differences can occur in fast pyrolysis bio-oil properties by applying different reactor technologies or configurations. The comparison to analytical pyrolysis method suggested that Py-GC/MS could serve as a rapid screening method for bio-oil composition when produced in fluid-bed reactors. Furthermore, hot vapor filtration generally resulted in the most favorable bio-oil product, with respect to water, solids, viscosity, and total acid number. These results can be helpful in understanding the variation in bio-oil production methods and their effects on bio-oil product composition.« less

BioWord: A sequence manipulation suite for Microsoft Word

PubMed Central

2012-01-01

Background The ability to manipulate, edit and process DNA and protein sequences has rapidly become a necessary skill for practicing biologists across a wide swath of disciplines. In spite of this, most everyday sequence manipulation tools are distributed across several programs and web servers, sometimes requiring installation and typically involving frequent switching between applications. To address this problem, here we have developed BioWord, a macro-enabled self-installing template for Microsoft Word documents that integrates an extensive suite of DNA and protein sequence manipulation tools. Results BioWord is distributed as a single macro-enabled template that self-installs with a single click. After installation, BioWord will open as a tab in the Office ribbon. Biologists can then easily manipulate DNA and protein sequences using a familiar interface and minimize the need to switch between applications. Beyond simple sequence manipulation, BioWord integrates functionality ranging from dyad search and consensus logos to motif discovery and pair-wise alignment. Written in Visual Basic for Applications (VBA) as an open source, object-oriented project, BioWord allows users with varying programming experience to expand and customize the program to better meet their own needs. Conclusions BioWord integrates a powerful set of tools for biological sequence manipulation within a handy, user-friendly tab in a widely used word processing software package. The use of a simple scripting language and an object-oriented scheme facilitates customization by users and provides a very accessible educational platform for introducing students to basic bioinformatics algorithms. PMID:22676326

BioWord: a sequence manipulation suite for Microsoft Word.

PubMed

Anzaldi, Laura J; Muñoz-Fernández, Daniel; Erill, Ivan

2012-06-07

The ability to manipulate, edit and process DNA and protein sequences has rapidly become a necessary skill for practicing biologists across a wide swath of disciplines. In spite of this, most everyday sequence manipulation tools are distributed across several programs and web servers, sometimes requiring installation and typically involving frequent switching between applications. To address this problem, here we have developed BioWord, a macro-enabled self-installing template for Microsoft Word documents that integrates an extensive suite of DNA and protein sequence manipulation tools. BioWord is distributed as a single macro-enabled template that self-installs with a single click. After installation, BioWord will open as a tab in the Office ribbon. Biologists can then easily manipulate DNA and protein sequences using a familiar interface and minimize the need to switch between applications. Beyond simple sequence manipulation, BioWord integrates functionality ranging from dyad search and consensus logos to motif discovery and pair-wise alignment. Written in Visual Basic for Applications (VBA) as an open source, object-oriented project, BioWord allows users with varying programming experience to expand and customize the program to better meet their own needs. BioWord integrates a powerful set of tools for biological sequence manipulation within a handy, user-friendly tab in a widely used word processing software package. The use of a simple scripting language and an object-oriented scheme facilitates customization by users and provides a very accessible educational platform for introducing students to basic bioinformatics algorithms.

Pyrene biodegradation with layer-by-layer assembly bio-microcapsules.

PubMed

Deng, Fucai; Zhang, Zhengfang; Yang, Chen; Guo, Chuling; Lu, Guining; Dang, Zhi

2017-04-01

Biotechnology is considered as a promising technology for the removal of polycyclic aromatic hydrocarbons from the environment. Free bacteria are often sensitive to some biotic and abiotic factors in the environment to the extent that their ability to effect biodegradation of organic pollutants, such as polycyclic aromatic hydrocarbons, is hampered. Consequently, it is imperative to carry out investigations into biological systems that will obviate or aid tolerance of bacteria to harsh environmental conditions. Chitosan/alginate bio-microcapsules produced using layer-by-layer (LBL) assembly method were tested for pyrene (PYR) biodegradation under harsh environmental conditions. Morphology observation indicated that the flake bio-microcapsules could be successfully prepared through LBL assembly method. Surface analysis showed that the bio-microcapsules had large fractions of mesopores. The results of the biodegradation experiments revealed that the 95% of 10mgL -1 PYR could be removed by the bacteria encapsulated chitosan/alginate bio-microcapsules in 3 days, which was higher than that of the free bacteria (59%). Compared to the free cells, the bacteria encapsulated chitosan/alginate bio-microcapsules produced 1-6 times higher PYR biodegradation rates at a high initial PYR concentration (50mgL -1 ) and extremely low pH values (pH =3) or temperatures (10°C or 40°C), as well as high salt stress. The results indicated that bacteria in microcapsules treatment gained a much higher tolerance to environmental stress and LBL bio-microcapsule could be promising candidate for remediating the organic pollutants. Copyright © 2016 Elsevier Inc. All rights reserved.

Bio-Oss® modified by calcitonin gene-related peptide promotes osteogenesis in vitro.

PubMed

Li, Yuanjing; Yang, Lan; Zheng, Zhichao; Li, Zhengmao; Deng, Tian; Ren, Wen; Wu, Caijuan; Guo, Lvhua

2017-11-01

Bio-Oss ® and α-calcitonin gene-related peptide (CGRP) are involved in osteogenesis. However, it has remained to be assessed how α-CGRP affects the effect of Bio-Oss. In the present study, primary osteoblasts were incubated with α-CGRP, Bio-Oss, α-GGRP-Bio-Oss or mimic-α-CGRP. The proliferation rate, mineralization nodules, alkaline phosphatase (ALP) activity and the expression of osteogenic genes were measured by a Cell Counting Kit-8 assay, Alizarin Red-S staining, ALP activity detection and reverse-transcription quantitative PCR as well as western blot analysis, respectively. The proliferation rate, ALP activity and the number of mineralization nodules were significantly increased in the α-CGRP-modified Bio-Oss group compared to that in the Bio-Oss group. The mRNA and protein levels of osteocalcin, Runt-related transcription factor-2 and ALP were significantly upregulated in the α-CGRP-Bio-Oss group compared with those in the Bio-Oss group. Furthermore, the effect of mimic-α-CGRP on osteogenesis was reduced as it carried a mutation. In conclusion, the present study was the first to demonstrate that Bio-Oss modified with CGRP contributed to osteogenesis and may provide a novel formulation applied in the clinic for restoration of large bone defects.

High-performance flexible strain sensor with bio-inspired crack arrays.

PubMed

Han, Zhiwu; Liu, Linpeng; Zhang, Junqiu; Han, Qigang; Wang, Kejun; Song, Honglie; Wang, Ze; Jiao, Zhibin; Niu, Shichao; Ren, Luquan

2018-06-12

Biomimetic sensor technology is always superior to existing human technologies. The scorpion, especially the forest scorpion, has a unique ability to detect subtle vibrations, which is attributed to the microcrack-shaped slit sensillum on its legs. Here, the biological sensing mechanism of the typical scorpion (Heterometrus petersii) was intensively studied in order to newly design and significantly improve the flexible strain sensors. Benefiting from the easy-crack property of polystyrene (PS) and using the solvent-induced swelling as well as double template transferring method, regular and controllable microcrack arrays were successfully fabricated on top of polydimethylsiloxane (PDMS). Using this method, any physical damage to PDMS could be effectively avoided. More fortunately, this bio-inspired crack arrays fabricated in this work also had a radial-like pattern similar to the slit sensillum of the scorpion, which was another unexpected imitation. The gauge factor (GF) of the sensor was conservatively evaluated at 5888.89 upon 2% strain and the response time was 297 ms. Afterward, it was demonstrated that the bio-inspired regular microcrack arrays could also significantly enhance the performance of traditional strain sensors, especially in terms of the sensitivity and response time. The practical applications, such as the detection of human motions and surface folding, were also tested in this work, with the results showing significant potential applications in numerous fields. This work changes the traditional waste cracks on some damaged products into valuable things for ultrasensitive mechanical sensors. Moreover, with this manufacturing technique, we could easily realize the simple, low cost and large-scale fabrication of advanced bioinpired sensors.

Hydrodeoxygenation of Pyrolysis Bio-Oil Over Ni Impregnated Mesoporous Materials.

PubMed

Lee, In-Gu; Lee, Heejin; Kang, Bo Sung; Kim, Young-Min; Kim, Sang Chai; Jung, Sang-Chul; Ko, Chang Hyun; Park, Young-Kwon

2018-02-01

The catalytic hydrodeoxygenation (HDO) of bio-oil over Ni-supported mesoporous materials was performed using a high pressure autoclave reactor. The actual pyrolysis oil of cork oak wood was used as a sample, and Ni/Al-SBA-15 and Ni/Al-MSU-F were used as catalysts. In addition, supercritical ethanol was added as solvent. Both Ni-supported mesoporous catalysts showed efficient HDO reaction ability. A higher heating value and pH of bio-oil were achieved by the HDO reaction over both catalysts and upgraded bio-oil had a lower viscosity. Compared to Ni/Al-MSU-F, Ni/Al- SBA-15 produced more upgraded bio-oil with a lower oxygen content and higher heating value via a catalytic HDO process.

BioSmalltalk: a pure object system and library for bioinformatics.

PubMed

Morales, Hernán F; Giovambattista, Guillermo

2013-09-15

We have developed BioSmalltalk, a new environment system for pure object-oriented bioinformatics programming. Adaptive end-user programming systems tend to become more important for discovering biological knowledge, as is demonstrated by the emergence of open-source programming toolkits for bioinformatics in the past years. Our software is intended to bridge the gap between bioscientists and rapid software prototyping while preserving the possibility of scaling to whole-system biology applications. BioSmalltalk performs better in terms of execution time and memory usage than Biopython and BioPerl for some classical situations. BioSmalltalk is cross-platform and freely available (MIT license) through the Google Project Hosting at http://code.google.com/p/biosmalltalk hernan.morales@gmail.com Supplementary data are available at Bioinformatics online.

The importance of assessing self-reported HIV status in bio-behavioural surveys.

PubMed

Johnston, Lisa G; Sabin, Miriam Lewis; Prybylski, Dimitri; Sabin, Keith; McFarland, Willi; Baral, Stefan; Kim, Andrea A; Raymond, H Fisher

2016-08-01

In bio-behavioural surveys measuring prevalence of infection with human immunodeficiency virus (HIV), respondents should be asked the results of their last HIV test. However, many government authorities, nongovernmental organizations, researchers and other civil society stakeholders have stated that respondents involved in such surveys should not be asked to self-report their HIV status. The reasons offered for not asking respondents to report their status are that responses may be inaccurate and that asking about HIV status may violate the respondents' human rights and exacerbate stigma and discrimination. Nevertheless, we contend that, in the antiretroviral therapy era, asking respondents in bio-behavioural surveys to self-report their HIV status is essential for measuring and improving access to - and coverage of - services for the care, treatment and prevention of HIV infection. It is also important for estimating the true size of the unmet needs in addressing the HIV epidemic and for interpreting the behaviours associated with the acquisition and transmission of HIV infection correctly. The data available indicate that most participants in health-related surveys are willing to respond to a question about HIV status - as one of possibly several sensitive questions about sexual and drug use behaviours. Ultimately, normalizing the self-reporting of HIV status could help the global community move from an era of so-called exceptionalism to one of destigmatization - and so improve the epidemic response worldwide.

BioInt: an integrative biological object-oriented application framework and interpreter.

PubMed

Desai, Sanket; Burra, Prasad

2015-01-01

BioInt, a biological programming application framework and interpreter, is an attempt to equip the researchers with seamless integration, efficient extraction and effortless analysis of the data from various biological databases and algorithms. Based on the type of biological data, algorithms and related functionalities, a biology-specific framework was developed which has nine modules. The modules are a compilation of numerous reusable BioADTs. This software ecosystem containing more than 450 biological objects underneath the interpreter makes it flexible, integrative and comprehensive. Similar to Python, BioInt eliminates the compilation and linking steps cutting the time significantly. The researcher can write the scripts using available BioADTs (following C++ syntax) and execute them interactively or use as a command line application. It has features that enable automation, extension of the framework with new/external BioADTs/libraries and deployment of complex work flows.

Upgrading of Intermediate Bio-Oil Produced by Catalytic Pyrolysis

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

Abdullah, Zia; Chadwell, Brad; Taha, Rachid

2015-06-30

The objectives of this project were to (1) develop a process to upgrade catalytic pyrolysis bio-oil, (2) investigate new upgrading catalysts suited for upgrading catalytic pyrolysis bio-oil, (3) demonstrate upgrading system operation for more than 1,000 hours using a single catalyst charge, and (4) produce a final upgraded product that can be blended to 30 percent by weight with petroleum fuels or that is compatible with existing petroleum refining operations. This project has, to the best of our knowledge, for the first time enabled a commercially viable bio-oil hydrotreatment process to produce renewable blend stock for transportation fuels.

Joint BioEnergy Institute

ScienceCinema

Keasling, Jay; Simmons, Blake; Tartaglino, Virginia; Baidoo, Edward; Kothari, Ankita

2018-05-11

The Joint BioEnergy Institute (JBEI) is a U.S. Department of Energy (DOE) Bioenergy Research Center dedicated to developing advanced biofuels—liquid fuels derived from the solar energy stored in plant biomass that can replace gasoline, diesel and jet fuels.

BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks

PubMed Central

Rialle, Stéphanie; Felicori, Liza; Dias-Lopes, Camila; Pérès, Sabine; El Atia, Sanaâ; Thierry, Alain R.; Amar, Patrick; Molina, Franck

2010-01-01

Motivation: Synthetic biology studies how to design and construct biological systems with functions that do not exist in nature. Biochemical networks, although easier to control, have been used less frequently than genetic networks as a base to build a synthetic system. To date, no clear engineering principles exist to design such cell-free biochemical networks. Results: We describe a methodology for the construction of synthetic biochemical networks based on three main steps: design, simulation and experimental validation. We developed BioNetCAD to help users to go through these steps. BioNetCAD allows designing abstract networks that can be implemented thanks to CompuBioTicDB, a database of parts for synthetic biology. BioNetCAD enables also simulations with the HSim software and the classical Ordinary Differential Equations (ODE). We demonstrate with a case study that BioNetCAD can rationalize and reduce further experimental validation during the construction of a biochemical network. Availability and implementation: BioNetCAD is freely available at http://www.sysdiag.cnrs.fr/BioNetCAD. It is implemented in Java and supported on MS Windows. CompuBioTicDB is freely accessible at http://compubiotic.sysdiag.cnrs.fr/ Contact: stephanie.rialle@sysdiag.cnrs.fr; franck.molina@sysdiag.cnrs.fr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20628073

Reliable Characterization for Pyrolysis Bio-Oils Leads to Enhanced

Science.gov Websites

Upgrading Methods | NREL Reliable Characterization for Pyrolysis Bio-Oils Leads to Enhanced Upgrading Methods Science and Technology Highlights Highlights in Research & Development Reliable Characterization for Pyrolysis Bio-Oils Leads to Enhanced Upgrading Methods Key Research Results Achievement As co

Report on the 5th International Bio-logging Symposium

DTIC Science & Technology

2014-09-30

LONG-TERM GOALS Bio-logging originated in the marine (polar) realm, which explains why marine mammals remain today the main biological models in...Wikelski as the convenor. The Proceedings of BLS5 will be published in two open-access BioMed Central (BMC) journals: Animal Biotelemetry (http

Efficacy of a sound-based intervention with a child with an autism spectrum disorder and auditory sensory over-responsivity.

PubMed

Gee, Bryan M; Thompson, Kelly; St John, Holly

2014-03-01

Sound-based interventions (SBIs) are being used by paediatric occupational therapists to help children with autism spectrum disorders and co-morbid sensory processing disorders. A limited yet growing body of evidence is emerging related to the efficacy of SBIs in reducing sensory processing deficits among paediatric clients with co-morbid conditions. The current study employed an ABA single-subject case-controlled design, implementing The Listening Program® with a 7-year-old child diagnosed with autism spectrum disorder who demonstrated auditory sensory over-responsivity (SOR). The intervention consisted of 10 weeks of psycho-acoustically modified classical music that was delivered using specialized headphones and amplifier and a standard CD player. Repeated measures were conducted during the A(1), B and A(2) phases of the study using the Sensory Processing Measure, a subjective caregiver questionnaire, and the Sensory Over-Responsivity Scales, an examiner-based assessment measure to track changes of the participant's auditory SOR-related behaviours. The results indicated that the participant exhibited a decrease in the number of negative (avoidant, verbal and physical negative) and self-stimulatory behaviours. The decreases in negative and self-stimulatory behaviour may have been due to the therapeutic effect of the repeated exposure to the Sensory Over-Responsivity Scales or The Listening Program SBI. Copyright © 2013 John Wiley & Sons, Ltd.

Bio-logging of physiological parameters in higher marine vertebrates

NASA Astrophysics Data System (ADS)

Ponganis, Paul J.

2007-02-01

Bio-logging of physiological parameters in higher marine vertebrates had its origins in the field of bio-telemetry in the 1960s and 1970s. The development of microprocessor technology allowed its first application to bio-logging investigations of Weddell seal diving physiology in the early 1980s. Since that time, with the use of increased memory capacity, new sensor technology, and novel data processing techniques, investigators have examined heart rate, temperature, swim speed, stroke frequency, stomach function (gastric pH and motility), heat flux, muscle oxygenation, respiratory rate, diving air volume, and oxygen partial pressure (P) during diving. Swim speed, heart rate, and body temperature have been the most commonly studied parameters. Bio-logging investigation of pressure effects has only been conducted with the use of blood samplers and nitrogen analyses on animals diving at isolated dive holes. The advantages/disadvantages and limitations of recording techniques, probe placement, calibration techniques, and study conditions are reviewed.

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

PubMed

Katayama, Toshiaki; Arakawa, Kazuharu; Nakao, Mitsuteru; Ono, Keiichiro; Aoki-Kinoshita, Kiyoko F; Yamamoto, Yasunori; Yamaguchi, Atsuko; Kawashima, Shuichi; Chun, Hong-Woo; Aerts, Jan; Aranda, Bruno; Barboza, Lord Hendrix; Bonnal, Raoul Jp; Bruskiewich, Richard; Bryne, Jan C; Fernández, José M; Funahashi, Akira; Gordon, Paul Mk; Goto, Naohisa; Groscurth, Andreas; Gutteridge, Alex; Holland, Richard; Kano, Yoshinobu; Kawas, Edward A; Kerhornou, Arnaud; Kibukawa, Eri; Kinjo, Akira R; Kuhn, Michael; Lapp, Hilmar; Lehvaslaiho, Heikki; Nakamura, Hiroyuki; Nakamura, Yasukazu; Nishizawa, Tatsuya; Nobata, Chikashi; Noguchi, Tamotsu; Oinn, Thomas M; Okamoto, Shinobu; Owen, Stuart; Pafilis, Evangelos; Pocock, Matthew; Prins, Pjotr; Ranzinger, René; Reisinger, Florian; Salwinski, Lukasz; Schreiber, Mark; Senger, Martin; Shigemoto, Yasumasa; Standley, Daron M; Sugawara, Hideaki; Tashiro, Toshiyuki; Trelles, Oswaldo; Vos, Rutger A; Wilkinson, Mark D; York, William; Zmasek, Christian M; Asai, Kiyoshi; Takagi, Toshihisa

2010-08-21

Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*

PubMed Central

2010-01-01

Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies. PMID:20727200

Intravenous Nicotine Self-Administration in Smokers: Dose-Response Function and Sex Differences.

PubMed

Jensen, Kevin P; DeVito, Elise E; Valentine, Gerald; Gueorguieva, Ralitza; Sofuoglu, Mehmet

2016-07-01

Sex differences in the sensitivity to nicotine may influence vulnerability to tobacco dependence. The goal of this study was to investigate the dose-response function for the reinforcing and subjective effects of intravenous nicotine in male and female smokers. Tobacco-dependent subjects (12 male and 14 female) participated in four experimental sessions in which they received sample infusions of saline and nicotine (0.1, 0.2, 0.3, or 0.4 mg doses) in a randomized double-blind crossover design. During each session, subjects first received the sample infusions, and heart rate (HR), blood pressure, and subjective stimulatory, pleasurable and aversive responses were monitored. Immediately following the sample infusions, subjects self-administered either nicotine or saline in six double-blind forced-choice trials. A sex by dose interaction was observed in the nicotine choice paradigm. Nicotine self-administration rate was negatively correlated with nicotine dose in males (males displayed choice preference for low doses of nicotine over high doses of nicotine), but no significant relationship between dose and choice preference was evident in females. Relative to placebo, sample doses of nicotine increased heart rate and blood pressure, and induced stimulatory, pleasurable, and aversive subjective effects. Diastolic blood pressure increased dose dependently in males, but not in females. These findings, which demonstrate sex differences in nicotine self-administration for doses that are near to the reinforcement threshold, suggest that male and female smokers may respond differently to the changes in nicotine doses available for self-administration.

Elsevier’s approach to the bioCADDIE 2016 Dataset Retrieval Challenge

PubMed Central

Scerri, Antony; Kuriakose, John; Deshmane, Amit Ajit; Stanger, Mark; Moore, Rebekah; Naik, Raj; de Waard, Anita

2017-01-01

Abstract We developed a two-stream, Apache Solr-based information retrieval system in response to the bioCADDIE 2016 Dataset Retrieval Challenge. One stream was based on the principle of word embeddings, the other was rooted in ontology based indexing. Despite encountering several issues in the data, the evaluation procedure and the technologies used, the system performed quite well. We provide some pointers towards future work: in particular, we suggest that more work in query expansion could benefit future biomedical search engines. Database URL: https://data.mendeley.com/datasets/zd9dxpyybg/1 PMID:29220454

Bio-power, Agamben, and emerging nursing knowledge.

PubMed

Georges, Jane M

2008-01-01

This philosophical article posits that an emerging theme in contemporary nursing epistemology is bio-power and proposes the use of philosopher Giorgio Agamben's perspectives as a useful approach for the future investigation of bio-power in nursing knowledge. Building upon Meleis' characterization of diversity as the most recent "milestone" of contemporary theoretical development of the nursing discipline, selected recent texts from the nursing literature are analyzed, and implications for future nursing knowledge in the context of Agamben's work are explored.

A micro-sized bio-solar cell for self-sustaining power generation.

PubMed

Lee, Hankeun; Choi, Seokheun

2015-01-21

Self-sustainable energy sources are essential for a wide array of wireless applications deployed in remote field locations. Due to their self-assembling and self-repairing properties, "biological solar (bio-solar) cells" are recently gaining attention for those applications. The bio-solar cell can continuously generate electricity from microbial photosynthetic and respiratory activities under day-night cycles. Despite the vast potential and promise of bio-solar cells, they, however, have not yet successfully been translated into commercial applications, as they possess persistent performance limitations and scale-up bottlenecks. Here, we report an entirely self-sustainable and scalable microliter-sized bio-solar cell with significant power enhancement by maximizing solar energy capture, bacterial attachment, and air bubble volume in well-controlled microchambers. The bio-solar cell has a ~300 μL single chamber defined by laser-machined poly(methyl methacrylate) (PMMA) substrates and it uses an air cathode to allow freely available oxygen to act as an electron acceptor. We generated a maximum power density of 0.9 mW m(-2) through photosynthetic reactions of cyanobacteria, Synechocystis sp. PCC 6803, which is the highest power density among all micro-sized bio-solar cells.

The effect of torrefaction on the chemistry of fast-pyrolysis bio-oil.

PubMed

Meng, Jiajia; Park, Junyeong; Tilotta, David; Park, Sunkyu

2012-05-01

Fast pyrolysis was performed on torrefied loblolly pine and the collected bio-oils were analyzed to compare the effect of the torrefaction treatment on their quality. The results of the analyses show that bio-oils produced from torrefied wood have improved oxygen-to-carbon ratios compared to those from the original wood with the penalty of a decrease in bio-oil yield. The extent of this improvement depends on the torrefaction severity. Based on the GC/MS analysis of the pyrolysis bio-oils, bio-oils produced from torrefied biomass show different compositions compared to that from the original wood. Specifically, the former becomes more concentrated in pyrolytic lignin with less water content than the latter. It was considered that torrefaction could be a potential upgrading method to improve the quality of bio-oil, which might be a useful feedstock for phenolic-based chemicals. Copyright © 2012 Elsevier Ltd. All rights reserved.

Stimulatory effect of insulin on 5alpha-reductase type 1 (SRD5A1) expression through an Akt-dependent pathway in ovarian granulosa cells.

PubMed

Kayampilly, Pradeep P; Wanamaker, Brett L; Stewart, James A; Wagner, Carrie L; Menon, K M J

2010-10-01

Elevated levels of 5α-reduced androgens have been shown to be associated with hyperandrogenism and hyperinsulinemia, the leading causes of ovulatory dysfunction in women. 5α-Dihydrotestosterone reduces ovarian granulosa cell proliferation by inhibiting FSH-mediated mitogenic signaling pathways. The present study examined the effect of insulin on 5α-reductase, the enzyme that catalyses the conversion of androgens to their 5α-derivatives. Granulosa cells isolated from immature rat ovaries were cultured in serum-free, phenol red-free DMEM-F12 media and treated with different doses of insulin (0, 0.1, 1.0, and 10.0 μg/ml) for different time intervals up to 12 h. The expression of 5α-reductase type 1 mRNA, the predominant isoform found in granulosa cells, showed a significant (P<0.05) increase in response to the insulin treatment up to 12 h compared with control. The catalytic activity of 5α-reductase enzyme was also stimulated in a dose-depended manner (P<0.05). Inhibiting the Akt-dependent signaling pathway abolished the insulin-mediated increase in 5α-reductase mRNA expression, whereas inhibition of the ERK-dependent pathway had no effect. The dose-dependent increase in 5α-reductase mRNA expression as well as catalytic activity seen in response to insulin treatment was also demonstrated in the human granulosa cell line (KGN). In addition to increased mRNA expression, a dose-dependent increase in 5α-reductase protein expression in response to insulin was also seen in KGN cells, which corroborated well with that of mRNA expression. These results suggest that elevated levels of 5α-reduced androgens seen in hyperinsulinemic conditions might be explained on the basis of a stimulatory effect of insulin on 5α-reductase in granulosa cells. The elevated levels of these metabolites, in turn, might adversely affect growth and proliferation of granulosa cells, thereby impairing follicle growth and ovulation.

Stimulatory Effect of Insulin on 5α-Reductase Type 1 (SRD5A1) Expression through an Akt-Dependent Pathway in Ovarian Granulosa Cells

PubMed Central

Kayampilly, Pradeep P.; Wanamaker, Brett L.; Stewart, James A.; Wagner, Carrie L.; Menon, K. M. J.

2010-01-01

Elevated levels of 5α-reduced androgens have been shown to be associated with hyperandrogenism and hyperinsulinemia, the leading causes of ovulatory dysfunction in women. 5α-Dihydrotestosterone reduces ovarian granulosa cell proliferation by inhibiting FSH-mediated mitogenic signaling pathways. The present study examined the effect of insulin on 5α-reductase, the enzyme that catalyses the conversion of androgens to their 5α-derivatives. Granulosa cells isolated from immature rat ovaries were cultured in serum-free, phenol red-free DMEM-F12 media and treated with different doses of insulin (0, 0.1, 1.0, and 10.0 μg/ml) for different time intervals up to 12 h. The expression of 5α-reductase type 1 mRNA, the predominant isoform found in granulosa cells, showed a significant (P < 0.05) increase in response to the insulin treatment up to 12 h compared with control. The catalytic activity of 5α-reductase enzyme was also stimulated in a dose-depended manner (P < 0.05). Inhibiting the Akt-dependent signaling pathway abolished the insulin-mediated increase in 5α-reductase mRNA expression, whereas inhibition of the ERK-dependent pathway had no effect. The dose-dependent increase in 5α-reductase mRNA expression as well as catalytic activity seen in response to insulin treatment was also demonstrated in the human granulosa cell line (KGN). In addition to increased mRNA expression, a dose-dependent increase in 5α-reductase protein expression in response to insulin was also seen in KGN cells, which corroborated well with that of mRNA expression. These results suggest that elevated levels of 5α-reduced androgens seen in hyperinsulinemic conditions might be explained on the basis of a stimulatory effect of insulin on 5α-reductase in granulosa cells. The elevated levels of these metabolites, in turn, might adversely affect growth and proliferation of granulosa cells, thereby impairing follicle growth and ovulation. PMID:20810561

Photofunctional hybrids of lanthanide functionalized bio-MOF-1 for fluorescence tuning and sensing.

PubMed

Shen, Xiang; Yan, Bing

2015-08-01

A series of luminescent Ln(3+)@bio-MOF-1 (Ln=Eu, Tb, bio-MOF-1=Zn8(ad)4(BPDC)6O⋅2Me2NH2 (ad=adeninate, BPDC=biphenyldicarboxylate)) are synthesized via postsynthetic cation exchange by encapsulating lanthanide ions into an anionic metal-organic framework (MOF), and their photophysical properties are studied. After loading 2-thenoyltrifluroacetone (TTA) as sensitized ligand by a gas diffusion ("ship-in-bottle") method, it is found that the luminescent intensity of Eu(3+) is enhanced. Especially, when loading two different lanthanide cations into bio-MOF-1, the luminescent color can be tuned to close white (light pink) light output. Additionally, bio-MOF-1 and Eu(3+)@bio-MOF-1 are selected as representative samples for sensing metal ions. When bio-MOF-1 is immersed in the aqueous solutions of different metal ions, it shows highly sensitive sensing for Fe(3+) as well as Eu(3+)@bio-MOF-1 immersed in the DMF solutions of different metal ion. The results are benefit for the further application of functionalized bio-MOFs in practical fields. Copyright © 2015 Elsevier Inc. All rights reserved.

Microbial bio-fuels: a solution to carbon emissions and energy crisis.

PubMed

Kumar, Arun; Kaushal, Sumit; Saraf, Shubhini A; Singh, Jay Shankar

2018-06-01

Increasing energy demand, limited fossil fuel resources and climate change have prompted development of alternative sustainable and economical fuel resources such as crop-based bio-ethanol and bio-diesel. However, there is concern over use of arable land that is used for food agriculture for creation of biofuel. Thus, there is a renewed interest in the use of microbes particularly microalgae for bio-fuel production. Microbes such as micro-algae and cyanobacteria that are used for biofuel production also produce other bioactive compounds under stressed conditions. Microbial agents used for biofuel production also produce bioactive compounds with antimicrobial, antiviral, anticoagulant, antioxidant, antifungal, anti-inflammatory and anticancer activity. Because of importance of such high-value compounds in aquaculture and bioremediation, and the potential to reduce carbon emissions and energy security, the biofuels produced by microbial biotechnology might substitute the crop-based bio-ethanol and bio-diesel production.

MSU-Northern Bio-Energy Center of Excellence

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

Kegel, Greg; Alcorn-Windy Boy, Jessica; Abedin, Md. Joynal

2014-09-30

MSU-Northern established the Bio-Energy Center (the Center) into a Regional Research Center of Excellence to address the obstacles concerning biofuels, feedstock, quality, conversion process, economic viability and public awareness. The Center built its laboratories and expertise in order to research and support product development and commercialization for the bio-energy industry in our region. The Center wanted to support the regional agricultural based economy by researching biofuels based on feedstock’s that can be grown in our region in an environmentally responsible manner. We were also interested in any technology that will improve the emissions and fuel economy performance of heavy dutymore » diesel engines. The Center had a three step approach to accomplish these goals: 1. Enhance the Center’s research and testing capabilities 2. Develop advanced biofuels from locally grown agricultural crops. 3. Educate and outreach for public understanding and acceptance of new technology. The Center was very successful in completing the tasks as outlined in the project plan. Key successes include discovering and patenting a new chemical conversion process for converting camelina oil to jet fuel, as well as promise in developing a heterogeneous Grubs catalyst to support the new chemical conversion process. The Center also successfully fragmented and deoxygenated naturally occurring lignin with a Ni-NHC catalyst, showing promise for further exploration of using lignin for fuels and fuel additives. This would create another value-added product for lignin that can be sourced from beetle kill trees or waste products from cellulose ethanol fuel facilities.« less

Direct detection of Mycobacterium tuberculosis rifampin resistance in bio-safe stained sputum smears.

PubMed

Lavania, Surabhi; Anthwal, Divya; Bhalla, Manpreet; Singh, Nagendra; Haldar, Sagarika; Tyagi, Jaya Sivaswami

2017-01-01

Direct smear microscopy of sputum forms the mainstay of TB diagnosis in resource-limited settings. Stained sputum smear slides can serve as a ready-made resource to transport sputum for molecular drug susceptibility testing. However, bio-safety is a major concern during transport of sputum/stained slides and for laboratory workers engaged in processing Mycobacterium tuberculosis infected sputum specimens. In this study, a bio-safe USP (Universal Sample Processing) concentration-based sputum processing method (Bio-safe method) was assessed on 87 M. tuberculosis culture positive sputum samples. Samples were processed for Ziehl-Neelsen (ZN) smear, liquid culture and DNA isolation. DNA isolated directly from sputum was subjected to an IS6110 PCR assay. Both sputum DNA and DNA extracted from bio-safe ZN concentrated smear slides were subjected to rpoB PCR and simultaneously assessed by DNA sequencing for determining rifampin (RIF) resistance. All sputum samples were rendered sterile by Bio-safe method. Bio-safe smears exhibited a 5% increment in positivity over direct smear with a 14% increment in smear grade status. All samples were positive for IS6110 and rpoB PCR. Thirty four percent samples were RIF resistant by rpoB PCR product sequencing. A 100% concordance (κ value = 1) was obtained between sequencing results derived from bio-safe smear slides and bio-safe sputum. This study demonstrates that Bio-safe method can address safety issues associated with sputum processing, provide an efficient alternative to sample transport in the form of bio-safe stained concentrated smear slides and can also provide information on drug (RIF) resistance by direct DNA sequencing.

Bio-oil upgrading strategies to improve PHA production from selected aerobic mixed cultures.

PubMed

Moita Fidalgo, Rita; Ortigueira, Joana; Freches, André; Pelica, João; Gonçalves, Magarida; Mendes, Benilde; Lemos, Paulo C

2014-06-25

Recent research on polyhydroxyalkanoates (PHAs) has focused on developing cost-effective production processes using low-value or industrial waste/surplus as substrate. One of such substrates is the liquid fraction resulting from pyrolysis processes, bio-oil. In this study, valorisation of bio-oil through PHA production was investigated. The impact of the complex bio-oil matrix on PHA production by an enriched mixed culture was examined. The performance of the direct utilization of pure bio-oil was compared with the utilization of three defined substrates contained in this bio-oil: acetate, glucose and xylose. When compared with acetate, bio-oil revealed lower capacity for polymer production as a result of a lower polymer yield on substrate and a lower PHA cell content. Two strategies for bio-oil upgrade were performed, anaerobic fermentation and vacuum distillation, and the resulting liquid streams were tested for polymer production. The first one was enriched in volatile fatty acids and the second one mainly on phenolic and long-chain fatty acids. PHA accumulation assays using the upgraded bio-oils attained polymer yields on substrate similar or higher than the one achieved with acetate, although with a lower PHA content. The capacity to use the enriched fractions for polymer production has yet to be optimized. The anaerobic digestion of bio-oil could also open-up the possibility to use the fermented bio-oil directly in the enrichment process of the mixed culture. This would increase the selective pressure toward an optimized PHA accumulating culture selection. Copyright © 2013 Elsevier B.V. All rights reserved.

Mild Biomass Liquefaction Process for Economic Production of Stabilized Refinery-Ready Bio-oil

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

Gangwal, Santosh; Meng, Jiajia; McCabe, Kevin

Southern Research (SR) in cooperation with U.S. Department of Energy (DOE), Bioenergy Technology Office (BETO), investigated a biomass liquefaction process for economic production of stabilized refinery-ready bio-oil. The project was awarded by DOE under a Funding Opportunity Announcement (DE-FOA-0000686) for Bio-oil Stabilization and Commoditization that intended to evaluate the feasibility of using bio-oil as a potential feedstock in an existing petroleum refinery. SR investigated Topic Area 1 of the FOA at Technology Readiness Level 2-3 to develop thermochemical liquefaction technologies for producing a bio-oil feedstock from high-impact biomass that can be utilized within a petroleum refinery. Bio-oil obtained from fastmore » pyrolysis of biomass is a green intermediate that can be further upgraded into a biofuel for blending in a petroleum refinery using a hydro-deoxygenation (HDO) route. Co-processing pyrolysis bio-oil in a petroleum refinery is an attractive approach to leverage the refinery’s existing capital. However, the petroleum industry is reluctant to accept pyrolysis bio-oil because of a lack of a standard definition for an acceptable bio-oil feedstock in existing refinery processes. Also per BETO’s multiyear program plan, fast pyrolysis-based bio-fuel is presently not cost competitive with petroleum-based transportation fuels. SR aims to develop and demonstrate a cost-effective low-severity thermal liquefaction and hydrodeoxygenation (HDO) process to convert woody biomass to stabilized bio-oils that can be directly blended with hydrotreater input streams in a petroleum refinery for production of gasoline and/or diesel range hydrocarbons. The specific project objectives are to demonstrate the processes at laboratory scale, characterize the bio-oil product and develop a plan in partnership with a refinery company to move the technology towards commercialization.« less

Bio-Based Polyurethane Containing Isosorbide for Use in Composites and Coatings

DTIC Science & Technology

2015-04-01

ARL-TR-7259 ● APR 2015 US Army Research Laboratory Bio-Based Polyurethane Containing Isosorbide for Use in Composites and...copyright notation hereon. ARL-TR-7259 ● APR 2015 US Army Research Laboratory Bio-Based Polyurethane Containing Isosorbide for Use...4. TITLE AND SUBTITLE Bio-Based Polyurethane Containing Isosorbide for Use in Composites and Coatings 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c

Development of vaccines for bio-warfare agents.

PubMed

Rosenthal, S R; Clifford, J C M

2002-01-01

There is a recognized need for the development of new vaccines (as well as other biologicals and drugs) to counteract the effects of a potential bio-terrorist or bio-warfare event in the U.S. domestic population and military forces. Regulation of products to protect against potential bio-warfare agents poses unique challenges since the usual measures of efficacy that require exposure to natural disease may not currently be possible, for epidemiological and ethical reasons. To help to address this issue, the FDA has published and requested comments on a proposed animal rule intended to address certain efficacy issues for new agents for use against lethal or permanently disabling toxic substances. Recent product development activity has focused on Bacillus anthracis (anthrax) and variola major (smallpox), agents that are regarded as highest priority in posing a risk to national security. FDA resources exist to assist vaccine developers with regard to the novel challenges posed in the dinical development of these products.

Processing and characterization of bio-based composites

NASA Astrophysics Data System (ADS)

Lu, Hong

Much research has focused on bio-based composites as a potential material to replace petroleum-based plastics. Considering the high price of Polyhydroxyalkanoates (PHAs), PHA/ Distiller's Dried Grains with Solubles (DDGS) composite is a promising economical and high-performance biodegradable material. In this paper, we discuss the effect of DDGS on PHA composites in balancing cost with material performance. Poly (lactic acid) PLA/DDGS composite is another excellent biodegradable composite, although as a bio-based polymer its degradation time is relatively long. The goal of this research is therefore to accelerate the degradation process for this material. Both bio-based composites were extruded through a twin-screw microcompounder, and the two materials were uniformly mixed. The morphology of the samples was examined using a Scanning Electron Microscope (SEM); thermal stability was determined with a Thermal Gravimetric Analyzer (TGA); other thermal properties were studied using Differential Scanning Calorimetry (DSC) and a Dynamic Mechanical Analyzer (DMA). Viscoelastic properties were also evaluated using a Rheometer.

Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format.

PubMed

Webb, Ryan L; Ma'ayan, Avi

2011-03-21

The World Wide Web plays a critical role in enabling molecular, cell, systems and computational biologists to exchange, search, visualize, integrate, and analyze experimental data. Such efforts can be further enhanced through the development of semantic web concepts. The semantic web idea is to enable machines to understand data through the development of protocol free data exchange formats such as Resource Description Framework (RDF) and the Web Ontology Language (OWL). These standards provide formal descriptors of objects, object properties and their relationships within a specific knowledge domain. However, the overhead of converting datasets typically stored in data tables such as Excel, text or PDF into RDF or OWL formats is not trivial for non-specialists and as such produces a barrier to seamless data exchange between researchers, databases and analysis tools. This problem is particularly of importance in the field of network systems biology where biochemical interactions between genes and their protein products are abstracted to networks. For the purpose of converting biochemical interactions into the BioPAX format, which is the leading standard developed by the computational systems biology community, we developed an open-source command line tool that takes as input tabular data describing different types of molecular biochemical interactions. The tool converts such interactions into the BioPAX level 3 OWL format. We used the tool to convert several existing and new mammalian networks of protein interactions, signalling pathways, and transcriptional regulatory networks into BioPAX. Some of these networks were deposited into PathwayCommons, a repository for consolidating and organizing biochemical networks. The software tool Sig2BioPAX is a resource that enables experimental and computational systems biologists to contribute their identified networks and pathways of molecular interactions for integration and reuse with the rest of the research community.

78 FR 5165 - First Phase of the Forest Planning Process for the Bio-Region

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-24

... DEPARTMENT OF AGRICULTURE Forest Service First Phase of the Forest Planning Process for the Bio... initiating the first phase of the forest planning process for the Bio-Region. SUMMARY: Come gather 'round... phase of the Bio-Regional Assessment has begun. DATES: The Bio-Regional Assessment Report will be...

Global gene expression in the bovine corpus luteum is altered after stimulatory and superovulatory treatments.

PubMed

Fátima, Luciana A; Baruselli, Pietro S; Gimenes, Lindsay U; Binelli, Mario; Rennó, Francisco P; Murphy, Bruce D; Papa, Paula C

2013-01-01

Equine chorionic gonadotrophin (eCG) has been widely used in superovulation and artificial insemination programmes and usually promotes an increase in corpus luteum (CL) volume and stimulates progesterone production. Therefore, to identify eCG-regulated genes in the bovine CL, the transcriptome was evaluated by microarray analysis and the expression of selected genes was validated by qPCR and western blot. Eighteen Nelore crossbred cows were divided into control (n=5), stimulated (n=6) and superovulated groups (n=7). Ovulation was synchronised using a progesterone device-based protocol. Stimulated animals received 400 IU of eCG at device removal and superovulated animals received 2000 IU of eCG 4 days prior. Corpora lutea were collected 7 days after gonadotrophin-releasing hormone administration. Overall, 242 transcripts were upregulated and 111 transcripts were downregulated in stimulated cows (P ≤ 0.05) and 111 were upregulated and 113 downregulated in superovulated cows compared to the control animals (1.5-fold, P ≤ 0.05). Among the differentially expressed genes, many were involved in lipid biosynthesis and progesterone production, such as PPARG, STAR, prolactin receptors and follistatin. In conclusion, eCG modulates gene expression differently depending on the treatment, i.e. stimulatory or superovulatory. Our data contribute to the understanding of the pathways involved in increased progesterone levels observed after eCG treatment.

Bio-based Polymer Foam from Soyoil

NASA Astrophysics Data System (ADS)

Bonnaillie, Laetitia M.; Wool, Richard P.

2006-03-01

The growing bio-based polymeric foam industry is presently lead by plant oil-based polyols for polyurethanes and starch foams. We developed a new resilient, thermosetting foam system with a bio-based content higher than 80%. The acrylated epoxidized soybean oil and its fatty acid monomers is foamed with pressurized carbon dioxide and cured with free-radical initiators. The foam structure and pore dynamics are highly dependent on the temperature, viscosity and extent of reaction. Low-temperature cure hinds the destructive pore coalescence and the application of a controlled vacuum results in foams with lower densities ˜ 0.1 g/cc, but larger cells. We analyze the physics of foam formation and stability, as well as the structure and mechanical properties of the cured foam using rigidity percolation theory. The parameters studied include temperature, vacuum applied, and cross-link density. Additives bring additional improvements: nucleating agents and surfactants help produce foams with a high concentration of small cells and low bulk density. Hard and soft thermosetting foams with a bio content superior to 80% are successfully produced and tested. Potential applications include foam-core composites for hurricane-resistant housing, structural reinforcement for windmill blades, and tissue scaffolds.

BioEnergy Science Center

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

None

The BioEnergy Science Center, led by Oak Ridge National Laboratory, has been making advances in biofuels for over a decade. These achievements in plant genomics, microbial engineering, biochemistry, and plant physiology will carry over into the Center for Bioenergy Innovation, a new Department of Energy bioenergy research center.

Calixarenes in bio-medical researches.

PubMed

Rodik, Roman V; Boyko, Vyacheslav I; Kalchenko, Vitaly I

2009-01-01

Application of calixarene derivatives in bio-medical researches is reviewed in this article. Antiviral, bactericidal, antithrombothic, antituberculosis, anticancer activity as well as specific protein complexation, membranotropic properties and toxicity of modified calixarenes are discussed.

Chemicals derived from pyrolysis bio-oils as antioxidants in fuels and lubricants

USDA-ARS?s Scientific Manuscript database

Softwood and hardwood lignins and hardwood were pyrolyzed to produce bio-oils to produce lignin-derived bio-oils of which phenols were the major component. These bio-oils were extracted with alkali to yield a range of lignin-related phenols having molecular weights (MWs) from 110 to 344. When tested...

BioXSD: the common data-exchange format for everyday bioinformatics web services.

PubMed

Kalas, Matús; Puntervoll, Pål; Joseph, Alexandre; Bartaseviciūte, Edita; Töpfer, Armin; Venkataraman, Prabakar; Pettifer, Steve; Bryne, Jan Christian; Ison, Jon; Blanchet, Christophe; Rapacki, Kristoffer; Jonassen, Inge

2010-09-15

The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of the resources offer programmatic web-service interface. However, efficient use of the resources is hampered by the lack of widely used, standard data-exchange formats for the basic, everyday bioinformatics data types. BioXSD has been developed as a candidate for standard, canonical exchange format for basic bioinformatics data. BioXSD is represented by a dedicated XML Schema and defines syntax for biological sequences, sequence annotations, alignments and references to resources. We have adapted a set of web services to use BioXSD as the input and output format, and implemented a test-case workflow. This demonstrates that the approach is feasible and provides smooth interoperability. Semantics for BioXSD is provided by annotation with the EDAM ontology. We discuss in a separate section how BioXSD relates to other initiatives and approaches, including existing standards and the Semantic Web. The BioXSD 1.0 XML Schema is freely available at http://www.bioxsd.org/BioXSD-1.0.xsd under the Creative Commons BY-ND 3.0 license. The http://bioxsd.org web page offers documentation, examples of data in BioXSD format, example workflows with source codes in common programming languages, an updated list of compatible web services and tools and a repository of feature requests from the community.

Infectious complications of Bio-Alcamid filler used for HIV-related facial lipoatrophy.

PubMed

Nadarajah, Jeya T; Collins, Micaela; Raboud, Janet; Su, DeSheng; Rao, Kavya; Loutfy, Mona R; Walmsley, Sharon

2012-12-01

Human immunodeficiency virus (HIV)-related facial lipoatrophy is a devastating adverse effect of antiretroviral therapy. At this time, the most viable treatment option is cosmetic surgery with synthetic fillers. Bio-Alcamid has many advantages over other fillers, and has become widely used. The objective of this study was to determine the incidence rate of infectious complications associated with Bio-Alcamid facial filler in patients with HIV-related facial lipoatrophy (FLA). This retrospective study identified patients who had received treatment with Bio-Alcamid, and reviewed their long-term outcomes. Two hundred sixty-seven patients with Bio-Alcamid were reviewed. Infectious complications were documented in 56 (19%) patients. The incidence rate of infection was 0.07 per patient-year of follow-up. Among patients with infections, the median time from first Bio-Alcamid treatment to infection was 32 months (interquartile range, 21-42). We did not find an association between the development of infection and the level of immune suppression by HIV. Surgical drainage in addition to antibiotics was required for the majority of patients. Potential risk factors for infection include severity of FLA and a preceding history of facial manipulation, including Bio-Alcamid touch-up treatments, cosmetic surgery, facial trauma, and dental work. Bio-Alcamid treatment of HIV-related FLA was associated with a high rate of infectious complications, often presenting years after treatment. Antibiotic prophylaxis should be considered in patients with Bio-Alcamid prior to dental work or facial manipulation.

The BioSentinel Bioanalytical Microsystem: Characterizing DNA Radiation Damage in Living Organisms Beyond Earth Orbit

NASA Technical Reports Server (NTRS)

Ricco, A. J.; Hanel, R.; Bhattacharya, S.; Boone, T.; Tan, M.; Mousavi, A.; Rademacher, A.; Schooley, A.; Klamm, B.; Benton, J.;

Process contribution evaluation for COD removal and energy production from molasses wastewater in a BioH2-BioCH4-MFC-integrated system.

PubMed

Yun, Jeonghee; Lee, Yun-Yeong; Choi, Hyung Joo; Cho, Kyung-Suk

2017-01-01

In this study, a three-stage-integrated process using the hydrogenic process (BioH 2 ), methanogenic process (BioCH 4 ), and a microbial fuel cell (MFC) was operated using molasses wastewater. The contribution of individual processes to chemical oxygen demand (COD) removal and energy production was evaluated. The three-stage integration system was operated at molasses of 20 g-COD L -1 , and each process achieved hydrogen production rate of 1.1 ± 0.24 L-H 2 L -1 day -1 , methane production rate of 311 ± 18.94 mL-CH 4 L -1 day -1 , and production rate per electrode surface area of 10.8 ± 1.4 g m -2 day -1 . The three-stage integration system generated energy production of 32.32 kJ g-COD -1 and achieved COD removal of 98 %. The contribution of BioH 2 , BioCH 4 , and the MFC reactor was 20.8, 72.2, and, 7.0 % of the total COD removal, and 18.7, 81.2, and 0.16 % of the total energy production, respectively. The continuous stirred-tank reactor BioH 2 at HRT of 1 day, up-flow anaerobic sludge blanket BioCH 4 at HRT of 2 days, and MFC reactor at HRT of 3 days were decided in 1:2:3 ratios of working volume under hydraulic retention time consideration. This integration system can be applied to various configurations depending on target wastewater inputs, and it is expected to enhance energy recovery and reduce environmental impact of the final effluent.

Heterotrimeric G Stimulatory Protein α Subunit Is Required for Intestinal Smooth Muscle Contraction in Mice.

PubMed

Qin, Xiaoteng; Liu, Shangming; Lu, Qiulun; Zhang, Meng; Jiang, Xiuxin; Hu, Sanyuan; Li, Jingxin; Zhang, Cheng; Gao, Jiangang; Zhu, Min-Sheng; Feil, Robert; Li, Huashun; Chen, Min; Weinstein, Lee S; Zhang, Yun; Zhang, Wencheng

2017-04-01

The α subunit of the heterotrimeric G stimulatory protein (Gsa), encoded by the guanine nucleotide binding protein, α-stimulating gene (Gnas, in mice), is expressed ubiquitously and mediates receptor-stimulated production of cyclic adenosine monophosphate and activation of the protein kinase A signaling pathway. We investigated the roles of Gsa in vivo in smooth muscle cells of mice. We performed studies of mice with Cre recombinase-mediated disruption of Gnas in smooth muscle cells (Gsa SMKO and SM22-CreER T2 , induced in adult mice by tamoxifen). Intestinal tissues were collected for histologic, biochemical, molecular, cell biology, and physiology analyses. Intestinal function was assessed in mice using the whole-gut transit time test. We compared gene expression patterns of intestinal smooth muscle from mice with vs without disruption of Gnas. Biopsy specimens from ileum of patients with chronic intestinal pseudo-obstruction and age-matched control biopsies were analyzed by immunohistochemistry. Disruption of Gnas in smooth muscle of mice reduced intestinal motility and led to death within 4 weeks. Tamoxifen-induced disruption of Gnas in adult mice impaired contraction of intestinal smooth muscle and peristalsis. More than 80% of these died within 3 months of tamoxifen exposure, with features of intestinal pseudo-obstruction characterized by chronic intestinal dilation and dysmotility. Gsa deficiency reduced intestinal levels of cyclic adenosine monophosphate and transcriptional activity of the cyclic adenosine monophosphate response element binding protein 1 (CREB1); this resulted in decreased expression of the forkhead box F1 gene (Foxf1) and protein, and contractile proteins, such as myosin heavy chain 11; actin, α2, smooth muscle, aorta; calponin 1; and myosin light chain kinase. We found decreased levels of Gsa, FOXF1, CREB1, and phosphorylated CREB1 proteins in intestinal muscle layers of patients with chronic intestinal pseudo

Crystal structure of human dual specificity phosphatase, JNK stimulatory phosphatase-1, at 1.5 A resolution.

PubMed

Yokota, Takehiro; Nara, Yukinori; Kashima, Akiko; Matsubara, Keiko; Misawa, Satoru; Kato, Ryohei; Sugio, Shigetoshi

2007-02-01

Human JNK stimulatory phosphatase-1 (JSP-1) is a novel member of dual specificity phosphatases. A C-terminus truncated JSP-1 was expressed in Escherichia coli and was crystallized using the sitting-drop vapor diffusion method. Thin-plate crystals obtained at 278 K belong to a monoclinic space group, C2, with unit-cell parameters a = 84.0 A, b = 49.3 A, c = 47.3 A, and beta = 119.5 degrees , and diffract up to 1.5 A resolution at 100 K. The structure of JSP-1 has a single compact (alpha/beta) domain, which consists of six alpha-helices and five beta-strands, and shows a conserved structural scaffold in regard to both DSPs and PTPs. A cleft formed by a PTP-loop at the active site is very shallow, and is occupied by one sulfonate compound, MES, at the bottom. In the binary complex structure of JSP-1 with MES, the conformations of three important segments in regard to the catalytic mechanism are not similar to those in PTP1B. JSP-1 has no loop corresponding to the Lys120-loop of PTP1B, and tryptophan residue corresponding to the substrate-stacking in PTP1B is substituted by alanine residue in JSP-1. Copyright 2006 Wiley-Liss, Inc.

BioRadioTransmitter: a self-powered wireless glucose-sensing system.

PubMed

Hanashi, Takuya; Yamazaki, Tomohiko; Tsugawa, Wakako; Ikebukuro, Kazunori; Sode, Koji

2011-09-01

Although an enzyme fuel cell can be utilized as a glucose sensor, the output power generated is too low to power a device such as a currently available transmitter and operating system, and an external power source is required for operating an enzyme-fuel-cell-based biosensing system. We proposed a novel biosensor that we named BioCapacitor, in which a capacitor serves as a transducer. In this study, we constructed a new BioCapacitor-based system with an added radio-transmitter circuit and a miniaturized enzyme fuel cell. A miniaturized direct-electron-transfer-type compartmentless enzyme fuel cell was constructed with flavin adenine dinucleotide-dependent glucose dehydrogenase complex-based anode and a bilirubin-oxidase-based cathode. For construction of a BioRadioTransmitter wireless sensing system, a capacitor, an ultra-low-voltage charge-pump-integrated circuit, and Hartley oscillator circuit were connected to the miniaturized enzyme fuel cell. A radio-receiver circuit, comprising two field-effect transistors and a coil as an antenna, was used to amplify the signal generated from the biofuel cells. Radio wave signals generated by the BioRadioTransmitter were received, amplified, and converted from alternate to direct current by the radio receiver. When the capacitor discharges in the presence of glucose, the BioRadioTransmitter generates a radio wave, which is monitored by a radio receiver connected wirelessly to the sensing device. Magnitude of the radio wave transmission frequency change observed at the radio receiver was correlated to glucose concentration in the fuel cells. We constructed a stand-alone, self-powered, wireless glucose-sensing system called a BioRadioTransmitter by using a radio transmitter in which the radio wave transmission frequency changes with the glucose concentration in the fuel cell. The BioRadioTransmitter is a significant advance toward construction of an implantable continuous glucose monitor. © 2011 Diabetes Technology Society.

Improve homology search sensitivity of PacBio data by correcting frameshifts.

PubMed

Du, Nan; Sun, Yanni

2016-09-01

Single-molecule, real-time sequencing (SMRT) developed by Pacific BioSciences produces longer reads than secondary generation sequencing technologies such as Illumina. The long read length enables PacBio sequencing to close gaps in genome assembly, reveal structural variations, and identify gene isoforms with higher accuracy in transcriptomic sequencing. However, PacBio data has high sequencing error rate and most of the errors are insertion or deletion errors. During alignment-based homology search, insertion or deletion errors in genes will cause frameshifts and may only lead to marginal alignment scores and short alignments. As a result, it is hard to distinguish true alignments from random alignments and the ambiguity will incur errors in structural and functional annotation. Existing frameshift correction tools are designed for data with much lower error rate and are not optimized for PacBio data. As an increasing number of groups are using SMRT, there is an urgent need for dedicated homology search tools for PacBio data. In this work, we introduce Frame-Pro, a profile homology search tool for PacBio reads. Our tool corrects sequencing errors and also outputs the profile alignments of the corrected sequences against characterized protein families. We applied our tool to both simulated and real PacBio data. The results showed that our method enables more sensitive homology search, especially for PacBio data sets of low sequencing coverage. In addition, we can correct more errors when comparing with a popular error correction tool that does not rely on hybrid sequencing. The source code is freely available at https://sourceforge.net/projects/frame-pro/ yannisun@msu.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Activation and characterization of waste coffee grounds as bio-sorbent

NASA Astrophysics Data System (ADS)

Mariana; Marwan; Mulana, F.; Yunardi; Ismail, T. A.; Hafdiansyah, M. F.

2018-03-01

As the city well known for its culture of coffee drinkers, modern and traditional coffee shops are found everywhere in Banda Aceh, Indonesia. High number of coffee shops in the city generates large quantities of spent coffee grounds as waste without any effort to convert them as other valuable products. In an attempt to reduce environmental problems caused by used coffee grounds, this research was conducted to utilize waste coffee grounds as an activated carbon bio-sorbent. The specific purpose of this research is to improve the performance of coffee grounds bio-sorbent through chemical and physical activation, and to characterize the produced bio-sorbent. Following physical activation by carbonization, a chemical activation was achieved by soaking the carbonized waste coffee grounds in HCl solvent and carbonization process. The activated bio-sorbent was characterized for its morphological properties using Scanning Electron Microscopy (SEM), its functional groups by Fourier Transform Infra-Red Spectrophotometer (FTIR), and its material characteristics using X-Ray Diffraction (XRD). Characterization of the activated carbon prepared from waste coffee grounds shows that it meets standard quality requirement in accordance with Indonesian National Standard, SNI 06-3730-1995. Activation process has modified the functional groups of the waste coffee grounds. Comparing to natural waste coffee grounds, the resulted bio-sorbent demonstrated a more porous surface morphology following activation process. Consequently, such bio-sorbent is a potential source to be used as an adsorbent for various applications.

Low-Severity Hydroprocessing to Stabilize Bio-oil: TechnoEconomic Assessment

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

Tews, Iva J.; Elliott, Douglas C.

The impetus for this study was the suggestion that recent developments in fast pyrolysis (FP) bio-oil production had indicated instability of the bio-oil in storage which might lead to unacceptable viscosity increases. Commercial operation of FP in Finland began in 2014 and the distribution of the bio-oil to isolated users has been proposed as the long-term plan. Stability of the shipped bio-oil therefore became a concern. Experimental results at PNNL with low-severity hydroprocessing of bio-oil for stabilization has validated a process in which the stability of the bio-oil could be improved, as measured by viscosity increase following storage of themore » product at 80 °C for 24h. In the work reported here the assessed process configuration consists of fast pyrolysis followed by low temperature and pressure hydroprocessing to produce a stable fuel oil product. The product could then be stored for an extended period of time without significant viscosity increase. This work was carried out as part of a collaborative project between Technical Research Centre of Finland (VTT) and Pacific Northwest National Laboratory (PNNL). The public funding agents for the work were Tekes in Finland and the Bioenergy Technologies Office of the U.S. Department of Energy. The effort was proposed as an evaluation of the process developed in earlier collaboration and jointly invented by VTT and PNNL researchers.« less

Characterization of un-hydrated and hydrated BioAggregate™ and MTA Angelus™.

PubMed

Camilleri, J; Sorrentino, F; Damidot, D

2015-04-01

BioAggregate™ is a novel material introduced for use as a root-end filling material. It is tricalcium silicate-based, free of aluminium and uses tantalum oxide as radiopacifier. BioAggregate contains additives to enhance the material performance. The purpose of this research was to characterize the un-hydrated and hydrated forms of BioAggregate using a combination of techniques, verify whether the additives if present affect the properties of the set material and compare these properties to those of MTA Angelus™. Un-hydrated and hydrated BioAggregate and MTA Angelus were assessed. Un-hydrated cement was tested for chemical composition, specific surface area, mineralogy and kinetics of hydration. The set material was investigated for mineralogy, microstructure and bioactivity. Scanning electron microscopy, X-ray energy dispersive spectroscopic analysis, X-ray fluorescence spectroscopy, X-ray diffraction and isothermal calorimetry were employed. The specific surface area was investigated using a gas adsorption method with nitrogen as the probe. BioAggregate was composed of tricalcium silicate, tantalum oxide, calcium phosphate and silicon dioxide and was free of aluminium. On hydration, the tricalcium silicate produced calcium silicate hydrate and calcium hydroxide. The former was deposited around the cement grains, while the latter reacted with the silicon dioxide to form additional calcium silicate hydrate. This resulted in reduction of calcium hydroxide in the aged cement. MTA Angelus reacted in a similar fashion; however, since it contained no additives, the calcium hydroxide was still present in the aged cement. Bioactivity was demonstrated by deposition of hydroxyapatite. BioAggregate exhibited a high specific surface area. Nevertheless, the reactivity determined by isothermal calorimetry appeared to be slow compared to MTA Angelus. The tantalum oxide as opposed to bismuth oxide was inert, and tantalum was not leached in solution. BioAggregate exhibited

Toxicity assessment of chlorpyrifos-degrading fungal bio-composites and their environmental risks.

PubMed

Liu, Jie; Zhang, Xiaoying; Yang, Mengran; Hu, Meiying; Zhong, Guohua

2018-02-01

Bioremediation techniques coupling with functional microorganisms have emerged as the most promising approaches for in-situ elimination of pesticide residue. However, the environmental safety of bio-products based on microorganisms or engineered enzymes was rarely known. Here, we described the toxicity assessment of two previously fabricated fungal bio-composites which were used for the biodegradation of chlorpyrifos, to clarify their potential risks on the environment and non-target organisms. Firstly, the acute and chronic toxicity of prepared bio-composites were evaluated using mice and rabbits, indicating neither acute nor chronic effect was induced via short-term or continuous exposure. Then, the acute mortality on zebrafish was investigated, which implied the application of fungal bio-composites had no lethal risk on aquatic organisms. Meanwhile, the assessment on soil organic matters suggested that no threat was posed to soil quality. Finally, by monitoring, the germination of cabbage was not affected by the exposure to two bio-products. Therefore, the application of fungal bio-composites for chlorpyrifos elimination cannot induce toxic risk to the environment and non-target organisms, which insured the safety of these engineered bio-products for realistic management of pesticide residue, and provided new insights for further development of bioremediation techniques based on functional microorganisms.