Biological and analytical variations of 16 parameters related to coagulation screening tests and the activity of coagulation factors.

PubMed

Chen, Qian; Shou, Weiling; Wu, Wei; Guo, Ye; Zhang, Yujuan; Huang, Chunmei; Cui, Wei

2015-04-01

To accurately estimate longitudinal changes in individuals, it is important to take into consideration the biological variability of the measurement. The few studies available on the biological variations of coagulation parameters are mostly outdated. We confirmed the published results using modern, fully automated methods. Furthermore, we added data for additional coagulation parameters. At 8:00 am, 12:00 pm, and 4:00 pm on days 1, 3, and 5, venous blood was collected from 31 healthy volunteers. A total of 16 parameters related to coagulation screening tests as well as the activity of coagulation factors were analyzed; these included prothrombin time, fibrinogen (Fbg), activated partial thromboplastin time, thrombin time, international normalized ratio, prothrombin time activity, activated partial thromboplastin time ratio, fibrin(-ogen) degradation products, as well as the activity of factor II, factor V, factor VII, factor VIII, factor IX, and factor X. All intraindividual coefficients of variation (CVI) values for the parameters of the screening tests (except Fbg) were less than 5%. Conversely, the CVI values for the activity of coagulation factors were all greater than 5%. In addition, we calculated the reference change value to determine whether a significant difference exists between two test results from the same individual. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Role of p21-activated kinases in cardiovascular development and function.

PubMed

Kelly, Mollie L; Astsaturov, Artyom; Chernoff, Jonathan

2013-11-01

p21-activated kinases (Paks) are a group of six serine/threonine kinases (Pak1-6) that are involved in a variety of biological processes. Recently, Paks, more specifically Pak1, -2, and -4, have been shown to play important roles in cardiovascular development and function in a range of model organisms including zebrafish and mice. These functions include proper morphogenesis and conductance of the heart, cardiac contractility, and development and integrity of the vasculature. The mechanisms underlying these effects are not fully known, but they likely differ among the various Pak isoforms and include both kinase-dependent and -independent functions. In this review, we discuss aspects of Pak function relevant to cardiovascular biology as well as potential therapeutic implications of small-molecule Pak inhibitors in cardiovascular disease.

Denosumab for bone diseases: translating bone biology into targeted therapy.

PubMed

Tsourdi, Elena; Rachner, Tilman D; Rauner, Martina; Hamann, Christine; Hofbauer, Lorenz C

2011-12-01

Signalling of receptor activator of nuclear factor-κB (RANK) ligand (RANKL) through RANK is a critical pathway to regulate the differentiation and activity of osteoclasts and, hence, a master regulator of bone resorption. Increased RANKL activity has been demonstrated in diseases characterised by excessive bone loss such as osteoporosis, rheumatoid arthritis and osteolytic bone metastases. The development and approval of denosumab, a fully MAB against RANKL, has heralded a new era in the treatment of bone diseases by providing a potent, targeted and reversible inhibitor of bone resorption. This article summarises the molecular and cellular biology of the RANKL/RANK system and critically reviews preclinical and clinical studies that have established denosumab as a promising novel therapy for metabolic and malignant bone diseases. We will discuss the potential indications for denosumab along with a critical review of safety and analyse its potential within the concert of established therapies.

A truncated Wnt7a retains full biological activity in skeletal muscle

NASA Astrophysics Data System (ADS)

von Maltzahn, Julia; Zinoviev, Radoslav; Chang, Natasha C.; Bentzinger, C. Florian; Rudnicki, Michael A.

2013-11-01

Wnt signaling has essential roles during embryonic development and tissue homoeostasis. Wnt proteins are post-translationally modified and the attachment of a palmitate moiety at two conserved residues is believed to be a prerequisite for the secretion and function of Wnt proteins. Here we demonstrate that a mammalian Wnt protein can be fully functional without palmitoylation. We generate a truncated Wnt7a variant, consisting of the C-terminal 137 amino acids lacking the conserved palmitoylation sites and show that it retains full biological activity in skeletal muscle. This includes binding to and signaling through its receptor Fzd7 to stimulate symmetric expansion of satellite stem cells by activating the planar-cell polarity pathway and inducing myofibre hypertrophy by signaling through the AKT/mTOR pathway. Furthermore, this truncated Wnt7a shows enhanced secretion and dispersion compared with the full-length protein. Together, these findings open important new avenues for the development of Wnt7a as a treatment for muscle-wasting diseases and have broad implications for the therapeutic use of Wnts as biologics.

PASylation: a biological alternative to PEGylation for extending the plasma half-life of pharmaceutically active proteins

PubMed Central

Schlapschy, Martin; Binder, Uli; Börger, Claudia; Theobald, Ina; Wachinger, Klaus; Kisling, Sigrid; Haller, Dirk; Skerra, Arne

2013-01-01

A major limitation of biopharmaceutical proteins is their fast clearance from circulation via kidney filtration, which strongly hampers efficacy both in animal studies and in human therapy. We have developed conformationally disordered polypeptide chains with expanded hydrodynamic volume comprising the small residues Pro, Ala and Ser (PAS). PAS sequences are hydrophilic, uncharged biological polymers with biophysical properties very similar to poly-ethylene glycol (PEG), whose chemical conjugation to drugs is an established method for plasma half-life extension. In contrast, PAS polypeptides offer fusion to a therapeutic protein on the genetic level, permitting Escherichia coli production of fully active proteins and obviating in vitro coupling or modification steps. Furthermore, they are biodegradable, thus avoiding organ accumulation, while showing stability in serum and lacking toxicity or immunogenicity in mice. We demonstrate that PASylation bestows typical biologics, such as interferon, growth hormone or Fab fragments, with considerably prolonged circulation and boosts bioactivity in vivo. PMID:23754528

Development of the Vinylogous Pictet-Spengler Cyclization and Total Synthesis of (±)-Lundurine A.

PubMed

Nash, Aaron; Qi, Xiangbing; Maity, Pradip; Owens, Kyle; Tambar, Uttam K

2018-04-16

A novel vinylogous Pictet-Spengler cyclization has been developed for the generation of indole-annulated medium-sized rings. The method enables the synthesis of tetrahydroazocinoindoles with a fully substituted carbon center, a prevalent structural motif in many biologically active alkaloids. The strategy has been applied to the total synthesis of (±)-lundurine A. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The application of Biological-Hydraulic coupled model for Tubificidae-microorganism interaction system

NASA Astrophysics Data System (ADS)

Zhong, Xiao; Sun, Peide; Song, Yingqi; Wang, Ruyi; Fang, Zhiguo

2010-11-01

Based on the fully coupled activated sludge model (FCASM), the novel model Tubificidae -Fully Coupled Activated Sludge Model-hydraulic (T-FCASM-Hydro), has been developed in our previous work. T-FCASM-Hydro not only describe the interactive system between Tubificidae and functional microorganisms for the sludge reduction and nutrient removal simultaneously, but also considere the interaction between biological and hydraulic field, After calibration and validation of T-FCASM-Hydro at Zhuji Feida-hongyu Wastewater treatment plant (WWTP) in Zhejiang province, T-FCASM-Hydro was applied for determining optimal operating condition in the WWTP. Simulation results showed that nitrogen and phosphorus could be removed efficiently, and the efficiency of NH4+-N removal enhanced with increase of DO concentration. At a certain low level of DO concentration in the aerobic stage, shortcut nitrification-denitrification dominated in the process of denitrification in the novel system. However, overhigh agitation (>6 mgṡL-1) could result in the unfavorable feeding behavior of Tubificidae because of the strong flow disturbance, which might lead to low rate of sludge reduction. High sludge reduction rate and high removal rate of nitrogen and phosphorus could be obtained in the new-style oxidation ditch when DO concentration at the aerobic stage with Tubificidae was maintained at 3.6 gṡm-3.

Node fingerprinting: an efficient heuristic for aligning biological networks.

PubMed

Radu, Alex; Charleston, Michael

2014-10-01

With the continuing increase in availability of biological data and improvements to biological models, biological network analysis has become a promising area of research. An emerging technique for the analysis of biological networks is through network alignment. Network alignment has been used to calculate genetic distance, similarities between regulatory structures, and the effect of external forces on gene expression, and to depict conditional activity of expression modules in cancer. Network alignment is algorithmically complex, and therefore we must rely on heuristics, ideally as efficient and accurate as possible. The majority of current techniques for network alignment rely on precomputed information, such as with protein sequence alignment, or on tunable network alignment parameters, which may introduce an increased computational overhead. Our presented algorithm, which we call Node Fingerprinting (NF), is appropriate for performing global pairwise network alignment without precomputation or tuning, can be fully parallelized, and is able to quickly compute an accurate alignment between two biological networks. It has performed as well as or better than existing algorithms on biological and simulated data, and with fewer computational resources. The algorithmic validation performed demonstrates the low computational resource requirements of NF.

Spectroscopic characteristic (FT-IR, FT-Raman, UV, 1H and 13C NMR), theoretical calculations and biological activity of alkali metal homovanillates

NASA Astrophysics Data System (ADS)

Samsonowicz, M.; Kowczyk-Sadowy, M.; Piekut, J.; Regulska, E.; Lewandowski, W.

2016-04-01

The structural and vibrational properties of lithium, sodium, potassium, rubidium and cesium homovanillates were investigated in this paper. Supplementary molecular spectroscopic methods such as: FT-IR, FT-Raman in the solid phase, UV and NMR were applied. The geometrical parameters and energies were obtained from density functional theory (DFT) B3LYP method with 6-311++G** basis set calculations. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned. Geometric and magnetic aromaticity indices, atomic charges, dipole moments, HOMO and LUMO energies were also calculated. The microbial activity of investigated compounds was tested against Bacillus subtilis (BS), Pseudomonas aeruginosa (PA), Escherichia coli (EC), Staphylococcus aureus (SA) and Candida albicans (CA). The relationship between the molecular structure of tested compounds and their antimicrobial activity was studied. The principal component analysis (PCA) was applied in order to attempt to distinguish the biological activities of these compounds according to selected band wavenumbers. Obtained data show that the FT-IR spectra can be a rapid and reliable analytical tool and a good source of information for the quantitative analysis of the relationship between the molecular structure of the compound and its biological activity.

Chemical composition and biological activity of essential oils of Origanum vulgare L. subsp. vulgare L. under different growth conditions.

PubMed

De Falco, Enrica; Mancini, Emilia; Roscigno, Graziana; Mignola, Enrico; Taglialatela-Scafati, Orazio; Senatore, Felice

2013-12-04

This research was aimed at investigating the essential oil production, chemical composition and biological activity of a crop of pink flowered oregano (Origanum vulgare L. subsp. vulgare L.) under different spatial distribution of the plants (single and binate rows). This plant factor was shown to affect its growth, soil covering, fresh biomass, essential oil amount and composition. In particular, the essential oil percentage was higher for the binate row treatment at the full bloom. The chemical composition of the oils obtained by hydrodistillation was fully characterized by GC and GC-MS. The oil from plants grown in single rows was rich in sabinene, while plants grown in double rows were richer in ocimenes. The essential oils showed antimicrobial action, mainly against Gram-positive pathogens and particularly Bacillus cereus and B. subtilis.

Spacer conformation in biologically active molecules. Part 2. Structure and conformation of 4-[2-(diphenylmethylamino)ethyl]-1-(2-methoxyphenyl) piperazine and its diphenylmethoxy analog—potential 5-HT 1A receptor ligands

NASA Astrophysics Data System (ADS)

Karolak-Wojciechowska, J.; Fruziński, A.; Czylkowski, R.; Paluchowska, M. H.; Mokrosz, M. J.

2003-09-01

As a part of studies on biologically active molecule structures with aliphatic linking chain, the structures of 4-[2-diphenylmethylamino)ethyl]-1-(2-methoxyphenyl)piperazine dihydrochloride ( 1) and 4-[2-diphenylmethoxy)ethyl]-1-(2-methoxyphenyl)piperazine fumarate ( 2) have been reported. In both compounds, four atomic non-all-carbons linking chains (N)C-C-X-C are present. The conformation of that linking spacer depends on the nature of the X-atom. The preferred conformation for chain with XNH has been found to be fully extended while for that with XO—the bend one. It was confirmed by conformational calculations (strain energy distribution and random search) and crystallographic data, including statistics from CCDC.

Plasticity and Activation of Spared Intraspinal Respiratory Circuits Following Spinal Cord Injury

DTIC Science & Technology

2015-10-01

scheduled to present these data at the Spring 2016 Experimental Biology Meeting in San Diego, CA, and thus fully anticipate that analysis will be...that had been deprived of descending drive from the brainstem from an acute cervical spinal cord injury in an endogenous rhythmic manner. To address...epidural stimulation. Major Task 3: Analysis of Tissue Responses to Microwire Implantation These experiments, which were incorporated into the revised

Biological Activities of Fusarochromanone: a Potent Anti-cancer Agent

DTIC Science & Technology

2014-09-03

experiments to more fully elucidate the detailed mechanism underlying this favorable feature of FC101. Like most other bioactive natural flavonoids , FC101...tribution, metabolism, and elimination of compounds in blood and tissues over time. FC101 is a flavonoid , and over 4,000 natural compounds have been... Flavonoids generally bind tightly to serum proteins (e.g., serum albumin) and thus substantial amounts are inaccessible to the desired bio- logical targets

Biological Opinion Compliance Report and Permit Activity Report

DTIC Science & Technology

1999-03-01

and thermoregulate themselves. Hatchlings will be kept in the brood boxes until their feather tracts are fullyfeathered (approximately 12-14 days) and...they are able to fully thermoregulate . Boxes will be cleaned and disinfected Monday and Thursday of each week using Germacertt"r nontoxic...and are able to feed and thermoregulate themselves, they will be transferred to the outdoor flight pen. The outdoor pen is 48 feet by 60 feet and

Towards fully automated Identification of Vesicle-Membrane Fusion Events in TIRF Microscopy

NASA Astrophysics Data System (ADS)

Vallotton, Pascal; James, David E.; Hughes, William E.

2007-11-01

Total Internal Reflection Fluorescence Microscopy (TIRFM) is imposing itself as the tool of choice for studying biological activity in close proximity to the plasma membrane. For example, the exquisite selectivity of TIRFM allows monitoring the diffusion of GFP-phogrin vesicles and their recruitment to the plasma membrane in pancreatic β-cells. We present a novel computer vision system for automatically identifying the elusive fusion events of GFP-phogrin vesicles with the plasma membrane. Our method is based on robust object tracking and matched filtering. It should accelerate the quantification of TIRFM data and allow the extraction of more biological information from image data to support research in diabetes and obesity.

Imaging fully hydrated whole cells by coherent x-ray diffraction microscopy.

PubMed

Nam, Daewoong; Park, Jaehyun; Gallagher-Jones, Marcus; Kim, Sangsoo; Kim, Sunam; Kohmura, Yoshiki; Naitow, Hisashi; Kunishima, Naoki; Yoshida, Takashi; Ishikawa, Tetsuya; Song, Changyong

2013-03-01

Nanoscale imaging of biological specimens in their native condition is of long-standing interest, in particular with direct, high resolution views of internal structures of intact specimens, though as yet progress has been limited. Here we introduce wet coherent x-ray diffraction microscopy capable of imaging fully hydrated and unstained biological specimens. Whole cell morphologies and internal structures better than 25 nm can be clearly visualized without contrast degradation.

Non-plaque-forming virions of Modified Vaccinia virus Ankara express viral genes.

PubMed

Lülf, Anna-Theresa; Freudenstein, Astrid; Marr, Lisa; Sutter, Gerd; Volz, Asisa

2016-12-01

In cell culture infections with vaccinia virus the number of counted virus particles is substantially higher than the number of plaques obtained by titration. We found that standard vaccine preparations of recombinant Modified Vaccinia virus Ankara produce only about 20-30% plaque-forming virions in fully permissive cell cultures. To evaluate the biological activity of the non-plaque-forming particles, we generated recombinant viruses expressing fluorescent reporter proteins under transcriptional control of specific viral early and late promoters. Live cell imaging and automated counting by fluorescent microscopy indicated that virtually all virus particles can enter cells and switch on viral gene expression. Although most of the non-plaque-forming infections are arrested at the level of viral early gene expression, we detected activation of late viral transcription in 10-20% of single infected cells. Thus, non-plaque-forming particles are biologically active, and likely contribute to the immunogenicity of vaccinia virus vaccines. Copyright © 2016 Elsevier Inc. All rights reserved.

Estimating the surface area of birds: using the homing pigeon (Columba livia) as a model.

PubMed

Perez, Cristina R; Moye, John K; Pritsos, Chris A

2014-05-08

Estimation of the surface area of the avian body is valuable for thermoregulation and metabolism studies as well as for assessing exposure to oil and other surface-active organic pollutants from a spill. The use of frozen carcasses for surface area estimations prevents the ability to modify the posture of the bird. The surface area of six live homing pigeons in the fully extended flight position was estimated using a noninvasive method. An equation was derived to estimate the total surface area of a pigeon based on its body weight. A pigeon's surface area in the fully extended flight position is approximately 4 times larger than the surface area of a pigeon in the perching position. The surface area of a bird is dependent on its physical position, and, therefore, the fully extended flight position exhibits the maximum area of a bird and should be considered the true surface area of a bird. © 2014. Published by The Company of Biologists Ltd | Biology Open.

Will systems biology offer new holistic paradigms to life sciences?

PubMed Central

Conti, Filippo; Valerio, Maria Cristina; Zbilut, Joseph P.

2008-01-01

A biological system, like any complex system, blends stochastic and deterministic features, displaying properties of both. In a certain sense, this blend is exactly what we perceive as the “essence of complexity” given we tend to consider as non-complex both an ideal gas (fully stochastic and understandable at the statistical level in the thermodynamic limit of a huge number of particles) and a frictionless pendulum (fully deterministic relative to its motion). In this commentary we make the statement that systems biology will have a relevant impact on nowadays biology if (and only if) will be able to capture the essential character of this blend that in our opinion is the generation of globally ordered collective modes supported by locally stochastic atomisms. PMID:19003440

Human Behavior and Cognition in Evolutionary Economics.

PubMed

Nelson, Richard R

2011-12-01

My brand of evolutionary economics recognizes, highlights, that modern economies are always in the process of changing, never fully at rest, with much of the energy coming from innovation. This perspective obviously draws a lot from Schumpeter. Continuing innovation, and the creative destruction that innovation engenders, is driving the system. There are winners and losers in the process, but generally the changes can be regarded as progress. The processes through which economic activity and performance evolve has a lot in common with evolution in biology. In particular, at any time the economy is marked by considerable variety, there are selection forces winnowing on that variety, but also continuing emergence of new ways of doing things and often economic actors. But there also are important differences from biological evolution. In particular, both innovation and selection are to a considerable degree purposive activities, often undertaken on the basis of relatively strong knowledge.

Peptide mimic for influenza vaccination using nonnatural combinatorial chemistry

PubMed Central

Miles, John J.; Tan, Mai Ping; Dolton, Garry; Galloway, Sarah A.E.; Laugel, Bruno; Makinde, Julia; Matthews, Katherine K.; Watkins, Thomas S.; Wong, Yide; Clark, Richard J.; Pentier, Johanne M.; Attaf, Meriem; Lissina, Anya; Ager, Ann; Gallimore, Awen; Gras, Stephanie; Rossjohn, Jamie; Burrows, Scott R.; Cole, David K.; Price, David A.

2018-01-01

Polypeptide vaccines effectively activate human T cells but suffer from poor biological stability, which confines both transport logistics and in vivo therapeutic activity. Synthetic biology has the potential to address these limitations through the generation of highly stable antigenic “mimics” using subunits that do not exist in the natural world. We developed a platform based on D–amino acid combinatorial chemistry and used this platform to reverse engineer a fully artificial CD8+ T cell agonist that mirrored the immunogenicity profile of a native epitope blueprint from influenza virus. This nonnatural peptide was highly stable in human serum and gastric acid, reflecting an intrinsic resistance to physical and enzymatic degradation. In vitro, the synthetic agonist stimulated and expanded an archetypal repertoire of polyfunctional human influenza virus–specific CD8+ T cells. In vivo, specific responses were elicited in naive humanized mice by subcutaneous vaccination, conferring protection from subsequent lethal influenza challenge. Moreover, the synthetic agonist was immunogenic after oral administration. This proof-of-concept study highlights the power of synthetic biology to expand the horizons of vaccine design and therapeutic delivery. PMID:29528337

Soy Pulp Extract Inhibits Angiotensin I-Converting Enzyme (ACE) Activity In Vitro: Evidence for Its Potential Hypertension-Improving Action.

PubMed

Nishibori, Naoyoshi; Kishibuchi, Reina; Morita, Kyoji

2017-05-04

Soy pulp, called "okara" in Japanese, is known as a by-product of the production of bean curd (tofu), and expected to contain a variety of biologically active substances derived from soybean. However, the biological activities of okara ingredients have not yet been fully understood, and the effectiveness of okara as a functional food seems necessary to be further evaluated. Then the effect of okara extract on angiotensin I-converting enzyme (ACE) activity was examined in vitro, and the extract was shown to cause the inhibition of ACE activity in a manner depending on its concentration. Kinetic analysis indicated that this enzyme inhibition was accompanied by an increase in the Km value without any change in Vmax. Further studies suggested that putative inhibitory substances contained in the extract might be heat stable and dialyzable, and recovered mostly in the peptide fraction obtained by a spin-column separation and a high performance liquid chromatography (HPLC) fractionation. Therefore, the extract was speculated to contain small-size peptides responsible for the inhibitory effect of okara extract on ACE activity, and could be expected to improve the hypertensive conditions by reducing the production of hypertensive peptide.

Translational applications of evaluating physiologic variability in human endotoxemia

PubMed Central

Scheff, Jeremy D.; Mavroudis, Panteleimon D.; Calvano, Steve E.; Androulakis, Ioannis P.

2012-01-01

Dysregulation of the inflammatory response is a critical component of many clinically challenging disorders such as sepsis. Inflammation is a biological process designed to lead to healing and recovery, ultimately restoring homeostasis; however, the failure to fully achieve those beneficial results can leave a patient in a dangerous persistent inflammatory state. One of the primary challenges in developing novel therapies in this area is that inflammation is comprised of a complex network of interacting pathways. Here, we discuss our approaches towards addressing this problem through computational systems biology, with a particular focus on how the presence of biological rhythms and the disruption of these rhythms in inflammation may be applied in a translational context. By leveraging the information content embedded in physiologic variability, ranging in scale from oscillations in autonomic activity driving short-term heart rate variability (HRV) to circadian rhythms in immunomodulatory hormones, there is significant potential to gain insight into the underlying physiology. PMID:23203205

Structural molecular biology: Recent results from neutron diffraction

NASA Astrophysics Data System (ADS)

Timmins, Peter A.

1995-02-01

Neutron diffraction is of importance in structural biology at several different levels of resolution. In most cases the unique possibility arising from deuterium labelling or contrast variation is of fundamental importance in providing information complementary to that which can be obtained from X-ray diffraction. At high resolution, neutron crystallography of proteins allows the location of hydrogen atoms in the molecule or of the hydration water, both of which may be central to biological activity. A major difficulty in this field has been the poor signal-to-noise ratio of the data arising not only from relatively low beam intensities and small crystals but, most importantly from the incoherent background due to hydrogen atoms in the sample. Modern methods of molecular biology now offer ways of producing fully deuterated proteins by cloning in bacteria grown on fully deuterated media. At a slightly lower resolution, there are a number of systems which may be ordered in one or two dimensions. This is the case in the purple membrane where neutron diffraction with deuterium labelling has complemented high resolution electron diffraction. Finally there is a class of very large macromolecular systems which can be crystallised and have been studied by X-ray diffraction but in which part of the structure is locally disordered and usually has insufficient contrast to be seen with X-rays. In this case the use of H 2O/D 2O contrast variation allows these components to be located. Examples of this are the nucleic acid in virus structures and detergent bound to membrane proteins.

Cost-effectiveness analysis of secukinumab for the treatment of active psoriatic arthritis: a Canadian perspective.

PubMed

Goeree, Ron; Chiva-Razavi, Sima; Gunda, Praveen; Graham, Christopher N; Miles, LaStella; Nikoglou, Efthalia; Jugl, Steffen M; Gladman, Dafna D

2018-02-01

The study evaluates the cost-effectiveness of secukinumab, a fully human monoclonal antibody that selectively neutralizes interleukin (IL)-17A, vs currently licensed biologic treatments in patients with active psoriatic arthritis (PsA) from a Canadian healthcare system perspective. A decision analytic semi-Markov model evaluated the cost-effectiveness of secukinumab 150 mg and 300 mg compared to subcutaneous biologics adalimumab, certolizumab pegol, etanercept, golimumab, and ustekinumab, and intravenous biologics infliximab and infliximab biosimilar in biologic-naive and biologic-experienced patients over a lifetime horizon. The response to treatments was evaluated after 12 weeks by PsA Response Criteria (PsARC) response rates. Non-responders or patients discontinuing initial-line of biologic treatment were allowed to switch to subsequent-line biologics. Model input parameters (Psoriasis Area Severity Index [PASI], Health Assessment Questionnaire [HAQ], withdrawal rates, costs, and resource use) were collected from clinical trials, published literature, and other Canadian sources. Benefits were expressed as quality-adjusted life years (QALYs). An annual discount rate of 5% was applied to costs and benefits. The robustness of the study findings were evaluated via sensitivity analyses. Biologic-naive patients treated with secukinumab achieved the highest number of QALYs (8.54) at the lowest cost (CAD 925,387) over a lifetime horizon vs all comparators. Secukinumab dominated all treatments, except for infliximab and its biosimilar, which achieved minimally more QALYs (8.58). However, infliximab and its biosimilar incurred more costs than secukinumab (infliximab: CAD 1,015,437; infliximab biosimilar: CAD 941,004), resulting in higher cost-effectiveness estimates relative to secukinumab. In the biologic-experienced population, secukinumab dominated all treatments as it generated more QALYs (8.89) at lower costs (CAD 954,692). Deterministic sensitivity analyses indicated the results were most sensitive to variation in PsARC response rates, change in HAQ, and utility values in both populations. Secukinumab is either dominant or cost-effective vs all licensed biologics for the treatment of active PsA in biologic-naive and biologic-experienced populations in Canada.

Blog construction as an effective tool in biochemistry active learning.

PubMed

Cubas Rolim, Estêvão; Martins de Oliveira, Julia; Dalvi, Luana T; Moreira, Daniel C; Garcia Caldas, Natasha; Fernandes Lobo, Felipe; André Polli, Démerson; Campos, Élida G; Hermes-Lima, Marcelo

2017-05-01

To boost active learning in undergraduate students, they were given the task of preparing blogs on topics of clinical biochemistry. This "experiment" lasted for 12 teaching-semesters (from 2008 to 2013), and included a survey on the blogs' usefulness at the end of each semester. The survey (applied in the 2008-2010 period) used a Likert-like questionnaire with eight questions and a 1-to-6 scale, from "totally disagree" to "fully agree." Answers of 428 students were analyzed and indicated overall approval of the blog activity: 86% and 35% of the responses scored 4-to-6 and 6, respectively. Considering the survey results, the high grades obtained by students on their blogs (averaging 8.3 in 2008-2010), and the significant increase in average grades of the clinical biochemistry exam after the beginning of the blog system (from 5.5 in 2007 to 6.4 in 2008-2010), we concluded that blogging activity on biochemistry is a promising tool for boosting active learning. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(3):205-215, 2017. © 2016 The International Union of Biochemistry and Molecular Biology.

Preparation and biological activities of anti-HER2 monoclonal antibodies with fully core-fucosylated homogeneous bi-antennary complex-type glycans.

PubMed

Tsukimura, Wataru; Kurogochi, Masaki; Mori, Masako; Osumi, Kenji; Matsuda, Akio; Takegawa, Kaoru; Furukawa, Kiyoshi; Shirai, Takashi

2017-12-01

Recently, the absence of a core-fucose residue in the N-glycan has been implicated to be important for enhancing antibody-dependent cellular cytotoxicity (ADCC) activity of immunoglobulin G monoclonal antibodies (mAbs). Here, we first prepared anti-HER2 mAbs having two core-fucosylated N-glycan chains with the single G2F, G1aF, G1bF, or G0F structure, together with those having two N-glycan chains with a single non-core-fucosylated corresponding structure for comparison, and determined their biological activities. Dissociation constants of mAbs with core-fucosylated N-glycans bound to recombinant Fcγ-receptor type IIIa variant were 10 times higher than those with the non-core-fucosylated N-glycans, regardless of core glycan structures. mAbs with the core-fucosylated N-glycans had markedly reduced ADCC activities, while those with the non-core-fucosylated N-glycans had high activities. These results indicate that the presence of a core-fucose residue in the N-glycan suppresses the binding to the Fc-receptor and the induction of ADCC of anti-HER2 mAbs.

Quantitative structure-activity relationship study of P2X7 receptor inhibitors using combination of principal component analysis and artificial intelligence methods.

PubMed

Ahmadi, Mehdi; Shahlaei, Mohsen

2015-01-01

P2X7 antagonist activity for a set of 49 molecules of the P2X7 receptor antagonists, derivatives of purine, was modeled with the aid of chemometric and artificial intelligence techniques. The activity of these compounds was estimated by means of combination of principal component analysis (PCA), as a well-known data reduction method, genetic algorithm (GA), as a variable selection technique, and artificial neural network (ANN), as a non-linear modeling method. First, a linear regression, combined with PCA, (principal component regression) was operated to model the structure-activity relationships, and afterwards a combination of PCA and ANN algorithm was employed to accurately predict the biological activity of the P2X7 antagonist. PCA preserves as much of the information as possible contained in the original data set. Seven most important PC's to the studied activity were selected as the inputs of ANN box by an efficient variable selection method, GA. The best computational neural network model was a fully-connected, feed-forward model with 7-7-1 architecture. The developed ANN model was fully evaluated by different validation techniques, including internal and external validation, and chemical applicability domain. All validations showed that the constructed quantitative structure-activity relationship model suggested is robust and satisfactory.

Quantitative structure–activity relationship study of P2X7 receptor inhibitors using combination of principal component analysis and artificial intelligence methods

PubMed Central

Ahmadi, Mehdi; Shahlaei, Mohsen

2015-01-01

P2X7 antagonist activity for a set of 49 molecules of the P2X7 receptor antagonists, derivatives of purine, was modeled with the aid of chemometric and artificial intelligence techniques. The activity of these compounds was estimated by means of combination of principal component analysis (PCA), as a well-known data reduction method, genetic algorithm (GA), as a variable selection technique, and artificial neural network (ANN), as a non-linear modeling method. First, a linear regression, combined with PCA, (principal component regression) was operated to model the structure–activity relationships, and afterwards a combination of PCA and ANN algorithm was employed to accurately predict the biological activity of the P2X7 antagonist. PCA preserves as much of the information as possible contained in the original data set. Seven most important PC's to the studied activity were selected as the inputs of ANN box by an efficient variable selection method, GA. The best computational neural network model was a fully-connected, feed-forward model with 7−7−1 architecture. The developed ANN model was fully evaluated by different validation techniques, including internal and external validation, and chemical applicability domain. All validations showed that the constructed quantitative structure–activity relationship model suggested is robust and satisfactory. PMID:26600858

Soluble microbial products (SMPs) release in activated sludge systems: a review

PubMed Central

2012-01-01

This review discusses the characterization, production and implications of soluble microbial products (SMPs) in biological wastewater treatment. The precise definition of SMPs is open to talk about, but is currently regarded as “the pool of organic compounds that are released into solution from substrate metabolism and biomass decay”'. Some of the SMPs have been identified as humic acids, polysaccharides, proteins, amino acids, antibiotics, extracellular enzymes and structural components of cells and products of energy metabolism. They adversely affect the kinetic activity, flocculating and settling properties of sludge. This review outlines some important findings with regard to biodegradability and treatability of SMPs and also the effect of process parameters on their production. As SMPs are produced during biological treatment process, their trace amounts normally remain in the effluent that defines the highest COD removal efficiency. Their presence in effluent represents a high potential risk of toxic by-product formation during chlorine disinfection. Studies have indicated that among all wastewater post-treatment processes, the adsorption by granular activated carbon combined with biologically induced degradation is the most effective method for removal of SMPs. However, it may be concludes that the knowledge regarding SMPs is still under progress and more work is required to fully understand their contribution to the treatment process. PMID:23369231

Soluble microbial products (SMPs) release in activated sludge systems: a review.

PubMed

Azami, Hamed; Sarrafzadeh, Mohammad Hossein; Mehrnia, Mohammad Reza

2012-12-18

This review discusses the characterization, production and implications of soluble microbial products (SMPs) in biological wastewater treatment. The precise definition of SMPs is open to talk about, but is currently regarded as "the pool of organic compounds that are released into solution from substrate metabolism and biomass decay"'. Some of the SMPs have been identified as humic acids, polysaccharides, proteins, amino acids, antibiotics, extracellular enzymes and structural components of cells and products of energy metabolism. They adversely affect the kinetic activity, flocculating and settling properties of sludge. This review outlines some important findings with regard to biodegradability and treatability of SMPs and also the effect of process parameters on their production. As SMPs are produced during biological treatment process, their trace amounts normally remain in the effluent that defines the highest COD removal efficiency. Their presence in effluent represents a high potential risk of toxic by-product formation during chlorine disinfection. Studies have indicated that among all wastewater post-treatment processes, the adsorption by granular activated carbon combined with biologically induced degradation is the most effective method for removal of SMPs. However, it may be concludes that the knowledge regarding SMPs is still under progress and more work is required to fully understand their contribution to the treatment process.

Simultaneous biological nutrient removal: evaluation of autotrophic denitrification, heterotrophic nitrification, and biological phosphorus removal in full-scale systems.

PubMed

Littleton, Helen X; Daigger, Glen T; Strom, Peter F; Cowan, Robert A

2003-01-01

Simultaneous biological nutrient removal (SBNR) is the biological removal of nitrogen and phosphorus in excess of that required for biomass synthesis in a biological wastewater treatment system without defined anaerobic or anoxic zones. Evidence is growing that significant SBNR can occur in many systems, including the aerobic zone of systems already configured for biological nutrient removal. Although SBNR systems offer several potential advantages, they cannot be fully realized until the mechanisms responsible for SBNR are better understood. Consequently, a research program was initiated with the basic hypothesis that three mechanisms might be responsible for SBNR: the reactor macroenvironment, the floc microenvironment, and novel microorganisms. Previously, the nutrient removal capabilities of seven full-scale, staged, closed-loop bioreactors known as Orbal oxidation ditches were evaluated. Chemical analysis and microbiological observations suggested that SBNR occurred in these systems. Three of these plants were further examined in this research to evaluate the importance of novel microorganisms, especially for nitrogen removal. A screening tool was developed to determine the relative significance of the activities of microorganisms capable of autotrophic denitrification and heterotrophic nitrification-aerobic denitrification in biological nutrient removal systems. The results indicated that novel microorganisms were not substantial contributors to SBNR in the plants studied. Phosphorus metabolism (anaerobic release, aerobic uptake) was also tested in one of the plants. Activity within the mixed liquor that was consistent with current theories for phosphorus-accumulating organisms (PAOs) was observed. Along with other observations, this suggests the presence of PAOs in the facilities studied.

Constitutive nitric oxide synthase activation is a significant route for nitroglycerin-mediated vasodilation

PubMed Central

Bonini, Marcelo G.; Stadler, Krisztian; de Oliveira Silva, Sueli; Corbett, Jean; Dore, Michael; Petranka, John; Fernandes, Denise C.; Tanaka, Leonardo Y.; Duma, Danielle; Laurindo, Francisco R. M.; Mason, Ronald P.

2008-01-01

The physiological effects of nitroglycerin as a potent vasodilator have long been documented. However, the molecular mechanisms by which nitroglycerin exerts its biological functions are still a matter of intense debate. Enzymatic pathways converting nitroglycerin to vasoactive compounds have been identified, but none of them seems to fully account for the reported clinical observations. Here, we demonstrate that nitroglycerin triggers constitutive nitric oxide synthase (NOS) activation, which is a major source of NO responsible for low-dose (1–10 nM) nitroglycerin-induced vasorelaxation. Our studies in cell cultures, isolated vessels, and whole animals identified endothelial NOS activation as a fundamental requirement for nitroglycerin action at pharmacologically relevant concentrations in WT animals. PMID:18562300

ANNUAL REPORT, JULY 1, 1958

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

None

1959-02-01

This annual report of Brookhaven National Laboratory describes its program and activities for the fiscal year 1958. The progress and trends of the research program are presented along with a description of the operational, service, and administrative activities of the Laboratory. The scientific and technical details of the many research and development activities are covered more fully in scientific and technical periodicals and in the quarterly scientific progress reports and other scientiflc reports of the Laboratory. A list of all publications for July 1, 1957 to June 30, 1958, is given. Status and progress are given in fields of physics,more » accelerator development, instrumentation, applied mathematics, chemistry, nuclear engineering, biology, and medical research. (For preceding period see BNL-462.) (W.D.M.)« less

Soft bio-integrated systems for continuous health monitoring

NASA Astrophysics Data System (ADS)

Raj, M.; Wei, P. H.; Morey, B.; Wang, X.; Keen, B.; DePetrillo, P.; Hsu, Y. Y.; Ghaffari, R.

2014-06-01

Electronically-enabled wearable systems that monitor physiological activity and electrophysiological activity hold the key to truly personalized medical care outside of the hospital setting. However, fundamental technical challenges exist in achieving medical systems that are comfortable, unobtrusive and fully integrated without external connections to bench top instruments. In particular, there is a fundamental mismatch in mechanical coupling between existing classes of rigid electronics and soft biological substrates, like the skin. Here we describe new mechanical and electrical design strategies for wearable devices with mechanical properties that approach that of biological tissue. These systems exploit stretchable networks of conformal sensors (i.e. electrodes, temperature sensors, and accelerometers) and associated circuitry (i.e. microcontroller, memory, voltage regulators, rechargeable battery, wireless communication modules) embedded in ultrathin, elastomeric substrates. Quantitative analyses of sensor performance and mechanics under tensile and torsional stresses illustrate the ability to mechanically couple with soft tissues in a way that is mechanically invisible to the user. Representative examples of these soft biointegrated systems can be applied for continuous sensing of muscle and movement activity in the home and ambulatory settings.

Mechanics of active surfaces

NASA Astrophysics Data System (ADS)

Salbreux, Guillaume; Jülicher, Frank

2017-09-01

We derive a fully covariant theory of the mechanics of active surfaces. This theory provides a framework for the study of active biological or chemical processes at surfaces, such as the cell cortex, the mechanics of epithelial tissues, or reconstituted active systems on surfaces. We introduce forces and torques acting on a surface, and derive the associated force balance conditions. We show that surfaces with in-plane rotational symmetry can have broken up-down, chiral, or planar-chiral symmetry. We discuss the rate of entropy production in the surface and write linear constitutive relations that satisfy the Onsager relations. We show that the bending modulus, the spontaneous curvature, and the surface tension of a passive surface are renormalized by active terms. Finally, we identify active terms which are not found in a passive theory and discuss examples of shape instabilities that are related to active processes in the surface.

Multiscale mechanobiology: computational models for integrating molecules to multicellular systems

PubMed Central

Mak, Michael; Kim, Taeyoon

2015-01-01

Mechanical signals exist throughout the biological landscape. Across all scales, these signals, in the form of force, stiffness, and deformations, are generated and processed, resulting in an active mechanobiological circuit that controls many fundamental aspects of life, from protein unfolding and cytoskeletal remodeling to collective cell motions. The multiple scales and complex feedback involved present a challenge for fully understanding the nature of this circuit, particularly in development and disease in which it has been implicated. Computational models that accurately predict and are based on experimental data enable a means to integrate basic principles and explore fine details of mechanosensing and mechanotransduction in and across all levels of biological systems. Here we review recent advances in these models along with supporting and emerging experimental findings. PMID:26019013

Bioculture System Validation

NASA Technical Reports Server (NTRS)

Sato, Kevin Y.

2012-01-01

The Bioculture System first flight will be to validate the performance of the hardware and its automated and manual operational capabilities in the space flight environment of the International Space Station. Biology, Engineering, and Operations tests will be conducted in the Bioculture System fully characterize its automated and manual functions to support cell culturing for short and long durations. No hypothesis-driven research will be conducted with biological sample, and the science leads have all provided their concurrence that none of the data they collect will be considered as proprietary and can be free distributed to the science community. The outcome of the validation flight will be to commission the hardware for use by the science community. This presentation will provide non-proprietary details about the Bioculture System and information about the activities for the first flight.

Entamoeba histolytica: a snapshot of current research and methods for genetic analysis

PubMed Central

Morf, Laura; Singh, Upinder

2012-01-01

Entamoeba histolytica represents one of the leading causes of parasitic death worldwide. Although identified as the causative agent of amebiasis since 1875, the molecular mechanisms by which the parasite causes disease are still not fully understood. Studying Entamoeba reveals insights into a eukaryotic cell that differs in many ways from better-studied model organisms. Thus, much can be learned from this protozoan parasite on evolution, cell biology and RNA biology. In this review we discuss selected research highlights in Entamoeba research and focus on the development of molecular biological techniques to study this pathogen. We end by highlighting some of the many questions that remain to be answered in order to fully understand this important human pathogen. PMID:22664276

Effect of guaianolides in the meiosis reinitiation of amphibian oocytes.

PubMed

Zapata-Martínez, J; Sánchez-Toranzo, G; Chaín, F; Catalán, C A N; Bühler, M I

2017-02-01

Sesquiterpene lactones (STLs) are a large and structurally diverse group of plant metabolites generally found in the Asteraceae family. STLs exhibit a wide spectrum of biological activities and it is generally accepted that their major mechanism of action is the alkylation of the thiol groups of biological molecules. The guaianolides is one of various groups of STLs. Anti-tumour and anti-migraine effects, an allergenic agent, an inhibitor of smooth muscle cells and of meristematic cell proliferation are only a few of the most commonly reported activities of STLs. In amphibians, fully grown ovarian oocytes are arrested at the beginning of meiosis I. Under stimulus with progesterone, this meiotic arrest is released and meiosis progresses to metaphase II, a process known as oocyte maturation. There are previous records of the inhibitory effect of dehydroleucodin (DhL), a guaianolide lactone, on the progression of meiosis. It has been also shown that DhL and its 11,13-dihydroderivative (2H-DhL; a mixture of epimers at C-11) act as blockers of the resumption of meiosis in fully grown ovarian oocytes from the amphibian Rhinella arenarum (formerly classified as Bufo arenarum). The aim of this study was to analyze the effect of four closely related guaianolides, i.e., DhL, achillin, desacetoxymatricarin and estafietin as possible inhibitors of meiosis in oocytes of amphibians in vitro and discuss some structure-activity relationships. It was found that the inhibitory effect on meiosis resumption is greater when the lactone has two potentially reactive centres, either a α,β-α',β'-diunsaturated cyclopentanone moiety or an epoxide group plus an exo-methylene-γ-lactone function.

Influence of chemical peeling on the skin stress response system.

PubMed

Kimura, Ayako; Kanazawa, Nobuo; Li, Hong-Jin; Yonei, Nozomi; Yamamoto, Yuki; Furukawa, Fukumi

2012-07-01

Skin stress response system (SSRS) involves corticotropin-releasing hormone (CRH) and proopiomelanocortin (POMC)-derived peptides, such as adrenocorticotropic hormone (ACTH), a-melanocyte-stimulating hormone (MSH) and b-endorphin that are locally generated in response to locally provided stressors or proinflammatory cytokines. This system would restrict tissue damage and restore local homoeostasis. Trichloroacetic acid (TCA) is one of the most widely used peeling agents and applied for cosmetic treatment of photodamaged skin. However, the biological mechanism responsible for TCA peeling has yet to be fully determined. While our investigation focused on the inflammation and wound healing pathways, in the recent study, we have examined involvement of the SSRS as the third pathway. Mostly depending on our findings that TCA peeling activates the SSRS by inducing the POMC expression of keratinocytes in the CRH-independent manner, together with the results reported by other researchers, we can say that the biological effect of POMC seems to be responsible for the TCA-induced epidermal SSRS activation. © 2012 John Wiley & Sons A/S.

Multi-scale Observation of Biological Interactions of Nanocarriers: from Nano to Macro

PubMed Central

Jin, Su-Eon; Bae, Jin Woo; Hong, Seungpyo

2010-01-01

Microscopic observations have played a key role in recent advancements in nanotechnology-based biomedical sciences. In particular, multi-scale observation is necessary to fully understand the nano-bio interfaces where a large amount of unprecedented phenomena have been reported. This review describes how to address the physicochemical and biological interactions of nanocarriers within the biological environments using microscopic tools. The imaging techniques are categorized based on the size scale of detection. For observation of the nano-scale biological interactions of nanocarriers, we discuss atomic force microscopy (AFM), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). For the micro to macro-scale (in vitro and in vivo) observation, we focus on confocal laser scanning microscopy (CLSM) as well as in vivo imaging systems such as magnetic resonance imaging (MRI), superconducting quantum interference devices (SQUIDs), and IVIS®. Additionally, recently developed combined techniques such as AFM-CLSM, correlative Light and Electron Microscopy (CLEM), and SEM-spectroscopy are also discussed. In this review, we describe how each technique helps elucidate certain physicochemical and biological activities of nanocarriers such as dendrimers, polymers, liposomes, and polymeric/inorganic nanoparticles, thus providing a toolbox for bioengineers, pharmaceutical scientists, biologists, and research clinicians. PMID:20232368

A 92-kDa human immunostimulatory protein.

PubMed Central

Fontan, E; Briend, E; Saklani-Jusforgues, H; d'Alayer, J; Vandekerckhove, J; Fauve, R M

1994-01-01

We purified to apparent homogeneity a human urinary glycoprotein of 92 kDa (HGP.92) that, administered intravenously at 250 micrograms/kg, fully protected mice against a lethal inoculum of Listeria monocytogenes. Since HGP.92 protected scid mice, which lack B and T lymphocytes, this increased resistance to Listeria did not appear to be lymphocyte mediated. Furthermore, inflammatory macrophages incubated with 6 nM HGP.92 inhibited the growth of Lewis carcinoma cells in vitro. These two activities appeared to depend on an oligosaccharide moiety, as they were lost after N-Glycanase treatment of HGP.92. Thus, the biological activity of HGP.92 was in some way related to a glycan moiety. Images PMID:8078887

Peptide-chaperone-directed transdermal protein delivery requires energy.

PubMed

Ruan, Renquan; Jin, Peipei; Zhang, Li; Wang, Changli; Chen, Chuanjun; Ding, Weiping; Wen, Longping

2014-11-03

The biologically inspired transdermal enhanced peptide TD1 has been discovered to specifically facilitate transdermal delivery of biological macromolecules. However, the biological behavior of TD1 has not been fully defined. In this study, we find that energy is required for the TD1-mediated transdermal protein delivery through rat and human skins. Our results show that the permeation activity of TD1-hEGF, a fusion protein composed of human epidermal growth factor (hEGF) and the TD1 sequence connected with a glycine-serine linker (GGGGS), can be inhibited by the energy inhibitor, rotenone or oligomycin. In addition, adenosine triphosphate (ATP), the essential energetic molecule in organic systems, can effectively facilitate the TD1 directed permeation of the protein-based drug into the skin in a dose-dependent fashion. Our results here demonstrate a novel energy-dependent permeation process during the TD1-mediated transdermal protein delivery that could be valuable for the future development of promising new transdermal drugs.

New functions and signaling mechanisms for the class of adhesion G protein–coupled receptors

PubMed Central

Liebscher, Ines; Ackley, Brian; Araç, Demet; Ariestanti, Donna M.; Aust, Gabriela; Bae, Byoung-il; Bista, Bigyan R.; Bridges, James P.; Duman, Joseph G.; Engel, Felix B.; Giera, Stefanie; Goffinet, André M.; Hall, Randy A.; Hamann, Jörg; Hartmann, Nicole; Lin, Hsi-Hsien; Liu, Mingyao; Luo, Rong; Mogha, Amit; Monk, Kelly R.; Peeters, Miriam C.; Prömel, Simone; Ressl, Susanne; Schiöth, Helgi B.; Sigoillot, Séverine M.; Song, Helen; Talbot, William S.; Tall, Gregory G.; White, James P.; Wolfrum, Uwe; Xu, Lei; Piao, Xianhua

2014-01-01

The class of adhesion G protein–coupled receptors (aGPCRs), with 33 human homologs, is the second largest family of GPCRs. In addition to a seven-transmembrane α-helix—a structural feature of all GPCRs—the class of aGPCRs is characterized by the presence of a large N-terminal extracellular region. In addition, all aGPCRs but one (GPR123) contain a GPCR autoproteolysis–inducing (GAIN) domain that mediates autoproteolytic cleavage at the GPCR autoproteolysis site (GPS) motif to generate N- and a C-terminal fragments (NTF and CTF, respectively) during protein maturation. Subsequently, the NTF and CTF are associated non-covalently as a heterodimer at the plasma membrane. While the biological function of the GAIN domain–mediated autocleavage is not fully understood, mounting evidence suggests that the NTF and CTF possess distinct biological activities in addition to their function as a receptor unit. We discuss recent advances in understanding the biological functions, signaling mechanisms, and disease associations of the aGPCRs. PMID:25424900

Review on fate and mechanism of removal of pharmaceutical pollutants from wastewater using biological approach.

PubMed

Tiwari, Bhagyashree; Sellamuthu, Balasubramanian; Ouarda, Yassine; Drogui, Patrick; Tyagi, Rajeshwar D; Buelna, Gerardo

2017-01-01

Due to research advancement and discoveries in the field of medical science, maintains and provides better human health and safer life, which lead to high demand for production of pharmaceutical compounds with a concomitant increase in population. These pharmaceutical (biologically active) compounds were not fully metabolized by the body and excreted out in wastewater. This micro-pollutant remains unchanged during wastewater treatment plant operation and enters into the receiving environment via the discharge of treated water. Persistence of pharmaceutical compounds in both surface and ground waters becomes a major concern due to their potential eco-toxicity. Pharmaceuticals (emerging micro-pollutants) deteriorate the water quality and impart a toxic effect on living organisms. Therefore, from last two decades, plenty of studies were conducted on the occurrence, impact, and removal of pharmaceutical residues from the environment. This review provides an overview on the fate and removal of pharmaceutical compounds via biological treatment process. Copyright © 2016 Elsevier Ltd. All rights reserved.

Recent Progress on Piezoelectric and Triboelectric Energy Harvesters in Biomedical Systems

PubMed Central

Zheng, Qiang; Shi, Bojing; Wang, Zhong Lin

2017-01-01

Implantable medical devices (IMDs) have become indispensable medical tools for improving the quality of life and prolonging the patient's lifespan. The minimization and extension of lifetime are main challenges for the development of IMDs. Current innovative research on this topic is focused on internal charging using the energy generated by the physiological environment or natural body activity. To harvest biomechanical energy efficiently, piezoelectric and triboelectric energy harvesters with sophisticated structural and material design have been developed. Energy from body movement, muscle contraction/relaxation, cardiac/lung motions, and blood circulation is captured and used for powering medical devices. Other recent progress in this field includes using PENGs and TENGs for our cognition of the biological processes by biological pressure/strain sensing, or direct intervention of them for some special self‐powered treatments. Future opportunities lie in the fabrication of intelligent, flexible, stretchable, and/or fully biodegradable self‐powered medical systems for monitoring biological signals and treatment of various diseases in vitro and in vivo. PMID:28725529

Isolation, structures, and structure - cytotoxic activity relationships of withanolides and physalins from Physalis angulata.

PubMed

Damu, Amooru G; Kuo, Ping-Chung; Su, Chung-Ren; Kuo, Tsung-Hsiao; Chen, Tzu-Hsuan; Bastow, Kenneth F; Lee, Kuo-Hsiung; Wu, Tian-Shung

2007-07-01

Phytochemical investigation of Physalis angulata was initiated following primary biological screening. Fractionation of CHCl3 and n-BuOH solubles of the MeOH extract from the whole plant was guided by in vitro cytotoxic activity assay using cultured HONE-1 and NUGC cells and led to the isolation of seven new withanolides, withangulatins B-H (1-7), and a new minor physalin, physalin W (8), along with 14 known compounds, including physaprun A, withaphysanolide, dihydrowithanolide E, physanolide A, withaphysalin A, and physalins B, D, F, G, I, J, T, U, and V. New compounds (1-8) were fully characterized by a combination of spectroscopic methods (1D and 2D NMR and MS) and the relative stereochemical assignments based on NOESY correlations and analysis of coupling constants. Biological evaluation of these compounds against a panel of human cancer cell lines showed broad cytotoxic activity. Withangulatin B (1) and physalins D (10) and F (11) displayed potent cytotoxic activity against a panel of human cancer cell lines with EC50 values ranging from 0.2 to 1.6 microg/mL. Structure-activity relationship analysis indicated that withanolides and physalins with 4beta-hydroxy-2-en-1-one and 5beta,6beta-epoxy moieties are potential cytotoxic agents.

Trust, Growth Mindset, and Student Commitment to Active Learning in a College Science Course.

PubMed

Cavanagh, Andrew J; Chen, Xinnian; Bathgate, Meghan; Frederick, Jennifer; Hanauer, David I; Graham, Mark J

2018-01-01

There is growing consensus regarding the effectiveness of active-learning pedagogies in college science courses. Less is known about ways that student-level factors contribute to positive outcomes in these contexts. The present study examines students' ( N = 245) trust in the instructor-defined as perceptions of their instructor's understanding, acceptance, and care-and students' attitudes toward learning within an anatomy and physiology course featuring active learning. Analyses indicate that student trust of instructor and students' views of their own intelligence are both associated with student commitment to, and engagement in, active learning. Student-reported trust of the instructor corresponded to final grade, while students' views of their own intelligence did not. In an active-learning context in which students are more fully engaged in the learning process, student trust of the instructor was an important contributor to desired student outcomes. © 2018 A. J. Cavanagh et al. CBE—Life Sciences Education © 2018 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Mapping sites of aspirin-induced acetylations in live cells by quantitative acid-cleavable activity-based protein profiling (QA-ABPP)

PubMed Central

Wang, Jigang; Zhang, Chong-Jing; Zhang, Jianbin; He, Yingke; Lee, Yew Mun; Chen, Songbi; Lim, Teck Kwang; Ng, Shukie; Shen, Han-Ming; Lin, Qingsong

2015-01-01

Target-identification and understanding of mechanism-of-action (MOA) are challenging for development of small-molecule probes and their application in biology and drug discovery. For example, although aspirin has been widely used for more than 100 years, its molecular targets have not been fully characterized. To cope with this challenge, we developed a novel technique called quantitative acid-cleavable activity-based protein profiling (QA-ABPP) with combination of the following two parts: (i) activity-based protein profiling (ABPP) and iTRAQ™ quantitative proteomics for identification of target proteins and (ii) acid-cleavable linker-based ABPP for identification of peptides with specific binding sites. It is known that reaction of aspirin with its target proteins leads to acetylation. We thus applied the above technique using aspirin-based probes in human cancer HCT116 cells. We identified 1110 target proteins and 2775 peptides with exact acetylation sites. By correlating these two sets of data, 523 proteins were identified as targets of aspirin. We used various biological assays to validate the effects of aspirin on inhibition of protein synthesis and induction of autophagy which were elicited from the pathway analysis of Aspirin target profile. This technique is widely applicable for target identification in the field of drug discovery and biology, especially for the covalent drugs. PMID:25600173

NOVEL CERAMIC MEMBRANE BIOREACTOR FOR LOW-FLOW SYSTEMS - PHASE I

EPA Science Inventory

Improved low-flow (50,000 gallons per day) sanitary wastewater treatment systems are needed. CeraMem Corporation's proposed approach includes a membrane bioreactor (MBR) using fully proven biological processes for biological oxygen demand oxidation and (optionally) fo...

Effects of a biologic agent in a patient with rheumatoid arthritis after treatment for methotrexate-associated B-cell lymphoma: a case report.

PubMed

Kuroda, Takeshi; Sato, Hiroe; Nakatsue, Takeshi; Wada, Yoko; Murakami, Shuichi; Nakano, Masaaki; Narita, Ichiei

2014-04-11

Several studies have suggested an increased risk of malignant tumor in patients with rheumatoid arthritis. It has been also reported that rheumatoid arthritis patients have a high incidence of lymphoma compared with the general population, and that patients receiving methotrexate, which is the anchor drug for rheumatoid arthritis treatment, can develop lymphoproliferative disease. Nevertheless, management of rheumatoid arthritis after treatment for methotrexate-associated lymphoma has not been fully investigated. We here report a patient with rheumatoid arthritis who developed malignant lymphoma associated with methotrexate therapy. Moreover, we describe the use of a biologic agent for a rheumatoid arthritis patient after treatment for lymphoma associated with methotrexate. A 60-year-old Japanese man with a 20-year history of rheumatoid arthritis was admitted to our hospital with a left inguinal tumor. Open biopsy was performed and a biopsy specimen revealed diffuse large B-cell lymphoma. As our patient had received methotrexate for 4 years, we diagnosed the lymphoproliferative disease as being methotrexate-related. This lymphoma was not associated with Epstein- Barr virus by Epstein-Barr virus-encoded ribonucleic acid in-situ hybridization, but this patient was an Epstein-Barr virus carrier, regarding serological testing. The lymphoma went into complete remission after 6 courses of rituximab plus cyclophosphamide, hydroxydaunorubicin, vincristine, and prednisone/prednisolone therapy. Two years later, however, rheumatoid arthritis activity gradually increased and was not controlled with salazosulfapyridine. Etanercept was administered in view of its possible effect on B-cells, and this reduced the level of disease activity without recurrence of lymphoma. The management of rheumatoid arthritis after treatment for methotrexate-associated lymphoma has not been fully investigated yet. Etanercept appeared to be safe because of its B-cell effect, but further observation is necessary to make a firm conclusion. Further accumulation of cases is needed to clarify which biologics are safe and effective for treatment of methotrexate-associated B-cell lymphoma.

Thieno[3,2-b]- and thieno[2,3-b]pyrrole bioisosteric analogues of the hallucinogen and serotonin agonist N,N-dimethyltryptamine.

PubMed

Blair, J B; Marona-Lewicka, D; Kanthasamy, A; Lucaites, V L; Nelson, D L; Nichols, D E

1999-03-25

The synthesis and biological activity of 6-[2-(N, N-dimethylamino)ethyl]-4H-thieno[3,2-b]pyrrole (3a) and 4-[2-(N, N-dimethylamino)ethyl]-6H-thieno[2,3-b]pyrrole (3b), thienopyrroles as potential bioisosteres of N,N-dimethyltryptamine (1a), are reported. Hallucinogen-like activity was evaluated in the two-lever drug discrimination paradigm using LSD- and DOI-trained rats. Neither 3a nor 3b substituted for LSD or DOI up to doses of 50 micromol/kg. By comparison, 1a fully substituted in LSD-trained rats. However, 3a and 3b fully substituted for the 5-HT1A agonist LY293284 ((-)-(4R)-6-acetyl-4-(di-n-propylamino)-1,3,4, 5-tetrahydrobenz[c,d]indole). Both 3a and 3b induced a brief "serotonin syndrome" and salivation, an indication of 5-HT1A receptor activation. At the cloned human 5-HT2A receptor 3b had about twice the affinity of 3a. At the cloned human 5-HT2B and 5-HT2C receptors, however, 3a had about twice the affinity of 3b. Therefore, thiophene lacks equivalence as a replacement for the phenyl ring in the indole nucleus of tryptamines that bind to 5-HT2 receptor subtypes and possess LSD-like behavioral effects. Whereas both of the thienopyrroles had lower affinity than the corresponding 1a at 5-HT2 receptors, 3a and 3b had significantly greater affinity than 1a at the 5-HT1A receptor. Thus, thienopyrrole does appear to serve as a potent bioisostere for the indole nucleus in compounds that bind to the serotonin 5-HT1A receptor. These differences in biological activity suggest that serotonin receptor isoforms are very sensitive to subtle changes in the electronic character of the aromatic systems of indole compounds.

Investigating habits: strategies, technologies and models

PubMed Central

Smith, Kyle S.; Graybiel, Ann M.

2014-01-01

Understanding habits at a biological level requires a combination of behavioral observations and measures of ongoing neural activity. Theoretical frameworks as well as definitions of habitual behaviors emerging from classic behavioral research have been enriched by new approaches taking account of the identification of brain regions and circuits related to habitual behavior. Together, this combination of experimental and theoretical work has provided key insights into how brain circuits underlying action-learning and action-selection are organized, and how a balance between behavioral flexibility and fixity is achieved. New methods to monitor and manipulate neural activity in real time are allowing us to have a first look “under the hood” of a habit as it is formed and expressed. Here we discuss ideas emerging from such approaches. We pay special attention to the unexpected findings that have arisen from our own experiments suggesting that habitual behaviors likely require the simultaneous activity of multiple distinct components, or operators, seen as responsible for the contrasting dynamics of neural activity in both cortico-limbic and sensorimotor circuits recorded concurrently during different stages of habit learning. The neural dynamics identified thus far do not fully meet expectations derived from traditional models of the structure of habits, and the behavioral measures of habits that we have made also are not fully aligned with these models. We explore these new clues as opportunities to refine an understanding of habits. PMID:24574988

Combined analytical approaches to define biodistribution and biological activity of semi-synthetic berberrubine, the active metabolite of natural berberine.

PubMed

Porru, Emanuele; Franco, Placido; Calabria, Donato; Spinozzi, Silvia; Roberti, Marinella; Caliceti, Cristiana; Roda, Aldo

2018-06-01

Berberine (BBR) is a natural alkaloid obtained from Berberis species plants, known for its protective effects against several diseases. Among the primary BBR metabolites, berberrubine (M1) showed the highest plasma concentration but few and conflicting data are available regarding its concentration in biological fluids related to its new potential activity on vascular cells. A combined analytical approach was applied to study biodistribution of M1 in comparison with BBR. The optimization of sample clean-up combined with a fully validated HPLC-ESI-MS/MS tailored for M1 allows sufficient detectability and accuracy to be reached in the different studied organs even when administered at low dose, comparable to that assumed by human. A predictive human vascular endothelial cell-based assay to measure intracellular xanthine oxidase has been developed and applied to study unexplored activities of M1 alongside other common activities. Results showed that oral M1 treatment exhibits higher plasma levels than BBR, reaching maximum concentration 400-fold higher than BBR (204 vs 0.5 ng/mL); moreover, M1 exhibits higher concentrations than BBR also in all the biological compartments analyzed. Noteworthy, the two compounds follow two different excretion routes: M1 through urine, while BBR through feces. In vitro studies demonstrated that M1 inhibited intracellular xanthine oxidase activity, one of the major sources of reactive oxygen species in vasculature, with an IC50 = 9.90 ± 0.01 μg/mL and reduced the expression of the inflammatory marker ICAM-1. These peculiar characteristics allow new perspectives to be opened up for the direct use of M1 instead of BBR in endothelial dysfunction treatment.

Medicinal chemistry and pharmacology of genus Tripterygium (Celastraceae)

PubMed Central

Brinker, Anita M.; Ma, Jun; Lipsky, Peter E.; Raskin, Ilya

2013-01-01

Plants in the genus Tripterygium, such as Tripterygium wilfordii Hook. f., have a long history of use in traditional Chinese medicine. In recent years there has been considerable interest in the use of Tripterygium extracts and of the main bioactive constituent, the diterpene triepoxide triptolide (1), to treat a variety of autoimmune and inflammation-related conditions. The main mode of action of the Tripterygium extracts and triptolide (1) is the inhibition of expression of proinflammatory genes such as those for interleukin-2 (IL-2), inducible nitric oxide synthase (iNOS), tumor necrosis factor-α (TNF-α), cyclooxygenase-2 (COX-2) and interferon-gamma (IFN-γ). The efficacy and safety of certain types of Tripterygium extracts were confirmed in human clinical trials in the US and abroad. Over 300 compounds have been identified in the genus Tripterygium, and many of these have been evaluated for biological activity. The overall activity of the extract is based on the interaction between its components. Therefore, the safety and efficacy of the extract cannot be fully mimicked by any individual constituent. This review discusses the biochemical composition and biological and pharmacological activities of Tripterygium extracts, and their main bioactive components. PMID:17250858

Medicinal chemistry and pharmacology of genus Tripterygium (Celastraceae).

PubMed

Brinker, Anita M; Ma, Jun; Lipsky, Peter E; Raskin, Ilya

2007-03-01

Plants in the genus Tripterygium, such as Tripterygium wilfordii Hook.f., have a long history of use in traditional Chinese medicine. In recent years there has been considerable interest in the use of Tripterygium extracts and of the main bioactive constituent, the diterpene triepoxide triptolide (1), to treat a variety of autoimmune and inflammation-related conditions. The main mode of action of the Tripterygium extracts and triptolide (1) is the inhibition of expression of proinflammatory genes such as those for interleukin-2 (IL-2), inducible nitric oxide synthase (iNOS), tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase-2 (COX-2) and interferon-gamma (IFN-gamma). The efficacy and safety of certain types of Tripterygium extracts were confirmed in human clinical trials in the US and abroad. Over 300 compounds have been identified in the genus Tripterygium, and many of these have been evaluated for biological activity. The overall activity of the extract is based on the interaction between its components. Therefore, the safety and efficacy of the extract cannot be fully mimicked by any individual constituent. This review discusses the biochemical composition and biological and pharmacological activities of Tripterygium extracts, and their main bioactive components.

Canatoxin, a toxic protein from jack beans (Canavalia ensiformis), is a variant form of urease (EC 3.5.1.5): biological effects of urease independent of its ureolytic activity.

PubMed Central

Follmer, C; Barcellos, G B; Zingali, R B; Machado, O L; Alves, E W; Barja-Fidalgo, C; Guimarães, J A; Carlini, C R

2001-01-01

Canatoxin is a toxic protein from Canavalia ensiformis seeds, lethal to mice (LD(50)=2 mg/kg) and insects. Further characterization of canatoxin showed that its main native form (184 kDa) is a non-covalently linked dimer of a 95 kDa polypeptide containing zinc and nickel. Partial sequencing of internal peptides indicated homology with urease (EC 3.5.1.5) from the same seed. Canatoxin has approx. 30% of urease's activity for urea, and K(m) of 2-7 mM. The proteins differ in their affinities for metal ions and were separated by affinity chromatography on a Zn(2+) matrix. Similar to canatoxin, urease activates blood platelets and interacts with glycoconjugates. In contrast with canatoxin, no lethality was seen in mice injected with urease (10 mg/kg). Pretreatment with p-hydroxymercuribenzoate irreversibly abolished the ureolytic activity of both proteins. On the other hand, p-hydroxymercuribenzoate-treated canatoxin was still lethal to mice, and both treated proteins were fully active in promoting platelet aggregation and binding to glycoconjugates. Taken together, our data indicate that canatoxin is a variant form of urease. Moreover, we show for the first time that these proteins display several biological effects that are unrelated to their enzymic activity for urea. PMID:11696010

Interleukin-17 inhibitors. A new era in treatment of psoriasis and other skin diseases.

PubMed

Wasilewska, Agnieszka; Winiarska, Marta; Olszewska, Małgorzata; Rudnicka, Lidia

2016-08-01

Psoriasis is a chronic skin disease caused by the excessive secretion of inflammatory cytokines. Available therapeutic options include biologic drugs such as tumor necrosis factor alpha inhibitors and interleukin 12/23 (IL-12/23) inhibitors. The recent discovery of IL-17, which contributes to development of psoriasis, opened new possibilities for further treatment modalities. Currently, one anti-IL17 biological agent is approved for the treatment - a fully human monoclonal antibody that targets IL-17A (secukinumab). Further clinical trials, including a humanized IgG4 specific for IL-17 (ixekizumab) and a fully human antibody that targets the IL-17 receptor A (brodalumab).

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.

Getting Beyond Getting Ready for Pandemic Influenza

DTIC Science & Technology

2009-01-01

more information, see: http://homeland.house.gov/Hearings/index.asp?ID=89. “…Emerging biological threats such as pandemic influenza or weaponized ...which we have no immediately available cure. Work is clearly underway to prepare for such a biological event.10 However, despite the fact that...Nation to fully withstand the impact of such a devastating widespread biological event. Pandemic influenza would destroy the security of our

Analysis of Cell Biomechanics Response to Gravity:A Fluids for Biology Study Utilizing NASA Glenns Zero Gravity Research Facility

NASA Technical Reports Server (NTRS)

Bomani, Bilal M. M.; Kassemi, Mohammad; Neumann, Eric S.

2016-01-01

It remains unclear how biological cells sense and respond to gravitational forces. Leading scientists state that a large gap exists in the understanding of physiological and molecular adaptation that occurs as biology enters the spaceflight realm. We are seeking a method to fully understand how cells sense microgravity/gravity and what triggers their response.

Biocharts: a visual formalism for complex biological systems

PubMed Central

Kugler, Hillel; Larjo, Antti; Harel, David

2010-01-01

We address one of the central issues in devising languages, methods and tools for the modelling and analysis of complex biological systems, that of linking high-level (e.g. intercellular) information with lower-level (e.g. intracellular) information. Adequate ways of dealing with this issue are crucial for understanding biological networks and pathways, which typically contain huge amounts of data that continue to grow as our knowledge and understanding of a system increases. Trying to comprehend such data using the standard methods currently in use is often virtually impossible. We propose a two-tier compound visual language, which we call Biocharts, that is geared towards building fully executable models of biological systems. One of the main goals of our approach is to enable biologists to actively participate in the computational modelling effort, in a natural way. The high-level part of our language is a version of statecharts, which have been shown to be extremely successful in software and systems engineering. The statecharts can be combined with any appropriately well-defined language (preferably a diagrammatic one) for specifying the low-level dynamics of the pathways and networks. We illustrate the language and our general modelling approach using the well-studied process of bacterial chemotaxis. PMID:20022895

Pattern Formation

NASA Astrophysics Data System (ADS)

Hoyle, Rebecca

2006-03-01

From the stripes of a zebra and the spots on a leopard's back to the ripples on a sandy beach or desert dune, regular patterns arise everywhere in nature. The appearance and evolution of these phenomena has been a focus of recent research activity across several disciplines. This book provides an introduction to the range of mathematical theory and methods used to analyse and explain these often intricate and beautiful patterns. Bringing together several different approaches, from group theoretic methods to envelope equations and theory of patterns in large-aspect ratio-systems, the book also provides insight behind the selection of one pattern over another. Suitable as an upper-undergraduate textbook for mathematics students or as a fascinating, engaging, and fully illustrated resource for readers in physics and biology, Rebecca Hoyle's book, using a non-partisan approach, unifies a range of techniques used by active researchers in this growing field. Accessible description of the mathematical theory behind fascinating pattern formation in areas such as biology, physics and materials science Collects recent research for the first time in an upper level textbook Features a number of exercises - with solutions online - and worked examples

Expression from cloned DNA of biologically active glycoprotein C of herpes simplex virus type 1 in mammalian cells.

PubMed

Ghosh-Choudhury, N; Butcher, M; Ghosh, H P

1990-03-01

A DNA fragment of the herpes simplex virus type 1 genome encoding glycoprotein C (gC-1) has been cloned into different eukaryotic expression vectors for transient and stable expression of the glycoprotein in a number of cell lines. All of these expression vectors use a non-HSV promoter, such as the adenovirus major late promoter or murine leukemia virus long terminal repeat promoter to express gC-1 in COS and CHO cells or 3T3 cells. The gC-1 protein synthesized was fully glycosylated with both N- and O-linked oligosaccharides. Synthesis of the mature 120K gC-1 glycoprotein involved partially glycosylated 100K and 105K proteins and the non-glycosylated 70K protein as intermediate molecules. Immunofluorescence studies showed that the expressed gC-1 was localized intracellularly in the nuclear envelope as well as on the cell surface. The expressed gC-1 was biologically active and could act as a receptor for the complement component C3b in the absence of other HSV proteins.

Real-time functional imaging for monitoring miR-133 during myogenic differentiation.

PubMed

Kato, Yoshio; Miyaki, Shigeru; Yokoyama, Shigetoshi; Omori, Shin; Inoue, Atsushi; Horiuchi, Machiko; Asahara, Hiroshi

2009-11-01

MicroRNAs (miRNAs) are a class of non-coding small RNAs that act as negative regulators of gene expression through sequence-specific interactions with the 3' untranslated regions (UTRs) of target mRNA and play various biological roles. miR-133 was identified as a muscle-specific miRNA that enhanced the proliferation of myoblasts during myogenic differentiation, although its activity in myogenesis has not been fully characterized. Here, we developed a novel retroviral vector system for monitoring muscle-specific miRNA in living cells by using a green fluorescent protein (GFP) that is connected to the target sequence of miR-133 via the UTR and a red fluorescent protein for normalization. We demonstrated that the functional promotion of miR-133 during myogenesis is visualized by the reduction of GFP carrying the miR-133 target sequence, suggesting that miR-133 specifically down-regulates its targets during myogenesis in accordance with its expression. Our cell-based miRNA functional assay monitoring miR-133 activity should be a useful tool in elucidating the role of miRNAs in various biological events.

Functionally-interdependent shape-switching nanoparticles with controllable properties

PubMed Central

Halman, Justin R.; Satterwhite, Emily; Roark, Brandon; Chandler, Morgan; Viard, Mathias; Ivanina, Anna; Bindewald, Eckart; Kasprzak, Wojciech K.; Panigaj, Martin; Bui, My N.; Lu, Jacob S.; Miller, Johann; Khisamutdinov, Emil F.; Shapiro, Bruce A.; Dobrovolskaia, Marina A.

2017-01-01

Abstract We introduce a new concept that utilizes cognate nucleic acid nanoparticles which are fully complementary and functionally-interdependent to each other. In the described approach, the physical interaction between sets of designed nanoparticles initiates a rapid isothermal shape change which triggers the activation of multiple functionalities and biological pathways including transcription, energy transfer, functional aptamers and RNA interference. The individual nanoparticles are not active and have controllable kinetics of re-association and fine-tunable chemical and thermodynamic stabilities. Computational algorithms were developed to accurately predict melting temperatures of nanoparticles of various compositions and trace the process of their re-association in silico. Additionally, tunable immunostimulatory properties of described nanoparticles suggest that the particles that do not induce pro-inflammatory cytokines and high levels of interferons can be used as scaffolds to carry therapeutic oligonucleotides, while particles with strong interferon and mild pro-inflammatory cytokine induction may qualify as vaccine adjuvants. The presented concept provides a simple, cost-effective and straightforward model for the development of combinatorial regulation of biological processes in nucleic acid nanotechnology. PMID:28108656

Phenolics from Winemaking By-Products Better Decrease VLDL-Cholesterol and Triacylglycerol Levels than Those of Red Wine in Wistar Rats.

PubMed

de Oliveira, Walkia Polliana; Biasoto, Aline Camarão Telles; Marques, Valquíria Fernanda; Dos Santos, Ieda Maria; Magalhães, Kedma; Correa, Luiz Claudio; Negro-Dellacqua, Melissa; Miranda, Maria Spínola; de Camargo, Adriano Costa; Shahidi, Fereidoon

2017-10-01

Winemaking by-products account for more than 30% of the grape production, but this inexpensive feedstock has not yet been fully exploited. Accordingly, we evaluated the potential biological activity of winemaking by-products produced with Syrah grapes in comparison with those of the wine produced using the same grape cultivar. Winemaking by-products showed higher contents of total anthocyanins, flavonols, stilbenes, and flavanols than red wine as evaluated by HPLC-DAD-FD (on a dry weight basis). In contrast, red wine was a better source of phenolic acids. However, the contribution of phenolic acids was minor for both samples. Furthermore, equivalent concentration of winemaking by-products (100 mg/kg/d) showed greater biological activity by than that of red wine by decreasing the levels of VLDL-cholesterol and triacylglycerols in Wistar rats. Therefore, this study supports the use of winemaking by-products as an economical source of bioactive phenolics with potential use in the food and nutraceutical industries. © 2017 Institute of Food Technologists®.

Development and implementation of coral reef biocriteria in U.S. jurisdictions.

PubMed

Bradley, Patricia; Fisher, William S; Bell, Heidi; Davis, Wayne; Chan, Valerie; LoBue, Charles; Wiltse, Wendy

2009-03-01

Coral reefs worldwide are declining at an alarming rate and are under continuous threat from both natural and anthropogenic environmental stressors. Warmer sea temperatures attributed to global climate change and numerous human activities at local scales place these valuable ecosystems at risk. Reefs provide numerous services, including shoreline protection, fishing, tourism and biological diversity, which are lost through physical damage, overfishing, and pollution. Pollution can be controlled under provisions of the Clean Water Act, but these options have not been fully employed to protect coral reefs. No U.S. jurisdiction has implemented coral reef biocriteria, which are narrative or quantitative water quality standards based on the condition of a biological resource or assemblage. The President's Ocean Action Plan directs the U.S. Environmental Protection Agency (EPA) to develop biological assessment methods and biological criteria for evaluating and maintaining the health of coral reef ecosystems. EPA has formed the Coral Reef Biocriteria Working Group (CRBWG) to foster development of coral reef biocriteria through focused research, evaluation and communication among Agency partners and U.S. jurisdictions. Ongoing CRBWG activities include development and evaluation of a rapid bioassessment protocol for application in biocriteria programs; development of a survey design and monitoring strategy for the U.S. Virgin Islands; comprehensive reviews of biocriteria approaches proposed by states and territories; and assembly of data from a variety of monitoring programs for additional metrics. Guidance documents are being prepared to assist U.S. jurisdictions in reaching protective and defensible biocriteria.

Aloysia citrodora Paláu (Lemon verbena): A review of phytochemistry and pharmacology.

PubMed

Bahramsoltani, Roodabeh; Rostamiasrabadi, Pourouchista; Shahpiri, Zahra; Marques, André M; Rahimi, Roja; Farzaei, Mohammad Hosein

2018-08-10

Aloysia citrodora Paláu (Lippia citriodora Kunth), commonly known as "lemon verbena" is a medicinal plant native to South America, North Africa, and South of Europe which is used by native people for several indications such as diarrhea, flatulence, insomnia, and rheumatism. Despite the wide biological activities of lemon verbena, there is no current review summarizing medicinal properties of the plant; thus, this paper aims to discuss current state of the art regarding the phytochemistry, pharmacology, and therapeutic applications of A. citrodora considering in vitro, in vivo, and clinical studies. Electronic databases including PubMed, Scifinder, Cochrane library, Scopus, and Science direct were searched with the scientific name of the plant and its synonyms, as well as the common name. All studies on the ethnobotany, phytochemistry, pharmacology, and clinical application of the plant until October 2017 were included in this review. Despite the few number of studies on the ethnopharmacology of the plant, A. citrodora is widely assessed regarding its phytochemistry and biological activities. Neral and geranial are the main ingredients of the essential oil; whereas verbascoside is the most significant component of the extract. Biological activities such as antioxidant, anxiolytic, neuroprotective, anticancer, anesthetic, antimicrobial, and sedative effects are proved in cell cultures, as well as animal studies. Several pharmacological activities have been reported for A. citrodora; however, the plant is not fully assessed regarding its safety and efficacy in human. Future well-designed human studies are essential to confirm the therapeutic benefits of this plant in clinical settings. Copyright © 2018 Elsevier B.V. All rights reserved.

A structured viroid RNA serves as a substrate for dicer-like cleavage to produce biologically active small RNAs but is resistant to RNA-induced silencing complex-mediated degradation.

PubMed

Itaya, Asuka; Zhong, Xuehua; Bundschuh, Ralf; Qi, Yijun; Wang, Ying; Takeda, Ryuta; Harris, Ann R; Molina, Carlos; Nelson, Richard S; Ding, Biao

2007-03-01

RNA silencing is a potent means of antiviral defense in plants and animals. A hallmark of this defense response is the production of 21- to 24-nucleotide viral small RNAs via mechanisms that remain to be fully understood. Many viruses encode suppressors of RNA silencing, and some viral RNAs function directly as silencing suppressors as counterdefense. The occurrence of viroid-specific small RNAs in infected plants suggests that viroids can trigger RNA silencing in a host, raising the question of how these noncoding and unencapsidated RNAs survive cellular RNA-silencing systems. We address this question by characterizing the production of small RNAs of Potato spindle tuber viroid (srPSTVds) and investigating how PSTVd responds to RNA silencing. Our molecular and biochemical studies provide evidence that srPSTVds were derived mostly from the secondary structure of viroid RNAs. Replication of PSTVd was resistant to RNA silencing, although the srPSTVds were biologically active in guiding RNA-induced silencing complex (RISC)-mediated cleavage, as shown with a sensor system. Further analyses showed that without possessing or triggering silencing suppressor activities, the PSTVd secondary structure played a critical role in resistance to RISC-mediated cleavage. These findings support the hypothesis that some infectious RNAs may have evolved specific secondary structures as an effective means to evade RNA silencing in addition to encoding silencing suppressor activities. Our results should have important implications in further studies on RNA-based mechanisms of host-pathogen interactions and the biological constraints that shape the evolution of infectious RNA structures.

[Synthesis and biological activity of substance P analogs].

PubMed

Liu, S Y; Zhong, M N; Dong, Y X; Li, Y L; Yuan, X M

1997-12-01

Substance P (SP) and its three analogs were synthesized through solid-phase procedure. The fully-protected peptide-resin was cleaved with anhydrous HF.--SH of Cys in [Cys5,9] SP(4-11) was protected with Acm, then deprotected through Iodine oxidation method, the disulfide bridge cyclization was formed subsequently. The crude product was purified on C18 RP-HPLC. The results of guinea-pig isolated ileum test (GPI) showed that the potency of the analogs was as follows: [AcGln5, Pro9] SP(5-11) > SP > SP(4-11) > [Cys5,9] SP(4-11). They induced GPI to contract very fast and showed the characteristics of tachykinin. On the writing test in mice, the results showed: [Cys5,9] SP(4-11) > SP > SP(4-11) > [AcGln5, Pro9] SP(5-11). The biological tests showed that the SP analogs have some extent of selectivity.

Biological and socioeconomic determinants of prediabetes in youth: an analysis using 2007 to 2011 Canadian Health Measures Surveys.

PubMed

Rodd, Celia; Feely, Allison; Dart, Allison; Sharma, Atul; McGavock, Jon

2018-06-13

To describe rates of prediabetes among youth in Canada and the associated social and biological characteristics. We analyzed the cross-sectional data from the first (2007-2009) and second (2009-2011) cycles of the Canadian Health Measures Survey (CHMS) for youth aged 6-19 years. Prediabetes was defined using the glycated hemoglobin (A1C) guidelines set out by the American Diabetes Association (ADA) and the Canadian Diabetes Association (CDA) of A1C ranges 5.7-6.4% (38.8-46.4 mmol/mol) and 6.0-6.4% (42.1-46.4 mmol/mol), respectively. An elevated A1C was observed in 22.8% of our sample (n = 3449) based on the ADA definition and 5.2% of youth using the CDA definition. Independent predictors in a fully adjusted model for prediabetes were non-White (odds ratio (OR) 2.62: 95% Confidence intervals 2.05-3.35), obese (OR 1.53: 1.19-1.96), less physically active youth (0.97: 0.95-0.99), and parents with high school education or less (1.34: 1.02-1.74). Moreover, significant regional variations were noted with higher rates for all regions except Ontario. Prediabetes is relatively common in Canada and associated with common biologic and socioeconomic factors. Importantly, regular physical activity was significantly associated with reduced odds of prediabetes. Targeted screening and continued emphasis on physical activity may help curb the increasing rates of prediabetes.

Chemical composition and biological activities of extracts and essential oil of Boswellia dalzielii leaves.

PubMed

Kohoude, Midéko Justin; Gbaguidi, Fernand; Agbani, Pierre; Ayedoun, Marc-Abel; Cazaux, Sylvie; Bouajila, Jalloul

2017-12-01

Boswellia dalzielii Hutch. (Burseraceae) is an aromatic plant. The leaves are used for beverage flavouring. This study investigates the chemical composition and biological activities of various extracts. The essential oil was prepared via hydrodistillation. Identification and quantification were realized via GC-MS and GC-FID. Consecutive extractions (cyclohexane, dichloromethane, ethyl acetate and methanol) were carried out and various chemical groups (phenolics, flavonoids, tannins, antocyanins and sugar) were quantified. The volatile compounds of organic extracts were identified before and after derivatization. Antioxidant, antihyperuricemia, anti-Alzheimer, anti-inflammatory and anticancer activities were evaluated. In the essential oil, 50 compounds were identified, including 3-carene (27.72%) and α-pinene (15.18%). 2,5-Dihydroxy acetophenone and β-d-xylopyranose were identified in the methanol extract. Higher phenolic (315.97 g GAE/kg dry mass) and flavonoid (37.19 g QE/kg dry mass) contents were observed in the methanol extract. The methanol extract has presented remarkable IC 50  =   6.10 mg/L for antiDPPH, 35.10 mg/L for antixanthine oxidase and 28.01 mg/L for anti-5-lipoxygenase. For acetylcholinesterase inhibition, the best IC 50 (76.20 and 67.10 mg/L) were observed, respectively, with an ethyl acetate extract and the essential oil. At 50 mg/L, the dichloromethane extract inhibited OVCAR-3 cell lines by 65.10%, while cyclohexane extract inhibited IGROV-1 cell lines by 92.60%. Biological activities were fully correlated with the chemical groups of the extracts. The ethyl acetate and methanol extracts could be considered as potential alternatives for use in dietary supplements for the prevention or treatment of diseases because of these extracts natural antioxidant, antihyperuricemic and anti-inflammatory activities.

A Quasi Experiment to Determine the Effectiveness of a "Partially Flipped" versus "Fully Flipped" Undergraduate Class in Genetics and Evolution.

PubMed

Adams, Alison E M; Garcia, Jocelyn; Traustadóttir, Tinna

2016-01-01

Two sections of Genetics and Evolution were taught by one instructor. One group (the fully flipped section) had the entire class period devoted to active learning (with background material that had to be watched before class), and the other group (the partially flipped section) had just a portion of class time spent on active learning (with the background material presented during class time). The same materials and assessments were used for both sections. Analysis of objective measures revealed that there was no significant difference between the learning outcomes of students in the two sections. There was no main effect of gender, major, or ethnicity on success in the whole cohort or in either section. There appeared to be a significant main effect of class standing, with freshmen performing significantly less well than sophomores, juniors, or seniors (who all performed equally well) in both sections (p < 0.01); however, this was a very preliminary observation, as there were very few freshmen in either section. The only predictor of success in the two sections was prior grade point average. An anonymous end-of-semester survey showed no significant difference between the two sections in interest in the subject matter. © 2016 A.E.M. Adams et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Entropic-elasticity-controlled dissociation and energetic-elasticity-controlled rupture induce catch-to-slip bonds in cell-adhesion molecules.

PubMed

Wei, YuJie

2008-03-01

We develop a physical model to describe the kinetic behavior in cell-adhesion molecules. Unbinding of noncovalent biological bonds is assumed to occur by both bond dissociation and bond rupture. Such a decomposition of debonding processes is a space decomposition of the debonding events. Dissociation under thermal fluctuation is nondirectional in a three-dimensional space, and its energy barrier to escape is not influenced by a tensile force, but the microstates that could lead to dissociation are changed by the tensile force; rupture happens along the tensile force direction. An applied force effectively lowers the energy barrier to escape along the loading direction. The lifetime of the biological bond, due to the two concurrent off rates, may grow with increasing tensile force to a moderate amount and then decrease with further increasing load. We hypothesize that a catch-to-slip bond transition is a generic feature in biological bonds. The model also predicts that catch bonds in a more flexible molecular structure have longer lifetimes and need less force to be fully activated.

Validated reversed phase LC method for quantitative analysis of polymethoxyflavones in citrus peel extracts.

PubMed

Wang, Zhenyu; Li, Shiming; Ferguson, Stephen; Goodnow, Robert; Ho, Chi-Tang

2008-01-01

Polymethoxyflavones (PMFs), which exist exclusively in the citrus genus, have biological activities including anti-inflammatory, anticarcinogenic, and antiatherogenic properties. A validated RPLC method was developed for quantitative analysis of six major PMFs, namely nobiletin, tangeretin, sinensetin, 5,6,7,4'-tetramethoxyflavone, 3,5,6,7,3',4'-hexamethoxyflavone, and 3,5,6,7,8,3',4'-heptamethoxyflavone. The polar embedded LC stationary phase was able to fully resolve the six analogues. The developed method was fully validated in terms of linearity, accuracy, precision, sensitivity, and system suitability. The LOD of the method was calculated as 0.15 microg/mL and the recovery rate was between 97.0 and 105.1%. This analytical method was successfully applied to quantify the individual PMFs in four commercially available citrus peel extracts (CPEs). Each extract shows significant difference in the PMF composition and concentration. This method may provide a simple, rapid, and reliable tool to help reveal the correlation between the bioactivity of the PMF extracts and the individual PMF content.

Sowing the Seeds of the Sciences: Our Gift to the Future

ERIC Educational Resources Information Center

Sillick, Audrey

2013-01-01

Audrey Sillick's article, first printed in 1988, provides a theory base for Maria Montessori's foundational emphasis on the biological sciences and the sustainability of a living, organic planet Earth as part of the educational process "of becoming more fully human." Ms. Sillick helps link primary-level biology with the special energy…

Development of the Biological Experimental Design Concept Inventory (BEDCI)

ERIC Educational Resources Information Center

Deane, Thomas; Nomme, Kathy; Jeffery, Erica; Pollock, Carol; Birol, Gulnur

2014-01-01

Interest in student conception of experimentation inspired the development of a fully validated 14-question inventory on experimental design in biology (BEDCI) by following established best practices in concept inventory (CI) design. This CI can be used to diagnose specific examples of non-expert-like thinking in students and to evaluate the…

Micro-Eukaryote Diversity in Freshwater Ponds That Harbor the Amphibian Pathogen "Batrachochytrium Dendrobatidis" ("Bd")

ERIC Educational Resources Information Center

Lauer, Antje; McConnel, Lonnie; Singh, Navdeep

2012-01-01

We designed a microbiology project that fully engaged undergraduate biology students, high school students, and their teachers in a summer research program as part of the Research Education Vitalizing Science University Program conducted at California State University Bakersfield. Modern molecular biological methods and microscopy were used to…

Proteome analysis of snake venom toxins: pharmacological insights.

PubMed

Georgieva, Dessislava; Arni, Raghuvir K; Betzel, Christian

2008-12-01

Snake venoms are an extremely rich source of pharmacologically active proteins with a considerable clinical and medical potential. To date, this potential has not been fully explored, mainly because of our incomplete knowledge of the venom proteome and the pharmacological properties of its components, in particular those devoid of enzymatic activity. This review summarizes the latest achievements in the determination of snake venom proteome, based primarily on the development of new strategies and techniques. Detailed knowledge of the venom toxin composition and biological properties of the protein constituents should provide the scaffold for the design of new more effective drugs for the treatment of the hemostatic system and heart disorders, inflammation, cancer and consequences of snake bites, as well as new tools for clinical diagnostic and assays of hemostatic parameters.

The sludge loading rate regulates the growth and release of heterotrophic bacteria resistant to six types of antibiotics in wastewater activated sludge.

PubMed

Yuan, Qing-Bin; Guo, Mei-Ting; Yang, Jian

2015-01-01

Wastewater treatment plants are considered as hot reservoirs of antimicrobial resistance. However, the fates of antibiotic-resistant bacteria during biological treatment processes and relevant influencing factors have not been fully understood. This study evaluated the effects of the sludge loading rate on the growth and release of six kinds of antibiotic-resistant bacteria in an activated sludge system. The results indicated that higher sludge loading rates amplified the growth of all six types of antibiotic resistant bacteria. The release of most antibiotic-resistant bacteria through both the effluent and biosolids was amplified with increased sludge loading rate. Biosolids were the main pattern for all antibiotic-resistant bacteria release in an activated sludge system, which was determined primarily by their growth in the activated sludge. A higher sludge loading rate reactor tended to retain more antibiotic resistance. An activated sludge system with lower sludge loading rates was considered more conducive to the control of antibiotic resistance.

Novel 2-Phenoxyanilide Congeners Derived from a Hit Structure of the TCAMS: Synthesis and Evaluation of Their in Vitro Activity against Plasmodium falciparum.

PubMed

Weidner, Thomas; Nasereddin, Abed; Preu, Lutz; Grünefeld, Johann; Dzikowski, Ron; Kunick, Conrad

2016-02-17

The Tres Cantos Antimalarial Compound Set (TCAMS) is a publicly available compound library which contains 13533 hit structures with confirmed activity against Plasmodium falciparum, the infective agent responsible for malaria tropica. The TCAMS provides a variety of starting points for the investigation of new antiplasmodial drug leads. One of the promising compounds is TCMDC-137332, which seemed to be a good starting point due to its antiplasmodial potency and its predicted physicochemical properties. Several new analogues based on a 2-phenoxyanilide scaffold were synthesized by standard amide coupling reactions and were fully characterized regarding their identity and purity by spectroscopic and chromatographic methods. Furthermore, the results of the biological evaluation of all congeners against Plasmodium falciparum NF54 strains are presented. The findings of our in vitro screening could not confirm the presumed nanomolar antiplasmodial activity of TCMDC-137332 and its derivatives.

A high-performance protocol for extraction of microplastics in fish.

PubMed

Karami, Ali; Golieskardi, Abolfazl; Choo, Cheng Keong; Romano, Nicholas; Ho, Yu Bin; Salamatinia, Babak

2017-02-01

So far, several classes of digesting solutions have been employed to extract microplastics (MPs) from biological matrices. However, the performance of digesting solutions across different temperatures has never been systematically investigated. In the first phase of the present study, we measured the efficiency of different oxidative agents (NaClO or H 2 O 2 ), bases (NaOH or KOH), and acids [HCl or HNO 3 ; concentrated and diluted (5%)] in digesting fish tissues at room temperature (RT, 25°C), 40, 50, or 60°C. In the second phase, the treatments that were efficient in digesting the biological materials (>95%) were evaluated for their compatibility with eight major plastic polymers (assessed through recovery rate, Raman spectroscopy analysis, and morphological changes). Among the tested solutions, NaClO, NaOH, and diluted acids did not result in a satisfactory digestion efficiency at any of the temperatures. The H 2 O 2 treatment at 50°C efficiently digested the biological materials, although it decreased the recovery rate of nylon-6 (NY6) and nylon-66 (NY66) and altered the colour of polyethylene terephthalate (PET) fragments. Similarly, concentrated HCl and HNO 3 treatments at RT fully digested the fish tissues, but also fully dissolved NY6 and NY66, and reduced the recovery rate of most or all of the polymers, respectively. Potassium hydroxide solution fully eliminated the biological matrices at all temperatures. However, at 50 and 60°C, it degraded PET, reduced the recovery rate of PET and polyvinyl chloride (PVC), and changed the colour of NY66. According to our results, treating biological materials with a 10% KOH solution and incubating at 40°C was both time and cost-effective, efficient in digesting biological materials, and had no impact on the integrity of the plastic polymers. Furthermore, coupling this treatment with NaI extraction created a promising protocol to isolate MPs from whole fish samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Characteristics of silver nanoparticles in vehicles for biological applications.

PubMed

Kejlová, Kristina; Kašpárková, Věra; Krsek, Daniel; Jírová, Dagmar; Kolářová, Hana; Dvořáková, Markéta; Tománková, Kateřina; Mikulcová, Veronika

2015-12-30

Silver nanoparticles (AgNPs) have been used for decades as anti-bacterial agents in various industrial fields such as cosmetics, health industry, food storage, textile coatings and environmental applications, although their toxicity is not fully recognized yet. Antimicrobial and catalytic activity of AgNPs depends on their size as well as structure, shape, size distribution, and physico-chemical environment. The unique properties of AgNPs require novel or modified toxicological methods for evaluation of their toxic potential combined with robust analytical methods for characterization of nanoparticles applied in relevant vehicles, e.g., culture medium with/without serum and phosphate buffered saline. Copyright © 2015 Elsevier B.V. All rights reserved.

Heterologous expression, protein folding and antibody recognition of a neurotoxin from the Mexican coral snake Micrurus laticorallis.

PubMed

Clement, Herlinda; Flores, Vianey; De la Rosa, Guillermo; Zamudio, Fernando; Alagon, Alejandro; Corzo, Gerardo

2016-01-01

The cysteine-rich neurotoxins from elapid venoms are primarily responsible for human and animal envenomation; however, their low concentration in the venom may hamper the production of efficient elapid antivenoms. Therefore, the aim of the present study was to produce fully active elapid neurotoxic immunogens for elapid antivenom production. Cysteine-rich neurotoxins showed recombinant expression in two strains of E. coli, and were purified using affinity chromatography and reverse-phase HPLC (rpHPLC). The cDNA of the four disulfide-bridged peptide neurotoxin Mlat1 was cloned into a modified expression vector, pQE30, which was transfected into two different E. coli strains. The recombinant toxin (HisrMlat1) was found only in inclusion bodies in M15 strain cells, and in both inclusion bodies and cytoplasm in Origami strain cells. The HisrMlat1 from inclusion bodies from M15 cells was solubilized using guanidine hydrochloride, and then purified by rpHPLC. It showed various contiguous fractions having the same molecular mass, indicating that HisrMlat1 was oxidized after cell extraction forming different misfolded disulfide bridge arrangements without biological activity. In vitro folding conditions of the misfolded HisrMlat1 generated a biologically active HisrMlat1. On the other hand, the HisrMlat1 from the cytoplasm from Origami cells was already soluble, and then purified by HPLC. It showed a single fraction with neurotoxic activity; so, no folding steps were needed. The in vitro folded HisrMlat1 from M15 cells and the cytoplasmic soluble HisrMlat1from Origami cells were indistinguishable in their structure and neurotoxicity. Rabbit polyclonal antibodies raised up against biologically active HisrMlat1 recognized the native Mlat1 (nMlat1) from the whole venom of M. laticorallis. In addition, HisrMlat1 was recognized by horse polyclonal antibodies obtained from the immunization of elapid species from sub-Saharan Africa. HisrMlat1 shows increased biological activities compared to the native peptide, and may be used as an immunizing agent in combination with other toxic components such phospholipases type A2 for elapid antivenom production.

Long-term movement patterns of a coral reef predator

NASA Astrophysics Data System (ADS)

Heupel, M. R.; Simpfendorfer, C. A.

2015-06-01

Long-term monitoring is required to fully define periodicity and patterns in animal movement. This is particularly relevant for defining what factors are driving the presence, location, and movements of individuals. The long-term movement and space use patterns of grey reef sharks, Carcharhinus amblyrhynchos, were examined on a whole of reef scale in the southern Great Barrier Reef to define whether movement and activity space varied through time. Twenty-nine C. amblyrhynchos were tracked for over 2 years to define movement patterns. All individuals showed high residency within the study site, but also had high roaming indices. This indicated that individuals remained in the region and used all of the monitored habitat (i.e., the entire reef perimeter). Use of space was consistent through time with high reuse of areas most of the year. Therefore, individuals maintained discrete home ranges, but undertook broader movements around the reef at times. Mature males showed greatest variation in movement with larger activity spaces and movement into new regions during the mating season (August-September). Depth use patterns also differed, suggesting behaviour or resource requirements varied between sexes. Examination of the long-term, reef-scale movements of C. amblyrhynchos has revealed that reproductive activity may play a key role in space use and activity patterns. It was unclear whether mating behaviour or an increased need for food to sustain reproductive activity and development played a greater role in these patterns. Reef shark movement patterns are becoming more clearly defined, but research is still required to fully understand the biological drivers for the observed patterns.

UK–South Asian patients’ experiences of and satisfaction toward receiving information about biologics in rheumatoid arthritis

PubMed Central

Kumar, Kanta; Raizada, Sabrina R; Mallen, Christian D; Stack, Rebecca J

2018-01-01

Background Rheumatoid arthritis (RA) causes painful joint inflammation and is incurable, but treatments control RA. Drug regimens are complex, and patients often do not take their medication as expected. Poor medication adherence can lead to poorly controlled disease and worse patient outcomes. Biologics treatments are expensive and require full engagement from patients. We have previously shown that patients from Black ethnic minority backgrounds do not fully engage into treatment plan. This study explored the patients’ experiences in and satisfaction toward receiving information about biologics and future support preferences in South Asian patients with RA. Methods Twenty South Asian patients with RA from Royal Wolverhampton Hospitals NHS Trust and Central Manchester University Hospitals NHS Foundation Trust participated in individual semistructured interviews. Interviews were transcribed and data were analyzed by using thematic analysis approach. Results Four overarching themes describe the patients’ experience in and satisfaction toward receiving information on biologics: 1) current provision of information regarding the “biologics journey” and understanding of RA: in this theme, non-English-speaking patients expressed heightened anxiety about stepping up to biologics; 2) experience and perceptions of biologics: many patients were positive about the biologic experience; however, there were patient-perceived delays in getting on to the biologics; 3) factors influencing willingness to try biologics: in this theme, a number of factors were identified including seeking advice from doctors abroad; and 4) recommendations on the desired information to fully understand the use of biologics: some patients valued group discussions, while others suggested receiving RA and biologic information through a video interaction. Conclusion This novel study provides insight into South Asian RA patients’ experiences in and satisfaction toward receiving information about biologics. South Asian patients with RA reported a range of perceptions about biologics and support preferences, many of which may not be shared with the non-South Asian population. PMID:29670337

Advances on plant-pathogen interactions from molecular toward systems biology perspectives.

PubMed

Peyraud, Rémi; Dubiella, Ullrich; Barbacci, Adelin; Genin, Stéphane; Raffaele, Sylvain; Roby, Dominique

2017-05-01

In the past 2 decades, progress in molecular analyses of the plant immune system has revealed key elements of a complex response network. Current paradigms depict the interaction of pathogen-secreted molecules with host target molecules leading to the activation of multiple plant response pathways. Further research will be required to fully understand how these responses are integrated in space and time, and exploit this knowledge in agriculture. In this review, we highlight systems biology as a promising approach to reveal properties of molecular plant-pathogen interactions and predict the outcome of such interactions. We first illustrate a few key concepts in plant immunity with a network and systems biology perspective. Next, we present some basic principles of systems biology and show how they allow integrating multiomics data and predict cell phenotypes. We identify challenges for systems biology of plant-pathogen interactions, including the reconstruction of multiscale mechanistic models and the connection of host and pathogen models. Finally, we outline studies on resistance durability through the robustness of immune system networks, the identification of trade-offs between immunity and growth and in silico plant-pathogen co-evolution as exciting perspectives in the field. We conclude that the development of sophisticated models of plant diseases incorporating plant, pathogen and climate properties represent a major challenge for agriculture in the future. © 2016 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

A Structured Viroid RNA Serves as a Substrate for Dicer-Like Cleavage To Produce Biologically Active Small RNAs but Is Resistant to RNA-Induced Silencing Complex-Mediated Degradation▿

PubMed Central

Itaya, Asuka; Zhong, Xuehua; Bundschuh, Ralf; Qi, Yijun; Wang, Ying; Takeda, Ryuta; Harris, Ann R.; Molina, Carlos; Nelson, Richard S.; Ding, Biao

2007-01-01

RNA silencing is a potent means of antiviral defense in plants and animals. A hallmark of this defense response is the production of 21- to 24-nucleotide viral small RNAs via mechanisms that remain to be fully understood. Many viruses encode suppressors of RNA silencing, and some viral RNAs function directly as silencing suppressors as counterdefense. The occurrence of viroid-specific small RNAs in infected plants suggests that viroids can trigger RNA silencing in a host, raising the question of how these noncoding and unencapsidated RNAs survive cellular RNA-silencing systems. We address this question by characterizing the production of small RNAs of Potato spindle tuber viroid (srPSTVds) and investigating how PSTVd responds to RNA silencing. Our molecular and biochemical studies provide evidence that srPSTVds were derived mostly from the secondary structure of viroid RNAs. Replication of PSTVd was resistant to RNA silencing, although the srPSTVds were biologically active in guiding RNA-induced silencing complex (RISC)-mediated cleavage, as shown with a sensor system. Further analyses showed that without possessing or triggering silencing suppressor activities, the PSTVd secondary structure played a critical role in resistance to RISC-mediated cleavage. These findings support the hypothesis that some infectious RNAs may have evolved specific secondary structures as an effective means to evade RNA silencing in addition to encoding silencing suppressor activities. Our results should have important implications in further studies on RNA-based mechanisms of host-pathogen interactions and the biological constraints that shape the evolution of infectious RNA structures. PMID:17202210

Biological activities of red propolis: a rewiew

PubMed

de Figueiredo, Sonia M; de Freitas, Marcia Christina Dornelas; de Oliveira, Daiana Teixeira; de Miranda, Marina Barcelos; Vieira-Filho, Sidney Augusto; Caligiorne, Rachel Basques

2018-02-23

• Background: The red propolis (RdProp) is a resin produced by Apis mellifera bees, which collect the reddish exudate on the surface of its botanic source, the species Dalbergiae castophyllum, popularly known in Brazil as "rabo de bugio". Considered as the 13th type of Brazilian propolis, this resin has been gaining prominence due to its natural composition, rich in bioactive substances not found in other types of propolis. • Objective: This review aims to address the most important characteristics of PV, its botanical origin, the main constituents, its biological properties and the patents related to this natural product. • Method: By means of the SciFinder, Google Patents, Patus® and Spacenet, scientific articles and patents involving the term "red propolis" were searched until August 2017 • Results: A number of biological properties, including antimicrobial, anti-inflammatory, antiparasitic, antitumor, antioxidant, metabolic and nutraceutical activities are attributed to RdProp, demonstrating the great potential of its use in the food, pharmaceutical and cosmetics industries. • Conclusion: The available papers are associated to pharmacological potential of RdProp, but the molecular mechanisms or bioactive compounds responsible for each activity have not yet been fully elucidated. The RdProp patents currently found are directed to components for the pharmaceutical industry (EP2070543A1; WO2014186851A1; FR3006589A1; CN1775277A; CN105797149A; CN1879859A), cosmetic (JP6012138B2; JP2008247830A; JP6012138B2) and food (JP5478392B2; CN101380052A; WO2006038690A1). Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Activation of photosynthesis and resistance to photoinhibition in cyanobacteria within biological desert crust.

PubMed

Harel, Yariv; Ohad, Itzhak; Kaplan, Aaron

2004-10-01

Filamentous cyanobacteria are the main primary producers in biological desert sand crusts. The cells are exposed to extreme environmental conditions including temperature, light, and diurnal desiccation/rehydration cycles. We have studied the kinetics of activation of photosynthesis during rehydration of the cyanobacteria, primarily Microcoleus sp., within crust samples collected in the Negev desert, Israel. We also investigated their susceptibility to photoinhibition. Activation of the photosynthetic apparatus, measured by fluorescence kinetics, thermoluminescence, and low temperature fluorescence emission spectra, did not require de novo protein synthesis. Over 50% of the photosystem II (PSII) activity, assembled phycobilisomes, and photosystem I (PSI) antennae were detected within less than 5 min of rehydration. Energy transfer to PSII and PSI by the respective antennae was fully established within 10 to 20 min of rehydration. The activation of a fraction of PSII population (about 20%-30%) was light and temperature-dependent but did not require electron flow to plastoquinone [was not inhibited by 3-(3,4-dichlorophenyl)-1,1-dimethylurea]. The cyanobacteria within the crusts are remarkably resistant to photoinhibition even in the absence of protein synthesis. The rate of PSII repair increased with light intensity and with time of exposure. Consequently, the extent of photoinhibition in high-light-exposed crusts reached a constant, relatively low, level. This is in contrast to model organisms such as Synechocystis sp. strain PCC 6803 where PSII activity declined continuously over the entire exposure to high illumination. Ability of the crust's organisms to rapidly activate photosynthesis upon rehydration and withstand photoinhibition under high light intensity may partly explain their ability to survive in this ecosystem.

GREEN TEA CATECHINS ARE POTENT SENSITIZERS OF RYANODINE RECEPTOR TYPE 1 (RYR1)

PubMed Central

Feng, Wei; Cherednichenko, Gennady; Ward, Chris W.; Padilla, Isela T.; Cabrales, Elaine; Lopez, José R.; Eltit, José M.; Allen, Paul D.; Pessah, Isaac N.

2010-01-01

Catechins, polyphenols extracted from green tea leaves, have a broad range of biological activities although the specific molecular mechanisms responsible are not known. At the high experimental concentrations typically used polyphenols bind to membrane phospholipid and also are easily auto-oxidized to generate superoxide anion and semiquinones, and can adduct to protein thiols. We report that the type 1 ryanodine receptor (RyR1) is a molecular target that responds to nanomolar (−)-epigallocatechin-3-gallate (EGCG) and (−)-epicatechin-3-gallate (ECG). Single channel analyses demonstrate EGCG (5-10nM) increases channel open probability (Po) 2-fold, by lengthening open dwell time. The degree of channel activation is concentration dependent and is rapidly and fully reversible. Four related catechins, EGCG, ECG, EGC ((−)-epigallocatechin) and EC ((−)-epicatechin) showed a rank order of activity toward RyR1 (EGCG>ECG>>EGC>>>EC). EGCG and ECG enhance the sensitivity of RyR1 to activation by ≤100μM cytoplasmic Ca2+ without altering inhibitory potency by >100μM Ca2+. EGCG as high as 10μM in the extracellular medium potentiated Ca2+ transient amplitudes evoked by electrical stimuli applied to intact myotubes and adult FDB fibers, without eliciting spontaneous Ca2+ release or slowing Ca2+ transient recovery. The results identify RyR1 as a sensitive target for the major tea catechins EGCG and ECG, and this interaction is likely to contribute to their observed biological activities. PMID:20471964

Safety, pharmacokinetics, and pharmacodynamics of RSLV-132, an RNase-Fc fusion protein in systemic lupus erythematosus: a randomized, double-blind, placebo-controlled study.

PubMed

Burge, D J; Eisenman, J; Byrnes-Blake, K; Smolak, P; Lau, K; Cohen, S B; Kivitz, A J; Levin, R; Martin, R W; Sherrer, Y; Posada, J A

2017-07-01

Blood-borne RNA circulating in association with autoantibodies is a potent stimulator of interferon production and immune system activation. RSLV-132 is a novel fully human biologic Fc fusion protein that is comprised of human RNase fused to the Fc domain of human IgG1. The drug is designed to remain in circulation and digest extracellular RNA with the aim of preventing activation of the immune system via Toll-like receptors and the interferon pathway. The present study describes the first clinical study of nuclease therapy in 32 subjects with systemic lupus erythematosus. The drug was well tolerated with a very favorable safety profile. The approximately 19-day serum half-life potentially supports once monthly dosing. There were no subjects in the study that developed anti-RSLV-132 antibodies. Decreases in B-cell activating factor correlated with decreases in disease activity in a subset of patients.

11-β hydroxysteroid type 1 knockout mice display an antidepressant-like phenotype in the forced swim test.

PubMed

Slattery, David A; Uzunov, Doncho P; Cryan, John F

2016-02-01

11β-dehydroxysteroid dehydrogenase (HSD) types 1 and 2, enzymes are involved in the activation and inactivation of glucocorticoids in vivo, respectively. Indirect evidence implicates two enzymes in the aetiology of depression but no study has directly assessed the potential role of 11 β-HSD1 in animal tests. We assessed 11 β-HSD1 knockout mice in the forced swim test (FST), tail suspension test (TST) and for locomotor activity. Genetic ablation of the 11β-HSD1 gene results in an antidepressant-like phenotype in the FST; the most widely utilised animal test of antidepressant activity, but not in the related TST. This may be related to the different biological substrates underlying these tests. The decreased FST immobility was not due to alterations in general activity. Taken together these results suggest that 11β-HSD1 may play an important role in depression-related behaviours and further studies are necessary to fully characterise its role in such behaviour.

Rapid adaptation of activated sludge bacteria into a glycogen accumulating biofilm enabling anaerobic BOD uptake.

PubMed

Hossain, Md Iqbal; Paparini, Andrea; Cord-Ruwisch, Ralf

2017-03-01

Glycogen accumulating organisms (GAO) are known to allow anaerobic uptake of biological oxygen demand (BOD) in activated sludge wastewater treatment systems. In this study, we report a rapid transition of suspended activated sludge biomass to a GAO dominated biofilm by selective enrichment using sequences of anaerobic loading followed by aerobic exposure of the biofilm to air. The study showed that within eight weeks, a fully operational, GAO dominated biofilm had developed, enabling complete anaerobic BOD uptake at a rate of 256mg/L/h. The oxygen uptake by the biofilm directly from the atmosphere had been calculated to provide significant energy savings. This study suggests that wastewater treatment plant operators can convert activated sludge systems readily into a "passive aeration" biofilm that avoids costly oxygen transfer to bulk wastewater solution. The described energy efficient BOD removal system provides an opportunity to be coupled with novel nitrogen removal processes such as anammox. Copyright © 2016. Published by Elsevier Ltd.

Production of bioactive chitosan oligosaccharides using the hypertransglycosylating chitinase-D from Serratia proteamaculans.

PubMed

Madhuprakash, Jogi; El Gueddari, Nour Eddine; Moerschbacher, Bruno M; Podile, Appa Rao

2015-12-01

The biological activities of chitosan and its oligosaccharides are greatly influenced by properties such as the degree of polymerization (DP), degree of acetylation (DA) and pattern of acetylation (PA). Here, structurally diverse chitosan oligosaccharides from chitosan polymers (DA=35% or 61%) were generated using Serratia proteamaculans wild-type chitinase D (SpChiD) and the W114A mutant which lacks transglycosylase activity. The crude oligosaccharide mixtures and purified fractions with specific DP and DA ranges were tested for their ability to induce an oxidative burst in rice cell suspension cultures. The crude mixtures were more active when produced by the W114A mutant whereas the purified fractions were more active when produced by wild-type SpChiD. Neither hydrolysis nor transglycosylation by SpChiD was inhibited in the presence of fully-deacetylated oligosaccharides, suggesting that SpChiD could be exploited to generate oligosaccharides with defined DA and PA values. Copyright © 2015 Elsevier Ltd. All rights reserved.

Multi-analysis strategy for metabolism of Andrographis paniculata in rat using liquid chromatography/quadrupole time-of-flight mass spectrometry.

PubMed

Li, Wenlan; Sun, Xiangming; Xu, Ying; Wang, Xuezhi; Bai, Jing; Ji, Yubin

2015-07-01

Compared with chemical drugs, it is a huge challenge to identify active ingredients of multicomponent traditional Chinese medicine (TCM). For most TCMs, metabolism investigation of absorbed constituents is a feasible way to clarify the active material basis. Although Andrographis paniculata (AP) has been extensively researched by domestic and foreign scholars, its metabolism has seldom been fully addressed to date. In this paper, high-performance liquid chromatography/quadrupole time-of-flight mass spectrometry was applied to analysis and characterization of AP metabolism in rat urine and feces samples after oral administration of ethanol extract. The differences in metabolites and metabolic pathways between the two biological samples were further compared. The chemical structures of 20 components were tentatively identified from drug-treated biological samples, including six prototype components and 14 metabolites, which underwent such main metabolic pathways as hydrolyzation, hydrogenation, dehydroxylation, deoxygenation, methylation, glucuronidation, sulfonation and sulfation. Two co-existing components were found in urine and feces samples, suggesting that some ingredients' metabolic processes were not unique. This study provides a comprehensive report on the metabolism of AP in rats, which will be helpful for understanding its mechanism. Copyright © 2014 John Wiley & Sons, Ltd.

Bioprospecting of Marine Macrophytes Using MS-Based Lipidomics as a New Approach

PubMed Central

Maciel, Elisabete; Leal, Miguel Costa; Lillebø, Ana Isabel; Domingues, Pedro; Domingues, Maria Rosário; Calado, Ricardo

2016-01-01

The marine environment supports a remarkable diversity of organisms which are a potential source of natural products with biological activities. These organisms include a wide variety of marine plants (from micro- to macrophytes), which have been used in the food and pharmaceutical industry. However, the biochemistry and biological activities of many of these macrophytes (namely macroalgae and halophytes, including seagrasses) are still far from being fully explored. Most popular bioactive components include polysaccharides, peptides, phenolics and fatty acids (FAs). Polar lipids (glycolipids, phospholipids and betaine lipids) are emerging as novel value-added bioactive phytochemicals, rich in n-3 FA, with high nutritional value and health beneficial effects for the prevention of chronic diseases. Polar lipids account various combinations of polar groups, fatty acyl chains and backbone structures. The polar lipidome of macrophytes is remarkably diverse, and its screening represents a significant analytical challenge. Modern research platforms, particularly mass spectrometry (MS)-based lipidomic approaches, have been recently used to address this challenge and are here reviewed. The application of lipidomics to address lipid composition of marine macrophytes will contribute to the stimulation of further research on this group and foster the exploration of novel applications. PMID:27005634

SH2 Domain-Based FRET Biosensor for Measuring BCR-ABL Activity in Living CML Cells.

PubMed

Fujioka, Mari; Asano, Yumi; Nakada, Shigeyuki; Ohba, Yusuke

2017-01-01

Fluorescent proteins (FPs) displaying distinct spectra have shed their light on a wide range of biological functions. Moreover, sophisticated biosensors engineered to contain single or multiple FPs, including Förster resonance energy transfer (FRET)-based biosensors, spatiotemporally reveal the molecular mechanisms underlying a variety of pathophysiological processes. However, their usefulness for applied life sciences has yet to be fully explored. Recently, our research group has begun to expand the potential of FPs from basic biological research to the clinic. Here, we describe a method to evaluate the responsiveness of leukemia cells from patients to tyrosine kinase inhibitors using a biosensor based on FP technology and the principle of FRET. Upon phosphorylation of the tyrosine residue of the biosensor, binding of the SH2 domain to phosphotyrosine induces conformational change of the biosensor and brings the donor and acceptor FPs into close proximity. Therefore, kinase activity and response to kinase inhibitors can be monitored by an increase and a decrease in FRET efficiency, respectively. As in basic research, this biosensor resolves hitherto arduous tasks and may provide innovative technological advances in clinical laboratory examinations. State-of-the-art detection devices that enable such innovation are also introduced.

Mechanical Fluidity of Fully Suspended Biological Cells

PubMed Central

Maloney, John M.; Lehnhardt, Eric; Long, Alexandra F.; Van Vliet, Krystyn J.

2013-01-01

Mechanical characteristics of single biological cells are used to identify and possibly leverage interesting differences among cells or cell populations. Fluidity—hysteresivity normalized to the extremes of an elastic solid or a viscous liquid—can be extracted from, and compared among, multiple rheological measurements of cells: creep compliance versus time, complex modulus versus frequency, and phase lag versus frequency. With multiple strategies available for acquisition of this nondimensional property, fluidity may serve as a useful and robust parameter for distinguishing cell populations, and for understanding the physical origins of deformability in soft matter. Here, for three disparate eukaryotic cell types deformed in the suspended state via optical stretching, we examine the dependence of fluidity on chemical and environmental influences at a timescale of ∼1 s. We find that fluidity estimates are consistent in the time and frequency domains under a structural damping (power-law or fractional-derivative) model, but not under an equivalent-complexity, lumped-component (spring-dashpot) model; the latter predicts spurious time constants. Although fluidity is suppressed by chemical cross-linking, we find that ATP depletion in the cell does not measurably alter the parameter, and we thus conclude that active ATP-driven events are not a crucial enabler of fluidity during linear viscoelastic deformation of a suspended cell. Finally, by using the capacity of optical stretching to produce near-instantaneous increases in cell temperature, we establish that fluidity increases with temperature—now measured in a fully suspended, sortable cell without the complicating factor of cell-substratum adhesion. PMID:24138852

Objectives | Office of Cancer Clinical Proteomics Research

Cancer.gov

The overall objective of CPTAC is to systematically identify proteins that derive from alterations in cancer genomes and related biological processes, in order to understand the molecular basis of cancer that is not fully elucidated or not possible through genomics and to accelerate the translation of molecular findings into the clinic.  This is to be achieved through enhancing our understanding of cancer genome biology by adding a complementary functional layer of protein biology (a “proteogenome” approach) that refines/prioritizes driver genes, enhances understanding of pathogenesis

Improving Synthetic Biology Communication: Recommended Practices for Visual Depiction and Digital Submission of Genetic Designs.

PubMed

Hillson, Nathan J; Plahar, Hector A; Beal, Jacob; Prithviraj, Ranjini

2016-06-17

Research is communicated more effectively and reproducibly when articles depict genetic designs consistently and fully disclose the complete sequences of all reported constructs. ACS Synthetic Biology is now providing authors with updated guidance and piloting a new tool and publication workflow that facilitate compliance with these recommended practices and standards for visual representation and data exchange.

Engaging Non-Science Majors by Integrating Biology and the Liberal Arts

ERIC Educational Resources Information Center

Bozzone, Donna M.; Doyle, Mary Beth

2017-01-01

We describe a pair of fully integrated courses designed to teach biology to non-majors in a manner that connects authentically to the liberal arts. The co-taught courses were organized around the question: What does it mean to be human? Students investigated this question in the context of three topics: dis/ability, race, and sex and gender. In…

You're Teaching, but How Do You Know They're Learning?

ERIC Educational Resources Information Center

Musante, Susan

2009-01-01

Although most instructors would like to believe that their students fully understand every biological concept explained in class, this is often not the case. Gary Wisehart, chair and professor of biology at San Diego City College, knows this from firsthand experience. "Students get very good at telling you what you want to hear," he says, "so it…

The role of the glycosyl moiety of myricetin derivatives in anti-HIV-1 activity in vitro.

PubMed

Ortega, Joseph T; Suárez, Alirica I; Serrano, Maria L; Baptista, Jani; Pujol, Flor H; Rangel, Hector R

2017-10-12

Plant extracts are sources of valuable compounds with biological activity, especially for the anti-proliferative activity against pathogens or tumor cells. Myricetin is a flavonoid found in several plants that has been described as an inhibitor of Human immunodeficiency virus type 1 (HIV-1) through its action against the HIV reverse transcriptase, but myricetin derivatives have not been fully studied. The aim of this study was to evaluate the anti-HIV-1 activity of glycosylated metabolites obtained from Marcetia taxifolia and derived from myricetin: myricetin rhamnoside and myricetin 3-(6-rhamnosylgalactoside). Compounds were obtained from organic extracts by maceration of aerial parts of M. taxifolia. All biological assays were performed in the MT4 cell line. Antiviral activity was measured as inhibition of p24 and reverse transcriptase with a fluorescent assay. Both flavonoids have antiviral activity in vitro, with an EC50 of 120 µM for myricetin 3-rhamnoside (MR) and 45 µM for myricetin 3-(6-rhamnosylgalactoside) (MRG), both significantly lower than the EC50 of myricetin (230 µM). Although both compounds inhibited the reverse transcriptase activity, with an IC50 of 10.6 µM for MR and 13.8 µM for MRG, myricetin was the most potent, with an IC50 of 7.6 µM, and an inhibition greater than 80%. Molecular docking approach showed correlation between the free energy of binding with the assays of enzyme inhibition. The results suggest that glycosylated moiety might enhance the anti-HIV-1 activity of myricetin, probably by favoring the internalization of the flavonoid into the cell. The inhibition of the HIV-1 reverse transcriptase is likely responsible for the antiviral activity.

Application of Time-Resolved Tryptophan Phosphorescence Spectroscopy to Protein Folding Studies.

NASA Astrophysics Data System (ADS)

Subramaniam, Vinod

This thesis presents studies of the protein folding problem, one of the most significant questions in contemporary biophysics. Sensitive biophysical techniques, including room temperature tryptophan phosphorescence, which reports on the local environment of the residue, and the lability of proteins to denaturation, a global parameter, were used to assess the validity of the traditional assumption that the biologically active state of a protein is the 'native' state, and to determine whether the pathways of folding in vitro lead to the folded state achieved in vivo. Phosphorescence techniques have also been extended to study, for the first time, emission from tryptophan residues engineered into specific positions as reporters of protein structure. During in vitro refolding of E. coli alkaline phosphatase and bovine 13-lactoglobulin, significant differences were found between the refolded proteins and the native conformations, which have no apparent effect on the biological functions. Slow conformational transitions, termed 'annealing,' that occur long after the return of enzyme activity of alkaline phosphatase are manifested in the retarded recovery of phosphorescence intensity, lifetime, and protein lability. While 'annealing' is not observed for beta -lactoglobulin, both phosphorescence and lability experiments reveal changes in the structure of the refolded protein, even though its biological activity, retinol binding, is fully recovered. This result suggests that the pathways of folding in vitro need not lead to the structure formed in vivo. We have used phosphorescence techniques to study the refolding of ribonuclease T1, which exhibits slow kinetics characteristic of proline isomerization. Furthermore, the ability to extract structural information from phosphorescent tryptophan probes engineered into selected regions represents an important advance in studying protein structure; we have reported the first such results from a mutant staphylococcal nuclease. The refolding data have been interpreted in the context of recent theoretical work on rugged energy landscape models of protein folding. Our results suggest that the barriers to folding can be as large as ~ 20 kcal-mol^{-1}, and imply that the conventional definition of the 'native' state as the biologically active conformation may need revision to acknowledge that the active state may represent a long-lived intermediate on the pathway to the native structure.

Widespread mechanosensing controls the structure behind the architecture in plants.

PubMed

Hamant, Olivier

2013-10-01

Mechanical forces play an instructing role for many aspects of animal cell biology, such as division, polarity and fate. Although the associated mechanoperception pathways still remain largely elusive in plants, physical cues have long been thought to guide development in parallel to biochemical factors. With the development of new imaging techniques, micromechanics tools and modeling approaches, the role of mechanical signals in plant development is now re-examined and fully integrated with modern cell biology. Using recent examples from the literature, I propose to use a multiscale perspective, from the whole plant down to the cell wall, to fully appreciate the diversity of developmental processes that depend on mechanical signals. Incidentally, this also illustrates how conceptually rich this field is. Copyright © 2013 Elsevier Ltd. All rights reserved.

Analysis of AtCry1 and Mutants

NASA Astrophysics Data System (ADS)

Burdick, Derek; Purvis, Adam; Ahmad, Margaret; Link, Justin J.; Engle, Dorothy

Cryptochrome is an incredibly versatile protein that influences numerous biological processes such as plant growth, bird migration, and sleep cycles. Due to the versatility of this protein, understanding the mechanism would allow for advances in numerous fields such as crop growth, animal behavior, and sleep disorders. It is known that cryptochrome requires blue light to function, but the exact processes in the regulation of biological activity are still not fully understood. It is believed that the c-terminal domain of the protein undergoes a conformational change when exposed to blue light which allows for biological function. Three different non-functioning mutants were tested during this study to gain insight on the mechanism of cryptochrome. Absorbance spectra showed a difference between two of the mutants and the wild type with one mutant showing little difference. Immunoprecipitation experiments were also conducted to identify the different c-terminal responses of the mutants. By studying non functioning mutants of this protein, the mechanism of the protein can be further characterized. This two-month research experience in Paris allowed us to experience international and interdisciplinary collaborations in science and immerse in a different culture. The Borcer Fund for Student Research, Xavier University, Cincinnati, OH, and John Hauck Foundation.

Aligning Goals, Assessments, and Activities: An Approach to Teaching PCR and Gel Electrophoresis

PubMed Central

Robertson, Amber L.; Batzli, Janet; Harris, Michelle; Miller, Sarah

2008-01-01

Polymerase chain reaction (PCR) and gel electrophoresis have become common techniques used in undergraduate molecular and cell biology labs. Although students enjoy learning these techniques, they often cannot fully comprehend and analyze the outcomes of their experiments because of a disconnect between concepts taught in lecture and experiments done in lab. Here we report the development and implementation of novel exercises that integrate the biological concepts of DNA structure and replication with the techniques of PCR and gel electrophoresis. Learning goals were defined based on concepts taught throughout the cell biology lab course and learning objectives specific to the PCR and gel electrophoresis lab. Exercises developed to promote critical thinking and target the underlying concepts of PCR, primer design, gel analysis, and troubleshooting were incorporated into an existing lab unit based on the detection of genetically modified organisms. Evaluative assessments for each exercise were aligned with the learning goals and used to measure student learning achievements. Our analysis found that the exercises were effective in enhancing student understanding of these concepts as shown by student performance across all learning goals. The new materials were particularly helpful in acquiring relevant knowledge, fostering critical-thinking skills, and uncovering prevalent misconceptions. PMID:18316813

Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon.

PubMed

Torelli, Emanuela; Kozyra, Jerzy Wieslaw; Gu, Jing-Ying; Stimming, Ulrich; Piantanida, Luca; Voïtchovsky, Kislon; Krasnogor, Natalio

2018-05-03

RNA presents intringuing roles in many cellular processes and its versatility underpins many different applications in synthetic biology. Nonetheless, RNA origami as a method for nanofabrication is not yet fully explored and the majority of RNA nanostructures are based on natural pre-folded RNA. Here we describe a biologically inert and uniquely addressable RNA origami scaffold that self-assembles into a nanoribbon by seven staple strands. An algorithm is applied to generate a synthetic De Bruijn scaffold sequence that is characterized by the lack of biologically active sites and repetitions larger than a predetermined design parameter. This RNA scaffold and the complementary staples fold in a physiologically compatible isothermal condition. In order to monitor the folding, we designed a new split Broccoli aptamer system. The aptamer is divided into two nonfunctional sequences each of which is integrated into the 5' or 3' end of two staple strands complementary to the RNA scaffold. Using fluorescence measurements and in-gel imaging, we demonstrate that once RNA origami assembly occurs, the split aptamer sequences are brought into close proximity forming the aptamer and turning on the fluorescence. This light-up 'bio-orthogonal' RNA origami provides a prototype that can have potential for in vivo origami applications.

Discovery and Characterization of a Highly Potent and Selective Aminopyrazoline-Based in Vivo Probe (BAY-598) for the Protein Lysine Methyltransferase SMYD2.

PubMed

Eggert, Erik; Hillig, Roman C; Koehr, Silke; Stöckigt, Detlef; Weiske, Jörg; Barak, Naomi; Mowat, Jeffrey; Brumby, Thomas; Christ, Clara D; Ter Laak, Antonius; Lang, Tina; Fernandez-Montalvan, Amaury E; Badock, Volker; Weinmann, Hilmar; Hartung, Ingo V; Barsyte-Lovejoy, Dalia; Szewczyk, Magdalena; Kennedy, Steven; Li, Fengling; Vedadi, Masoud; Brown, Peter J; Santhakumar, Vijayaratnam; Arrowsmith, Cheryl H; Stellfeld, Timo; Stresemann, Carlo

2016-05-26

Protein lysine methyltransferases have recently emerged as a new target class for the development of inhibitors that modulate gene transcription or signaling pathways. SET and MYND domain containing protein 2 (SMYD2) is a catalytic SET domain containing methyltransferase reported to monomethylate lysine residues on histone and nonhistone proteins. Although several studies have uncovered an important role of SMYD2 in promoting cancer by protein methylation, the biology of SMYD2 is far from being fully understood. Utilization of highly potent and selective chemical probes for target validation has emerged as a concept which circumvents possible limitations of knockdown experiments and, in particular, could result in an improved exploration of drug targets with a complex underlying biology. Here, we report the development of a potent, selective, and cell-active, substrate-competitive inhibitor of SMYD2, which is the first reported inhibitor suitable for in vivo target validation studies in rodents.

Reverse Genetics and High Throughput Sequencing Methodologies for Plant Functional Genomics

PubMed Central

Ben-Amar, Anis; Daldoul, Samia; Reustle, Götz M.; Krczal, Gabriele; Mliki, Ahmed

2016-01-01

In the post-genomic era, increasingly sophisticated genetic tools are being developed with the long-term goal of understanding how the coordinated activity of genes gives rise to a complex organism. With the advent of the next generation sequencing associated with effective computational approaches, wide variety of plant species have been fully sequenced giving a wealth of data sequence information on structure and organization of plant genomes. Since thousands of gene sequences are already known, recently developed functional genomics approaches provide powerful tools to analyze plant gene functions through various gene manipulation technologies. Integration of different omics platforms along with gene annotation and computational analysis may elucidate a complete view in a system biology level. Extensive investigations on reverse genetics methodologies were deployed for assigning biological function to a specific gene or gene product. We provide here an updated overview of these high throughout strategies highlighting recent advances in the knowledge of functional genomics in plants. PMID:28217003

Approach/avoidance in dreams.

PubMed

Malcolm-Smith, Susan; Koopowitz, Sheri; Pantelis, Eleni; Solms, Mark

2012-03-01

The influential threat simulation theory (TST) asserts that dreaming yields adaptive advantage by providing a virtual environment in which threat-avoidance may be safely rehearsed. We have previously found the incidence of biologically threatening dreams to be around 20%, with successful threat avoidance occurring in approximately one-fifth of such dreams. TST asserts that threat avoidance is over-represented relative to other possible dream contents. To begin assessing this issue, we contrasted the incidence of 'avoidance' dreams with that of their opposite: 'approach' dreams. Because TST states that the threat-avoidance function is only fully activated in ecologically valid (biologically threatening) contexts, we also performed this contrast for populations living in both high- and low-threat environments. We find that 'approach' dreams are significantly more prevalent across both contexts. We suggest these results are more consistent with the view that dreaming is generated by reward-seeking systems than by fear-conditioning systems, although reward-seeking is clearly not the only factor determining the content of dreams. Copyright © 2011 Elsevier Inc. All rights reserved.

Nucleophilic catalysis of acylhydrazone equilibration for protein-directed dynamic covalent chemistry

PubMed Central

Bhat, Venugopal T.; Caniard, Anne M.; Luksch, Torsten; Brenk, Ruth; Campopiano, Dominic J.; Greaney, Michael F.

2010-01-01

Dynamic covalent chemistry uses reversible chemical reactions to set up an equilibrating network of molecules at thermodynamic equilibrium, which can adjust its composition in response to any agent capable of altering the free energy of the system. When the target is a biological macromolecule, such as a protein, the process corresponds to the protein directing the synthesis of its own best ligand. Here, we demonstrate that reversible acylhydrazone formation is an effective chemistry for biological dynamic combinatorial library formation. In the presence of aniline as a nucleophilic catalyst, dynamic combinatorial libraries equilibrate rapidly at pH 6.2, are fully reversible, and may be switched on or off by means of a change in pH. We have interfaced these hydrazone dynamic combinatorial libraries with two isozymes from the glutathione S-transferase class of enzyme, and observed divergent amplification effects, where each protein selects the best-fitting hydrazone for the hydrophobic region of its active site. PMID:20489719

KEEPING AN EYE ON RETINOBLASTOMA CONTROL OF HUMAN EMBRYONIC STEM CELLS

PubMed Central

Conklin, Jamie F.; Sage, Julien

2010-01-01

Human embryonic stem cells (hESCs) hold great promise in regenerative medicine. However, before the full potential of these cells is achieved, major basic biological questions need to be addressed. In particular, there are still gaps in our knowledge of the molecular mechanisms underlying the derivation of hESCs from blastocysts, the regulation of the undifferentiated, pluripotent state, and the control of differentiation into specific lineages. Furthermore, we still do not fully understand the tumorigenic potential of hESCs, limiting their use in regenerative medicine. The RB pathway is a key signaling module that controls cellular proliferation, cell survival, chromatin structure, and cellular differentiation in mammalian cells. Members of the RB pathway are important regulators of hESC biology and manipulation of the activity of this pathway may provide novel means to control the fate of hESCs. Here we review what is known about the expression and function of members of the RB pathway in hESCs and discuss areas of interest in this field. PMID:19760644

[Psychosomatics is "expensive"].

PubMed

Hnízdil, J; Savlík, J

2005-01-01

Experience shoves that number of diseases where recognition and treatment is without limits of classical medicine is rising, however it is fully within the competence of psychosomatic approach. It does not concern the classical classification into organic and functional defects, but it concerns the possibility of complex approach. The theorem of "diagnosis per exclusionem" is still valid, as well as it is true that the means of medicine end at its biological limitations. We consider stressing in our article that psychosomatic diseases or psychosomatic patients do not exist and psychosomatics is not and independent specialization. Psychosomatics is, as inseparable unity of psychic and somatic activities, each human being. Complex biopsychosocial (psychosomatic) approach is the way of thinking and work, which considers human in unrepeatable oneness and context of his life. It does not mean to underestimate objective biological findings and results of instrumentally investigation, but their implanting into the complex network of consequences of the patient's life in order to choose the most appropriate methods of the care of the individual in healthiness and disease.

Differential regulation of EGFR-MAPK signaling by deoxycholic acid (DCA) and ursodeoxycholic acid (UDCA) in colon cancer.

PubMed

Centuori, Sara M; Martinez, Jesse D

2014-10-01

A high-fat diet coincides with increased levels of bile acids. This increase in bile acids, particularly deoxycholic acid (DCA), has been strongly associated with the development of colon cancer. Conversely, ursodeoxycholic acid (UDCA) may have chemopreventive properties. Although structurally similar, DCA and UDCA present different biological and pathological effects in colon cancer progression. The differential regulation of cancer by these two bile acids is not yet fully understood. However, one possible explanation for their diverging effects is their ability to differentially regulate signaling pathways involved in the multistep progression of colon cancer, such as the epidermal growth factor receptor (EGFR)-mitogen-activated protein kinase (MAPK) pathway. This review will examine the biological effects of DCA and UDCA on colon cancer development, as well as the diverging effects of these bile acids on the oncogenic signaling pathways that play a role in colon cancer development, with a particular emphasis on bile acid regulation of the EGFR-MAPK pathway.

Differential regulation of EGFR-MAPK signaling by deoxycholic acid (DCA) and ursodeoxycholic acid (UDCA) in colon cancer

PubMed Central

Centuori, Sara M.; Martinez, Jesse D.

2014-01-01

A high fat diet coincides with elevated levels of bile acids. This elevation of bile acids, particularly deoxycholic acid (DCA), has been strongly associated with the development of colon cancer. Conversely, ursodeoxycholic acid (UDCA) may have chemopreventive properties. Although structurally similar, DCA and UDCA present different biological and pathological effects in colon cancer progression. The differential regulation of cancer by these two bile acids is not yet fully understood. However, one possible explanation for their diverging effects is their ability to differentially regulate signaling pathways involved in the multistep progression of colon cancer, such as the epidermal growth factor receptor (EGFR) mitogen-activated protein kinase (MAPK) pathway. This review will examine the biological effects of DCA and UDCA on colon cancer development, as well as the diverging effects of these bile acids on the oncogenic signaling pathways that play a role in colon cancer development, with a particular emphasis on bile acid regulation of the EGFR-MAPK pathway. PMID:25027205

Production of Functional Glucagon-Secreting α-Cells From Human Embryonic Stem Cells

PubMed Central

Rezania, Alireza; Riedel, Michael J.; Wideman, Rhonda D.; Karanu, Francis; Ao, Ziliang; Warnock, Garth L.; Kieffer, Timothy J.

2011-01-01

OBJECTIVE Differentiation of human embryonic stem (hES) cells to fully developed cell types holds great therapeutic promise. Despite significant progress, the conversion of hES cells to stable, fully differentiated endocrine cells that exhibit physiologically regulated hormone secretion has not yet been achieved. Here we describe an efficient differentiation protocol for the in vitro conversion of hES cells to functional glucagon-producing α- cells. RESEARCH DESIGN AND METHODS Using a combination of small molecule screening and empirical testing, we developed a six-stage differentiation protocol for creating functional α-cells. An extensive in vitro and in vivo characterization of the differentiated cells was performed. RESULTS A high rate of synaptophysin expression (>75%) and robust expression of glucagon and the α-cell transcription factor ARX was achieved. After a transient polyhormonal state in which cells coexpress glucagon and insulin, maturation in vitro or in vivo resulted in depletion of insulin and other β-cell markers with concomitant enrichment of α-cell markers. After transplantation, these cells secreted fully processed, biologically active glucagon in response to physiologic stimuli including prolonged fasting and amino acid challenge. Moreover, glucagon release from transplanted cells was sufficient to reduce demand for pancreatic glucagon, resulting in a significant decrease in pancreatic α-cell mass. CONCLUSIONS These results indicate that fully differentiated pancreatic endocrine cells can be created via stepwise differentiation of hES cells. These cells may serve as a useful screening tool for the identification of compounds that modulate glucagon secretion as well as those that promote the transdifferentiation of α-cells to β-cells. PMID:20971966

Furin is a chemokine-modifying enzyme: in vitro and in vivo processing of CXCL10 generates a C-terminally truncated chemokine retaining full activity.

PubMed

Hensbergen, Paul J; Verzijl, Dennis; Balog, Crina I A; Dijkman, Remco; van der Schors, Roel C; van der Raaij-Helmer, Elizabeth M H; van der Plas, Mariena J A; Leurs, Rob; Deelder, André M; Smit, Martine J; Tensen, Cornelis P

2004-04-02

Chemokines comprise a class of structurally related proteins that are involved in many aspects of leukocyte migration under basal and inflammatory conditions. In addition to the large number of genes, limited processing of these proteins by a variety of enzymes enhances the complexity of the total spectrum of chemokine variants. We have recently shown that the native chemokine CXCL10 is processed at the C terminus, thereby shedding the last four amino acids. The present study was performed to elucidate the mechanism in vivo and in vitro and to study the biological activity of this novel isoform of CXCL10. Using a combination of protein purification and mass spectrometric techniques, we show that the production of C-terminally truncated CXCL10 by primary keratinocytes is inhibited in vivo by a specific inhibitor of pro-protein convertases (e.g. furin) but not by inhibition of matrix metalloproteinases. Moreover, CXCL10 is processed by furin in vitro, which is abrogated by a mutation in the furin recognition site. Using GTPgammaS binding, Ca(2+) mobilization, and chemotaxis assays, we demonstrate that the C-terminally truncated CXCL10 variant is a potent ligand for CXCR3. Moreover, the inverse agonist activity on the virally encoded receptor ORF74 and the direct antibacterial activity of CXCL10 are fully retained. Hence, we have identified furin as a novel chemokine-modifying enzyme in vitro and most probably also in vivo, generating a C-terminally truncated CXCL10, which fully retains its (inverse) agonistic properties.

Synthetic Biology: Engineering Living Systems from Biophysical Principles.

PubMed

Bartley, Bryan A; Kim, Kyung; Medley, J Kyle; Sauro, Herbert M

2017-03-28

Synthetic biology was founded as a biophysical discipline that sought explanations for the origins of life from chemical and physical first principles. Modern synthetic biology has been reinvented as an engineering discipline to design new organisms as well as to better understand fundamental biological mechanisms. However, success is still largely limited to the laboratory and transformative applications of synthetic biology are still in their infancy. Here, we review six principles of living systems and how they compare and contrast with engineered systems. We cite specific examples from the synthetic biology literature that illustrate these principles and speculate on their implications for further study. To fully realize the promise of synthetic biology, we must be aware of life's unique properties. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Robots Make Intelligent Teachers

ERIC Educational Resources Information Center

Trotter, Robert J.

1973-01-01

Discussion of the use of teaching machines to help a child learn the basics of geometry. Fully developed educational modules for such subjects as physics, biology, physiology and linguistics are forth-coming. (EB)

Organic micropollutants paracetamol and ibuprofen-toxicity, biodegradation, and genetic background of their utilization by bacteria.

PubMed

Żur, Joanna; Piński, Artur; Marchlewicz, Ariel; Hupert-Kocurek, Katarzyna; Wojcieszyńska, Danuta; Guzik, Urszula

2018-06-19

Currently, analgesics and nonsteroidal anti-inflammatory drugs (NSAIDs) are classified as one of the most emerging group of xenobiotics and have been detected in various natural matrices. Among them, monocyclic paracetamol and ibuprofen, widely used to treat mild and moderate pain are the most popular. Since long-term adverse effects of these xenobiotics and their biological and pharmacokinetic activity especially at environmentally relevant concentrations are better understood, degradation of such contaminants has become a major concern. Moreover, to date, conventional wastewater treatment plants (WWTPs) are not fully adapted to remove that kind of micropollutants. Bioremediation processes, which utilize bacterial strains with increased degradation abilities, seem to be a promising alternative to the chemical methods used so far. Nevertheless, despite the wide prevalence of paracetamol and ibuprofen in the environment, toxicity and mechanism of their microbial degradation as well as genetic background of these processes remain not fully characterized. In this review, we described the current state of knowledge about toxicity and biodegradation mechanisms of paracetamol and ibuprofen and provided bioinformatics analysis concerning the genetic bases of these xenobiotics decomposition.

Analysis of galactosemia-linked mutations of GALT enzyme using a computational biology approach.

PubMed

Facchiano, A; Marabotti, A

2010-02-01

We describe the prediction of the structural and functional effects of mutations on the enzyme galactose-1-phosphate uridyltransferase related to the genetic disease galactosemia, using a fully computational approach. One hundred and seven single-point mutants were simulated starting from the structural model of the enzyme obtained by homology modeling methods. Several bioinformatics programs were then applied to each resulting mutant protein to analyze the effect of the mutations. The mutations have a direct effect on the active site, or on the dimer assembly and stability, or on the monomer stability. We describe how mutations may exert their effect at a molecular level by altering H-bonds, salt bridges, secondary structure or surface features. The alteration of protein stability, at level of monomer and/or dimer, is the main effect observed. We found an agreement between our results and the functional experimental data available in literature for some mutants. The data and analyses for all the mutants are fully available in the web-accessible database hosted at http://bioinformatica.isa.cnr.it/GALT.

Nature's chemical signatures in human olfaction: a foodborne perspective for future biotechnology.

PubMed

Dunkel, Andreas; Steinhaus, Martin; Kotthoff, Matthias; Nowak, Bettina; Krautwurst, Dietmar; Schieberle, Peter; Hofmann, Thomas

2014-07-07

The biocatalytic production of flavor naturals that determine chemosensory percepts of foods and beverages is an ever challenging target for academic and industrial research. Advances in chemical trace analysis and post-genomic progress at the chemistry-biology interface revealed odor qualities of nature's chemosensory entities to be defined by odorant-induced olfactory receptor activity patterns. Beyond traditional views, this review and meta-analysis now shows characteristic ratios of only about 3 to 40 genuine key odorants for each food, from a group of about 230 out of circa 10 000 food volatiles. This suggests the foodborn stimulus space has co-evolved with, and roughly match our circa 400 olfactory receptors as best natural agonists. This perspective gives insight into nature's chemical signatures of smell, provides the chemical odor codes of more than 220 food samples, and beyond addresses industrial implications for producing recombinants that fully reconstruct the natural odor signatures for use in flavors and fragrances, fully immersive interactive virtual environments, or humanoid bioelectronic noses. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Lipidomic Approaches towards Deciphering Glycolipids from Microalgae as a Reservoir of Bioactive Lipids

PubMed Central

da Costa, Elisabete; Silva, Joana; Mendonça, Sofia Hoffman; Abreu, Maria Helena; Domingues, Maria Rosário

2016-01-01

In recent years, noteworthy research has been performed around lipids from microalgae. Among lipids, glycolipids (GLs) are quite abundant in microalgae and are considered an important source of fatty acids (FAs). GLs are rich in 16- and 18-carbon saturated and unsaturated fatty acids and often contain polyunsaturated fatty acids (PUFAs) like n-3 α-linolenic (ALA 18:3), eicosapentaenoic (EPA, 20:5) and docosahexaenoic (DHA, 22:6). GLs comprise three major classes: monogalactosyldiacyl glycerolipids (MGDGs), digalactosyl diacylglycerolipids (DGDGs) and sulfoquinovosyl diacylglycerolipids (SQDGs), whose composition in FA directly depends on the growth conditions. Some of these lipids are high value-added compounds with antitumoral, antimicrobial and anti-inflammatory activities and also with important nutritional significance. To fully explore GLs’ bioactive properties it is necessary to fully characterize their structure and to understand the relation between the structure and their biological properties, which can be addressed using modern mass spectrometry (MS)-based lipidomic approaches. This review will focus on the up-to-date FA composition of GLs identified by MS-based lipidomics and their potential as phytochemicals. PMID:27213410

Mitsunobu alkylation of cancerostatic 5-fluorouridine with (2E)-10-hydroxydec-2-enoic acid, a fatty acid from royal jelly with multiple biological activities.

PubMed

Ottenhaus, Vanessa; Rosemeyer, Helmut

2015-09-01

5-Fluorouridine (1) - a nucleoside antimetabolite with strong cancerostatic properties - was protected i) at the 2'- and 3'-OH groups with a heptan-4-ylidene residue and ii) at the 5'-OH group with a (4-methoxyphenyl)(diphenyl)methyl residue. This fully protected compound, 3, was submitted to a Mitsunobu reaction with the N-hydroxysuccinimide (NHS) ester, 5, of (2E)-10-hydroxydec-2-enoic acid (4) which gave nucleolipid 6. The latter was detritylated with Cl2 CHCOOH to yield the co-drug 7 as NHS ester. Copyright © 2015 Verlag Helvetica Chimica Acta AG, Zürich.

Structure-function analyses unravel distinct effects of allosteric inhibitors of HIV-1 integrase on viral maturation and integration.

PubMed

Bonnard, Damien; Le Rouzic, Erwann; Eiler, Sylvia; Amadori, Céline; Orlov, Igor; Bruneau, Jean-Michel; Brias, Julie; Barbion, Julien; Chevreuil, Francis; Spehner, Danièle; Chasset, Sophie; Ledoussal, Benoit; Moreau, François; Saïb, Ali; Klaholz, Bruno P; Emiliani, Stéphane; Ruff, Marc; Zamborlini, Alessia; Benarous, Richard

2018-04-20

Recently, a new class of HIV-1 integrase (IN) inhibitors with a dual mode of action, called IN-LEDGF/p75 allosteric inhibitors (INLAIs), was described. Designed to interfere with the IN-LEDGF/p75 interaction during viral integration, unexpectedly, their major impact was on virus maturation. This activity has been linked to induction of aberrant IN multimerization, whereas inhibition of the IN-LEDGF/p75 interaction accounts for weaker antiretroviral effect at integration. Because these dual activities result from INLAI binding to IN at a single binding site, we expected that these activities co-evolved together, driven by the affinity for IN. Using an original INLAI, MUT-A, and its activity on an Ala-125 (A125) IN variant, we found that these two activities on A125-IN can be fully dissociated: MUT-A-induced IN multimerization and the formation of eccentric condensates in viral particles, which are responsible for inhibition of virus maturation, were lost, whereas inhibition of the IN-LEDGF/p75 interaction and consequently integration was fully retained. Hence, the mere binding of INLAI to A125 IN is insufficient to promote the conformational changes of IN required for aberrant multimerization. By analyzing the X-ray structures of MUT-A bound to the IN catalytic core domain (CCD) with or without the Ala-125 polymorphism, we discovered that the loss of IN multimerization is due to stabilization of the A125-IN variant CCD dimer, highlighting the importance of the CCD dimerization energy for IN multimerization. Our study reveals that affinity for the LEDGF/p75-binding pocket is not sufficient to induce INLAI-dependent IN multimerization and the associated inhibition of viral maturation. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Serine Protease Inhibitors in Ticks: An Overview of Their Role in Tick Biology and Tick-Borne Pathogen Transmission.

PubMed

Blisnick, Adrien A; Foulon, Thierry; Bonnet, Sarah I

2017-01-01

New tick and tick-borne pathogen control approaches that are both environmentally sustainable and which provide broad protection are urgently needed. Their development, however, will rely on a greater understanding of tick biology, tick-pathogen, and tick-host interactions. The recent advances in new generation technologies to study genomes, transcriptomes, and proteomes has resulted in a plethora of tick biomacromolecular studies. Among these, many enzyme inhibitors have been described, notably serine protease inhibitors (SPIs), whose importance in various tick biological processes is only just beginning to be fully appreciated. Among the multiple active substances secreted during tick feeding, SPIs have been shown to be directly involved in regulation of inflammation, blood clotting, wound healing, vasoconstriction and the modulation of host defense mechanisms. In light of these activities, several SPIs were examined and were experimentally confirmed to facilitate tick pathogen transmission. In addition, to prevent coagulation of the ingested blood meal within the tick alimentary canal, SPIs are also involved in blood digestion and nutrient extraction from the meal. The presence of SPIs in tick hemocytes and their involvement in tick innate immune defenses have also been demonstrated, as well as their implication in hemolymph coagulation and egg development. Considering the involvement of SPIs in multiple crucial aspects of tick-host-pathogen interactions, as well as in various aspects of the tick parasitic lifestyle, these molecules represent highly suitable and attractive targets for the development of effective tick control strategies. Here we review the current knowledge regarding this class of inhibitors in tick biology and tick-borne pathogen transmission, and their potential as targets for future tick control trials.

Serine Protease Inhibitors in Ticks: An Overview of Their Role in Tick Biology and Tick-Borne Pathogen Transmission

PubMed Central

Blisnick, Adrien A.; Foulon, Thierry; Bonnet, Sarah I.

2017-01-01

New tick and tick-borne pathogen control approaches that are both environmentally sustainable and which provide broad protection are urgently needed. Their development, however, will rely on a greater understanding of tick biology, tick-pathogen, and tick-host interactions. The recent advances in new generation technologies to study genomes, transcriptomes, and proteomes has resulted in a plethora of tick biomacromolecular studies. Among these, many enzyme inhibitors have been described, notably serine protease inhibitors (SPIs), whose importance in various tick biological processes is only just beginning to be fully appreciated. Among the multiple active substances secreted during tick feeding, SPIs have been shown to be directly involved in regulation of inflammation, blood clotting, wound healing, vasoconstriction and the modulation of host defense mechanisms. In light of these activities, several SPIs were examined and were experimentally confirmed to facilitate tick pathogen transmission. In addition, to prevent coagulation of the ingested blood meal within the tick alimentary canal, SPIs are also involved in blood digestion and nutrient extraction from the meal. The presence of SPIs in tick hemocytes and their involvement in tick innate immune defenses have also been demonstrated, as well as their implication in hemolymph coagulation and egg development. Considering the involvement of SPIs in multiple crucial aspects of tick-host-pathogen interactions, as well as in various aspects of the tick parasitic lifestyle, these molecules represent highly suitable and attractive targets for the development of effective tick control strategies. Here we review the current knowledge regarding this class of inhibitors in tick biology and tick-borne pathogen transmission, and their potential as targets for future tick control trials. PMID:28589099

Fourier transform Raman spectroscopy of synthetic and biological calcium phosphates.

PubMed

Sauer, G R; Zunic, W B; Durig, J R; Wuthier, R E

1994-05-01

Fourier-transform (FT) Raman spectroscopy was used to characterize the organic and mineral components of biological and synthetic calcium phosphate minerals. Raman spectroscopy provides information on biological minerals that is complimentary to more widely used infrared methodologies as some infrared-inactive vibrational modes are Raman-active. The application of FT-Raman technology has, for the first time, enabled the problems of high sample fluorescence and low signal-to-noise that are inherent in calcified tissues to be overcome. Raman spectra of calcium phosphates are dominated by a very strong band near 960 cm-1 that arises from the symmetric stretching mode (v1) of the phosphate group. Other Raman-active phosphate vibrational bands are seen at approximately 1075 (v3), 590 (v4), and 435 cm-1 (v2). Minerals containing acidic phosphate groups show additional vibrational modes. The different calcium phosphate mineral phases can be distinguished from one another by the relative positions and shapes of these bands in the Raman spectra. FT-Raman spectra of nascent, nonmineralized matrix vesicles (MV) show a distinct absence of the phosphate v1 band even though these structures are rich in calcium and phosphate. Similar results were seen with milk casein and synthetic Ca-phosphatidyl-serine-PO4 complexes. Hence, the phosphate and/or acidic phosphate ions in these noncrystalline biological calcium phosphates is in a molecular environment that differs from that in synthetic amorphous calcium phosphate. In MV, the first distinct mineral phase to form contained acidic phosphate bands similar to those seen in octacalcium phosphate. The mineral phase present in fully mineralized MV was much more apatitic, resembling that found in bones and teeth.(ABSTRACT TRUNCATED AT 250 WORDS)

Aryldiones incorporating a [1,4,5]oxadiazepane ring. Part 2: chemistry and biology of the cereal herbicide pinoxaden.

PubMed

Muehlebach, Michel; Cederbaum, Fredrik; Cornes, Derek; Friedmann, Adrian A; Glock, Jutta; Hall, Gavin; Indolese, Adriano F; Kloer, Daniel P; Le Goupil, Gael; Maetzke, Thomas; Meier, Hans; Schneider, Rudolf; Stoller, André; Szczepanski, Henry; Wendeborn, Sebastian; Widmer, Hansjuerg

2011-12-01

Pinoxaden is a new cereal herbicide that provides outstanding levels of post-emergence activity against a broad spectrum of grass weed species for worldwide selective use in both wheat and barley. Factors influencing activity and tolerance to pinoxaden were in part linked to distinct structural parts of the active ingredient. Three complementary contributions that decisively impact upon the herbicidal potency against grasses were identified: a preferred 2,6-diethyl-4-methyl aromatic substitution pattern, a dione area suitable for proherbicide formation and beneficial adjuvant effects. The uptake and translocation pattern of pinoxaden when coapplied with its tailored adjuvant were analysed by autoradiography, indicating extensive and rapid penetration, followed by effective distribution throughout the plant. Crop injury reduction on incorporation of the [1,4,5]oxadiazepane ring into the aryldione template was reinforced with safener technology. Comparative studies on the behaviour of pinoxaden applied either alone or in combination with the safener cloquintocet-mexyl demonstrated that addition of the safener resulted in significant enhancement of metabolic degradation in wheat and barley, providing excellent crop tolerance and a substantial selectivity margin without adverse effects on weed control. The biological potential of pinoxaden and its active principle pinoxaden dione in terms of grass weed control and tolerance in cereals was fully exploited by inclusion of the safener cloquintocet-mexyl in the formulation in combination with a specific and tailor-made tank-mix adjuvant based on methylated rape seed oil. Copyright © 2011 Society of Chemical Industry.

Extraction of temporally correlated features from dynamic vision sensors with spike-timing-dependent plasticity.

PubMed

Bichler, Olivier; Querlioz, Damien; Thorpe, Simon J; Bourgoin, Jean-Philippe; Gamrat, Christian

2012-08-01

A biologically inspired approach to learning temporally correlated patterns from a spiking silicon retina is presented. Spikes are generated from the retina in response to relative changes in illumination at the pixel level and transmitted to a feed-forward spiking neural network. Neurons become sensitive to patterns of pixels with correlated activation times, in a fully unsupervised scheme. This is achieved using a special form of Spike-Timing-Dependent Plasticity which depresses synapses that did not recently contribute to the post-synaptic spike activation, regardless of their activation time. Competitive learning is implemented with lateral inhibition. When tested with real-life data, the system is able to extract complex and overlapping temporally correlated features such as car trajectories on a freeway, after only 10 min of traffic learning. Complete trajectories can be learned with a 98% detection rate using a second layer, still with unsupervised learning, and the system may be used as a car counter. The proposed neural network is extremely robust to noise and it can tolerate a high degree of synaptic and neuronal variability with little impact on performance. Such results show that a simple biologically inspired unsupervised learning scheme is capable of generating selectivity to complex meaningful events on the basis of relatively little sensory experience. Copyright © 2012 Elsevier Ltd. All rights reserved.

Towards the development of tumor necrosis factor (TNF) sensitizers: making TNF work against cancer.

PubMed

Mocellin, Simone; Pilati, Pierluigi; Nitti, Donato

2007-01-01

Although TNF antitumor activity has been demonstrated in many preclinical models and in non-comparative clinical trials, no evidence exists that TNF-based treatments increase patient survival. Moreover, due to systemic toxicity, TNF can only be administered through sophisticated locoregional drug-delivery systems in patients with some types of organ-confined solid tumors; as a corollary, the impossibility to administer TNF through the systemic route does not allow to test the effectiveness of this cytokine in other clinical settings for the treatment of a broader spectrum of tumor types. A challenge many researchers are tackling is to dissect the cascade of molecular events underlying tumor sensitivity to TNF so to fully explore the anticancer potential of this molecule. The rationale for the development of strategies aimed at sensitizing malignant cells to TNF is to exploit tumor-specific molecular derangements to modulate TNF biological activities and ultimately maximize its tumor-selective cytotoxicity. This would not only enhance the anticancer activity of current TNF-based locoregional regimens, but would also open the avenue to the systemic administration of this cytokine and thus to a much wider clinical experimentation of TNF in the oncology field. In this review we first summarize the molecular biology of TNF and its cancer-related properties; then, the available findings regarding some among the most promising and best characterized TNF sensitizers are overviewed.

Omeprazole, a specific inhibitor of gastric (H/sup +/-K/sup +/)-ATPase, is a H/sup +/-activated oxidizing agent of sulfhydryl groups

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

Im, W.B.; Sih, J.C.; Blakeman, D.P.

1985-04-25

Omeprazole (5-methoxy-2-(((4-methoxy-3,5- dimethylpyridinyl)methyl)sulfinyl)-1H-benzimidazole) appeared to inhibit gastric (H/sup +/-K/sup +/)-ATPase by oxidizing its essential sulfhydryl groups, since the gastric ATPase inactivated by the drug in vivo or in vitro recovered its K+-dependent ATP hydrolyzing activity upon incubation with mercaptoethanol. Biological reducing agents like cysteine or glutathione, however, were unable to reverse the inhibitory effect of omeprazole. Moreover, acidic environments enhanced the potency of omeprazole. The chemical reactivity of omeprazole with mercaptans is also consistent with the biological action of omeprazole. The N-sulfenylated compound reacted at neutral pH with another stoichiometric amount of ethyl mercaptan to produce omeprazole sulfide quantitatively. Themore » gastric polypeptides of 100 kilodaltons representing (H/sup +/-K/sup +/)-ATPase in the rat gastric mucosa or isolated hog gastric membranes were covalently labeled with (/sup 14/C)omeprazole. The radioactive label bound to the ATPase, however, could not be displaced by mercaptoethanol under the identical conditions where the ATPase activity was fully restored. These observations suggest that the essential sulfhydryl groups which reacted with omeprazole did not form a stable covalent bond with the drug, but rather that they further reacted with adjacent sulfhydryl groups to form disulfides which could be reduced by mercaptoethanol.« less

Stimulation of Wound Healing by Electroactive, Antibacterial, and Antioxidant Polyurethane/Siloxane Dressing Membranes: In Vitro and in Vivo Evaluations.

PubMed

Gharibi, Reza; Yeganeh, Hamid; Rezapour-Lactoee, Alireza; Hassan, Zuhair M

2015-11-04

A series of novel polyurethane/siloxane-based wound dressing membranes was prepared through sol-gel reaction of methoxysilane end-functionalized urethane prepolymers composed of castor oil and ricinoleic methyl ester as well as methoxysilane functional aniline tetramer (AT) moieties. The samples were fully characterized and their physicochemical, mechanical, electrical, and biological properties were assayed. The biological activity of these dressings against fibroblast cells and couple of microbes was also studied. It was revealed that samples that displayed electroactivity by introduction of AT moieties showed a broad range of antimicrobial activity toward different microorganisms, promising antioxidant (radical scavenging) efficiency and significant activity for stimulation of fibroblast cell growth and proliferation. Meanwhile, these samples showed appropriate tensile strength and ability for maintaining a moist environment over a wound by controlled equilibrium water absorption and water vapor transmission rate. The selected electroactive dressing was subjected to an in vivo assay using a rat animal model and the wound healing process was monitored and compared with analogous dressing without AT moieties. The recorded results showed that the electroactive dressings induced an increase in the rate of wound contraction, promoted collagen deposition, and encouraged vascularization in the wounded area. On the basis of the results of in vitro and in vivo assays, the positive influence of designed dressings for accelerated healing of a wound model was confirmed.

Mexican Arnica (Heterotheca inuloides Cass. Asteraceae: Astereae): Ethnomedical uses, chemical constituents and biological properties.

PubMed

Rodríguez-Chávez, José Luis; Egas, Verónica; Linares, Edelmira; Bye, Robert; Hernández, Tzasna; Espinosa-García, Francisco J; Delgado, Guillermo

2017-01-04

Heterotheca inuloides Cass. (Asteraceae) has been traditionally used to treat a wide range of diseases in Mexico in the treatment of rheumatism, topical skin inflammation, muscular pain colic, and other painful conditions associated with inflammatory processes, additionally has been used to treat dental diseases, and gastrointestinal disorders. This species has also been used for the treatment of cancer and diabetes. This review provides up-to-date information on the botanical characterization, traditional uses, chemical constituents, as well as the biolological activities of H. inuloides. A literature search was conducted by analyzing the published scientific material. Information related to H. inuloides was collected from various primary information sources, including books, published articles in peer-reviewed journals, monographs, theses and government survey reports. The electronic search of bibliographic information was gathered from accepted scientific databases such as Scienfinder, ISI Web of Science, Scielo, LILACS, Redalyc, Pubmed, SCOPUS and Google Scholar. To date, more than 140 compounds have been identified from H. inuloides, including cadinane sesquiterpenes, flavonoids, phytosterols, triterpenes, benzoic acid derivatives, and other types of compounds. Many biological properties associated with H. inuloides. Many studies have shown that the extracts and some compounds isolated from this plant exhibit a broad spectrum of biological activities such as antioxidant, antitumor, anti-inflammatory, cytotoxic, and chelating activities, as well as insecticidal and phytotoxic activity. To date, reports on the toxicity of H. inuloides are limited. A comprehensive analysis of the literature obtained through the above-mentioned sources confirmed that ethnomedical uses of H. inuloides have been recorded in Mexico to treat rheumatism, pain, and conditions associated with inflammatory processes. Pharmacological studies have demonstrated the activity of certain compounds associated with the traditional use of the plant such as the anti-inflammatory and cytotoxic activities of the species. The available literature showed that cadinene sesquiterpenes are the major bioactive components of H. inuloides with potential pharmacological activities. Further investigations are needed to fully understand the mode of action of the major active constituents. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

A Biomechanical Comparison of Proportional Electromyography Control to Biological Torque Control Using a Powered Hip Exoskeleton.

PubMed

Young, Aaron J; Gannon, Hannah; Ferris, Daniel P

2017-01-01

Despite a large increase in robotic exoskeleton research, there are few studies that have examined human performance with different control strategies on the same exoskeleton device. Direct comparison studies are needed to determine how users respond to different types of control. The purpose of this study was to compare user performance using a robotic hip exoskeleton with two different controllers: a controller that targeted a biological hip torque profile and a proportional myoelectric controller. We tested both control approaches on 10 able-bodied subjects using a pneumatically powered hip exoskeleton. The state machine controller targeted a biological hip torque profile. The myoelectric controller used electromyography (EMG) of lower limb muscles to produce a proportional control signal for the hip exoskeleton. Each subject performed two 30-min exoskeleton walking trials (1.0 m/s) using each controller and a 10-min trial with the exoskeleton unpowered. During each trial, we measured subjects' metabolic cost of walking, lower limb EMG profiles, and joint kinematics and kinetics (torques and powers) using a force treadmill and motion capture. Compared to unassisted walking in the exoskeleton, myoelectric control significantly reduced metabolic cost by 13% ( p  = 0.005) and biological hip torque control reduced metabolic cost by 7% ( p  = 0.261). Subjects reduced muscle activity relative to the unpowered condition for a greater number of lower limb muscles using myoelectric control compared to the biological hip torque control. More subjects subjectively preferred the myoelectric controller to the biological hip torque control. Myoelectric control had more advantages (metabolic cost and muscle activity reduction) compared to a controller that targeted a biological torque profile for walking with a robotic hip exoskeleton. However, these results were obtained with a single exoskeleton device with specific control configurations while level walking at a single speed. Further testing on different exoskeleton hardware and with more varied experimental protocols, such as testing over multiple types of terrain, is needed to fully elucidate the potential benefits of myoelectric control for exoskeleton technology.

Are attractors 'strange', or is life more complicated than the simple laws of physics?

PubMed

Pogun, S

2001-01-01

Interesting and intriguing questions involve complex systems whose properties cannot be explained fully by reductionist approaches. Last century was dominated by physics, and applying the simple laws of physics to biology appeared to be a practical solution to understand living organisms. However, although some attributes of living organisms involve physico-chemical properties, the genetic program and evolutionary history of complex biological systems make them unique and unpredictable. Furthermore, there are and will be 'unobservable' phenomena in biology which have to be accounted for.

Heritability and genetic correlations of personality traits in a wild population of yellow-bellied marmots (Marmota flaviventris).

PubMed

Petelle, M B; Martin, J G A; Blumstein, D T

2015-10-01

Describing and quantifying animal personality is now an integral part of behavioural studies because individually distinctive behaviours have ecological and evolutionary consequences. Yet, to fully understand how personality traits may respond to selection, one must understand the underlying heritability and genetic correlations between traits. Previous studies have reported a moderate degree of heritability of personality traits, but few of these studies have either been conducted in the wild or estimated the genetic correlations between personality traits. Estimating the additive genetic variance and covariance in the wild is crucial to understand the evolutionary potential of behavioural traits. Enhanced environmental variation could reduce heritability and genetic correlations, thus leading to different evolutionary predictions. We estimated the additive genetic variance and covariance of docility in the trap, sociability (mirror image stimulation), and exploration and activity in two different contexts (open-field and mirror image simulation experiments) in a wild population of yellow-bellied marmots (Marmota flaviventris). We estimated both heritability of behaviours and of personality traits and found nonzero additive genetic variance in these traits. We also found nonzero maternal, permanent environment and year effects. Finally, we found four phenotypic correlations between traits, and one positive genetic correlation between activity in the open-field test and sociability. We also found permanent environment correlations between activity in both tests and docility and exploration in the MIS test. This is one of a handful of studies to adopt a quantitative genetic approach to explain variation in personality traits in the wild and, thus, provides important insights into the potential variance available for selection. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Duplication of the genome in normal and cancer cell cycles.

PubMed

Bandura, Jennifer L; Calvi, Brian R

2002-01-01

It is critical to discover the mechanisms of normal cell cycle regulation if we are to fully understand what goes awry in cancer cells. The normal eukaryotic cell tightly regulates the activity of origins of DNA replication so that the genome is duplicated exactly once per cell cycle. Over the last ten years much has been learned concerning the cell cycle regulation of origin activity. It is now clear that the proteins and cell cycle mechanisms that control origin activity are largely conserved from yeast to humans. Despite this conservation, the composition of origins of DNA replication in higher eukaryotes remains ill defined. A DNA consensus for predicting origins has yet to emerge, and it is of some debate whether primary DNA sequence determines where replication initiates. In this review we outline what is known about origin structure and the mechanism of once per cell cycle DNA replication with an emphasis on recent advances in mammalian cells. We discuss the possible relevance of these regulatory pathways for cancer biology and therapy.

An overview of Japanese CELSS research activities

NASA Technical Reports Server (NTRS)

Nitta, Keiji

1987-01-01

Development of Controlled Ecological Life Support System (CELSS) technology is inevitable for future long duration stays of human beings in space, for lunar base construction and for manned Mars flight programs. CELSS functions can be divided into 2 categories, Environmental Control and Material Recycling. Temperature, humidity, total atmospheric pressure and partial pressure of oxygen and carbon dioxide, necessary for all living things, are to be controlled by the environment control function. This function can be performed by technologies already developed and used as the Environment Control Life Support System (ECLSS) of Space Shuttle and Space Station. As for material recycling, matured technologies have not yet been established for fully satisfying the specific metabolic requirements of each living thing including human beings. Therefore, research activities for establishing CELSS technology should be focused on material recycling technologies using biological systems such as plants and animals and physico-chemical systems, for example, a gas recycling system, a water purifying and recycling system and a waste management system. Japanese research activities were conducted and will be continued accordingly.

Learning Biological Networks via Bootstrapping with Optimized GO-based Gene Similarity

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

Taylor, Ronald C.; Sanfilippo, Antonio P.; McDermott, Jason E.

2010-08-02

Microarray gene expression data provide a unique information resource for learning biological networks using "reverse engineering" methods. However, there are a variety of cases in which we know which genes are involved in a given pathology of interest, but we do not have enough experimental evidence to support the use of fully-supervised/reverse-engineering learning methods. In this paper, we explore a novel semi-supervised approach in which biological networks are learned from a reference list of genes and a partial set of links for these genes extracted automatically from PubMed abstracts, using a knowledge-driven bootstrapping algorithm. We show how new relevant linksmore » across genes can be iteratively derived using a gene similarity measure based on the Gene Ontology that is optimized on the input network at each iteration. We describe an application of this approach to the TGFB pathway as a case study and show how the ensuing results prove the feasibility of the approach as an alternate or complementary technique to fully supervised methods.« less

Rapid Detection of Thrombin and Other Protease Activity Directly in Whole Blood

NASA Astrophysics Data System (ADS)

Yu, Johnson Chung Sing

Thrombin is a serine protease that plays a key role in the clotting cascade to promote hemostasis following injury to the endothelium. From a clinical diagnostic perspective, in-vivo thrombin activity is linked to various blood clotting disorders, as well as cardiovascular disease (DVT, arteriosclerosis, etc). Thus, the ability to rapidly measure protease activity directly in whole blood will provide important new diagnostics, and clinical researchers with a powerful tool to further elucidate the relationship between circulating protease levels and disease. The ultimate goal is to design novel point of care (POC) diagnostic devices that are capable of monitoring protease activities directly in whole blood and biological sample. A charge-changing substrate specific to the thrombin enzyme was engineered and its functionality was confirmed by a series of experiments. This led to the preliminary design, construction, and testing of two device platforms deemed fully functional for the electrophoretic separation and focusing of charged peptide fragments. The concept of using the existing charge-changing substrate platform for bacterial protease detection was also investigated. Certain strains of E coli are associated with severe symptoms such as abdominal cramps, bloody diarrhea, and vomiting. The OmpT protease is expressed on the outer membrane of E coli and plays a role in the cleavage of antimicrobial peptides, the degradation of recombinant heterologous proteins, and the activation of plasminogen in the host. Thus, a synthetic peptide substrate specific to the OmpT protease was designed and modeled for the purpose of detecting E coli in biological sample.

Main Strategies of Plant Expression System Glycoengineering for Producing Humanized Recombinant Pharmaceutical Proteins.

PubMed

Rozov, S M; Permyakova, N V; Deineko, E V

2018-03-01

Most the pharmaceutical proteins are derived not from their natural sources, rather their recombinant analogs are synthesized in various expression systems. Plant expression systems, unlike mammalian cell cultures, combine simplicity and low cost of procaryotic systems and the ability for posttranslational modifications inherent in eucaryotes. More than 50% of all human proteins and more than 40% of the currently used pharmaceutical proteins are glycosylated, that is, they are glycoproteins, and their biological activity, pharmacodynamics, and immunogenicity depend on the correct glycosylation pattern. This review examines in detail the similarities and differences between N- and O-glycosylation in plant and mammalian cells, as well as the effect of plant glycans on the activity, pharmacokinetics, immunity, and intensity of biosynthesis of pharmaceutical proteins. The main current strategies of glycoengineering of plant expression systems aimed at obtaining fully humanized proteins for pharmaceutical application are summarized.

The effect of activated carbon addition on membrane bioreactor processes for wastewater treatment and reclamation - A critical review.

PubMed

Skouteris, George; Saroj, Devendra; Melidis, Paraschos; Hai, Faisal I; Ouki, Sabèha

2015-06-01

This review concentrates on the effect of activated carbon (AC) addition to membrane bioreactors (MBRs) treating wastewaters. Use of AC-assisted MBRs combines adsorption, biodegradation and membrane filtration. This can lead to advanced removal of recalcitrant pollutants and mitigation of membrane fouling. The relative contribution of adsorption and biodegradation to overall removal achieved by an AC-assisted MBR process can vary, and "biological AC" may not fully develop due to competition of target pollutants with bulk organics in wastewater. Thus periodic replenishment of spent AC is necessary. Sludge retention time (SRT) governs the frequency of spent AC withdrawal and addition of fresh AC, and is an important parameter that significantly influences the performance of AC-assisted MBRs. Of utmost importance is AC dosage because AC overdose may aggravate membrane fouling, increase sludge viscosity, impair mass transfer and reduce sludge dewaterability. Copyright © 2015 Elsevier Ltd. All rights reserved.

Sulfation effect on levan polysaccharide chains structure with molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Coskunkan, Binnaz; Turgut, Deniz; Rende, Deniz; Malta, Seyda; Baysal, Nihat; Ozisik, Rahmi; Toksoy-Oner, Ebru

Diversity in conformations and structural heterogeneity make polysaccharides the most challenging biopolymer type for experimental and theoretical characterization studies. Levan is a biopolymer chain that consists of fructose rings with β(2-6) linkages. It is a glycan that has great potential as a functional biopolymer in foods, feeds, cosmetics, pharmaceutical and chemical industries. Sulfated polysaccharides are group of macromolecules with sulfated groups in their hydroxyl parts with a range of important biological properties. Sulfate groups and their positions have a major effect on anticoagulant activity. It is reported that sulfate modified levan has anticoagulant activity such as heparin. In the current study, the effect of sulfation on the structure and dynamics of unmodified and sulfate modified levan are investigated via fully atomistic Molecular Dynamics simulations in aqueous media and varying salt concentrations at 310 K. This material is based upon work supported by the National Science Foundation under Grant No. CMMI-1538730.

Selenium-containing organic nanoparticles as silent precursors for ultra-sensitive thiol-responsive transmembrane anion transport.

PubMed

Lang, Chao; Zhang, Xin; Dong, Zeyuan; Luo, Quan; Qiao, Shanpeng; Huang, Zupeng; Fan, Xiaotong; Xu, Jiayun; Liu, Junqiu

2016-02-07

An anion transporter with a selenoxide group was able to form nanoparticles in water, whose activity was fully turned off due to the aggregation effect. The formed nanoparticles have a uniform size and can be readily dispersed in water at high concentrations. Turn-on of the nanoparticles by reducing molecules is proposed to be a combined process, including the reduction of selenoxide to selenide, disassembly of the nanoparticles and location of the transporter to the lipid membrane. Accordingly, a special acceleration phase can be observed in the turn-on kinetic curves. Since turn-on of the nanoparticles is quantitatively related to the amount of reductant, the nanoparticles can be activated in a step-by-step manner. Due to the sensibility of this system to thiols, cysteine can be detected at low nanomolar concentrations. This ultra-sensitive thiol-responsive transmembrane anion transport system is quite promising in biological applications.

Seamless integration of dose-response screening and flow chemistry: efficient generation of structure-activity relationship data of β-secretase (BACE1) inhibitors.

PubMed

Werner, Michael; Kuratli, Christoph; Martin, Rainer E; Hochstrasser, Remo; Wechsler, David; Enderle, Thilo; Alanine, Alexander I; Vogel, Horst

2014-02-03

Drug discovery is a multifaceted endeavor encompassing as its core element the generation of structure-activity relationship (SAR) data by repeated chemical synthesis and biological testing of tailored molecules. Herein, we report on the development of a flow-based biochemical assay and its seamless integration into a fully automated system comprising flow chemical synthesis, purification and in-line quantification of compound concentration. This novel synthesis-screening platform enables to obtain SAR data on b-secretase (BACE1) inhibitors at an unprecedented cycle time of only 1 h instead of several days. Full integration and automation of industrial processes have always led to productivity gains and cost reductions, and this work demonstrates how applying these concepts to SAR generation may lead to a more efficient drug discovery process. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Recombinant porcine epidermal growth factor-secreting Lactococcus lactis promotes the growth performance of early-weaned piglets

PubMed Central

2014-01-01

Background Epidermal growth factor (EGF) is an important growth factor in regulation of cell proliferation, differentiation, survival and apoptosis. Studies showed that food-grade Lactococcus lactis (L. lactis) and NICE expression system have superior performance in exogenous protein expression. This study aimed to construct and express porcine EGF (pEGF), and use L. lactis as vehicle for producing and delivering pEGF. Furthermore, investigating biological activity of pEGF and exploring applications feasibility of combination effects of L. lactis and pEGF on early weaned piglets’ production. Results A recombinant Lactococcus lactis which produced and secreted pEGF at 1000 ng/ml in culture supernatant was generated. Secreted pEGF was a fully biologically active protein, as demonstrated by its capacity to stimulate L929 mouse fibroblast cell line proliferation in vitro. For in vivo study, forty piglets were randomly allocated to control, antibiotic control, empty vector-expressing L. lactis (LL-EV) and pEGF-secreting L. lactis (LL-pEGF). After 14 d of rearing, final body weight and average daily gain in LL-pEGF were greater (P < 0.05, 8.95 vs. 8.37 kg, 206.1 vs. 157.7 g/day, respectively) than those in control, but no significant differences between LL-pEGF, LL-EV and antibiotic control. Overall period average daily feed intake was higher in LL-pEGF, LL-EV and antibiotic control than in control (P < 0.05, 252.9, 255.6, 250.0, 207.3 g/day, respectively). No significant difference was observed on ADFI/ADG. LL-pEGF increased villous height in the duodenum, jejunum and ileum than in control and LL-EV (P < 0.05). Sucrase in the 3 intestinal segments, aminopeptidase A in the duodenum and Jejunum, aminopeptidase N and dipeptidase IV in the duodenum in LL-pEGF were higher than those in control (P < 0.05). Furthermore, Escherichia coli and Enterococcus counts decreased in the ileum and Lactobacillus increased in the ileum and cecum digesta in LL-pEGF compare with the control (P < 0.05). Lactobacillus increased in the cecum in LL-EV compared with control and antibiotic control (P < 0.05). Conclusion We have generated a recombinant Lactococcus lactis which produced and secreted fully biologically active porcine EGF. Oral administration of pEGF-secreting L. lactis had beneficial effects on intestinal health and performance of early-weaned piglets. PMID:25142032

A spectrum of pharmacological activity in some biologically active peptides

PubMed Central

Bisset, G. W.; Lewis, G. P.

1962-01-01

The actions of bradykinin, angiotensin, oxytocin, vasopressin and substance P have been examined both on isolated smooth muscle preparations and in vivo. It was found that the isolated rat uterus and guinea-pig ileum can be used to distinguish between oxytocin and bradykinin and that the isolated rat colon and hen rectal caecum are almost specific test preparations for substance P. All the peptides were active on peripheral blood vessels, bradykinin, substance P and oxytocin causing vasodilatation and vasopressin and angiotensin vasoconstriction; bradykinin, substance P and angiotensin also caused an increase in capillary permeability in guinea-pigs. Only bradykinin and substance P were active in low concentrations in producing pain when applied to an exposed blister base. These two peptides were also active in causing bronchoconstriction. Oxytocin and vasopressin were the only peptides having milk-ejecting or antidiuretic activity which could be dissociated from cardiovascular effects. The spectrum of activity displayed by these peptides is in agreement with those functions which have been established for vasopressin and oxytocin and with those suggested, but not yet fully accepted, for bradykinin and angiotensin. It also indicates a possible function for substance P based on its vascular and permeability effects. ImagesFig. 6 PMID:13869527

Methods to examine reproductive biology in free-ranging, fully-marine mammals.

PubMed

Lanyon, Janet M; Burgess, Elizabeth A

2014-01-01

Historical overexploitation of marine mammals, combined with present-day pressures, has resulted in severely depleted populations, with many species listed as threatened or endangered. Understanding breeding patterns of threatened marine mammals is crucial to assessing population viability, potential recovery and conservation actions. However, determining reproductive parameters of wild fully-marine mammals (cetaceans and sirenians) is challenging due to their wide distributions, high mobility, inaccessible habitats, cryptic lifestyles and in many cases, large body size and intractability. Consequently, reproductive biologists employ an innovative suite of methods to collect useful information from these species. This chapter reviews historic, recent and state-of-the-art methods to examine diverse aspects of reproduction in fully-aquatic mammals.

Tagging and purifying proteins to teach molecular biology and advanced biochemistry.

PubMed

Roecklein-Canfield, Jennifer A; Lopilato, Jane

2004-11-01

Two distinct courses, "Molecular Biology" taught by the Biology Department and "Advanced Biochemistry" taught by the Chemistry Department, complement each other and, when taught in a coordinated and integrated way, can enhance student learning and understanding of complex material. "Molecular Biology" is a comprehensive lecture-based course with a 3-h laboratory once a week, while "Advanced Biochemistry" is a completely laboratory-based course with lecture fully integrated around independent student projects. Both courses emphasize and utilize cutting-edge technology. Teaching across departmental boundaries allows students access to faculty expertise and techniques rarely used at the undergraduate level, namely the tagging of proteins and their use in protein purification. Copyright © 2004 International Union of Biochemistry and Molecular Biology, Inc.

Scientists' opinions on the global status and management of biological diversity.

PubMed

Rudd, Murray A

2011-12-01

The large investments needed if loss of biological diversity is to be stemmed will likely lead to increased public and political scrutiny of conservation strategies and the science underlying them. It is therefore crucial to understand the degree of consensus or divergence among scientists on core scientific perceptions and strategies most likely to achieve given objectives. I developed an internet survey designed to elucidate the opinions of conservation scientists. Conservation scientists (n =583) were unanimous (99.5%) in their view that a serious loss of biological diversity is likely, very likely, or virtually certain. Scientists' agreement that serious loss is very likely or virtually certain ranged from 72.8% for Western Europe to 90.9% for Southeast Asia. Tropical coral ecosystems were perceived as the most seriously affected by loss of biological diversity; 88.0% of respondents familiar with that ecosystem type agreed that a serious loss is very likely or virtually certain. With regard to conservation strategies, scientists most often viewed understanding how people and nature interact in certain contexts and the role of biological diversity in maintaining ecosystem function as their priorities. Protection of biological diversity for its cultural and spiritual values and because of its usefulness to humans were low priorities, which suggests that many scientists do not fully support the utilitarian concept of ecosystem services. Many scientists expressed a willingness to consider conservation triage, engage in active conservation interventions, and consider reframing conservation goals and measures of success for conservation of biological diversity in an era of climate change. Although some heterogeneity of opinion is evident, results of the survey show a clear consensus within the scientific community on core issues of the extent and geographic scope of loss of biological diversity and on elements that may contribute to successful conservation strategies in the future. ©2011 Society for Conservation Biology.

Noise impact on wildlife: An environmental impact assessment

NASA Technical Reports Server (NTRS)

Bender, A.

1977-01-01

Various biological effects of noise on animals are discussed and a systematic approach for an impact assessment is developed. Further research is suggested to fully quantify noise impact on the species and its ecosystem.

Nano-hydroxyapatite modulates osteoblast lineage commitment by stimulation of DNA methylation and regulation of gene expression

PubMed Central

Ha, Shin-Woo; Jang, Hae Lin; Nam, Ki Tae; Beck, George R.

2015-01-01

Hydroxyapatite (HA) is the primary structural component of the skeleton and dentition. Under biological conditions, HA does not occur spontaneously and therefore must be actively synthesized by mineralizing cells such as osteoblasts. The mechanism(s) by which HA is actively synthesized by cells and deposited to create a mineralized matrix are not fully understood and the consequences of mineralization on cell function are even less well understood. HA can be chemically synthesized (HAp) and is therefore currently being investigated as a promising therapeutic biomaterial for use as a functional scaffold and implant coating for skeletal repair and dental applications. Here we investigated the biological effects of nano-HAp (10×100 nm) on the lineage commitment and differentiation of bone forming osteoblasts. Exposure of early stage differentiating osteoblasts resulted in dramatic and sustained changes in gene expression, both increased and decreased, whereas later stage osteoblasts were much less responsive. Analysis of the promoter region one of the most responsive genes, alkaline phosphatase, identified the stimulation of DNA methylation following cell exposure to nano-HAp. Collectively, the results reveal the novel epigenetic regulation of cell function by nano-HAp which has significant implication on lineage determination as well as identifying a novel potential therapeutic use of nanomaterials. PMID:26141836

Tocopherol composition of deodorization distillates and their antioxidative activity.

PubMed

Nogala-Kalucka, Malgorzata; Korczak, Jozef; Wagner, Karl-Heinz; Elmadfa, Ibrahim

2004-02-01

During the last stage of plant oil refining, deodorization distillates containing very important biological substances such as tocopherols, sterols, terpenoids or hydrocarbons are formed as a by-products. This study aimed at evaluating the content and antioxidant capacity of tocopherol concentrates from deodorization distillates obtained after the refining of rapeseed, soybean and sunflower oil. The majority of the matrix substances were eliminated from deodorization distillates by freezing with an acetone solution at -70 degrees C. The tocopherol concentrates obtained in this way contained approximately fivefold more tocopherols than the quantity in condensates after deodorization. Antioxidant activity was investigated by observing the peroxide value at 25 degrees C and using the Oxidograph test. The test medium was lard enriched with the tocopherol concentrates of the three plant oils versus single, synthetic alpha-, gamma- and delta-tocopherols (-T), which served for comparison. In these model systems, all investigated tocopherol concentrates exhibited antioxidant capacity. Their antioxidant effect was significantly lower than that of single delta-T and gamma-T, but significantly higher than alpha-T. The results prove that natural tocopherol concentrates obtained from plant oils are valuable food antioxidants and they also increase the biological and nutritional value of food especially when administered to animal fats or food of animal origin. Tocopherol concentrates can fully replace synthetic antioxidants that have been used thus far.

Enzymatic production of defined chitosan oligomers with a specific pattern of acetylation using a combination of chitin oligosaccharide deacetylases

NASA Astrophysics Data System (ADS)

Hamer, Stefanie Nicole; Cord-Landwehr, Stefan; Biarnés, Xevi; Planas, Antoni; Waegeman, Hendrik; Moerschbacher, Bruno Maria; Kolkenbrock, Stephan

2015-03-01

Chitin and chitosan oligomers have diverse biological activities with potentially valuable applications in fields like medicine, cosmetics, or agriculture. These properties may depend not only on the degrees of polymerization and acetylation, but also on a specific pattern of acetylation (PA) that cannot be controlled when the oligomers are produced by chemical hydrolysis. To determine the influence of the PA on the biological activities, defined chitosan oligomers in sufficient amounts are needed. Chitosan oligomers with specific PA can be produced by enzymatic deacetylation of chitin oligomers, but the diversity is limited by the low number of chitin deacetylases available. We have produced specific chitosan oligomers which are deacetylated at the first two units starting from the non-reducing end by the combined use of two different chitin deacetylases, namely NodB from Rhizobium sp. GRH2 that deacetylates the first unit and COD from Vibrio cholerae that deacetylates the second unit starting from the non-reducing end. Both chitin deacetylases accept the product of each other resulting in production of chitosan oligomers with a novel and defined PA. When extended to further chitin deacetylases, this approach has the potential to yield a large range of novel chitosan oligomers with a fully defined architecture.

Discovery of functional interactions among actin regulators by analysis of image fluctuations in an unperturbed motile cell system.

PubMed

Isogai, Tadamoto; Danuser, Gaudenz

2018-05-26

Cell migration is driven by propulsive forces derived from polymerizing actin that pushes and extends the plasma membrane. The underlying actin network is constantly undergoing adaptation to new mechano-chemical environments and intracellular conditions. As such, mechanisms that regulate actin dynamics inherently contain multiple feedback loops and redundant pathways. Given the highly adaptable nature of such a system, studies that use only perturbation experiments (e.g. knockdowns, overexpression, pharmacological activation/inhibition, etc.) are challenged by the nonlinearity and redundancy of the pathway. In these pathway configurations, perturbation experiments at best describe the function(s) of a molecular component in an adapting (e.g. acutely drug-treated) or fully adapted (e.g. permanent gene silenced) cell system, where the targeted component now resides in a non-native equilibrium. Here, we propose how quantitative live-cell imaging and analysis of constitutive fluctuations of molecular activities can overcome these limitations. We highlight emerging actin filament barbed-end biology as a prime example of a complex, nonlinear molecular process that requires a fluctuation analytic approach, especially in an unperturbed cellular system, to decipher functional interactions of barbed-end regulators, actin polymerization and membrane protrusion.This article is part of the theme issue 'Self-organization in cell biology'. © 2018 The Author(s).

Nano-hydroxyapatite modulates osteoblast lineage commitment by stimulation of DNA methylation and regulation of gene expression.

PubMed

Ha, Shin-Woo; Jang, Hae Lin; Nam, Ki Tae; Beck, George R

2015-10-01

Hydroxyapatite (HA) is the primary structural component of the skeleton and dentition. Under biological conditions, HA does not occur spontaneously and therefore must be actively synthesized by mineralizing cells such as osteoblasts. The mechanism(s) by which HA is actively synthesized by cells and deposited to create a mineralized matrix are not fully understood and the consequences of mineralization on cell function are even less well understood. HA can be chemically synthesized (HAp) and is therefore currently being investigated as a promising therapeutic biomaterial for use as a functional scaffold and implant coating for skeletal repair and dental applications. Here we investigated the biological effects of nano-HAp (10 × 100 nm) on the lineage commitment and differentiation of bone forming osteoblasts. Exposure of early stage differentiating osteoblasts resulted in dramatic and sustained changes in gene expression, both increased and decreased, whereas later stage osteoblasts were much less responsive. Analysis of the promoter region one of the most responsive genes, alkaline phosphatase, identified the stimulation of DNA methylation following cell exposure to nano-HAp. Collectively, the results reveal the novel epigenetic regulation of cell function by nano-HAp which has significant implication on lineage determination as well as identifying a novel potential therapeutic use of nanomaterials. Published by Elsevier Ltd.

From Diabetes Care to Diabetes Cure—The Integration of Systems Biology, eHealth, and Behavioral Change

PubMed Central

van Ommen, Ben; Wopereis, Suzan; van Empelen, Pepijn; van Keulen, Hilde M.; Otten, Wilma; Kasteleyn, Marise; Molema, Johanna J. W.; de Hoogh, Iris M.; Chavannes, Niels H.; Numans, Mattijs E.; Evers, Andrea W. M.; Pijl, Hanno

2018-01-01

From a biological view, most of the processes involved in insulin resistance, which drives the pathobiology of type 2 diabetes, are reversible. This theoretically makes the disease reversible and curable by changing dietary habits and physical activity, particularly when adopted early in the disease process. Yet, this is not fully implemented and exploited in health care due to numerous obstacles. This article reviews the state of the art in all areas involved in a diabetes cure-focused therapy and discusses the scientific and technological advancements that need to be integrated into a systems approach sustainable lifestyle-based healthcare system and economy. The implementation of lifestyle as cure necessitates personalized and sustained lifestyle adaptations, which can only be established by a systems approach, including all relevant aspects (personalized diagnosis and diet, physical activity and stress management, self-empowerment, motivation, participation and health literacy, all facilitated by blended care and ehealth). Introduction of such a systems approach in type 2 diabetes therapy not only requires a concerted action of many stakeholders but also a change in healthcare economy, with new winners and losers. A “call for action” is put forward to actually initiate this transition. The solution provided for type 2 diabetes is translatable to other lifestyle-related disorders. PMID:29403436

From Diabetes Care to Diabetes Cure-The Integration of Systems Biology, eHealth, and Behavioral Change.

PubMed

van Ommen, Ben; Wopereis, Suzan; van Empelen, Pepijn; van Keulen, Hilde M; Otten, Wilma; Kasteleyn, Marise; Molema, Johanna J W; de Hoogh, Iris M; Chavannes, Niels H; Numans, Mattijs E; Evers, Andrea W M; Pijl, Hanno

2017-01-01

From a biological view, most of the processes involved in insulin resistance, which drives the pathobiology of type 2 diabetes, are reversible. This theoretically makes the disease reversible and curable by changing dietary habits and physical activity, particularly when adopted early in the disease process. Yet, this is not fully implemented and exploited in health care due to numerous obstacles. This article reviews the state of the art in all areas involved in a diabetes cure-focused therapy and discusses the scientific and technological advancements that need to be integrated into a systems approach sustainable lifestyle-based healthcare system and economy. The implementation of lifestyle as cure necessitates personalized and sustained lifestyle adaptations, which can only be established by a systems approach, including all relevant aspects (personalized diagnosis and diet, physical activity and stress management, self-empowerment, motivation, participation and health literacy, all facilitated by blended care and ehealth). Introduction of such a systems approach in type 2 diabetes therapy not only requires a concerted action of many stakeholders but also a change in healthcare economy, with new winners and losers. A "call for action" is put forward to actually initiate this transition. The solution provided for type 2 diabetes is translatable to other lifestyle-related disorders.

The Bio-Logic and machinery of plant morphogenesis.

PubMed

Niklas, Karl J

2003-04-01

Morphogenesis (the development of organic form) requires signal-trafficking and cross-talking across all levels of organization to coordinate the operation of metabolic and genomic networked systems. Many biologists are currently converging on the pictorial conventions of computer scientists to render biological signaling as logic circuits supervising the operation of one or more signal-activated metabolic or gene networks. This approach can redact and simplify complex morphogenetic phenomena and allows for their aggregation into diagrams of larger, more "global" networked systems. This conceptualization is discussed in terms of how logic circuits and signal-activated subsystems work, and it is illustrated for examples of increasingly more complex morphogenetic phenomena, e.g., auxin-mediated cell expansion, entry into the mitotic cell cycle phases, and polar/lateral intercellular auxin transport. For each of these phenomena, a posited circuit/subsystem diagram draws rapid attention to missing components, either in the logic circuit or in the subsystem it supervises. These components must be identified experimentally if each of these basic phenomena is to be fully understood. Importantly, the power of the circuit/subsystem approach to modeling developmental phenomena resides not in its pictorial appeal but in the mathematical tools that are sufficiently strong to reveal and quantify the synergistics of networked systems and thus foster a better understanding of morphogenesis.

Fully solution-processed organic light-emitting electrochemical cells (OLEC) with inkjet-printed micro-lenses for disposable lab-on-chip applications at ambient conditions

NASA Astrophysics Data System (ADS)

Shu, Zhe; Pabst, Oliver; Beckert, Erik; Eberhardt, Ramona; Tünnermann, Andreas

2016-02-01

Microfluidic lab-on-chip devices can be used for chemical and biological analyses such as DNA tests or environmental monitoring. Such devices integrate most of the basic functionalities needed for scientific analysis on a microfluidic chip. When using such devices, cost and space-intensive lab equipment is no longer necessary. However, in order to make a monolithic and cost-efficient/disposable microfluidic sensing device, direct integration of the excitation light source for fluorescent sensing is often required. To achieve this, we introduce a fully solution processable deviation of OLEDs, organic light-emitting electrochemical cells (OLECs), as a low-cost excitation light source for a disposable microfluidic sensing platform. By mixing metal ions and a solid electrolyte with light-emitting polymers as active materials, an in-situ doping and in-situ PN-junction can be generated within a three layer sandwich device. Thanks to this doping effect, work function adaptation is not necessary and air-stable electrode can be used. An ambient manufacturing process for fully solution-processed OLECs is presented, which consist of a spin-coated blue light-emitting polymer plus dopants on an ITO cathode and an inkjet-printed PEDOT:PSS transparent top anode. A fully transparent blue OLEC is able to obtain light intensity > 2500 cd/m2 under pulsed driving mode and maintain stable after 1000 cycles, which fulfils requirements for simple fluorescent on-chip sensing applications. However, because of the large refractive index difference between substrates and air, about 80% of emitted light is trapped inside the device. Therefore, inkjet printed micro-lenses on the rear side are introduced here to further increase light-emitting brightness.

The paradigm of IL-6: from basic science to medicine.

PubMed

Naka, Tetsuji; Nishimoto, Norihiro; Kishimoto, Tadamitsu

2002-01-01

IL-6 is a pleiotropic cytokine with a wide range of biological activities in immune regulation, hematopoiesis, inflammation, and oncogenesis. Its activities are shared by IL-6-related cytokines such as leukemia inhibitory factor and oncostatin M. The pleiotropy and redundancy of IL-6 functions have been identified by using a unique receptor system comprising two functional proteins: an IL-6 receptor (IL-6R) and gp130, the common signal transducer of cytokines related to IL-6. Signal transduction through gp130 is mediated by two pathways: the JAK-STAT (Janus family tyrosine kinase-signal transducer and activator of transcription) pathway and the Ras mitogen-activated protein kinase pathway. The negative regulators of IL-6 signaling have also been identified, although the physiological roles of the molecules are not yet fully understood. The pathological roles of IL-6 have also been clarified in various disease conditions, such as inflammatory, autoimmune, and malignant diseases. On the basis of the findings, a new therapeutic approach to block the IL-6 signal using humanized anti-IL-6R antibody for rheumatoid arthritis, Castleman's disease, and multiple myeloma has been attempted.

Explicit modeling of marine biogeochemical influence on primary sea spray aerosol composition, and cloud impacts

NASA Astrophysics Data System (ADS)

Burrows, S. M.; Elliott, S.; Liu, X.; Ogunro, O. O.; Easter, R. C.; Rasch, P. J.

2013-12-01

Aerosol concentrations and their cloud nucleation activity in remote ocean regions represent an important uncertainty in current models of global climate. In particular, the impact of marine biological activity on the primary submicron sea spray aerosol is not yet fully understood, and existing knowledge has not yet been fully integrated into climate modeling efforts. We present recent results addressing two aspects of this problem. First, we present an estimate of the concentrations of ice-nucleation active particles derived from ocean biological material, and show that these may dominate IN concentrations in the remote marine boundary layer, particularly over the Southern Ocean. (Burrows et al., ACP, 2013a) Second, we present a novel framework for parameterizing the fractionation of marine organic matter into sea spray. The framework models aerosol organic enrichment as resulting from Langmuir adsorption of surface-active macromolecules at the surface of bursting bubbles. Distributions of macromolecular classes are estimated using output from a global marine biogeochemistry model (Burrows et al., in prep, 2013b; Elliott et al., submitted, 2013). The proposed parameterization independently produces relationships between chlorophyll-a and the sea spray organic mass fraction that are similar to existing empirical parameterizations in highly productive bloom regions, but which differ between seasons and ocean regions as a function of ocean biogeochemical variables. Future work should focus on further evaluating and improving the parameterization based on laboratory and field experiments, as well as on further investigation of the atmospheric implications of the predicted sea spray aerosol chemistry. Field experiments in the Southern Ocean and other remote ocean locations would be especially valuable in evaluating and improving these parameterizations. Burrows, S. M., Hoose, C., Pöschl, U., and Lawrence, M. G.: Ice nuclei in marine air: biogenic particles or dust?, Atmos. Chem. Phys., 13, 245-267, doi:10.5194/acp-13-245-2013, 2013a. Burrows, S. M., Elliott, S., Ogunro, O. and Rasch, P.: A framework for modeling the organic fractionation of the sea spray aerosol, in prep., 2013b. Elliott, S., S. Burrows, C. Deal, X. Liu, M. Long, O. Oluwaseun, L. Russell, and O. Wingenter, Prospects for the simulation of macromolecular surfactant chemistry in the ocean-atmosphere, submitted, 2013b.

What Makes the Optimal Wound Healing Material? A Review of Current Science and Introduction of a Synthetic Nanofabricated Wound Care Scaffold.

PubMed

MacEwan, Matthew R; MacEwan, Sarah; Kovacs, Tamas R; Batts, Joel

2017-10-02

Wound matrix materials are used to improve the regeneration of dermal and epidermal layers in both acute and chronic wounds. Contemporary wound matrices are primarily composed of biologic materials such as processed xenogeneic and allogeneic tissues. Unfortunately, existing biologic wound matrices possess multiple limitations including poor longevity, durability, strength, and enzymatic resistance required for persistent support for new tissue formation. A fully-synthetic, resorbable electrospun material (Restrata Wound Matrix, Acera, St.Louis, Missouri ) that exhibits structural similarities to the native extracellular matrix offers a new approach to the treatment of acute and chronic wounds. This novel matrix is the first product to combine the advantages of synthetic construction (e.g. resistance to enzymatic degradation, excellent biocompatibility, strength/durability and controlled degradation) with the positive attributes of biologic materials (e.g. biomimetic architecture similar to human extracellular matrix (ECM), fibrous architecture optimized to support cellular migration and proliferation, engineered porosity to encourage tissue ingrowth and vascularization). These features allow RWM to achieve rapid and complete healing of full-thickness wounds that, in preclinical studies, is comparable to Integra Bilayer Wound Matrix (Integra LifeSciences, Plainsboro, New Jersey), a gold standard biologic material with diverse clinical indications in the wound care. Together, this review suggests that the RWM offers a unique fully-synthetic alternative to existing biologic matrices that is effective, widely available, easy to store, simple to apply and low cost.

Emerging therapeutic delivery capabilities and challenges utilizing enzyme/protein packaged bacterial vesicles.

PubMed

Alves, Nathan J; Turner, Kendrick B; Medintz, Igor L; Walper, Scott A

2015-07-01

Nanoparticle-based therapeutics are poised to play a critical role in treating disease. These complex multifunctional drug delivery vehicles provide for the passive and active targeted delivery of numerous small molecule, peptide and protein-derived pharmaceuticals. This article will first discuss some of the current state of the art nanoparticle classes (dendrimers, lipid-based, polymeric and inorganic), highlighting benefits/drawbacks associated with their implementation. We will then discuss an emerging class of nanoparticle therapeutics, bacterial outer membrane vesicles, that can provide many of the nanoparticle benefits while simplifying assembly. Through molecular biology techniques; outer membrane vesicle hijacking potentially allows for stringent control over nanoparticle production allowing for targeted protein packaged nanoparticles to be fully synthesized by bacteria.

Databases for multilevel biophysiology research available at Physiome.jp.

PubMed

Asai, Yoshiyuki; Abe, Takeshi; Li, Li; Oka, Hideki; Nomura, Taishin; Kitano, Hiroaki

2015-01-01

Physiome.jp (http://physiome.jp) is a portal site inaugurated in 2007 to support model-based research in physiome and systems biology. At Physiome.jp, several tools and databases are available to support construction of physiological, multi-hierarchical, large-scale models. There are three databases in Physiome.jp, housing mathematical models, morphological data, and time-series data. In late 2013, the site was fully renovated, and in May 2015, new functions were implemented to provide information infrastructure to support collaborative activities for developing models and performing simulations within the database framework. This article describes updates to the databases implemented since 2013, including cooperation among the three databases, interactive model browsing, user management, version management of models, management of parameter sets, and interoperability with applications.

Noise-driven neuromorphic tuned amplifier.

PubMed

Fanelli, Duccio; Ginelli, Francesco; Livi, Roberto; Zagli, Niccoló; Zankoc, Clement

2017-12-01

We study a simple stochastic model of neuronal excitatory and inhibitory interactions. The model is defined on a directed lattice and internodes couplings are modulated by a nonlinear function that mimics the process of synaptic activation. We prove that such a system behaves as a fully tunable amplifier: the endogenous component of noise, stemming from finite size effects, seeds a coherent (exponential) amplification across the chain generating giant oscillations with tunable frequencies, a process that the brain could exploit to enhance, and eventually encode, different signals. On a wider perspective, the characterized amplification process could provide a reliable pacemaking mechanism for biological systems. The device extracts energy from the finite size bath and operates as an out of equilibrium thermal machine, under stationary conditions.

Astaxanthin as a Potential Neuroprotective Agent for Neurological Diseases

PubMed Central

Wu, Haijian; Niu, Huanjiang; Shao, Anwen; Wu, Cheng; Dixon, Brandon J.; Zhang, Jianmin; Yang, Shuxu; Wang, Yirong

2015-01-01

Neurological diseases, which consist of acute injuries and chronic neurodegeneration, are the leading causes of human death and disability. However, the pathophysiology of these diseases have not been fully elucidated, and effective treatments are still lacking. Astaxanthin, a member of the xanthophyll group, is a red-orange carotenoid with unique cell membrane actions and diverse biological activities. More importantly, there is evidence demonstrating that astaxanthin confers neuroprotective effects in experimental models of acute injuries, chronic neurodegenerative disorders, and neurological diseases. The beneficial effects of astaxanthin are linked to its oxidative, anti-inflammatory, and anti-apoptotic characteristics. In this review, we will focus on the neuroprotective properties of astaxanthin and explore the underlying mechanisms in the setting of neurological diseases. PMID:26378548

Airborne multicamera system for geo-spatial applications

NASA Astrophysics Data System (ADS)

Bachnak, Rafic; Kulkarni, Rahul R.; Lyle, Stacey; Steidley, Carl W.

2003-08-01

Airborne remote sensing has many applications that include vegetation detection, oceanography, marine biology, geographical information systems, and environmental coastal science analysis. Remotely sensed images, for example, can be used to study the aftermath of episodic events such as the hurricanes and floods that occur year round in the coastal bend area of Corpus Christi. This paper describes an Airborne Multi-Spectral Imaging System that uses digital cameras to provide high resolution at very high rates. The software is based on Delphi 5.0 and IC Imaging Control's ActiveX controls. Both time and the GPS coordinates are recorded. Three successful test flights have been conducted so far. The paper present flight test results and discusses the issues being addressed to fully develop the system.

C. elegans network biology: a beginning.

PubMed Central

Piano, Fabio; Gunsalus, Kristin C; Hill, David E; Vidal, Marc

2006-01-01

The architecture and dynamics of molecular networks can provide an understanding of complex biological processes complementary to that obtained from the in-depth study of single genes and proteins. With a completely sequenced and well-annotated genome, a fully characterized cell lineage, and powerful tools available to dissect development, Caenorhabditis elegans, among metazoans, provides an optimal system to bridge cellular and organismal biology with the global properties of macromolecular networks. This chapter considers omic technologies available for C. elegans to describe molecular networks--encompassing transcriptional and phenotypic profiling as well as physical interaction mapping--and discusses how their individual and integrated applications are paving the way for a network-level understanding of C. elegans biology. PMID:18050437

Wireless Performance of a Fully Passive Neurorecording Microsystem Embedded in Dispersive Human Head Phantom

NASA Technical Reports Server (NTRS)

Schwerdt, Helen N.; Chae, Junseok; Miranda, Felix A.

2012-01-01

This paper reports the wireless performance of a biocompatible fully passive microsystem implanted in phantom media simulating the dispersive dielectric properties of the human head, for potential application in recording cortical neuropotentials. Fully passive wireless operation is achieved by means of backscattering electromagnetic (EM) waves carrying 3rd order harmonic mixing products (2f(sub 0) plus or minus f(sub m)=4.4-4.9 GHZ) containing targeted neuropotential signals (fm approximately equal to 1-1000 Hz). The microsystem is enclosed in 4 micrometer thick parylene-C for biocompatibility and has a footprint of 4 millimeters x 12 millimeters x 500 micrometers. Preliminary testing of the microsystem implanted in the lossy biological simulating media results in signal-to-noise ratio's (SNR) near 22 (SNR approximately equal to 38 in free space) for millivolt level neuropotentials, demonstrating the potential for fully passive wireless microsystems in implantable medical applications.

Considerations on Directive 98/8 of the European Commission - the biocide directive.

PubMed

Patryn, Rafał; Jarosz, Mirosław J; Włoszczak-Szubzda, Anna; Sak, Jarosław; Pawlikowski, Jakub

2011-01-01

Nowadays, versatile human activity requires the development of technologies in the chemical and biological industries that ultimately enable an increase in human activity, and help create the living conditions in the domain of human civilization. Increasing this activity very frequently requires the implementation of new technologies concerning the active elimination of numerous threats and obstacles which are found in the human and natural environment. The concept of so-called biocidal products has been introduced into the European legislation as long as ten years ago, defining them as various types of 'chemical substances or microorganisms which can deter, render harmless, or exert a controlling eff ect on any harmful organism, by chemical or biological means'. They can be added to other materials (typically liquids) to protect them against biological infestation and growth. Biocidal products - due to their specificity, toxicity and composition - create a serious risk for human and animal life and health, as well as for the natural environment, it is therefore fully justified to have legal regulations concerning such biocides. Because biocidal products are intended to kill living organisms, and as such, many biocidal products pose a significant risk to human health and welfare, and have significant adverse eff ects on the natural environment. Great care is required when handling biocides and appropriate protective clothing and equipment should be used. Currently, Directive 98/8/EC is a comprehensive set of legal regulations concerning biocidal products, their specificity, principles relating to their placing on the market, and guidelines for their control. It is worth emphasizing that Directive 98/8/EC implements the clampdown on poisoning cases with biocides, the duty of which was passed to the so-called Centres of Consultation and Toxicological Information. These centres provide round-the-clock (24-hour) medical consultation and assistance in cases of poisonings with these products. The presented study constitutes an in-depth presentation and analysis of the European law concerning biocides and the current regulations applying to them.

Real-Time Tracking the Synthesis and Degradation of Albumin in Complex Biological Systems with a near-Infrared Fluorescent Probe.

PubMed

Jin, Qiang; Feng, Lei; Zhang, Shui-Jun; Wang, Dan-Dan; Wang, Fang-Jun; Zhang, Yi; Cui, Jing-Nan; Guo, Wen-Zhi; Ge, Guang-Bo; Yang, Ling

2017-09-19

In this study, a novel fluorescent detection system for biological sensing of human albumin (HA) was developed on the basis of the pseudoesterase activity and substrate preference of HA. The designed near-infrared (NIR) fluorescent probe (DDAP) could be effectively hydrolyzed by HA, accompanied by significant changes in both color and fluorescence spectrum. The sensing mechanism was fully investigated by fluorescence spectroscopy, NMR, and mass spectra. DDAP exhibited excellent selectivity and sensitivity toward HA over a variety of human plasma proteins, hydrolases, and abundant biomolecules found in human body. The probe has been successfully applied to measure native HA in diluted plasma samples and the secreted HA in the hepatocyte culture supernatant. DDAP has also been used for fluorescence imaging of HA reabsorption in living renal cells, and the results show that the probe exhibits good cell permeability, low cytotoxicity and high imaging resolution. Furthermore, DDAP has been successfully used for real-time tracking the uptaking and degradation of albumin in ex vivo mouse kidney models for the first time. All these results clearly demonstrated that DDAP-based assay held great promise for real-time sensing and tracking HA in complex biological systems, which would be very useful for basic researches and clinical diagnosis of HA-associated diseases.

Microfluidics as a new tool in radiation biology

PubMed Central

Lacombe, Jerome; Phillips, Shanna Leslie; Zenhausern, Frederic

2016-01-01

Ionizing radiations interact with molecules at the cellular and molecular levels leading to several biochemical modifications that may be responsible for biological effects on tissue or whole organisms. The study of these changes is difficult because of the complexity of the biological response(s) to radiations and the lack of reliable models able to mimic the whole molecular phenomenon and different communications between the various cell networks, from the cell activation to the macroscopic effect at the tissue or organismal level. Microfluidics, the science and technology of systems that can handle small amounts of fluids in confined and controlled environment, has been an emerging field for several years. Some microfluidic devices, even at early stages of development, may already help radiobiological research by proposing new approaches to study cellular, tissue and total-body behavior upon irradiation. These devices may also be used in clinical biodosimetry since microfluidic technology is frequently developed for integrating complex bioassay chemistries into automated user-friendly, reproducible and sensitive analyses. In this review, we discuss the use, numerous advantages, and possible future of microfluidic technology in the field of radiobiology. We will also examine the disadvantages and required improvements for microfluidics to be fully practical in radiation research and to become an enabling tool for radiobiologists and radiation oncologists. PMID:26704304

Microfluidics as a new tool in radiation biology.

PubMed

Lacombe, Jerome; Phillips, Shanna Leslie; Zenhausern, Frederic

2016-02-28

Ionizing radiations interact with molecules at the cellular and molecular levels leading to several biochemical modifications that may be responsible for biological effects on tissue or whole organisms. The study of these changes is difficult because of the complexity of the biological response(s) to radiations and the lack of reliable models able to mimic the whole molecular phenomenon and different communications between the various cell networks, from the cell activation to the macroscopic effect at the tissue or organismal level. Microfluidics, the science and technology of systems that can handle small amounts of fluids in confined and controlled environment, has been an emerging field for several years. Some microfluidic devices, even at early stages of development, may already help radiobiological research by proposing new approaches to study cellular, tissue and total-body behavior upon irradiation. These devices may also be used in clinical biodosimetry since microfluidic technology is frequently developed for integrating complex bioassay chemistries into automated user-friendly, reproducible and sensitive analyses. In this review, we discuss the use, numerous advantages, and possible future of microfluidic technology in the field of radiobiology. We will also examine the disadvantages and required improvements for microfluidics to be fully practical in radiation research and to become an enabling tool for radiobiologists and radiation oncologists. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

An Allosteric Cross-Talk Between the Activation Loop and the ATP Binding Site Regulates the Activation of Src Kinase

NASA Astrophysics Data System (ADS)

Pucheta-Martínez, Encarna; Saladino, Giorgio; Morando, Maria Agnese; Martinez-Torrecuadrada, Jorge; Lelli, Moreno; Sutto, Ludovico; D'Amelio, Nicola; Gervasio, Francesco Luigi

2016-04-01

Phosphorylation of the activation loop is a fundamental step in the activation of most protein kinases. In the case of the Src tyrosine kinase, a prototypical kinase due to its role in cancer and its historic importance, phosphorylation of tyrosine 416 in the activation loop is known to rigidify the structure and contribute to the switch from the inactive to a fully active form. However, whether or not phosphorylation is able per-se to induce a fully active conformation, that efficiently binds ATP and phosphorylates the substrate, is less clear. Here we employ a combination of solution NMR and enhanced-sampling molecular dynamics simulations to fully map the effects of phosphorylation and ATP/ADP cofactor loading on the conformational landscape of Src tyrosine kinase. We find that both phosphorylation and cofactor binding are needed to induce a fully active conformation. What is more, we find a complex interplay between the A-loop and the hinge motion where the phosphorylation of the activation-loop has a significant allosteric effect on the dynamics of the C-lobe.

Uptake and bio-reactivity of polystyrene nanoparticles is affected by surface modifications, ageing and LPS adsorption: in vitro studies on neural tissue cells

NASA Astrophysics Data System (ADS)

Murali, Kumarasamy; Kenesei, Kata; Li, Yang; Demeter, Kornél; Környei, Zsuzsanna; Madarász, Emilia

2015-02-01

Because of their capacity of crossing an intact blood-brain barrier and reaching the brain through an injured barrier or via the nasal epithelium, nanoparticles have been considered as vehicles to deliver drugs and as contrast materials for brain imaging. The potential neurotoxicity of nanoparticles, however, is not fully explored. Using particles with a biologically inert polystyrene core material, we investigated the role of the chemical composition of particle surfaces in the in vitro interaction with different neural cell types. PS NPs within a size-range of 45-70 nm influenced the metabolic activity of cells depending on the cell-type, but caused toxicity only at extremely high particle concentrations. Neurons did not internalize particles, while microglial cells ingested a large amount of carboxylated but almost no PEGylated NPs. PEGylation reduced the protein adsorption, toxicity and cellular uptake of NPs. After storage (shelf-life >6 months), the toxicity and cellular uptake of NPs increased. The altered biological activity of ``aged'' NPs was due to particle aggregation and due to the adsorption of bioactive compounds on NP surfaces. Aggregation by increasing the size and sedimentation velocity of NPs results in increased cell-targeted NP doses. The ready endotoxin adsorption which cannot be prevented by PEG coating, can render the particles toxic. The age-dependent changes in otherwise harmless NPs could be the important sources for variability in the effects of NPs, and could explain the contradictory data obtained with ``identical'' NPs.Because of their capacity of crossing an intact blood-brain barrier and reaching the brain through an injured barrier or via the nasal epithelium, nanoparticles have been considered as vehicles to deliver drugs and as contrast materials for brain imaging. The potential neurotoxicity of nanoparticles, however, is not fully explored. Using particles with a biologically inert polystyrene core material, we investigated the role of the chemical composition of particle surfaces in the in vitro interaction with different neural cell types. PS NPs within a size-range of 45-70 nm influenced the metabolic activity of cells depending on the cell-type, but caused toxicity only at extremely high particle concentrations. Neurons did not internalize particles, while microglial cells ingested a large amount of carboxylated but almost no PEGylated NPs. PEGylation reduced the protein adsorption, toxicity and cellular uptake of NPs. After storage (shelf-life >6 months), the toxicity and cellular uptake of NPs increased. The altered biological activity of ``aged'' NPs was due to particle aggregation and due to the adsorption of bioactive compounds on NP surfaces. Aggregation by increasing the size and sedimentation velocity of NPs results in increased cell-targeted NP doses. The ready endotoxin adsorption which cannot be prevented by PEG coating, can render the particles toxic. The age-dependent changes in otherwise harmless NPs could be the important sources for variability in the effects of NPs, and could explain the contradictory data obtained with ``identical'' NPs. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr06849a

Composting of the solid fraction of digestate derived from pig slurry: Biological processes and compost properties

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

Tambone, Fulvia, E-mail: fulvia.tambone@unimi.it; Terruzzi, Laura; Scaglia, Barbara

Highlights: • Anaerobic digestion leads to the production of a biologically stable digestate. • Solid–liquid separation produces a solid fraction having high fertilizer value. • Composting process shows low biological activity due to high biological stability of digestate. • Solid digestate fraction can be composted in a short time or used directly as organic fertilizer. - Abstract: The aim of this paper was to assess the characteristics of the solid fractions (SF) obtained by mechanical separation of digestate, their compostability and compost quality. To do so, the SF of digestates obtained from anaerobic digestion of pig slurry, energy crops andmore » agro-industrial residues were sampled in five plants located in Northern Italy. Results obtained indicated that anaerobic digestion by itself promoted the high biological stability of biomasses with a Potential Dynamic Respiration Index (PDRI) close to 1000 mgO{sub 2} kg V S{sup −1} h{sup −1}. Subsequent composting of digestates, with an added bulking agent, did not give remarkably different results, and led only to a slight modification of the characteristics of the initial non-composted mixtures; the composts obtained fully respected the legal limits for high quality compost. Chemical studies of organic matter composition of the biomasses by using CP MAS {sup 13}C NMR, indicated that the compost was composed of a high relative content of O-alkyl-C (71.47% of total C) (cellulose and hemicelluloses) and a low alkyl-C (12.42%) (i.e. volatile fatty acids, steroid-like molecules, aliphatic biopolymers and proteins)« less

Bill E. Kunkle Interdisciplinary Beef Symposium: Overlapping physiological responses and endocrine biomarkers that are indicative of stress responsiveness and immune function in beef cattle.

PubMed

Carroll, J A; Burdick Sanchez, N C

2014-12-01

Acknowledgment that modern livestock production systems impose stress on animals has been accepted by the scientific community and producers. As the economic burden has increased for livestock producers, expectations for animal performance have increased, thus placing more strain on the entire production system. Whether or not periodic exposure to stress within the production system jeopardizes the well-being of animals continues to be an area of debate largely because of the inability to accurately quantify the magnitude and severity of the stress response on other biological systems. Adding to the confusion is the fact that activation of the stress axis can be both beneficial and detrimental to the body depending on the duration of the stress response and the frequency at which an animal is exposed to stressful stimuli. Few would argue that continuous long-term stress inhibits livestock productivity and overall well-being. Less clear is whether or not occasional exposure to acute stress jeopardizes the productivity and well-being of livestock. To fully appreciate the complexity associated with activation of the stress axis and the overall biological impact on the body, one must delve deep into the scientific literature and examine the science in an unbiased manner. It is imperative to appreciate and understand that activation of the stress axis is an essential survival mechanism necessary to maintain homeostasis during biologically challenging times. Acute activation of the stress axis leads to repartitioning of energy to organs and tissues essential for coping with stress, redirection of blood flow from the peripheral to large muscle groups, decreased digestive function, and priming of the immune system to prepare for subsequent infections. Conversely, chronic activation of the stress axis disrupts digestive function, causes catabolism of muscle and adipose tissue, and suppresses overall immune function, thus making an animal more susceptible to disease. But what parameters are needed to distinguish periods of acute stress from those of chronic stress, and what biological markers are the best indicators of "stress" in an animal? Although there are a plethora of physiological responses and endocrine biomarkers that can be quantified, an integrative tool that has been readily embraced by scientists and producers as an effective and efficient indicator of the duration and magnitude of stress that an animal is experiencing has yet to be identified.

Honey, Propolis, and Royal Jelly: A Comprehensive Review of Their Biological Actions and Health Benefits

PubMed Central

Sammugam, Lakhsmi; Ramesh, Nagesvari

2017-01-01

Background There are several health benefits that honeybee products such as honey, propolis, and royal jelly claim toward various types of diseases in addition to being food. Scope and Approach In this paper, the effects of honey, propolis, and royal jelly on different metabolic diseases, cancers, and other diseases have been reviewed. The modes of actions of these products have also been illustrated for purposes of better understanding. Key Findings and Conclusions An overview of honey, propolis, and royal jelly and their biological potentials was highlighted. The potential health benefits of honey, such as microbial inhibition, wound healing, and its effects on other diseases, are described. Propolis has been reported to have various health benefits related to gastrointestinal disorders, allergies, and gynecological, oral, and dermatological problems. Royal jelly is well known for its protective effects on reproductive health, neurodegenerative disorders, wound healing, and aging. Nevertheless, the exact mechanisms of action of honey, propolis, and royal jelly on the abovementioned diseases and activities have not been not fully elucidated, and further research is warranted to explain their exact contributions. PMID:28814983

Copper-catalysed enantioselective stereodivergent synthesis of amino alcohols.

PubMed

Shi, Shi-Liang; Wong, Zackary L; Buchwald, Stephen L

2016-04-21

The chirality, or 'handedness', of a biologically active molecule can alter its physiological properties. Thus it is routine procedure in the drug discovery and development process to prepare and fully characterize all possible stereoisomers of a drug candidate for biological evaluation. Despite many advances in asymmetric synthesis, developing general and practical strategies for obtaining all possible stereoisomers of an organic compound that has multiple contiguous stereocentres remains a challenge. Here, we report a stereodivergent copper-based approach for the expeditious construction of amino alcohols with high levels of chemo-, regio-, diastereo- and enantioselectivity. Specifically, we synthesized these amino-alcohol products using sequential, copper-hydride-catalysed hydrosilylation and hydroamination of readily available enals and enones. This strategy provides a route to all possible stereoisomers of the amino-alcohol products, which contain up to three contiguous stereocentres. We leveraged catalyst control and stereospecificity simultaneously to attain exceptional control of the product stereochemistry. Beyond the immediate utility of this protocol, our strategy could inspire the development of methods that provide complete sets of stereoisomers for other valuable synthetic targets.

Honey, Propolis, and Royal Jelly: A Comprehensive Review of Their Biological Actions and Health Benefits.

PubMed

Pasupuleti, Visweswara Rao; Sammugam, Lakhsmi; Ramesh, Nagesvari; Gan, Siew Hua

2017-01-01

There are several health benefits that honeybee products such as honey, propolis, and royal jelly claim toward various types of diseases in addition to being food. In this paper, the effects of honey, propolis, and royal jelly on different metabolic diseases, cancers, and other diseases have been reviewed. The modes of actions of these products have also been illustrated for purposes of better understanding. An overview of honey, propolis, and royal jelly and their biological potentials was highlighted. The potential health benefits of honey, such as microbial inhibition, wound healing, and its effects on other diseases, are described. Propolis has been reported to have various health benefits related to gastrointestinal disorders, allergies, and gynecological, oral, and dermatological problems. Royal jelly is well known for its protective effects on reproductive health, neurodegenerative disorders, wound healing, and aging. Nevertheless, the exact mechanisms of action of honey, propolis, and royal jelly on the abovementioned diseases and activities have not been not fully elucidated, and further research is warranted to explain their exact contributions.

Shot-noise Limited Faraday Rotation Spectroscopy for Detection of Nitric Oxide Isotopes in Breath, Urine, and Blood

PubMed Central

Wang, Yin; Nikodem, Michal; Zhang, Eric; Cikach, Frank; Barnes, Jarrod; Comhair, Suzy; Dweik, Raed A.; Kao, Christina; Wysocki, Gerard

2015-01-01

Measurement of NO and/or its metabolites in the various body compartments has transformed our understanding of biology. The inability of the current NO measurement methods to account for naturally occurring and experimental NO isotopes, however, has prevented the scientific community from fully understating NO metabolism in vivo. Here we present a mid-IR Faraday rotation spectrometer (FRS) for detection of NO isotopes. The instrument utilizes a novel dual modulation/demodulation (DM) FRS method which exhibits noise performance at only 2 times the fundamental quantum shot-noise level and provides the record sensitivity in its class. This is achieved with a system that is fully autonomous, robust, transportable, and does not require cryogenic cooling. The DM-FRS enables continuous monitoring of nitric oxide isotopes with the detection limits of 3.72 ppbv/Hz1/2 to14NO and 0.53 ppbv/Hz1/2 to15NO using only 45 cm active optical path. This DM-FRS measurement method can be used to improve the performance of conventional FRS sensors targeting other radical species. The feasibility of the instrument to perform measurements relevant to studies of NO metabolism in humans is demonstrated. PMID:25767064

Molecular mechanisms of immunosuppression by cyclosporins.

PubMed

Zenke, G; Baumann, G; Wenger, R; Hiestand, P; Quesniaux, V; Andersen, E; Schreier, M H

1993-06-23

Despite the successful clinical application of the immunosuppressive drug cyclosporin A (CsA, Sandimmun), its precise mechanism of action in the process of T cell activation remains elusive. CsA binds to the high-affinity cytosolic receptor cyclophilin whose peptidyl-prolyl cis-trans isomerase activity is inhibited upon binding. The linkage of this effect with the inhibition of the T cell receptor-mediated signal transduction pathway, which leads to a suppression of lymphokine gene transcription, is still unclear. We analyzed the relationship between cyclophilin-binding and immunosuppressive activity (e.g., effect on IL-2 transcription) of cyclosporin derivatives in vitro. The results show that binding to cyclophilin is required, but not sufficient for immunosuppression. Cyclosporin analogues which completely lack immunosuppressive activity but fully retained their cyclophilin-binding capacity antagonize the immunosuppressive activity of CsA. These derivatives inhibit the isomerase activity of cyclophilin, which clearly demonstrates that inhibition of the cyclophilin isomerase activity does not lead to immunosuppression. In analogy to the other immunosuppressants of microbial origin, FK-506 and rapamycin, a specific structure of the "effector" domain of CsA, which is unrelated to the cyclophilin-binding domain, determines the biological activity. In the nucleus, CsA interferes with the DNA-binding of inducible transcription factors to their respective DNA motifs within lymphokine promoters by affecting intracellular translocation of transcription factor subunits.

Prediction of Antibacterial Activity from Physicochemical Properties of Antimicrobial Peptides

PubMed Central

Melo, Manuel N.; Ferre, Rafael; Feliu, Lídia; Bardají, Eduard; Planas, Marta; Castanho, Miguel A. R. B.

2011-01-01

Consensus is gathering that antimicrobial peptides that exert their antibacterial action at the membrane level must reach a local concentration threshold to become active. Studies of peptide interaction with model membranes do identify such disruptive thresholds but demonstrations of the possible correlation of these with the in vivo onset of activity have only recently been proposed. In addition, such thresholds observed in model membranes occur at local peptide concentrations close to full membrane coverage. In this work we fully develop an interaction model of antimicrobial peptides with biological membranes; by exploring the consequences of the underlying partition formalism we arrive at a relationship that provides antibacterial activity prediction from two biophysical parameters: the affinity of the peptide to the membrane and the critical bound peptide to lipid ratio. A straightforward and robust method to implement this relationship, with potential application to high-throughput screening approaches, is presented and tested. In addition, disruptive thresholds in model membranes and the onset of antibacterial peptide activity are shown to occur over the same range of locally bound peptide concentrations (10 to 100 mM), which conciliates the two types of observations. PMID:22194847

Building an Undergraduate STEM Team Using Team-Based Learning Leading to the Production of a Storyboard Appropriate for Elementary Students

NASA Astrophysics Data System (ADS)

Cutright, Teresa J.; Evans, Edward; Brantner, Justin S.

2014-06-01

A unique undergraduate team that spans five different engineering disciplines, chemistry, biology, and mathematics was formed. The team was formed to promote cross-disciplinary learning, to improve retention, and to prepare the students for the kind of problems they will face in their careers. This paper describes the variety of activities used over 2 years to tie the team together, as well as afford opportunities to develop team-building skills. The activities described highlight the critical elements of a faculty leader whose own work is interdisciplinary, correct balance of disciplines in the team, and sufficient time for team development. The use of external feedback was essential for all activities. Clearly defined goals and hard deadlines were critical for the completion of individual activities, as well as developing a healthy team environment. Although the student cohort has learned from the activities, more time is needed to assess whether the students have become a fully efficient team. Furthermore, an additional cohort would be needed to assess whether the approach was able to assist with student's interest in STEM and their desire to help other people.

Stability of human interferon-beta 1: oligomeric human interferon-beta 1 is inactive but is reactivated by monomerization.

PubMed

Utsumi, J; Yamazaki, S; Kawaguchi, K; Kimura, S; Shimizu, H

1989-10-05

Human interferon-beta 1 is extremely stable is a low ionic strength solution of pH 2 such as 10 mM HCl at 37 degrees C. However, the presence of 0.15 M NaCl led to a remarkable loss of antiviral activity. The molecular-sieve high-performance liquid chromatography revealed that, whereas completely active human interferon-beta 1 eluted as a 25 kDa species (monomeric form), the inactivated preparation eluted primarily as a 90 kDa species (oligomeric form). The specific activity (units per mg protein) of the oligomeric form was approx. 10% of that of the monomeric form. This observation shows that oligomeric human interferon-beta 1 is apparently in an inactive form. When the oligomeric eluate was resolved by polyacrylamide gel containing sodium dodecyl sulphate (SDS), it appeared to be monomeric under non-reducing conditions. Monomerization of the oligomeric human interferon-beta 1 by treatment with 1% SDS, fully regenerated its antiviral activity. These results suggest that the inactivation of the human interferon-beta 1 preparation was caused by its oligomerization via hydrophobic interactions without the formation of intermolecular disulphide bonds. These oligomers can be dissociated by SDS to restore biological activity.

Catalytically Active Guanylyl Cyclase B Requires Endoplasmic Reticulum-mediated Glycosylation, and Mutations That Inhibit This Process Cause Dwarfism.

PubMed

Dickey, Deborah M; Edmund, Aaron B; Otto, Neil M; Chaffee, Thomas S; Robinson, Jerid W; Potter, Lincoln R

2016-05-20

C-type natriuretic peptide activation of guanylyl cyclase B (GC-B), also known as natriuretic peptide receptor B or NPR2, stimulates long bone growth, and missense mutations in GC-B cause dwarfism. Four such mutants (L658F, Y708C, R776W, and G959A) bound (125)I-C-type natriuretic peptide on the surface of cells but failed to synthesize cGMP in membrane GC assays. Immunofluorescence microscopy also indicated that the mutant receptors were on the cell surface. All mutant proteins were dephosphorylated and incompletely glycosylated, but dephosphorylation did not explain the inactivation because the mutations inactivated a "constitutively phosphorylated" enzyme. Tunicamycin inhibition of glycosylation in the endoplasmic reticulum or mutation of the Asn-24 glycosylation site decreased GC activity, but neither inhibition of glycosylation in the Golgi by N-acetylglucosaminyltransferase I gene inactivation nor PNGase F deglycosylation of fully processed GC-B reduced GC activity. We conclude that endoplasmic reticulum-mediated glycosylation is required for the formation of an active catalytic, but not ligand-binding domain, and that mutations that inhibit this process cause dwarfism. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Silibinin phosphodiester glyco-conjugates: Synthesis, redox behaviour and biological investigations.

PubMed

Romanucci, Valeria; Agarwal, Chapla; Agarwal, Rajesh; Pannecouque, Christophe; Iuliano, Mauro; De Tommaso, Gaetano; Caruso, Tonino; Di Fabio, Giovanni; Zarrelli, Armando

2018-04-01

New silibinin phosphodiester glyco-conjugates were synthesized by efficient phosphoramidite chemistry and were fully characterized by 2D-NMR. A wide-ranging study focused on the determination of their pKa and E° values as well as on their radical scavenging activities by different assays (DPPH, ABTS + and HRSA) was conducted. The new glyco-conjugates are more water-soluble than silibinin, and their radical scavenging activities are higher than those of silibinin. The conjugation therefore improves both the water solubilities and antioxidant activities of the flavonolignan moieties. The serum stability was evaluated under physiological conditions, and the glyco-conjugates degraded with half-lives of 40-70 h, making them useful in pro-drug approaches. We started by treating androgen-dependent prostate cancer (PCa) LNCaP cells and then expanded our studies to androgen-independent PCa PC3 and DU145 cells. In most cases, the new derivatives significantly reduced both total and live cell numbers, albeit at different levels. Anti-HIV activities were evaluated and the glucosamine-phosphate silibinin derivative showed higher activity (IC 50  = 73 μM) than silibinin. Copyright © 2018 Elsevier Inc. All rights reserved.

Biological properties of solid free form designed ceramic scaffolds with BMP-2: in vitro and in vivo evaluation.

PubMed

Abarrategi, Ander; Moreno-Vicente, Carolina; Martínez-Vázquez, Francisco Javier; Civantos, Ana; Ramos, Viviana; Sanz-Casado, José Vicente; Martínez-Corriá, Ramón; Perera, Fidel Hugo; Mulero, Francisca; Miranda, Pedro; López-Lacomba, José Luís

2012-01-01

Porous ceramic scaffolds are widely studied in the tissue engineering field due to their potential in medical applications as bone substitutes or as bone-filling materials. Solid free form (SFF) fabrication methods allow fabrication of ceramic scaffolds with fully controlled pore architecture, which opens new perspectives in bone tissue regeneration materials. However, little experimentation has been performed about real biological properties and possible applications of SFF designed 3D ceramic scaffolds. Thus, here the biological properties of a specific SFF scaffold are evaluated first, both in vitro and in vivo, and later scaffolds are also implanted in pig maxillary defect, which is a model for a possible application in maxillofacial surgery. In vitro results show good biocompatibility of the scaffolds, promoting cell ingrowth. In vivo results indicate that material on its own conducts surrounding tissue and allow cell ingrowth, thanks to the designed pore size. Additional osteoinductive properties were obtained with BMP-2, which was loaded on scaffolds, and optimal bone formation was observed in pig implantation model. Collectively, data show that SFF scaffolds have real application possibilities for bone tissue engineering purposes, with the main advantage of being fully customizable 3D structures.

Biological Properties of Solid Free Form Designed Ceramic Scaffolds with BMP-2: In Vitro and In Vivo Evaluation

PubMed Central

Abarrategi, Ander; Moreno-Vicente, Carolina; Martínez-Vázquez, Francisco Javier; Civantos, Ana; Ramos, Viviana; Sanz-Casado, José Vicente; Martínez-Corriá, Ramón; Perera, Fidel Hugo; Mulero, Francisca; Miranda, Pedro; López-Lacomba, José Luís

2012-01-01

Porous ceramic scaffolds are widely studied in the tissue engineering field due to their potential in medical applications as bone substitutes or as bone-filling materials. Solid free form (SFF) fabrication methods allow fabrication of ceramic scaffolds with fully controlled pore architecture, which opens new perspectives in bone tissue regeneration materials. However, little experimentation has been performed about real biological properties and possible applications of SFF designed 3D ceramic scaffolds. Thus, here the biological properties of a specific SFF scaffold are evaluated first, both in vitro and in vivo, and later scaffolds are also implanted in pig maxillary defect, which is a model for a possible application in maxillofacial surgery. In vitro results show good biocompatibility of the scaffolds, promoting cell ingrowth. In vivo results indicate that material on its own conducts surrounding tissue and allow cell ingrowth, thanks to the designed pore size. Additional osteoinductive properties were obtained with BMP-2, which was loaded on scaffolds, and optimal bone formation was observed in pig implantation model. Collectively, data show that SFF scaffolds have real application possibilities for bone tissue engineering purposes, with the main advantage of being fully customizable 3D structures. PMID:22470527

[Biotechnological advances in monoclonal antibody therapy: the RANK ligand inhibitor antibody].

PubMed

Kiss, Emese; Kuluncsics, Zénó; Kiss, Zoltán; Poór, Gyula

2010-12-26

Biological drugs have been used since the middle of the last century in medicine. Nowadays we are witnesses of the intensive development and wider administration of these drugs in clinical practice. Around 250 biological drugs are available and more than 350 million patients have been treated since their marketed authorization. Among the biologics there are protein based macromolecules, which mass production can be performed with the help of biotechnology. This term referring to the use of living organisms for production of molecules, was introduced by the Hungarian engineer, Károly Ereky. The present review focuses on the research, production and development of monoclonal antibodies manufactured by biotechnology. Some steps of this development have changed our immunological knowledge and the outcome of several diseases. The development of antibodies was highly recognized by two Nobel prizes. Authors detail the structure and functions of immunoglobulins, and their development, including fully human monoclonal antibodies. The RANKL inhibitor denosumab, a fully human IgG2 monoclonal antibody belongs to this latter group and it is available for treatment of osteoporosis. Authors also summarize the basic process of bone metabolism and the benefits of RANK ligand inhibition.

Identification of Ina proteins from Fusarium acuminatum

NASA Astrophysics Data System (ADS)

Scheel, Jan Frederik; Kunert, Anna Theresa; Pöschl, Ulrich; Fröhlich-Nowoisky, Janine

2015-04-01

Freezing of water above -36° C is based on ice nucleation activity (INA) mediated by ice nucleators (IN) which can be of various origins. Beside mineral IN, biological particles are a potentially important source of atmospheric IN. The best-known biological IN are common plant-associated bacteria. The IN activity of these bacteria is induced by a surface protein on the outer cell membrane, which is fully characterized. In contrast, much less is known about the nature of fungal IN. The fungal genus Fusarium is widely spread throughout the earth. It belongs to the Ascomycota and is one of the most severe fungal pathogens. It can affect a variety of organisms from plants to animals including humans. INA of Fusarium was already described about 30 years ago and INA of Fusarium as well as other fungal genera is assumed to be mediated by proteins or at least to contain a proteinaceous compound. Although many efforts were made the precise INA machinery of Fusarium and other fungal species including the proteins and their corresponding genes remain unidentified. In this study preparations from living fungal samples of F. acuminatum were fractionated by liquid chromatography and IN active fractions were identified by freezing assays. SDS-page and de novo sequencing by mass spectrometry were used to identify the primary structure of the protein. Preliminary results show that the INA protein of F. acuminatum is contained in the early size exclusion chromatography fractions indicating a high molecular size. Moreover we could identify a single protein band from IN active fractions at 130-145 kDa corresponding to sizes of IN proteins from bacterial species. To our knowledge this is for the first time an isolation of a single protein from in vivo samples, which can be assigned as IN active from Fusarium.

Assessment of preparation time with fully-liquid versus non-fully liquid paediatric hexavalent vaccines. A time and motion study.

PubMed

De Coster, Ilse; Fournie, Xavier; Faure, Céline; Ziani, Eddy; Nicolas, Laurence; Soubeyrand, Benoit; Van Damme, Pierre

2015-07-31

Simplified vaccine preparation steps would save time and reduce potential immunisation errors. The aim of the study was to assess vaccine preparation time with fully-liquid hexavalent vaccine (DTaP-IPV-HB-PRP-T, Sanofi Pasteur MSD) versus non-fully liquid hexavalent vaccine that needs reconstitution (DTPa-HBV-IPV/Hib, GlaxoSmithKline Biologicals). Ninety-six Health Care Professionals (HCPs) participated in a randomised, cross-over, open-label, time and motion study in Belgium (2014). HCPs prepared each vaccine in a cross-over manner with a wash-out period of 3-5min. An independent nurse assessed preparation time and immunisation errors by systematic review of the videos. HCPs satisfaction and preference were evaluated by a self-administered questionnaire. Average preparation time was 36s for the fully-liquid vaccine and 70.5s for the non-fully liquid vaccine. The time saved using the fully-liquid vaccine was 34.5s (p≤0.001). On 192 preparations, 57 immunisation errors occurred: 47 in the non-fully liquid vaccine group (including one missing reconstitution of Hib component), 10 in the fully-liquid vaccine group. 71.9% of HCPs were very or somewhat satisfied with the ease of handling of both vaccines; 66.7% and 67.7% were very or somewhat satisfied with speed of preparation in the fully-liquid vaccine and the non-fully liquid vaccine groups, respectively. Almost all HCPs (97.6%) stated they would prefer the use of the fully-liquid vaccine in their daily practice. Preparation of a fully-liquid hexavalent vaccine can be completed in half the time necessary to prepare a non-fully liquid vaccine. The simplicity of the fully-liquid hexavalent vaccine preparation helps optimise reduction of immunisation errors. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

20 CFR 404.111 - When we consider a person fully insured based on World War II active military or naval service.

Code of Federal Regulations, 2011 CFR

2011-04-01

... on World War II active military or naval service. 404.111 Section 404.111 Employees' Benefits SOCIAL... Quarters of Coverage Fully Insured Status § 404.111 When we consider a person fully insured based on World... States during World War II; (b) The person died within three years after separation from service and...

Managing unexpected events in the manufacturing of biologic medicines.

PubMed

Grampp, Gustavo; Ramanan, Sundar

2013-08-01

The manufacturing of biologic medicines (biologics) requires robust process and facility design, rigorous regulatory compliance, and a well-trained workforce. Because of the complex attributes of biologics and their sensitivity to production and handling conditions, manufacturing of these medicines also requires a high-reliability manufacturing organization. As required by regulators, such an organization must monitor the state-of-control for the manufacturing process. A high-reliability organization also invests in an experienced and fully engaged technical support staff and fosters a management culture that rewards in-depth analysis of unexpected results, robust risk assessments, and timely and effective implementation of mitigation measures. Such a combination of infrastructure, technology, human capital, management, and a science-based operations culture does not occur without a strong organizational and financial commitment. These attributes of a high-reliability biologics manufacturer are difficult to achieve and may be differentiating factors as the supply of biologics diversifies in future years.

Sequence-based classification and identification of fungi

USDA-ARS?s Scientific Manuscript database

Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomi...

Crossword: A Fully Automated Algorithm for the Segmentation and Quality Control of Protein Microarray Images

PubMed Central

2015-01-01

Biological assays formatted as microarrays have become a critical tool for the generation of the comprehensive data sets required for systems-level understanding of biological processes. Manual annotation of data extracted from images of microarrays, however, remains a significant bottleneck, particularly for protein microarrays due to the sensitivity of this technology to weak artifact signal. In order to automate the extraction and curation of data from protein microarrays, we describe an algorithm called Crossword that logically combines information from multiple approaches to fully automate microarray segmentation. Automated artifact removal is also accomplished by segregating structured pixels from the background noise using iterative clustering and pixel connectivity. Correlation of the location of structured pixels across image channels is used to identify and remove artifact pixels from the image prior to data extraction. This component improves the accuracy of data sets while reducing the requirement for time-consuming visual inspection of the data. Crossword enables a fully automated protocol that is robust to significant spatial and intensity aberrations. Overall, the average amount of user intervention is reduced by an order of magnitude and the data quality is increased through artifact removal and reduced user variability. The increase in throughput should aid the further implementation of microarray technologies in clinical studies. PMID:24417579

Operation of the Australian Store.Synchrotron for macromolecular crystallography

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

Meyer, Grischa R.; Aragão, David; Mudie, Nathan J.

2014-10-01

The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The service automatically receives and archives raw diffraction data, related metadata and preliminary results of automated data-processing workflows. Data are able to be shared with collaborators and opened to the public. In the nine months since its deployment in August 2013, the service has handled over 22.4 TB of raw data (∼1.7 million diffraction images). Severalmore » real examples from the Australian crystallographic community are described that illustrate the advantages of the approach, which include real-time online data access and fully redundant, secure storage. Discoveries in biological sciences increasingly require multidisciplinary approaches. With this in mind, Store.Synchrotron has been developed as a component within a greater service that can combine data from other instruments at the Australian Synchrotron, as well as instruments at the Australian neutron source ANSTO. It is therefore envisaged that this will serve as a model implementation of raw data archiving and dissemination within the structural biology research community.« less

Fully Screen-Printed, Large-Area, and Flexible Active-Matrix Electrochromic Displays Using Carbon Nanotube Thin-Film Transistors.

PubMed

Cao, Xuan; Lau, Christian; Liu, Yihang; Wu, Fanqi; Gui, Hui; Liu, Qingzhou; Ma, Yuqiang; Wan, Haochuan; Amer, Moh R; Zhou, Chongwu

2016-11-22

Semiconducting single-wall carbon nanotubes are ideal semiconductors for printed electronics due to their advantageous electrical and mechanical properties, intrinsic printability in solution, and desirable stability in air. However, fully printed, large-area, high-performance, and flexible carbon nanotube active-matrix backplanes are still difficult to realize for future displays and sensing applications. Here, we report fully screen-printed active-matrix electrochromic displays employing carbon nanotube thin-film transistors. Our fully printed backplane shows high electrical performance with mobility of 3.92 ± 1.08 cm 2 V -1 s -1 , on-off current ratio I on /I off ∼ 10 4 , and good uniformity. The printed backplane was then monolithically integrated with an array of printed electrochromic pixels, resulting in an entirely screen-printed active-matrix electrochromic display (AMECD) with good switching characteristics, facile manufacturing, and long-term stability. Overall, our fully screen-printed AMECD is promising for the mass production of large-area and low-cost flexible displays for applications such as disposable tags, medical electronics, and smart home appliances.

Positively charged mini-protein Zbasic2 as a highly efficient silica binding module: opportunities for enzyme immobilization on unmodified silica supports.

PubMed

Bolivar, Juan M; Nidetzky, Bernd

2012-07-03

Silica is a highly attractive support material for protein immobilization in a wide range of biotechnological and biomedical-analytical applications. Without suitable derivatization, however, the silica surface is not generally usable for attachment of proteins. We show here that Z(basic2) (a three α-helix bundle mini-protein of 7 kDa size that exposes clustered positive charges from multiple arginine residues on one side) functions as highly efficient silica binding module (SBM), allowing chimeras of target protein with SBM to become very tightly attached to underivatized glass at physiological pH conditions. We used two enzymes, d-amino acid oxidase and sucrose phosphorylase, to demonstrate direct immobilization of Z(basic2) protein from complex biological samples with extremely high selectivity. Immobilized enzymes displayed full biological activity, suggesting that their binding to the glass surface had occurred in a preferred orientation via the SBM. We also show that charge complementarity was the main principle of affinity between SBM and glass surface, and Z(basic2) proteins were bound in a very strong, yet fully reversible manner, presumably through multipoint noncovalent interactions. Z(basic2) proteins were immobilized on porous glass in a loading of 30 mg protein/g support or higher, showing that attachment via the SBM combines excellent binding selectivity with a technically useful binding capacity. Therefore, Z(basic2) and silica constitute a fully orthogonal pair of binding module and insoluble support for oriented protein immobilization, and this opens up new opportunities for the application of silica-based materials in the development of supported heterogeneous biocatalysts.

20 CFR 404.111 - When we consider a person fully insured based on World War II active military or naval service.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false When we consider a person fully insured based on World War II active military or naval service. 404.111 Section 404.111 Employees' Benefits SOCIAL SECURITY ADMINISTRATION FEDERAL OLD-AGE, SURVIVORS AND DISABILITY INSURANCE (1950- ) Insured Status and Quarters of Coverage Fully Insured Status §...

High resolution labeling of cholinergic nerve terminals using a specific fully active biotinylated botulinum neurotoxin type A.

PubMed

Arribas, M; Blasi, J; Egea, G; Fariñas, I; Solsona, C; Marsal, J

1993-12-15

We report here on the synthesis and characterization of a fully active biotinylated derivative of the botulinum neurotoxin type A. Different ratios of biotin: botulinum toxin were tested to optimize derivatizing conditions and a ratio of 35:1 was selected for further experiments. The average number of biotin groups per toxin molecule was estimated to be 7.8, occurring at both heavy and light chains, and almost all externally located and easily accessible to recognition by streptavidin. The modified toxin retained its toxicity and its ability to interact with biological membranes. Apart from its suitability for detection in Western blots and in microtiter well plates, biotinylated botulinum toxin proved to be adequate for morphological labeling studies at both light and electron microscopy. Peroxidase histochemistry in cryostat sections of intoxicated rat hemidiaphragm muscles showed a distinct labeling of end-plates. Electron microscopy studies were performed on the electric organ of Torpedo marmorata using colloidal gold-conjugated streptavidin for detection. After intoxication of electric organ fragments with the modified toxin, gold labels were found associated with the presynaptic plasma membrane of nerve terminals and with the membrane of synaptic vesicles. Moreover, the distribution of biotinylated botulinum toxin binding sites over the membrane of synaptosomes isolated from the electric organ of Torpedo and their relationship with intramembrane particles were analyzed using the replica-staining label-fracture technique. It was found that the toxin is never associated with intramembrane particles.

Genetic and Genomic Toolbox of Zea mays

PubMed Central

Nannas, Natalie J.; Dawe, R. Kelly

2015-01-01

Maize has a long history of genetic and genomic tool development and is considered one of the most accessible higher plant systems. With a fully sequenced genome, a suite of cytogenetic tools, methods for both forward and reverse genetics, and characterized phenotype markers, maize is amenable to studying questions beyond plant biology. Major discoveries in the areas of transposons, imprinting, and chromosome biology came from work in maize. Moving forward in the post-genomic era, this classic model system will continue to be at the forefront of basic biological study. In this review, we outline the basics of working with maize and describe its rich genetic toolbox. PMID:25740912

PathJam: a new service for integrating biological pathway information.

PubMed

Glez-Peña, Daniel; Reboiro-Jato, Miguel; Domínguez, Rubén; Gómez-López, Gonzalo; Pisano, David G; Fdez-Riverola, Florentino

2010-10-28

Biological pathways are crucial to much of the scientific research today including the study of specific biological processes related with human diseases. PathJam is a new comprehensive and freely accessible web-server application integrating scattered human pathway annotation from several public sources. The tool has been designed for both (i) being intuitive for wet-lab users providing statistical enrichment analysis of pathway annotations and (ii) giving support to the development of new integrative pathway applications. PathJam’s unique features and advantages include interactive graphs linking pathways and genes of interest, downloadable results in fully compatible formats, GSEA compatible output files and a standardized RESTful API.

Lobster eye as a collector for water window microscopy

NASA Astrophysics Data System (ADS)

Pina, L.; Maršíková, V.; Inneman, A.; Nawaz, M. F.; Jančárek, A.; Havlíková, R.

2017-08-01

Imaging in EUV, SXR and XR spectral bands of radiation is of increasing interest. Material science, biology and hot plasma are examples of relevant fast developing areas. Applications include spectroscopy, astrophysics, Soft X-ray Ray metrology, Water Window microscopy, radiography and tomography. Especially Water Window imaging has still not fully recognized potential in biology and medicine microscopy applications. Theoretical study and design of Lobster Eye (LE) optics as a collector for water window (WW) microscopy and comparison with a similar size ellipsoidal mirror condensor are presented.

Canakinumab for the treatment of cryopyrin-associated periodic syndromes.

PubMed

Walsh, Garry M

2009-10-01

Familial cold-induced autoinflammatory syndrome, Muckle-Wells syndrome and neonatal-onset multisystem inflammatory disease make up cryopyrin-associated periodic syndromes (CAPS). These are autoinflammatory inherited disorders caused by autosomal dominant gain-of-function mutations in the NLRP3 gene, located on chromosome 1q44. Cryopyrin/NALP3/NLRP3 is an essential component of intracellular inflammasomes that activate caspase-1, which in turn converts interleukin-1beta (IL-1beta) to its active form. IL-1beta is a potent cytokine that activates diverse elements of the immune and inflammatory systems leading to the pathogenic changes characteristic of CAPS. There is therefore much interest in the development of IL-1beta blocking agents as novel biologic treatments for these conditions. Canakinumab (ACZ-885; Ilaris, Novartis Pharma) is a fully humanized monoclonal antibody (mAb) specific for IL-1beta and is indicated for a wide range of inflammatory disorders including CAPS. This review will assess the utility of canakinumab as a treatment for CAPS. Copyright 2009 Prous Science, S.A.U. or its licensors. All rights reserved.

Gamabufotalin, a major derivative of bufadienolide, inhibits VEGF-induced angiogenesis by suppressing VEGFR-2 signaling pathway.

PubMed

Tang, Ning; Shi, Lei; Yu, Zhenlong; Dong, Peipei; Wang, Chao; Huo, Xiaokui; Zhang, Baojing; Huang, Shanshan; Deng, Sa; Liu, Kexin; Ma, Tonghui; Wang, Xiaobo; Wu, Lijun; Ma, Xiao-Chi

2016-01-19

Gamabufotalin (CS-6), a main active compound isolated from Chinese medicine Chansu, has been shown to strongly inhibit cancer cell growth and inflammatory response. However, its effects on angiogenesis have not been known yet. Here, we sought to determine the biological effects of CS-6 on signaling mechanisms during angiogenesis. Our present results fully demonstrate that CS-6 could significantly inhibit VEGF triggered HUVECs proliferation, migration, invasion and tubulogenesis in vitro and blocked vascularization in Matrigel plugs impregnated in C57/BL6 mice as well as reduced vessel density in human lung tumor xenograft implanted in nude mice. Computer simulations revealed that CS-6 interacted with the ATP-binding sites of VEGFR-2 using molecular docking. Furthermore, western blot analysis indicated that CS-6 inhibited VEGF-induced phosphorylation of VEGFR-2 kinase and suppressed the activity of VEGFR-2-mediated signaling cascades. Therefore, our studies demonstrated that CS-6 inhibited angiogenesis by inhibiting the activation of VEGFR-2 signaling pathways and CS-6 could be a potential candidate in angiogenesis-related disease therapy.

STUDIES ON THE CHEMICAL NATURE OF THE SUBSTANCE INDUCING TRANSFORMATION OF PNEUMOCOCCAL TYPES

PubMed Central

Avery, Oswald T.; MacLeod, Colin M.; McCarty, Maclyn

1944-01-01

1. From Type III pneumococci a biologically active fraction has been isolated in highly purified form which in exceedingly minute amounts is capable under appropriate cultural conditions of inducing the transformation of unencapsulated R variants of Pneumococcus Type II into fully encapsulated cells of the same specific type as that of the heat-killed microorganisms from which the inducing material was recovered. 2. Methods for the isolation and purification of the active transforming material are described. 3. The data obtained by chemical, enzymatic, and serological analyses together with the results of preliminary studies by electrophoresis, ultracentrifugation, and ultraviolet spectroscopy indicate that, within the limits of the methods, the active fraction contains no demonstrable protein, unbound lipid, or serologically reactive polysaccharide and consists principally, if not solely, of a highly polymerized, viscous form of desoxyribonucleic acid. 4. Evidence is presented that the chemically induced alterations in cellular structure and function are predictable, type-specific, and transmissible in series. The various hypotheses that have been advanced concerning the nature of these changes are reviewed. PMID:19871359

Structural analysis and biological activity of a highly regular glycosaminoglycan from Achatina fulica.

PubMed

Liu, Jie; Zhou, Lutan; He, Zhicheng; Gao, Na; Shang, Feineng; Xu, Jianping; Li, Zi; Yang, Zengming; Wu, Mingyi; Zhao, Jinhua

2018-02-01

Edible snails have been widely used as a health food and medicine in many countries. A unique glycosaminoglycan (AF-GAG) was purified from Achatina fulica. Its structure was analyzed and characterized by chemical and instrumental methods, such as Fourier transform infrared spectroscopy, analysis of monosaccharide composition, and 1D/2D nuclear magnetic resonance spectroscopy. Chemical composition analysis indicated that AF-GAG is composed of iduronic acid (IdoA) and N-acetyl-glucosamine (GlcNAc) and its average molecular weight is 118kDa. Structural analysis clarified that the uronic acid unit in glycosaminoglycan (GAG) is the fully epimerized and the sequence of AF-GAG is →4)-α-GlcNAc (1→4)-α-IdoA2S (1→. Although its structure with a uniform repeating disaccharide is similar to those of heparin and heparan sulfate, this GAG is structurally highly regular and homogeneous. Anticoagulant activity assays indicated that AF-GAG exhibits no anticoagulant activities, but considering its structural characteristic, other bioactivities such as heparanase inhibition may be worthy of further study. Copyright © 2017 Elsevier Ltd. All rights reserved.

Simultaneous structure-activity studies and arming of natural products by C-H amination reveal cellular targets of eupalmerin acetate.

PubMed

Li, Jing; Cisar, Justin S; Zhou, Cong-Ying; Vera, Brunilda; Williams, Howard; Rodríguez, Abimael D; Cravatt, Benjamin F; Romo, Daniel

2013-06-01

Natural products have a venerable history of, and enduring potential for the discovery of useful biological activity. To fully exploit this, the development of chemical methodology that can functionalize unique sites within these complex structures is highly desirable. Here, we describe the use of rhodium(II)-catalysed C-H amination reactions developed by Du Bois to carry out simultaneous structure-activity relationship studies and arming (alkynylation) of natural products at 'unfunctionalized' positions. Allylic and benzylic C-H bonds in the natural products undergo amination while olefins undergo aziridination, and tertiary amine-containing natural products are converted to amidines by a C-H amination-oxidation sequence or to hydrazine sulfamate zwitterions by an unusual N-amination. The alkynylated derivatives are ready for conversion into cellular probes that can be used for mechanism-of-action studies. Chemo- and site-selectivity was studied with a diverse library of natural products. For one of these-the marine-derived anticancer diterpene, eupalmerin acetate-quantitative proteome profiling led to the identification of several protein targets in HL-60 cells, suggesting a polypharmacological mode of action.

Plant Development, Auxin, and the Subsystem Incompleteness Theorem

PubMed Central

Niklas, Karl J.; Kutschera, Ulrich

2012-01-01

Plant morphogenesis (the process whereby form develops) requires signal cross-talking among all levels of organization to coordinate the operation of metabolic and genomic subsystems operating in a larger network of subsystems. Each subsystem can be rendered as a logic circuit supervising the operation of one or more signal-activated system. This approach simplifies complex morphogenetic phenomena and allows for their aggregation into diagrams of progressively larger networks. This technique is illustrated here by rendering two logic circuits and signal-activated subsystems, one for auxin (IAA) polar/lateral intercellular transport and another for IAA-mediated cell wall loosening. For each of these phenomena, a circuit/subsystem diagram highlights missing components (either in the logic circuit or in the subsystem it supervises) that must be identified experimentally if each of these basic plant phenomena is to be fully understood. We also illustrate the “subsystem incompleteness theorem,” which states that no subsystem is operationally self-sufficient. Indeed, a whole-organism perspective is required to understand even the most simple morphogenetic process, because, when isolated, every biological signal-activated subsystem is morphogenetically ineffective. PMID:22645582

Simultaneous structure-activity studies and arming of natural products by C-H amination reveal cellular targets of eupalmerin acetate

NASA Astrophysics Data System (ADS)

Li, Jing; Cisar, Justin S.; Zhou, Cong-Ying; Vera, Brunilda; Williams, Howard; Rodríguez, Abimael D.; Cravatt, Benjamin F.; Romo, Daniel

2013-06-01

Natural products have a venerable history of, and enduring potential for the discovery of useful biological activity. To fully exploit this, the development of chemical methodology that can functionalize unique sites within these complex structures is highly desirable. Here, we describe the use of rhodium(II)-catalysed C-H amination reactions developed by Du Bois to carry out simultaneous structure-activity relationship studies and arming (alkynylation) of natural products at ‘unfunctionalized’ positions. Allylic and benzylic C-H bonds in the natural products undergo amination while olefins undergo aziridination, and tertiary amine-containing natural products are converted to amidines by a C-H amination-oxidation sequence or to hydrazine sulfamate zwitterions by an unusual N-amination. The alkynylated derivatives are ready for conversion into cellular probes that can be used for mechanism-of-action studies. Chemo- and site-selectivity was studied with a diverse library of natural products. For one of these—the marine-derived anticancer diterpene, eupalmerin acetate—quantitative proteome profiling led to the identification of several protein targets in HL-60 cells, suggesting a polypharmacological mode of action.

Health Promoting Effects of Brassica-Derived Phytochemicals: From Chemopreventive and Anti-Inflammatory Activities to Epigenetic Regulation

PubMed Central

Wagner, Anika Eva; Terschluesen, Anna Maria; Rimbach, Gerald

2013-01-01

A high intake of brassica vegetables may be associated with a decreased chronic disease risk. Health promoting effects of Brassicaceae have been partly attributed to glucosinolates and in particular to their hydrolyzation products including isothiocyanates. In vitro and in vivo studies suggest a chemopreventive activity of isothiocyanates through the redox-sensitive transcription factor Nrf2. Furthermore, studies in cultured cells, in laboratory rodents, and also in humans support an anti-inflammatory effect of brassica-derived phytochemicals. However, the underlying mechanisms of how these compounds mediate their health promoting effects are yet not fully understood. Recent findings suggest that brassica-derived compounds are regulators of epigenetic mechanisms. It has been shown that isothiocyanates may inhibit histone deacetylase transferases and DNA-methyltransferases in cultured cells. Only a few papers have dealt with the effect of brassica-derived compounds on epigenetic mechanisms in laboratory animals, whereas data in humans are currently lacking. The present review aims to summarize the current knowledge regarding the biological activities of brassica-derived phytochemicals regarding chemopreventive, anti-inflammatory, and epigenetic pathways. PMID:24454992

Metabolic recycling of ammonia via glutamate dehydrogenase supports breast cancer biomass

PubMed Central

Spinelli, Jessica B.; Yoon, Haejin; Ringel, Alison E.; Jeanfavre, Sarah; Clish, Clary B.; Haigis, Marcia C.

2017-01-01

Ammonia is a ubiquitous by-product of cellular metabolism, however the biological consequences of ammonia production are not fully understood, especially in cancer. We find that ammonia is not merely a toxic waste product, but is recycled into central amino acid metabolism to maximize nitrogen utilization. Cancer cells primarily assimilated ammonia through reductive amination catalyzed by glutamate dehydrogenase (GDH), and secondary reactions enabled other amino acids, such as proline and aspartate, to directly acquire this nitrogen. Metabolic recycling of ammonia accelerated proliferation of breast cancer. In mice, ammonia accumulated in the tumor microenvironment, and was used directly to generate amino acids through GDH activity. These data show that ammonia not only is a secreted waste product, but a fundamental nitrogen source that can support tumor biomass. PMID:29025995

Self-renewal molecular mechanisms of colorectal cancer stem cells.

PubMed

Pan, Tianhui; Xu, Jinghong; Zhu, Yongliang

2017-01-01

Colorectal cancer stem cells (CCSCs) represent a small fraction of the colorectal cancer cell population that possess self-renewal and multi-lineage differentiation potential and drive tumorigenicity. Self-renewal is essential for the malignant biological behaviors of colorectal cancer stem cells. While the self-renewal molecular mechanisms of colorectal cancer stem cells are not yet fully understood, the aberrant activation of signaling pathways, such as Wnt, Notch, transforming growth factor-β (TGF-β)/bone morphogenetic protein (BMP) and Hedgehog-Gli (HH-GLI), specific roles mediated by cell surface markers and micro-environmental factors are involved in the regulation of self-renewal. The elucidation of the molecular mechanisms behind self-renewal may lead to the development of novel targeted interventions for the treatment of colorectal cancer.

STREAMS TO RIVERS: THE NEXT GENERATION OF ECOSYSTEM MONITORING

EPA Science Inventory

The historical focus in aquatic ecosystems has been on sampling methods oriented toward surveys of wadeable streams or smaller rivers. However, to fully assess the condition of the nations waters, methods are needed for systems above and below this scale. Biological communities...

Thyrotropin-releasing hormone controls mitochondrial biology in human epidermis.

PubMed

Knuever, Jana; Poeggeler, Burkhard; Gáspár, Erzsébet; Klinger, Matthias; Hellwig-Burgel, Thomas; Hardenbicker, Celine; Tóth, Balázs I; Bíró, Tamás; Paus, Ralf

2012-03-01

Mitochondrial capacity and metabolic potential are under the control of hormones, such as thyroid hormones. The most proximal regulator of the hypothalamic-pituitary-thyroid (HPT) axis, TRH, is the key hypothalamic integrator of energy metabolism via its impact on thyroid hormone secretion. Here, we asked whether TRH directly modulates mitochondrial functions in normal, TRH-receptor-positive human epidermis. Organ-cultured human skin was treated with TRH (5-100 ng/ml) for 12-48 h. TRH significantly increased epidermal immunoreactivity for the mitochondria-selective subunit I of respiratory chain complex IV (MTCO1). This resulted from an increased MTCO1 transcription and protein synthesis and a stimulation of mitochondrial biogenesis as demonstrated by transmission electron microscopy and TRH-enhanced mitochondrial DNA synthesis. TRH also significantly stimulated the transcription of several other mitochondrial key genes (TFAM, HSP60, and BMAL1), including the master regulator of mitochondrial biogenesis (PGC-1α). TRH significantly enhanced mitochondrial complex I and IV enzyme activity and enhanced the oxygen consumption of human skin samples, which shows that the stimulated mitochondria are fully vital because the main source for cellular oxygen consumption is mitochondrial endoxidation. These findings identify TRH as a potent, novel neuroendocrine stimulator of mitochondrial activity and biogenesis in human epidermal keratinocytes in situ. Thus, human epidermis offers an excellent model for dissecting neuroendocrine controls of human mitochondrial biology under physiologically relevant conditions and for exploring corresponding clinical applications.

Tuning CRISPR-Cas9 Gene Drives in Saccharomyces cerevisiae

PubMed Central

Roggenkamp, Emily; Giersch, Rachael M.; Schrock, Madison N.; Turnquist, Emily; Halloran, Megan; Finnigan, Gregory C.

2018-01-01

Control of biological populations is an ongoing challenge in many fields, including agriculture, biodiversity, ecological preservation, pest control, and the spread of disease. In some cases, such as insects that harbor human pathogens (e.g., malaria), elimination or reduction of a small number of species would have a dramatic impact across the globe. Given the recent discovery and development of the CRISPR-Cas9 gene editing technology, a unique arrangement of this system, a nuclease-based “gene drive,” allows for the super-Mendelian spread and forced propagation of a genetic element through a population. Recent studies have demonstrated the ability of a gene drive to rapidly spread within and nearly eliminate insect populations in a laboratory setting. While there are still ongoing technical challenges to design of a more optimal gene drive to be used in wild populations, there are still serious ecological and ethical concerns surrounding the nature of this powerful biological agent. Here, we use budding yeast as a safe and fully contained model system to explore mechanisms that might allow for programmed regulation of gene drive activity. We describe four conserved features of all CRISPR-based drives and demonstrate the ability of each drive component—Cas9 protein level, sgRNA identity, Cas9 nucleocytoplasmic shuttling, and novel Cas9-Cas9 tandem fusions—to modulate drive activity within a population. PMID:29348295

A recombinant 63-kDa form of Bacillus anthracis protective antigen produced in the yeast Saccharomyces cerevisiae provides protection in rabbit and primate inhalational challenge models of anthrax infection.

PubMed

Hepler, Robert W; Kelly, Rosemarie; McNeely, Tessie B; Fan, Hongxia; Losada, Maria C; George, Hugh A; Woods, Andrea; Cope, Leslie D; Bansal, Alka; Cook, James C; Zang, Gina; Cohen, Steven L; Wei, Xiaorong; Keller, Paul M; Leffel, Elizabeth; Joyce, Joseph G; Pitt, Louise; Schultz, Loren D; Jansen, Kathrin U; Kurtz, Myra

2006-03-06

Infection by Bacillus anthracis is preventable by prophylactic vaccination with several naturally derived and recombinant vaccine preparations. Existing data suggests that protection is mediated by antibodies directed against the protective antigen (PA) component of the anthrax toxin complex. PA is an 83-kDa protein cleaved in vivo to yield a biologically active 63-kDa protein. In an effort to evaluate the potential of yeast as an expression system for the production of recombinant PA, and to determine if the yeast-purified rPA63 can protect from a lethal inhalational challenge, the sequence of the 63-kDa form of PA was codon-optimized and expressed in the yeast Saccharomyces cerevisiae. Highly purified rPA63 isolated from Saccharomyces under denaturing conditions demonstrated reduced biological activity in a macrophage-killing assay compared to non-denatured rPA83 purified from Escherichia coli. Rabbits and non-human primates (NHP) immunized with rPA63 and later challenged with a lethal dose of B. anthracis spores were generally protected from infection. These results indicate that epitopes present in the 63-kDa from of PA can protect rabbits and non-human primates from a lethal spore challenge, and further suggest that a fully functional rPA63 is not required in order to provide these epitopes.

Melanocyte biology and function with reference to oral melanin hyperpigmentation in HIV-seropositive subjects.

PubMed

Feller, Liviu; Chandran, Rakesh; Kramer, Beverley; Khammissa, Razia A G; Altini, Mario; Lemmer, Johan

2014-09-01

The color of normal skin and of oral mucosa is not determined by the number of melanocytes in the epithelium but rather by their melanogenic activity. Pigmented biopolymers or melanins are synthesized in melanosomes. Tyrosinase is the critical enzyme in the biosynthesis of both brown/black eumelanin and yellow/red pheomelanin. The number of the melanosomes within the melanocytes, the type of melanin within the melanosomes, and the efficacy of the transfer of melanosomes from the melanocytes to the neighboring keratinocytes all play an important role in tissue pigmentation. Melanin production is regulated by locally produced factors including proopiomelanocortin and its derivative peptides, particularly alpha-melanocyte-stimulating hormone (α-MSH), melanocortin 1 receptor (MC1R), adrenergic and cholinergic agents, growth factors, cytokines, and nitric oxide. Both eumelanin and pheomelanin can be produced by the same melanocytes, and the proportion of the two melanin types is influenced by the degree of functional activity of the α-MSH/MC1R intracellular pathway. The cause of HIV oral melanosis is not fully understood but may be associated with HIV-induced cytokine dysregulation, with the medications commonly prescribed to HIV-seropositive persons, and with adrenocortical dysfunction, which is not uncommon in HIV-seropositive subjects with AIDS. The purpose of this article is to discuss some aspects of melanocyte biology and HIV-associated oral melanin hyperpigmentation.

Our Selections and Decisions: Inherent Features of the Nervous System?

NASA Astrophysics Data System (ADS)

Rösler, Frank

The chapter summarizes findings on the neuronal bases of decisionmaking. Taking the phenomenon of selection it will be explained that systems built only from excitatory and inhibitory neuron (populations) have the emergent property of selecting between different alternatives. These considerations suggest that there exists a hierarchical architecture with central selection switches. However, in such a system, functions of selection and decision-making are not localized, but rather emerge from an interaction of several participating networks. These are, on the one hand, networks that process specific input and output representations and, on the other hand, networks that regulate the relative activation/inhibition of the specific input and output networks. These ideas are supported by recent empirical evidence. Moreover, other studies show that rather complex psychological variables, like subjective probability estimates, expected gains and losses, prediction errors, etc., do have biological correlates, i.e., they can be localized in time and space as activation states of neural networks and single cells. These findings suggest that selections and decisions are consequences of an architecture which, seen from a biological perspective, is fully deterministic. However, a transposition of such nomothetic functional principles into the idiographic domain, i.e., using them as elements for comprehensive 'mechanistic' explanations of individual decisions, seems not to be possible because of principle limitations. Therefore, individual decisions will remain predictable by means of probabilistic models alone.

Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site

PubMed Central

Sunden, Fanny; Peck, Ariana; Salzman, Julia; Ressl, Susanne; Herschlag, Daniel

2015-01-01

Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called ‘catalytic residues’ are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes. DOI: http://dx.doi.org/10.7554/eLife.06181.001 PMID:25902402

Signal acquisition and analysis for cortical control of neuroprosthetics.

PubMed

Tillery, Stephen I Helms; Taylor, Dawn M

2004-12-01

Work in cortically controlled neuroprosthetic systems has concentrated on decoding natural behaviors from neural activity, with the idea that if the behavior could be fully decoded it could be duplicated using an artificial system. Initial estimates from this approach suggested that a high-fidelity signal comprised of many hundreds of neurons would be required to control a neuroprosthetic system successfully. However, recent studies are showing hints that these systems can be controlled effectively using only a few tens of neurons. Attempting to decode the pre-existing relationship between neural activity and natural behavior is not nearly as important as choosing a decoding scheme that can be more readily deployed and trained to generate the desired actions of the artificial system. These artificial systems need not resemble or behave similarly to any natural biological system. Effective matching of discrete and continuous neural command signals to appropriately configured device functions will enable effective control of both natural and abstract artificial systems using compatible thought processes.

Opioid receptor probes derived from cycloaddition of the hallucinogen natural product salvinorin A.

PubMed

Lozama, Anthony; Cunningham, Christopher W; Caspers, Michael J; Douglas, Justin T; Dersch, Christina M; Rothman, Richard B; Prisinzano, Thomas E

2011-04-25

As part of our continuing efforts toward more fully understanding the structure-activity relationships of the neoclerodane diterpene salvinorin A, we report the synthesis and biological characterization of unique cycloadducts through [4+2] Diels-Alder cycloaddition. Microwave-assisted methods were developed and successfully employed, aiding in functionalizing the chemically sensitive salvinorin A scaffold. This demonstrates the first reported results for both cycloaddition of the furan ring and functionalization via microwave-assisted methodology of the salvinorin A skeleton. The cycloadducts yielded herein introduce electron-withdrawing substituents and bulky aromatic groups into the C-12 position. Kappa opioid (KOP) receptor space was explored through aromatization of the bent oxanorbornadiene system possessed by the cycloadducts to a planar phenyl ring system. Although dimethyl- and diethylcarboxylate analogues 5 and 6 retain some affinity and selectivity for KOP receptors and are full agonists, their aromatized counterparts 13 and 14 have reduced affinity for KOP receptors. The methods developed herein signify a novel approach toward rapidly probing the structure-activity relationships of furan-containing natural products.

Exploiting NanoLuc luciferase for smartphone-based bioluminescence cell biosensor for (anti)-inflammatory activity and toxicity.

PubMed

Cevenini, Luca; Calabretta, Maria Maddalena; Lopreside, Antonia; Tarantino, Giuseppe; Tassoni, Annalisa; Ferri, Maura; Roda, Aldo; Michelini, Elisa

2016-12-01

The availability of smartphones with high-performance digital image sensors and processing power has completely reshaped the landscape of point-of-need analysis. Thanks to the high maturity level of reporter gene technology and the availability of several bioluminescent proteins with improved features, we were able to develop a bioluminescence smartphone-based biosensing platform exploiting the highly sensitive NanoLuc luciferase as reporter. A 3D-printed smartphone-integrated cell biosensor based on genetically engineered Hek293T cells was developed. Quantitative assessment of (anti)-inflammatory activity and toxicity of liquid samples was performed with a simple and rapid add-and-measure procedure. White grape pomace extracts, known to contain several bioactive compounds, were analyzed, confirming the suitability of the smartphone biosensing platform for analysis of untreated complex biological matrices. Such approach could meet the needs of small medium enterprises lacking fully equipped laboratories for first-level safety tests and rapid screening of new bioactive products. Graphical abstract Smartphone-based bioluminescence cell biosensor.

Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site

DOE PAGES

Sunden, Fanny; Peck, Ariana; Salzman, Julia; ...

2015-04-22

Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called ‘catalytic residues’ are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modesmore » of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes.« less

Synthesis, characterization and biocidal activity of new organotin complexes of 2-(3-oxocyclohex-1-enyl)benzoic acid.

PubMed

Vieira, Flaviana T; de Lima, Geraldo M; Maia, José R da S; Speziali, Nivaldo L; Ardisson, José D; Rodrigues, Leonardo; Correa, Ary; Romero, Oscar B

2010-03-01

The reaction of 1,3-cyclohexadione with 2-aminobenzoic acid has produced the 2-(3-oxocyclohex-1-enyl)benzoic acid (HOBz). Subsequent reactions of the ligand with organotin chlorides led to [Me(2)Sn(OBz)O](2) (1), [Bu(2)Sn(OBz)O](2) (2), [Ph(2)Sn(OBz)O](2) (3), [Me(3)Sn(OBz)] (4), [Bu(3)Sn(OBz)] (5) and [Ph(3)Sn(OBz)] (6). All complexes have been fully characterized. In addition the structure of complexes (2) and (4) have been authenticated by X-ray crystallography. The biological activity of all derivatives has been screened against Cryptococcus neoformans and Candida albicans. In addition we have performed toxicological testes employing human kidney cell. The complexes (3), (5) and (6) displayed the best values of inhibition of the fungus growing, superior to ketoconazole. Compound (5) presented promising results in view of the antifungal and cytotoxicity assays. Copyright (c) 2009 Elsevier Masson SAS. All rights reserved.

Investigation of antioxidant capacity of the extracts of bilberry (VACCINUM MYRTILLIS L.) by voltammetry

NASA Astrophysics Data System (ADS)

Vtorushina, A. N.; Nikonova, E. D.

2016-02-01

This paper deals with the urgent issue of the search of new drugs based on plant raw materials that have an influence on various stages of oxidation processes occurring in the human body. The aim of this paper is to determine the antioxidant activity of the bilberry extracts that are used in the medicine practice by a cathodic voltammetry method. We consider the influence of water and alcohol bilberry extracts on the process of oxygen electroreduction. From these extracts the most activity relation to the process of cathodic oxygen reduction showed alcohol (40%) bilberry extract. It was also stated that the alcohol extract of bilberry has a greater antioxidant activity than other known antioxidants such as ascorbic acid, glucose, dihydroquercetin. Thus, after consideration of a number of plant objects, we showed the possibility of applying the method of cathodic voltammetry for the determination of total antioxidant activity of plant material and identifying and highlighting the most perspective sources of biologically active substances (BAS), as well as the ability of identifying extractants that fully extract BAS from plant raw materials. The activity data of extracts of plant raw materials gives an opportunity of establishing an effective yield phytopreparation based on bilberry that has an antioxidant effect.

Pattern Formation on Networks: from Localised Activity to Turing Patterns

PubMed Central

McCullen, Nick; Wagenknecht, Thomas

2016-01-01

Networks of interactions between competing species are used to model many complex systems, such as in genetics, evolutionary biology or sociology and knowledge of the patterns of activity they can exhibit is important for understanding their behaviour. The emergence of patterns on complex networks with reaction-diffusion dynamics is studied here, where node dynamics interact via diffusion via the network edges. Through the application of a generalisation of dynamical systems analysis this work reveals a fundamental connection between small-scale modes of activity on networks and localised pattern formation seen throughout science, such as solitons, breathers and localised buckling. The connection between solutions with a single and small numbers of activated nodes and the fully developed system-scale patterns are investigated computationally using numerical continuation methods. These techniques are also used to help reveal a much larger portion of of the full number of solutions that exist in the system at different parameter values. The importance of network structure is also highlighted, with a key role being played by nodes with a certain so-called optimal degree, on which the interaction between the reaction kinetics and the network structure organise the behaviour of the system. PMID:27273339

Tracking transcriptional activities with high-content epifluorescent imaging

NASA Astrophysics Data System (ADS)

Hua, Jianping; Sima, Chao; Cypert, Milana; Gooden, Gerald C.; Shack, Sonsoles; Alla, Lalitamba; Smith, Edward A.; Trent, Jeffrey M.; Dougherty, Edward R.; Bittner, Michael L.

2012-04-01

High-content cell imaging based on fluorescent protein reporters has recently been used to track the transcriptional activities of multiple genes under different external stimuli for extended periods. This technology enhances our ability to discover treatment-induced regulatory mechanisms, temporally order their onsets and recognize their relationships. To fully realize these possibilities and explore their potential in biological and pharmaceutical applications, we introduce a new data processing procedure to extract information about the dynamics of cell processes based on this technology. The proposed procedure contains two parts: (1) image processing, where the fluorescent images are processed to identify individual cells and allow their transcriptional activity levels to be quantified; and (2) data representation, where the extracted time course data are summarized and represented in a way that facilitates efficient evaluation. Experiments show that the proposed procedure achieves fast and robust image segmentation with sufficient accuracy. The extracted cellular dynamics are highly reproducible and sensitive enough to detect subtle activity differences and identify mechanisms responding to selected perturbations. This method should be able to help biologists identify the alterations of cellular mechanisms that allow drug candidates to change cell behavior and thereby improve the efficiency of drug discovery and treatment design.

Understanding Kombucha Tea Fermentation: A Review.

PubMed

Villarreal-Soto, Silvia Alejandra; Beaufort, Sandra; Bouajila, Jalloul; Souchard, Jean-Pierre; Taillandier, Patricia

2018-03-01

Kombucha is a beverage of probable Manchurian origins obtained from fermented tea by a microbial consortium composed of several bacteria and yeasts. This mixed consortium forms a powerful symbiosis capable of inhibiting the growth of potentially contaminating bacteria. The fermentation process also leads to the formation of a polymeric cellulose pellicle due to the activity of certain strains of Acetobacter sp. The tea fermentation process by the microbial consortium was able to show an increase in certain biological activities which have been already studied; however, little information is available on the characterization of its active components and their evolution during fermentation. Studies have also reported that the use of infusions from other plants may be a promising alternative. Kombucha is a traditional fermented tea whose consumption has increased in the recent years due to its multiple functional properties such as anti-inflammatory potential and antioxidant activity. The microbiological composition of this beverage is quite complex and still more research is needed in order to fully understand its behavior. This study comprises the chemical and microbiological composition of the tea and the main factors that may affect its production. © 2018 Institute of Food Technologists®.

Suppression of p53 Activity through the Cooperative Action of Ski and Histone Deacetylase SIRT1*

PubMed Central

Inoue, Yasumichi; Iemura, Shun-ichiro; Natsume, Tohru; Miyazawa, Keiji; Imamura, Takeshi

2011-01-01

Ski was originally identified as an oncogene based on the fact that Ski overexpression transformed chicken and quail embryo fibroblasts. Consistent with these proposed oncogenic roles, Ski is overexpressed in various human tumors. However, whether and how Ski functions in mammalian tumorigenesis has not been fully investigated. Here, we show that Ski interacts with p53 and attenuates the biological functions of p53. Ski overexpression attenuated p53-dependent transactivation, whereas Ski knockdown enhanced the transcriptional activity of p53. Interestingly, Ski bound to the histone deacetylase SIRT1 and stabilized p53-SIRT1 interaction to promote p53 deacetylation, which subsequently decreased the DNA binding activity of p53. Consistent with the ability of Ski to inactivate p53, overexpressing Ski desensitized cells to genotoxic drugs and Nutlin-3, a small-molecule antagonist of Mdm2 that stabilizes p53 and activates the p53 pathway, whereas knocking down Ski increased the cellular sensitivity to these agents. These results indicate that Ski negatively regulates p53 and suggest that the p53-Ski-SIRT1 axis is an attractive target for cancer therapy. PMID:21149449

N2 non-thermal atmospheric pressure plasma promotes wound healing in vitro and in vivo: Potential modulation of adhesion molecules and matrix metalloproteinase-9.

PubMed

Kang, Sung Un; Choi, Jae Won; Chang, Jae Won; Kim, Kang Il; Kim, Yeon Soo; Park, Ju Kyeong; Kim, Yang Eun; Lee, Yun Sang; Yang, Sang Sik; Kim, Chul-Ho

2017-02-01

Advances in physics and biology have made it possible to apply non-thermal atmospheric pressure plasma (NTP) in the biomedical field. Although accumulating evidence suggests that NTP has various medicinal effects, such as facilitating skin wound healing on exposed tissue while minimizing undesirable tissue damage, the underlying molecular mechanisms are not fully understood. In this study, NTP generated from N 2 optimized wound healing in the scratch wound healing assay. In addition, matrix metalloproteinase (MMP)-9 expression and enzyme activity increased and the urokinase-type plasminogen activator (uPA) system was activated after NTP treatment. We also showed that NTP treatment increased Slug and TCF8/ZEB1 expression and decreased that of E-cadherin, suggesting induction of the epithelial-to-mesenchymal transition (EMT). The effect of N 2 NTP was verified on rat wound model. Taken together, these results suggest that N 2 NTP promotes wound healing by inducing the EMT and activating the MMP-9/uPA system. These findings show the therapeutic potential of NTP for skin wound healing. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Broadening the Scope of Dental Education.

ERIC Educational Resources Information Center

Loe, Harald

1992-01-01

Scientific and technological advances affecting dental education in the near future are examined, including the growing role of saliva in diagnosis, direct imaging methods, biomaterials research, computer-aided design and manufacturing, molecular biology, and new restorative dentistry. It is argued that dentistry should be a fully recognized…

Analytical methods in environmental effects-directed investigations of effluents.

PubMed

Hewitt, L Mark; Marvin, Chris H

2005-05-01

Effluent discharges are released into aquatic environments as complex mixtures for which there is commonly either no knowledge of the toxic components or a lack of understanding of how known toxicants interact with other effluent components. Effects-directed investigations consist of chemical extraction and iterative fractionation steps directed by a biological endpoint that is designed to permit the identification or characterization of the chemical classes or compounds in a complex mixture responsible for the observed biological activity. Our review of the literature on effects-directed analyses of effluents for non-mutagenic as well as mutagenic endpoints showed that common extraction and concentration methods have been used. Since the mid-1980s, the methods have evolved from the use of XAD resins to C18 solid-phase extraction (SPE). Blue cotton, blue rayon, and blue chitin have been used specifically for investigations of mutagenic activity where polycyclic compounds were involved or suspected. After isolation, subsequent fractionations have been accomplished using SPE or a high-pressure liquid chromatography (HPLC) system commonly fitted with a C18 reverse-phase column. Substances in active fractions are characterized by gas chromatography/mass spectrometry (GC-MS) and/or other spectrometric techniques for identification. LC-MS methods have been developed for difficult-to-analyze polar substances identified from effects-directed studies, but the potential for LC-MS to identify unknown polar compounds has yet to be fully realized. Salmonella-based assays (some miniaturized) have been coupled with fractionation methods for most studies aimed at identifying mutagenic fractions and chemical classes in mixtures. Effects-directed investigations of mutagens have focused mostly on drinking water and sewage, whereas extensive investigations of non-mutagenic effects have also included runoff, pesticides, and pulp mill effluents. The success of effects-directed investigations should be based on a realistic initial objective of each project. Identification of chemical classes associated with the measured biological endpoint is frequently achievable; however, confirmation of individual compounds is much more difficult and not always a necessary goal of effects-directed chemical analysis.

Small Active Radiation Monitor

NASA Technical Reports Server (NTRS)

Badhwar, Gautam D.

2004-01-01

A device, named small active radiation monitor, allows on-orbit evaluations during periods of increased radiation, after extravehicular activities, or at predesignated times for crews on such long-duration space missions as on the International Space Station. It also permits direct evaluation of biological doses, a task now performed using a combination of measurements and potentially inaccurate simulations. Indeed the new monitor can measure a full array of radiation levels, from soft x-rays to hard galactic cosmic-ray particles. With refinement, it will benefit commercial (nuclear power-plant workers, airline pilots, medical technicians, physicians/dentists, and others) and military personnel as well as the astronauts for whom thermoluminescent dosimeters are inadequate. Civilian and military personnel have long since graduated from film badges to thermoluminescent dosimeters. Once used, most dosimeters must be returned to a central facility for processing, a step that can take days or even weeks. While this suffices for radiation workers for whom exposure levels are typically very low and of brief duration, it does not work for astronauts. Even in emergencies and using express mail, the results can often be delayed by as much as 24 hours. Electronic dosimeters, which are the size of electronic oral thermometers, and tattlers, small electronic dosimeters that sound an alarm when the dose/dose rate exceeds preset values, are also used but suffer disadvantages similar to those of thermoluminescent dosimeters. None of these devices fully answers the need of rapid monitoring during the space missions. Instead, radiation is monitored by passive detectors, which are read out after the missions. Unfortunately, these detectors measure only the absorbed dose and not the biologically relevant dose equivalent. The new monitor provides a real-time readout, a time history of radiation exposures (both absorbed dose and biologically relevant dose equivalent), and a count of the number of particles passing through a unit area. Better still, the monitor can be used anywhere.

Proton and gallium(III) binding properties of a biologically active salicylidene acylhydrazide.

PubMed

Hakobyan, Shoghik; Boily, Jean-François; Ramstedt, Madeleine

2014-09-01

Bacterial biofilm formation causes a range of problems in our society, especially in health care. Salicylidene acylhydrazides (hydrazones) are promising antivirulence drugs targeting secretion systems used during bacterial infection of host cells. When mixed with the gallium ion they become especially potent as bacterial and biofilm growth-suppressing agents, although the mechanisms through which this occurs are not fully understood. At the base of this uncertainty lies the nature of hydrazone-metal interactions. This study addresses this issue by resolving the equilibrium speciation of hydrazone-gallium aqueous solutions. The protonation constants of the target 2-oxo-2-[N-(2,4,6-trihydroxy-benzylidene)-hydrazino]-acetamide (ME0163) hydrazone species and of its 2,4,6-trihydroxybenzaldehyde and oxamic acid hydrazide building blocks were determined by UV-visible spectrophotometry to achieve this goal. These studies show that the hydrazone is an excessively strong complexing agent for gallium and that its antivirulence properties are predominantly ascribed to monomeric 1:1Ga-ME0163 complexes of various Ga hydrolysis and ME0163 protonation states. The chelation of Ga(III) to the hydrazone also increased the stability of the compounds against acid-induced hydrolysis, making this group of compounds very interesting for biological applications where the Fe-antagonist action of both Ga(III) and the hydrazone can be combined for enhanced biological effect. Copyright © 2014. Published by Elsevier Inc.

Macronutrient intake regulates sexual conflict in decorated crickets.

PubMed

Rapkin, J; Jensen, K; Lane, S M; House, C M; Sakaluk, S K; Hunt, J

2016-02-01

Sexual conflict results in a diversity of sex-specific adaptations, including chemical additions to ejaculates. Male decorated crickets (Gryllodes sigillatus) produce a gelatinous nuptial gift (the spermatophylax) that varies in size and free amino acid composition, which influences a female's willingness to fully consume this gift. Complete consumption of this gift maximizes sperm transfer through increased retention of the sperm-containing ampulla, but hinders post-copulatory mate choice. Here, we examine the effects of protein (P) and carbohydrate (C) intake on the weight and amino acid composition of the spermatophylax that describes its gustatory appeal to the female, as well as the ability of this gift to regulate sexual conflict via ampulla attachment time. Nutrient intake had similar effects on the expression of these traits with each maximized at a high intake of nutrients with a P : C ratio of 1 : 1.3. Under dietary choice, males actively regulated their nutrient intake but this regulation did not coincide with the peak of the nutritional landscape for any trait. Our results therefore demonstrate that a balanced intake of nutrients is central to regulating sexual conflict in G. sigillatus, but males are constrained from reaching the optima needed to bias the outcome of this conflict in their favour. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Sequence-specific 1H-NMR assignments for the aromatic region of several biologically active, monomeric insulins including native human insulin.

PubMed

Roy, M; Lee, R W; Kaarsholm, N C; Thøgersen, H; Brange, J; Dunn, M F

1990-06-12

The aromatic region of the 1H-FT-NMR spectrum of the biologically fully-potent, monomeric human insulin mutant, B9 Ser----Asp, B27 Thr----Glu has been investigated in D2O. At 1 to 5 mM concentrations, this mutant insulin is monomeric above pH 7.5. Coupling and amino acid classification of all aromatic signals is established via a combination of homonuclear one- and two-dimensional methods, including COSY, multiple quantum filters, selective spin decoupling and pH titrations. By comparisons with other insulin mutants and with chemically modified native insulins, all resonances in the aromatic region are given sequence-specific assignments without any reliance on the various crystal structures reported for insulin. These comparisons also give the sequence-specific assignments of most of the aromatic resonances of the mutant insulins B16 Tyr----Glu, B27 Thr----Glu and B25 Phe----Asp and the chemically modified species des-(B23-B30) insulin and monoiodo-Tyr A14 insulin. Chemical dispersion of the assigned resonances, ring current perturbations and comparisons at high pH have made possible the assignment of the aromatic resonances of human insulin, and these studies indicate that the major structural features of the human insulin monomer (including those critical to biological function) are also present in the monomeric mutant.

Bothrops jararaca envenomation: Pathogenesis of hemostatic disturbances and intravascular hemolysis.

PubMed

Senise, Luana V; Yamashita, Karine M; Santoro, Marcelo L

2015-11-01

To attain fully functional biological activity, vitamin-K dependent coagulation factors (VKDCF) are γ-carboxylated prior to secretion from liver. Warfarin impairs the γ-carboxylation, and consequently their physiological function. Bothrops jararaca snake venom (BjV) contains several activators of blood coagulation, especially procoagulant enzymes (prothrombin and factor X activators) and thrombin-like enzymes. In order to clarify the relative contribution of prothrombin and factor X activators to the hemostatic disturbances occurring during experimental B. jararaca envenomation, warfarin was used to deplete VKDCF, prior to BjV administration. Male Wistar rats were pretreated with saline (Sal) or warfarin (War) and inoculated subsequently with BjV or saline, thus forming four groups: Sal + Sal (negative control), Sal + BjV (positive control), War + Sal (warfarinization control), and War + BjV. Three hours after inoculation, prothrombin and factor X levels fell 40% and 50%, respectively; levels of both factors decreased more than 97% in the War + Sal and War + BjV groups. Platelet counts dropped 93% and 76% in Sal + BjV and War + BjV, respectively, and plasma fibrinogen levels decreased 86% exclusively in Sal + BjV. After 6 and 24 h, platelet counts and fibrinogen levels increased progressively. A dramatic augmentation in plasma hemoglobin levels and the presence of schizocytes and microcytes in the Sal + BjV group indicated the development of intravascular hemolysis, which was prevented by warfarin pretreatment. Our findings show that intravascular thrombin generation has the foremost role in the pathogenesis of coagulopathy and intravascular hemolysis, but not in the development of thrombocytopenia, in B. jararaca envenomation in rats; in addition, fibrinogenases (metalloproteinases) may contribute to coagulopathy more than thrombin-like enzymes. © 2015 by the Society for Experimental Biology and Medicine.

Synthesis, structure and catechol-oxidase activity of copper(II) complexes of 17-hydroxy-16-(N-3-oxo-prop-1-enyl)amino steroids.

PubMed

Wegner, Rainer; Dubs, Manuela; Görls, Helmar; Robl, Christian; Schönecker, Bruno; Jäger, Ernst-G

2002-09-01

Copper is next to iron the most important element in the biological transport, storage and in redox reactions of dioxygen. A bioanalogous activation of dioxygen with copper complexes is used for catalytical epoxidation, allylic hydroxylation and oxidative coupling of aromatic substrates, for example. With stereochemical information in form of chiral ligands, enantioselective reactions may be possible. Another aspect of interest on copper catalyzed reactions with dioxygen is that the exact mechanism and biological function of some enzymes (especially catechol oxidase) is yet not fully clear. For studies mimicking the copper-containing catechol oxidase appropriate chiral steroid ligands with defined stereochemistry and conformation have been synthesized. The four diastereomeric 16,17-aminoalcohols of the 3-methoxy-estra-1,3,5(10)-triene series have been condensed with salicylic aldehyde and different beta-ketoenols to the chiral ligand types 1-5. These compounds with different steric and electronic properties and different arrangements of the neighboring hydroxy and nitrogen functions were reacted with copper(II) acetate to copper complexes. The structure of these complexes will be discussed. The bioanalogous oxidation of 3,5-di-tbutyl-catechol (dtbc) to the corresponding quinone was catalyzed by most of the complexes, indicating their ability to activate dioxygen. The trans configurations c and d showed an activity one magnitude higher than the cis configurations a and b. Comparing compounds with the same diastereomeric configuration, the main influence was that of the peripheral R(1-3) substituents at the beta-ketoenaminic group which are useful for the fine-tuning of the properties of the copper atoms like redox potential and Lewis acidity.

Efficient reinforcement learning of a reservoir network model of parametric working memory achieved with a cluster population winner-take-all readout mechanism.

PubMed

Cheng, Zhenbo; Deng, Zhidong; Hu, Xiaolin; Zhang, Bo; Yang, Tianming

2015-12-01

The brain often has to make decisions based on information stored in working memory, but the neural circuitry underlying working memory is not fully understood. Many theoretical efforts have been focused on modeling the persistent delay period activity in the prefrontal areas that is believed to represent working memory. Recent experiments reveal that the delay period activity in the prefrontal cortex is neither static nor homogeneous as previously assumed. Models based on reservoir networks have been proposed to model such a dynamical activity pattern. The connections between neurons within a reservoir are random and do not require explicit tuning. Information storage does not depend on the stable states of the network. However, it is not clear how the encoded information can be retrieved for decision making with a biologically realistic algorithm. We therefore built a reservoir-based neural network to model the neuronal responses of the prefrontal cortex in a somatosensory delayed discrimination task. We first illustrate that the neurons in the reservoir exhibit a heterogeneous and dynamical delay period activity observed in previous experiments. Then we show that a cluster population circuit decodes the information from the reservoir with a winner-take-all mechanism and contributes to the decision making. Finally, we show that the model achieves a good performance rapidly by shaping only the readout with reinforcement learning. Our model reproduces important features of previous behavior and neurophysiology data. We illustrate for the first time how task-specific information stored in a reservoir network can be retrieved with a biologically plausible reinforcement learning training scheme. Copyright © 2015 the American Physiological Society.

Systematic network assessment of the carcinogenic activities of cadmium

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

Chen, Peizhan; Duan, Xiaohua; Li, Mian

Cadmium has been defined as type I carcinogen for humans, but the underlying mechanisms of its carcinogenic activity and its influence on protein-protein interactions in cells are not fully elucidated. The aim of the current study was to evaluate, systematically, the carcinogenic activity of cadmium with systems biology approaches. From a literature search of 209 studies that performed with cellular models, 208 proteins influenced by cadmium exposure were identified. All of these were assessed by Western blotting and were recognized as key nodes in network analyses. The protein-protein functional interaction networks were constructed with NetBox software and visualized with Cytoscapemore » software. These cadmium-rewired genes were used to construct a scale-free, highly connected biological protein interaction network with 850 nodes and 8770 edges. Of the network, nine key modules were identified and 60 key signaling pathways, including the estrogen, RAS, PI3K-Akt, NF-κB, HIF-1α, Jak-STAT, and TGF-β signaling pathways, were significantly enriched. With breast cancer, colorectal and prostate cancer cellular models, we validated the key node genes in the network that had been previously reported or inferred form the network by Western blotting methods, including STAT3, JNK, p38, SMAD2/3, P65, AKT1, and HIF-1α. These results suggested the established network was robust and provided a systematic view of the carcinogenic activities of cadmium in human. - Highlights: • A cadmium-influenced network with 850 nodes and 8770 edges was established. • The cadmium-rewired gene network was scale-free and highly connected. • Nine modules were identified, and 60 key signaling pathways related to cadmium-induced carcinogenesis were found. • Key mediators in the network were validated in multiple cellular models.« less

Shock wave treatment enhances cell proliferation and improves wound healing by ATP release-coupled extracellular signal-regulated kinase (ERK) activation.

PubMed

Weihs, Anna M; Fuchs, Christiane; Teuschl, Andreas H; Hartinger, Joachim; Slezak, Paul; Mittermayr, Rainer; Redl, Heinz; Junger, Wolfgang G; Sitte, Harald H; Rünzler, Dominik

2014-09-26

Shock wave treatment accelerates impaired wound healing in diverse clinical situations. However, the mechanisms underlying the beneficial effects of shock waves have not yet been fully revealed. Because cell proliferation is a major requirement in the wound healing cascade, we used in vitro studies and an in vivo wound healing model to study whether shock wave treatment influences proliferation by altering major extracellular factors and signaling pathways involved in cell proliferation. We identified extracellular ATP, released in an energy- and pulse number-dependent manner, as a trigger of the biological effects of shock wave treatment. Shock wave treatment induced ATP release, increased Erk1/2 and p38 MAPK activation, and enhanced proliferation in three different cell types (C3H10T1/2 murine mesenchymal progenitor cells, primary human adipose tissue-derived stem cells, and a human Jurkat T cell line) in vitro. Purinergic signaling-induced Erk1/2 activation was found to be essential for this proliferative effect, which was further confirmed by in vivo studies in a rat wound healing model where shock wave treatment induced proliferation and increased wound healing in an Erk1/2-dependent fashion. In summary, this report demonstrates that shock wave treatment triggers release of cellular ATP, which subsequently activates purinergic receptors and finally enhances proliferation in vitro and in vivo via downstream Erk1/2 signaling. In conclusion, our findings shed further light on the molecular mechanisms by which shock wave treatment exerts its beneficial effects. These findings could help to improve the clinical use of shock wave treatment for wound healing. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Biological iron oxidation by Gallionella spp. in drinking water production under fully aerated conditions.

PubMed

de Vet, W W J M; Dinkla, I J T; Rietveld, L C; van Loosdrecht, M C M

2011-11-01

Iron oxidation under neutral conditions (pH 6.5-8) may be a homo- or heterogeneous chemically- or a biologically-mediated process. The chemical oxidation is supposed to outpace the biological process under slightly alkaline conditions (pH 7-8). The iron oxidation kinetics and growth of Gallionella spp. - obligatory chemolithotrophic iron oxidizers - were assessed in natural, organic carbon-containing water, in continuous lab-scale reactors and full-scale groundwater trickling filters in the Netherlands. From Gallionella cell numbers determined by qPCR, balances were made for all systems. The homogeneous chemical iron oxidation occurred in accordance with the literature, but was retarded by a low water temperature (13 °C). The contribution of the heterogeneous chemical oxidation was, despite the presence of freshly formed iron oxyhydroxides, much lower than in previous studies in ultrapure water. This could be caused by the adsorption of natural organic matter (NOM) on the iron oxide surfaces. In the oxygen-saturated natural water with a pH ranging from 6.5 to 7.7, Gallionella spp. grew uninhibited and biological iron oxidation was an important, and probably the dominant, process. Gallionella growth was not even inhibited in a full-scale filter after plate aeration. From this we conclude that Gallionella spp. can grow under neutral pH and fully aerated conditions when the chemical iron oxidation is retarded by low water temperature and inhibition of the autocatalytic iron oxidation. Copyright © 2011 Elsevier Ltd. All rights reserved.

Public attitudes toward legally coerced biological treatments of criminals

PubMed Central

Berryessa, Colleen M.; Chandler, Jennifer A.; Reiner, Peter

2016-01-01

Abstract How does the public view the offer of a biological treatment in lieu of prison for criminal offenders? Using the contrastive vignette technique, we explored this issue, using mixed-methods analysis to measure concerns regarding changing the criminal's personality, the coercive nature of the offer, and the safety of the proposed treatment. Overall, we found that of the three variables, the safety of the pill had the strongest effect on public acceptance of a biological intervention. Indeed, it was notable that the public was relatively sanguine about coercive offers of biological agents, as well as changing the personality of criminals. While respondents did not fully endorse such coercive offers, neither were they outraged by the use of biological treatments of criminals in lieu of incarceration. These results are discussed in the context of the retributive and rehabilitative sentiments of the public, and legal jurisprudence in the arena of human rights law. PMID:28852535

Public attitudes toward legally coerced biological treatments of criminals.

PubMed

Berryessa, Colleen M; Chandler, Jennifer A; Reiner, Peter

2016-12-01

How does the public view the offer of a biological treatment in lieu of prison for criminal offenders? Using the contrastive vignette technique, we explored this issue, using mixed-methods analysis to measure concerns regarding changing the criminal's personality, the coercive nature of the offer, and the safety of the proposed treatment. Overall, we found that of the three variables, the safety of the pill had the strongest effect on public acceptance of a biological intervention. Indeed, it was notable that the public was relatively sanguine about coercive offers of biological agents, as well as changing the personality of criminals. While respondents did not fully endorse such coercive offers, neither were they outraged by the use of biological treatments of criminals in lieu of incarceration. These results are discussed in the context of the retributive and rehabilitative sentiments of the public, and legal jurisprudence in the arena of human rights law.

It’s More Than Stamp Collecting: How Genome Sequencing Can Unify Biological Research

PubMed Central

Richards, Stephen

2015-01-01

The availability of reference genome sequences, especially the human reference, has revolutionized the study of biology. However, whilst the genomes of some species have been fully sequenced, a wide range of biological problems still cannot be effectively studied for lack of genome sequence information. Here, I identify neglected areas of biology and describe how both targeted species sequencing and more broad taxonomic surveys of the tree of life can address important biological questions. I enumerate the significant benefits that would accrue from sequencing a broader range of taxa, as well as discuss the technical advances in sequencing and assembly methods that would allow for wide-ranging application of whole-genome analysis. Finally, I suggest that in addition to “Big Science” survey initiatives to sequence the tree of life, a modified infrastructure-funding paradigm would better support reference genome sequence generation for research communities most in need. PMID:26003218

It's more than stamp collecting: how genome sequencing can unify biological research.

PubMed

Richards, Stephen

2015-07-01

The availability of reference genome sequences, especially the human reference, has revolutionized the study of biology. However, while the genomes of some species have been fully sequenced, a wide range of biological problems still cannot be effectively studied for lack of genome sequence information. Here, I identify neglected areas of biology and describe how both targeted species sequencing and more broad taxonomic surveys of the tree of life can address important biological questions. I enumerate the significant benefits that would accrue from sequencing a broader range of taxa, as well as discuss the technical advances in sequencing and assembly methods that would allow for wide-ranging application of whole-genome analysis. Finally, I suggest that in addition to 'big science' survey initiatives to sequence the tree of life, a modified infrastructure-funding paradigm would better support reference genome sequence generation for research communities most in need. Copyright © 2015 Elsevier Ltd. All rights reserved.

Biological interaction of living cells with COSAN-based synthetic vesicles

PubMed Central

Tarrés, Màrius; Canetta, Elisabetta; Paul, Eleanor; Forbes, Jordan; Azzouni, Karima; Viñas, Clara; Teixidor, Francesc; Harwood, Adrian J.

2015-01-01

Cobaltabisdicarbollide (COSAN) [3,3′-Co(1,2-C2B9H11)2]−, is a complex boron-based anion that has the unusual property of self-assembly into membranes and vesicles. These membranes have similar dimensions to biological membranes found in cells, and previously COSAN has been shown to pass through synthetic lipid membranes and those of living cells without causing breakdown of membrane barrier properties. Here, we investigate the interaction of this inorganic membrane system with living cells. We show that COSAN has no immediate effect on cell viability, and cells fully recover when COSAN is removed following exposure for hours to days. COSAN elicits a range of cell biological effects, including altered cell morphology, inhibition of cell growth and, in some cases, apoptosis. These observations reveal a new biology at the interface between inorganic, synthetic COSAN membranes and naturally occurring biological membranes. PMID:25588708

Biological interaction of living cells with COSAN-based synthetic vesicles.

PubMed

Tarrés, Màrius; Canetta, Elisabetta; Paul, Eleanor; Forbes, Jordan; Azzouni, Karima; Viñas, Clara; Teixidor, Francesc; Harwood, Adrian J

2015-01-15

Cobaltabisdicarbollide (COSAN) [3,3'-Co(1,2-C2B9H11)2](-), is a complex boron-based anion that has the unusual property of self-assembly into membranes and vesicles. These membranes have similar dimensions to biological membranes found in cells, and previously COSAN has been shown to pass through synthetic lipid membranes and those of living cells without causing breakdown of membrane barrier properties. Here, we investigate the interaction of this inorganic membrane system with living cells. We show that COSAN has no immediate effect on cell viability, and cells fully recover when COSAN is removed following exposure for hours to days. COSAN elicits a range of cell biological effects, including altered cell morphology, inhibition of cell growth and, in some cases, apoptosis. These observations reveal a new biology at the interface between inorganic, synthetic COSAN membranes and naturally occurring biological membranes.

The South Central Superpave Center: Report of Activities

DOT National Transportation Integrated Search

1998-12-01

The planning of the South Central Superpave Center (SCSC) began in mid-1994. The Center hired its first staff in early 1995 and was fully staffed by June 1995, at which point it became fully operational. This report describes SCSC activities that too...

Synthesis, characterization and evaluation of 1,3,5-triazine aminobenzoic acid derivatives for their antimicrobial activity.

PubMed

Al-Zaydi, Khadijah M; Khalil, Hosam H; El-Faham, Ayman; Khattab, Sherine N

2017-05-10

Replacement of chloride ions in cyanuric chloride give several variants of 1,3,5-triazine derivatives which were investigated as biologically active small molecules. These compounds exhibit antimalarial, antimicrobial, anti-cancer and anti-viral activities, among other beneficial properties. On the other hand, treatment of bacterial infections remains a challenging therapeutic problem because of the emerging infectious diseases and the increasing number of multidrug-resistant microbial pathogens. As multidrug-resistant bacterial strains proliferate, the necessity for effective therapy has stimulated research into the design and synthesis of novel antimicrobial molecules. 1,3,5-Triazine 4-aminobenzoic acid derivatives were prepared by conventional method or by using microwave irradiation. Using microwave irradiation gave the desired products in less time, good yield and higher purity. Esterification of the 4-aminobenzoic acid moiety afforded methyl ester analogues. The s-triazine derivatives and their methyl ester analogues were fully characterized by FT-IR, NMR ( 1 H-NMR and 13 C-NMR), mass spectra and elemental analysis. All the synthesized compounds were evaluated for their antimicrobial activity. Some tested compounds showed promising activity against Staphylococcus aureus and Escherichia coli. Three series of mono-, di- and trisubstituted s-triazine derivatives and their methyl ester analogues were synthesized and fully characterized. All the synthesized compounds were evaluated for their antimicrobial activity. Compounds (10), (16), (25) and (30) have antimicrobial activity against S. aureus comparable to that of ampicillin, while the activity of compound (13) is about 50% of that of ampicillin. Compounds (13) and (14) have antimicrobial activity against E. coli comparable to that of ampicillin, while the activity of compounds (9-12) and (15) is about 50% of that of ampicillin. Furthermore, minimum inhibitory concentrations values for clinical isolates of compounds (10), (13), (14), (16), (25) and (30) were measured. Compounds (10) and (13) were more active against MRSA and E. coli than ampicillin. Invitro cytotoxicity results revealed that compounds (10) and (13) were nontoxic up to 250 µg/mL (with SI = 10) and 125 µg/mL (with SI = 5), respectively. Graphical abstract Three series of mono-, di- and trisubstituted s-triazine derivatives and their methyl ester analogues were synthesized and evaluated for their antimicrobial activity. Several compounds have antimicrobial activity against S. aureus and E. coli comparable to that of ampicillin.

Recent advances in lipid separations and structural elucidation using mass spectrometry combined with ion mobility spectrometry, ion-molecule reactions and fragmentation approaches

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

Zheng, Xueyun; Smith, Richard D.; Baker, Erin S.

Lipids are a vital class of molecules that play important and varied roles in biological processes. Fully understanding lipid roles, however, is extremely difficult since the number and diversity of lipid species is immense, with cells expressing hundreds of enzymes that synthesize tens of thousands of different lipids. While recent advances in chromatography and high resolution mass spectrometry have greatly progressed the understanding of lipid species and functions, effectively separating many lipids still remains problematic. Isomeric lipids have made lipid characterization especially difficult and occur due to subclasses having the same chemical composition, or species having multiple acyl chains connectivitiesmore » (sn-1, sn-2, or sn-3), double bond positions and orientations (cis or trans), and functional group stereochemistry (R versus S). Fully understanding the roles of lipids in biological processes therefore requires separating and evaluating how isomers change in biological and environmental samples. To address this challenge, ion mobility spectrometry separations, ion-molecule reactions and fragmentation techniques have increasingly been added to lipid analysis workflows to improve identifications. In this manuscript, we review the current state of these approaches and their capabilities for improving the identification of specific lipid species.« less

'Necessary and sufficient' in biology is not necessarily necessary - confusions and erroneous conclusions resulting from misapplied logic in the field of biology, especially neuroscience.

PubMed

Yoshihara, Motojiro; Yoshihara, Motoyuki

In this article, we describe an incorrect use of logic which involves the careless application of the 'necessary and sufficient' condition originally used in formal logic. This logical fallacy is causing frequent confusion in current biology, especially in neuroscience. In order to clarify this problem, we first dissect the structure of this incorrect logic (which we refer to as 'misapplied-N&S') to show how necessity and sufficiency in misapplied-N&S are not matching each other. Potential pitfalls of utilizing misapplied-N&S are exemplified by cases such as the discrediting of command neurons and other potentially key neurons, the distorting of truth in optogenetic studies, and the wrongful justification of studies with little meaning. In particular, the use of the word 'sufficient' in optogenetics tends to generate misunderstandings by opening up multiple interpretations. To avoid the confusion caused by the misleading logic, we now recommend using 'indispensable and inducing' instead of using 'necessary and sufficient.' However, we ultimately recommend fully articulating the limits of what our experiments suggest, not relying on such simple phrases. Only after this problem is fully understood and more rigorous language is demanded, can we finally interpret experimental results in an accurate way.

Detection of motile micro-organisms in biological samples by means of a fully automated image processing system

NASA Astrophysics Data System (ADS)

Alanis, Elvio; Romero, Graciela; Alvarez, Liliana; Martinez, Carlos C.; Hoyos, Daniel; Basombrio, Miguel A.

2001-08-01

A fully automated image processing system for detection of motile microorganism is biological samples is presented. The system is specifically calibrated for determining the concentration of Trypanosoma Cruzi parasites in blood samples of mice infected with Chagas disease. The method can be adapted for use in other biological samples. A thin layer of blood infected by T. cruzi parasites is examined in a common microscope in which the images of the vision field are taken by a CCD camera and temporarily stored in the computer memory. In a typical field, a few motile parasites are observable surrounded by blood red cells. The parasites have low contrast. Thus, they are difficult to detect visually but their great motility betrays their presence by the movement of the nearest neighbor red cells. Several consecutive images of the same field are taken, decorrelated with each other where parasites are present, and digitally processed in order to measure the number of parasites present in the field. Several fields are sequentially processed in the same fashion, displacing the sample by means of step motors driven by the computer. A direct advantage of this system is that its results are more reliable and the process is less time consuming than the current subjective evaluations made visually by technicians.

Mammalian Exo1 encodes both structural and catalytic functions that play distinct roles in essential biological processes

PubMed Central

Schaetzlein, Sonja; Chahwan, Richard; Avdievich, Elena; Roa, Sergio; Wei, Kaichun; Eoff, Robert L.; Sellers, Rani S.; Clark, Alan B.; Kunkel, Thomas A.; Scharff, Matthew D.; Edelmann, Winfried

2013-01-01

Mammalian Exonuclease 1 (EXO1) is an evolutionarily conserved, multifunctional exonuclease involved in DNA damage repair, replication, immunoglobulin diversity, meiosis, and telomere maintenance. It has been assumed that EXO1 participates in these processes primarily through its exonuclease activity, but recent studies also suggest that EXO1 has a structural function in the assembly of higher-order protein complexes. To dissect the enzymatic and nonenzymatic roles of EXO1 in the different biological processes in vivo, we generated an EXO1-E109K knockin (Exo1EK) mouse expressing a stable exonuclease-deficient protein and, for comparison, a fully EXO1-deficient (Exo1null) mouse. In contrast to Exo1null/null mice, Exo1EK/EK mice retained mismatch repair activity and displayed normal class switch recombination and meiosis. However, both Exo1-mutant lines showed defects in DNA damage response including DNA double-strand break repair (DSBR) through DNA end resection, chromosomal stability, and tumor suppression, indicating that the enzymatic function is required for those processes. On a transformation-related protein 53 (Trp53)-null background, the DSBR defect caused by the E109K mutation altered the tumor spectrum but did not affect the overall survival as compared with p53-Exo1null mice, whose defects in both DSBR and mismatch repair also compromised survival. The separation of these functions demonstrates the differential requirement for the structural function and nuclease activity of mammalian EXO1 in distinct DNA repair processes and tumorigenesis in vivo. PMID:23754438

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

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.

Exploring the Capacity of Water Framework Directive Indices to Assess Ecosystem Services in Fluvial and Riparian Systems: Towards a Second Implementation Phase.

PubMed

Vidal-Abarca, M R; Santos-Martín, F; Martín-López, B; Sánchez-Montoya, M M; Suárez Alonso, M L

2016-06-01

We explored the capacity of the biological and hydromorphological indices used in the Water Framework Directive (WFD) to assess ecosystem services by evaluating the ecological status of Spanish River Basins. This analysis relies on an exhaustive bibliography review which showed scientific evidence of the interlinkages between some ecosystem services and different hydromorphological and biological elements which have been used as indices in the WFD. Our findings indicate that, of a total of 38 ecosystem services analyzed, biological and hydromorphological indices can fully evaluate four ecosystem services. In addition, 18 ecosystem services can be partly evaluated by some of the analyzed indices, while 11 are not related with the indices. While Riparian Forest Quality was the index that was able to assess the largest number of ecosystem services (N = 12), the two indices of macrophytes offered very poor guarantees. Finally, biological indices related to diatoms and aquatic invertebrates and the Fluvial Habitat Index can be related with 7, 6, and 6 ecosystem services, respectively. Because the WFD indices currently used in Spain are not able to assess most of the ecosystem services analyzed, we suggest that there is potential to develop the second phase of the WFD implementation taking this approach into consideration. The incorporation of the ecosystem services approach into the WFD could provide the framework for assess the impacts of human activities on the quality of fluvial ecosystems and could give insights for water and watershed management in order to guarantee the delivery of multiple ecosystem services.

Trace elements at the intersection of marine biological and geochemical evolution

USGS Publications Warehouse

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

2016-01-01

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

Meat science: From proteomics to integrated omics towards system biology.

PubMed

D'Alessandro, Angelo; Zolla, Lello

2013-01-14

Since the main ultimate goal of farm animal raising is the production of proteins for human consumption, research tools to investigate proteins play a major role in farm animal and meat science. Indeed, proteomics has been applied to the field of farm animal science to monitor in vivo performances of livestock animals (growth performances, fertility, milk quality etc.), but also to further our understanding of the molecular processes at the basis of meat quality, which are largely dependent on the post mortem biochemistry of the muscle, often in a species-specific way. Post mortem alterations to the muscle proteome reflect the biological complexity of the process of "muscle to meat conversion," a process that, despite decades of advancements, is all but fully understood. This is mainly due to the enormous amounts of variables affecting meat tenderness per se, including biological factors, such as animal species, breed specific-characteristic, muscle under investigation. However, it is rapidly emerging that the tender meat phenotype is not only tied to genetics (livestock breeding selection), but also to extrinsic factors, such as the rearing environment, feeding conditions, physical activity, administration of hormonal growth promotants, pre-slaughter handling and stress, post mortem handling. From this intricate scenario, biochemical approaches and systems-wide integrated investigations (metabolomics, transcriptomics, interactomics, phosphoproteomics, mathematical modeling), which have emerged as complementary tools to proteomics, have helped establishing a few milestones in our understanding of the events leading from muscle to meat conversion. The growing integration of omics disciplines in the field of systems biology will soon contribute to take further steps forward. Copyright © 2012 Elsevier B.V. All rights reserved.

Electrical Chips for Biological Point-of-Care Detection.

PubMed

Reddy, Bobby; Salm, Eric; Bashir, Rashid

2016-07-11

As the future of health care diagnostics moves toward more portable and personalized techniques, there is immense potential to harness the power of electrical signals for biological sensing and diagnostic applications at the point of care. Electrical biochips can be used to both manipulate and sense biological entities, as they can have several inherent advantages, including on-chip sample preparation, label-free detection, reduced cost and complexity, decreased sample volumes, increased portability, and large-scale multiplexing. The advantages of fully integrated electrical biochip platforms are particularly attractive for point-of-care systems. This review summarizes these electrical lab-on-a-chip technologies and highlights opportunities to accelerate the transition from academic publications to commercial success.

Space Biophysics: Accomplishments, Trends, Challenges

NASA Technical Reports Server (NTRS)

Smith, Jeffrey D.

2015-01-01

Physics and biology are inextricably linked. All the chemical and biological processes of life are dutifully bound to follow the rules and laws of physics. In space, these physical laws seem to turn on their head and biological systems, from microbes to humans, adapt and evolve in myriad ways to cope with the changed physical influences of the space environment. Gravity is the most prominent change in space that influences biology. In microgravity, the physical processes of sedimentation, density-driven convective flow, influence of surface tension and fluid pressure profoundly influence biology at the molecular and cellular level as well as at the whole-body level. Gravity sensing mechanisms are altered, structural and functional components of biology (such as bone and muscle) are reduced and changes in the way fluids and gasses behave also drive the way microbial systems and biofilms grow as well as the way plants and animals adapt. The radiation environment also effects life in space. Solar particle events and high energy cosmic radiation can cause serious damage to DNA and other biomolecules. The results can cause mutation, cellular damage or death, leading to health consequences of acute radiation damage or long-term health consequences such as increased cancer risk. Space Biophysics is the study and utilization of physical changes in space that cause changes in biological systems. The unique physical environment in space has been used successfully to grow high-quality protein crystals and 3D tissue cultures that could not be grown in the presence of unidirectional gravitational acceleration here on Earth. All biological processes that change in space have their root in a biophysical alteration due to microgravity and/or the radiation environment of space. In order to fully-understand the risks to human health in space and to fully-understand how humans, plants, animals and microbes can safely and effectively travel and eventually live for long periods beyond the protective environment of Earth, the biophysical properties underlying these changes must be studied, characterized and understood. This lecture reviews the current state of NASA biophysics research accomplishments and identifies future trends and challenges for biophysics research on the International Space Station and beyond.

Translating human biology (introduction to special issue).

PubMed

Brewis, Alexandra A; Mckenna, James J

2015-01-01

Introducing a special issue on "Translating Human Biology," we pose two basic questions: Is human biology addressing the most critical challenges facing our species? How can the processes of translating our science be improved and innovated? We analyze articles published in American Journal of Human Biology from 2004-2013, and find there is very little human biological consideration of issues related to most of the core human challenges such as water, energy, environmental degradation, or conflict. There is some focus on disease, and considerable focus on food/nutrition. We then introduce this special volume with reference to the following articles that provide exemplars for the process of how translation and concern for broader context and impacts can be integrated into research. Human biology has significant unmet potential to engage more fully in translation for the public good, through consideration of the topics we focus on, the processes of doing our science, and the way we present our domain expertise. © 2014 Wiley Periodicals, Inc.

In vivo architectonic stability of fully de novo designed protein-only nanoparticles.

PubMed

Céspedes, María Virtudes; Unzueta, Ugutz; Tatkiewicz, Witold; Sánchez-Chardi, Alejandro; Conchillo-Solé, Oscar; Álamo, Patricia; Xu, Zhikun; Casanova, Isolda; Corchero, José Luis; Pesarrodona, Mireia; Cedano, Juan; Daura, Xavier; Ratera, Imma; Veciana, Jaume; Ferrer-Miralles, Neus; Vazquez, Esther; Villaverde, Antonio; Mangues, Ramón

2014-05-27

The fully de novo design of protein building blocks for self-assembling as functional nanoparticles is a challenging task in emerging nanomedicines, which urgently demand novel, versatile, and biologically safe vehicles for imaging, drug delivery, and gene therapy. While the use of viruses and virus-like particles is limited by severe constraints, the generation of protein-only nanocarriers is progressively reachable by the engineering of protein-protein interactions, resulting in self-assembling functional building blocks. In particular, end-terminal cationic peptides drive the organization of structurally diverse protein species as regular nanosized oligomers, offering promise in the rational engineering of protein self-assembling. However, the in vivo stability of these constructs, being a critical issue for their medical applicability, needs to be assessed. We have explored here if the cross-molecular contacts between protein monomers, generated by end-terminal cationic peptides and oligohistidine tags, are stable enough for the resulting nanoparticles to overcome biological barriers in assembled form. The analyses of renal clearance and biodistribution of several tagged modular proteins reveal long-term architectonic stability, allowing systemic circulation and tissue targeting in form of nanoparticulate material. This observation fully supports the value of the engineered of protein building blocks addressed to the biofabrication of smart, robust, and multifunctional nanoparticles with medical applicability that mimic structure and functional capabilities of viral capsids.

Engineering protein self-assembling in protein-based nanomedicines for drug delivery and gene therapy.

PubMed

Ferrer-Miralles, Neus; Rodríguez-Carmona, Escarlata; Corchero, José Luis; García-Fruitós, Elena; Vázquez, Esther; Villaverde, Antonio

2015-06-01

Lack of targeting and improper biodistribution are major flaws in current drug-based therapies that prevent reaching high local concentrations of the therapeutic agent. Such weaknesses impose the administration of high drug doses, resulting in undesired side effects, limited efficacy and enhanced production costs. Currently, missing nanosized containers, functionalized for specific cell targeting will be then highly convenient for the controlled delivery of both conventional and innovative drugs. In an attempt to fill this gap, health-focused nanotechnologies have put under screening a growing spectrum of materials as potential components of nanocages, whose properties can be tuned during fabrication. However, most of these materials pose severe biocompatibility concerns. We review in this study how proteins, the most versatile functional macromolecules, can be conveniently exploited and adapted by conventional genetic engineering as efficient building blocks of fully compatible nanoparticles for drug delivery and how selected biological activities can be recruited to mimic viral behavior during infection. Although engineering of protein self-assembling is still excluded from fully rational approaches, the exploitation of protein nano-assemblies occurring in nature and the direct manipulation of protein-protein contacts in bioinspired constructs open intriguing possibilities for further development. These methodologies empower the construction of new and potent vehicles that offer promise as true artificial viruses for efficient and safe nanomedical applications.

[Antagonistic interactions between saprotrophic fungi and geohelminths. 2. Saprotrophic fungi in biocontrol of parasitic geohelminths of humans and animals].

PubMed

Jaborowska-Jarmoluk, Magdalena; Mazurkiewicz-Zapałowicz, Kinga; Kołodziejczyk, Lidia

2009-01-01

The soils ecosystem plays an important role in the epidemiology of geohelminth diseases of humans and animals. Soil contamination with ova of the parasitic geohelminths represents a global public health-hazard issue. Biological agents have been thought to control the infective forms of parasites present in the soil. Biocontrol of geohelminths represents an alternative to pesticides (i.e., nematicides), which are not efficient in killing infective nematode forms and, additionally, result in the environment pollution and long-term disturbances in the soil ecosystem homeostasis. The degree of the inhibiting effect of soil saprotrophic fungi on geohelminth embryonic development varies and depends on the species. A number of fungi cause various morphological disorders in the embryos of developing parasitic nematodes, but also have an ovicidal effect. Although the nature of the antagonism between fungi and other living organisms has not been fully explained, it is certain that mycotoxins and fungal enzymes constitute its important components. Considering the studies carried out so far, the antagonistic effect of mold fungi against the infective stages of geohelminths can be fully recommended as a real control factor, especially as these saprotrophs represent a natural factor within the soil environment, that is of particular biochemical activity.

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

Nelson, Cassandra E.; Rogowski, Artur; Morland, Carl

Degradation of polysaccharides forms an essential arc in the carbon cycle, provides a percentage of our daily caloric intake, and is a major driver in the renewable chemical industry. Microorganisms proficient at degrading insoluble polysaccharides possess large numbers of carbohydrate active enzymes, many of which have been categorized as functionally redundant. Here we present data that suggests that carbohydrate active enzymes that have overlapping enzymatic activities can have unique, non-overlapping biological functions in the cell. Our comprehensive study to understand cellodextrin utilization in the soil saprophyte Cellvibrio japonicus found that only one of four predicted β-glucosidases is required in amore » physiological context. Gene deletion analysis indicated that only the cel3B gene product is essential for efficient cellodextrin utilization in C. japonicus and is constitutively expressed at high levels. Interestingly, expression of individual β-glucosidases in Escherichia coli K-12 enabled this non-cellulolytic bacterium to be fully capable of using cellobiose as a sole carbon source. Furthermore, enzyme kinetic studies indicated that the Cel3A enzyme is significantly more active than the Cel3B enzyme on the oligosaccharides but not disaccharides. Finally, our approach for parsing related carbohydrate active enzymes to determine actual physiological roles in the cell can be applied to other polysaccharide-degradation systems.« less

Unconventional food regeneration in space - Opportunities for microbial food production

NASA Technical Reports Server (NTRS)

Petersen, Gene R.; Schubert, Wayne W.; Seshan, P. K.; Dunlop, Eric H.

1987-01-01

The possible role of microbial species in regenerating food is considered, and three areas where microbial systems can be used in controlled ecological life support systems are discussed. Microbial species can serve as the biological portion of hybrid chemical/biological schemes for primary food products, as a means more fully to utilize waste materials from agronomical food production, and as a source of nutritional supplements to conventional plant foods. Work accomplished in each of these areas is described. The role of microgravity fermenters in this technology is addressed.

Larva and pupa of Megatoma (s. str.) undata (Linnaeus, 1758) with remarks on biology and economic importance (Coleoptera, Dermestidae).

PubMed

Kadej, Marcin

2017-01-01

An updated description of the final larval instar and pupa of Megatoma (s. str.) undata (Linnaeus, 1758) (Coleoptera: Dermestidae) is presented. Several morphological characteristics of M. undata larvae are documented and discussed: antenna, epipharynx, mandibula, maxilla, ligula with labial palpi, hastisetae, terga, and condition of the antecostal suture. The paper is fully illustrated and includes some important additions to extend notes on this species available in the references. Summarised data about biology, economic importance, and distribution of M. undata are also provided.

Nonlinear interferometric vibrational imaging of biological tissue

NASA Astrophysics Data System (ADS)

Jiang, Zhi; Marks, Daniel L.; Geddes, Joseph B., III; Boppart, Stephen A.

2008-02-01

We demonstrate imaging with the technique of nonlinear interferometric vibrational imaging (NIVI). Experimental images using this instrumentation and method have been acquired from both phantom and biological tissues. In our system, coherent anti-Stokes Raman scattering (CARS) signals are detected by spectral interferometry, which is able to fully restore high resolution Raman spectrum on each focal spot of a sample covering multiple Raman bands using broadband pump and Stokes laser beams. Spectral-domain detection has been demonstrated and allows for a significant increase in image acquiring speed, in signal-to-noise, and in interferometric signal stability.

Neutral evolution in a biological population as diffusion in phenotype space: reproduction with local mutation but without selection.

PubMed

Lawson, Daniel John; Jensen, Henrik Jeldtoft

2007-03-02

The process of "evolutionary diffusion," i.e., reproduction with local mutation but without selection in a biological population, resembles standard diffusion in many ways. However, evolutionary diffusion allows the formation of localized peaks that undergo drift, even in the infinite population limit. We relate a microscopic evolution model to a stochastic model which we solve fully. This allows us to understand the large population limit, relates evolution to diffusion, and shows that independent local mutations act as a diffusion of interacting particles taking larger steps.

Postextraction Alveolar Ridge Preservation: Biological Basis and Treatments

PubMed Central

Pagni, Giorgio; Pellegrini, Gaia; Giannobile, William V.; Rasperini, Giulio

2012-01-01

Following tooth extraction, the alveolar ridge undergoes an inevitable remodeling process that influences implant therapy of the edentulous area. Socket grafting is a commonly adopted therapy for the preservation of alveolar bone structures in combination or not with immediate implant placement although the biological bases lying behind this treatment modality are not fully understood and often misinterpreted. This review is intended to clarify the literature support to socket grafting in order to provide practitioners with valid tools to make a conscious decision of when and why to recommend this therapy. PMID:22737169

Enhancing interdisciplinary mathematics and biology education: a microarray data analysis course bridging these disciplines.

PubMed

Tra, Yolande V; Evans, Irene M

2010-01-01

BIO2010 put forth the goal of improving the mathematical educational background of biology students. The analysis and interpretation of microarray high-dimensional data can be very challenging and is best done by a statistician and a biologist working and teaching in a collaborative manner. We set up such a collaboration and designed a course on microarray data analysis. We started using Genome Consortium for Active Teaching (GCAT) materials and Microarray Genome and Clustering Tool software and added R statistical software along with Bioconductor packages. In response to student feedback, one microarray data set was fully analyzed in class, starting from preprocessing to gene discovery to pathway analysis using the latter software. A class project was to conduct a similar analysis where students analyzed their own data or data from a published journal paper. This exercise showed the impact that filtering, preprocessing, and different normalization methods had on gene inclusion in the final data set. We conclude that this course achieved its goals to equip students with skills to analyze data from a microarray experiment. We offer our insight about collaborative teaching as well as how other faculty might design and implement a similar interdisciplinary course.

Cellular pH regulators: potentially promising molecular targets for cancer chemotherapy.

PubMed

Izumi, Hiroto; Torigoe, Takayuki; Ishiguchi, Hiroshi; Uramoto, Hidetaka; Yoshida, Yoichiro; Tanabe, Mizuho; Ise, Tomoko; Murakami, Tadashi; Yoshida, Takeshi; Nomoto, Minoru; Kohno, Kimitoshi

2003-12-01

One of the major obstacles to the successful treatment of cancer is the complex biology of solid tumour development. Although regulation of intracellular pH has been shown to be critically important for many cellular functions, pH regulation has not been fully investigated in the field of cancer. It has, however, been shown that cellular pH is crucial for biological functions such as cell proliferation, invasion and metastasis, drug resistance and apoptosis. Hypoxic conditions are often observed during the development of solid tumours and lead to intracellular and extracellular acidosis. Cellular acidosis has been shown to be a trigger in the early phase of apoptosis and leads to activation of endonucleases inducing DNA fragmentation. To avoid intracellular acidification under such conditions, pH regulators are thought to be up-regulated in tumour cells. Four major types of pH regulator have been identified: the proton pump, the sodium-proton exchanger family (NHE), the bicarbonate transporter family (BCT) and the monocarboxylate transporter family (MCT). Here, we describe the structure and function of pH regulators expressed in tumour tissue. Understanding pH regulation in tumour cells may provide new ways of inducing tumour-specific apoptosis, thus aiding cancer chemotherapy.

A quantitative image cytometry technique for time series or population analyses of signaling networks.

PubMed

Ozaki, Yu-ichi; Uda, Shinsuke; Saito, Takeshi H; Chung, Jaehoon; Kubota, Hiroyuki; Kuroda, Shinya

2010-04-01

Modeling of cellular functions on the basis of experimental observation is increasingly common in the field of cellular signaling. However, such modeling requires a large amount of quantitative data of signaling events with high spatio-temporal resolution. A novel technique which allows us to obtain such data is needed for systems biology of cellular signaling. We developed a fully automatable assay technique, termed quantitative image cytometry (QIC), which integrates a quantitative immunostaining technique and a high precision image-processing algorithm for cell identification. With the aid of an automated sample preparation system, this device can quantify protein expression, phosphorylation and localization with subcellular resolution at one-minute intervals. The signaling activities quantified by the assay system showed good correlation with, as well as comparable reproducibility to, western blot analysis. Taking advantage of the high spatio-temporal resolution, we investigated the signaling dynamics of the ERK pathway in PC12 cells. The QIC technique appears as a highly quantitative and versatile technique, which can be a convenient replacement for the most conventional techniques including western blot, flow cytometry and live cell imaging. Thus, the QIC technique can be a powerful tool for investigating the systems biology of cellular signaling.

Single-Molecule Imaging of Cellular Signaling

NASA Astrophysics Data System (ADS)

De Keijzer, Sandra; Snaar-Jagalska, B. Ewa; Spaink, Herman P.; Schmidt, Thomas

Single-molecule microscopy is an emerging technique to understand the function of a protein in the context of its natural environment. In our laboratory this technique has been used to study the dynamics of signal transduction in vivo. A multitude of signal transduction cascades are initiated by interactions between proteins in the plasma membrane. These cascades start by binding a ligand to its receptor, thereby activating downstream signaling pathways which finally result in complex cellular responses. To fully understand these processes it is important to study the initial steps of the signaling cascades. Standard biological assays mostly call for overexpression of the proteins and high concentrations of ligand. This sets severe limits to the interpretation of, for instance, the time-course of the observations, given the large temporal spread caused by the diffusion-limited binding processes. Methods and limitations of single-molecule microscopy for the study of cell signaling are discussed on the example of the chemotactic signaling of the slime-mold Dictyostelium discoideum. Single-molecule studies, as reviewed in this chapter, appear to be one of the essential methodologies for the full spatiotemporal clarification of cellular signaling, one of the ultimate goals in cell biology.

Enhancing Interdisciplinary Mathematics and Biology Education: A Microarray Data Analysis Course Bridging These Disciplines

PubMed Central

Evans, Irene M.

2010-01-01

BIO2010 put forth the goal of improving the mathematical educational background of biology students. The analysis and interpretation of microarray high-dimensional data can be very challenging and is best done by a statistician and a biologist working and teaching in a collaborative manner. We set up such a collaboration and designed a course on microarray data analysis. We started using Genome Consortium for Active Teaching (GCAT) materials and Microarray Genome and Clustering Tool software and added R statistical software along with Bioconductor packages. In response to student feedback, one microarray data set was fully analyzed in class, starting from preprocessing to gene discovery to pathway analysis using the latter software. A class project was to conduct a similar analysis where students analyzed their own data or data from a published journal paper. This exercise showed the impact that filtering, preprocessing, and different normalization methods had on gene inclusion in the final data set. We conclude that this course achieved its goals to equip students with skills to analyze data from a microarray experiment. We offer our insight about collaborative teaching as well as how other faculty might design and implement a similar interdisciplinary course. PMID:20810954

PRP For the Treatment of Cartilage Pathology

PubMed Central

Kon, Elizaveta; Filardo, Giuseppe; Di Matteo, Berardo; Marcacci, Maurilio

2013-01-01

In recent years biological strategies are being more widely used to treat cartilage lesions. One of the most exploited novel treatments is Platelet-rich Plasma (PRP), whose high content of growth factors is supposed to determine a regenerative stimulus to cartilaginous tissue. Despite many promising in vitro and in vivo studies, when discussing clinical application a clear indication for the use of PRP cannot be assessed. There are initial encouraging clinical data, but only a few randomized controlled trials have been published, so it is not possible to fully endorse this kind of approach for the treatment of cartilage pathology. Furthermore, study comparison is very difficult due to the great variability in PRP preparation methods, cell content and concentration, storage modalities, activation methods and even application protocols. These factors partially explain the lack of high quality controlled trials up to now. This paper discusses the main aspects concerning the basic biology of PRP, the principal sources of variability, and summarizes the available literature on PRP use, both in surgical and conservative treatments. Based on current evidence, PRP treatment should only be indicated for low-grade cartilage degeneration and in case of failure of more traditional conservative approaches. PMID:23730375

In vivo visualisation of different modes of action of biological DMARDs inhibiting osteoclastic bone resorption.

PubMed

Matsuura, Yoshinobu; Kikuta, Junichi; Kishi, Yuika; Hasegawa, Tetsuo; Okuzaki, Daisuke; Hirano, Toru; Minoshima, Masafumi; Kikuchi, Kazuya; Kumanogoh, Atsushi; Ishii, Masaru

2018-04-28

Osteoclasts play critical roles in inflammatory bone destruction. Precursor cell migration, cell differentiation, and functional cell activation are all in play. Biological disease-modifying antirheumatic drugs (DMARDs) have been shown to significantly inhibit both bone erosion as well as synovitis, although how such agents reduce osteoclastic bone destruction in vivo has not been fully explained. Here, we used an intravital time-lapse imaging technique to directly visualise mature osteoclasts and their precursors, and explored how different biological DMARDs acted in vivo . Lipopolysaccharide (LPS) was injected into the calvarial periosteum of fluorescent reporter mice to induce inflammatory bone destruction. Time-lapse imaging was performed via intravital multiphoton microscopy 5 days after LPS injection. Biological DMARDs, including monoclonal antibodies (mAbs) against the interleukin (IL) 6 receptor (IL-6R) and tumour necrosis factor α (TNFα), or cytotoxic T-lymphocyte-associated protein 4 (CTLA4)-Ig, were intraperitoneally administered at the time of LPS injection. We determined CD80/86 expression levels in mature osteoclasts and their precursors by flow cytometry, quantitative PCR and immunohistochemistry. Of the biologicals tested, anti-IL-6R and anti-TNFα mAbs affected mature osteoclasts and switched bone-resorbing osteoclasts to non-resorbing cells. CTLA4-Ig had no action on mature osteoclasts but mobilised osteoclast precursors, eliminating their firm attachment to bone surfaces. In agreement with these results, CD80/86 (the target molecules of CTLA4-Ig) were prominently expressed only in osteoclast precursor cells, being suppressed during osteoclast maturation. Intravital imaging revealed that various biological DMARDs acted at specific therapeutic time points during osteoclastic bone destruction, with different efficacies. These results enable us to grasp the real modes of action of drugs, optimising the usage of drug regimens. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Ethical Imagination in Peace Studies: Beyond the Seville Statement.

ERIC Educational Resources Information Center

Rivage-Seul, M.

1989-01-01

Asks reader to look beyond Seville Statement, Social Darwinism, and utopian ideals and come to understand ethical imagination more fully as it relates to peace studies. Examines Seville Statement and its opposition to Social Darwinism. Explains how ethical imagination serves to provide radical alternative to biological determinism. (Author/NB)

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

Holm, Christian; Gompper, Gerhard; Dill, Ken A.

This special issue highlights new developments in theory and coarse-graining in biological and synthetic macromolecules and membranes. Such approaches give unique insights into the principles and design of the structures, dynamics, and assembly processes of these complex fluids and soft materials, where the length and time scales are often prohibitively long for fully atomistic modeling.

Use of metabolomics for the chemotaxonomy of legume-associated Ascochyta and allied genera

USDA-ARS?s Scientific Manuscript database

Chemotaxonomy and the comparative analysis of metabolic features of fungi have the potential to provide valuable information relating to ecology and evolution, but have not been fully explored in fungal biology. Here, we investigated the chemical diversity of legume-associated Ascochyta and Phoma sp...

Teachers' Concerns about Biotechnology Education

ERIC Educational Resources Information Center

Borgerding, Lisa A.; Sadler, Troy D.; Koroly, Mary Jo

2013-01-01

The impacts of biotechnology are found in nearly all sectors of society from health care and food products to environmental issues and energy sources. Despite the significance of biotechnology within the sciences, it has not become a prominent trend in science education. In this study, we seek to more fully identify biology teachers' concerns…

Report of the Action Committee on Bioengineering.

ERIC Educational Resources Information Center

Schein, Martin W.

Bioengineering has been defined as "the application of knowledge gained by a cross fertilization of engineering and the biological sciences so that both will be more fully utilized for the benefit of mankind." Bioengineering has at least six areas of application: (1) medical engineering, (2) environmental health engineering, (3)…

The advances and perspectives of recombinant protein production in the silk gland of silkworm Bombyx mori.

PubMed

Xu, Hanfu

2014-10-01

The silk gland of silkworm Bombyx mori, is one of the most important organs that has been fully studied and utilized so far. It contributes finest silk fibers to humankind. The silk gland has excellent ability of synthesizing silk proteins and is a kind tool to produce some useful recombinant proteins, which can be widely used in the biological, biotechnical and pharmaceutical application fields. It's a very active area to express recombinant proteins using the silk gland as a bioreactor, and great progress has been achieved recently. This review recapitulates the progress of producing recombinant proteins and silk-based biomaterials in the silk gland of silkworm in addition to the construction of expression systems. Current challenges and future trends in the production of valuable recombinant proteins using transgenic silkworms are also discussed.

Crystallization and preliminary X-ray diffraction analysis of the lectin from Dioclea rostrata Benth seeds

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

Delatorre, Plínio; Departamento de Ciências Biológicas, Universidade Regional do Cariri, Crato, CE 63195-000; Nascimento, Kyria Santiago

2006-02-01

D. rostrata lectin was crystallized by hanging-drop vapor diffusion. The crystal belongs to the orthorhombic space group I222 and diffracted to 1.87 Å resolution. Lectins from the Diocleinae subtribe (Leguminosae) are highly similar proteins that promote various biological activities with distinctly differing potencies. The structural basis for this experimental data is not yet fully understood. Dioclea rostrata lectin was purified and crystallized by hanging-drop vapour diffusion at 293 K. The crystal belongs to the orthorhombic space group I222, with unit-cell parameters a = 61.51, b = 88.22, c = 87.76 Å. Assuming the presence of one monomer per asymmetric unit,more » the solvent content was estimated to be about 47.9%. A complete data set was collected at 1.87 Å resolution.« less

Bacteriocins from Lactobacillus plantarum – production, genetic organization and mode of action

PubMed Central

Todorov, Svetoslav D.

2009-01-01

Bacteriocins are biologically active proteins or protein complexes that display a bactericidal mode of action towards usually closely related species. Numerous strains of bacteriocin producing Lactobacillus plantarum have been isolated in the last two decades from different ecological niches including meat, fish, fruits, vegetables, and milk and cereal products. Several of these plantaricins have been characterized and the aminoacid sequence determined. Different aspects of the mode of action, fermentation optimization and genetic organization of the bacteriocin operon have been studied. However, numerous of bacteriocins produced by different Lactobacillus plantarum strains have not been fully characterized. In this article, a brief overview of the classification, genetics, characterization, including mode of action and production optimization for bacteriocins from Lactic Acid Bacteria in general, and where appropriate, with focus on bacteriocins produced by Lactobacillus plantarum, is presented. PMID:24031346

Swertiajaponin as an anti-browning and antioxidant flavonoid.

PubMed

Moon, Kyoung Mi; Lee, Bonggi; Cho, Won-Kyung; Lee, Bong-Seon; Kim, Choon Young; Ma, Jin Yeul

2018-06-30

Enzymatic browning is a major issue that needs to be solved in the food industry. Although swertiajaponin is a flavonoid rich in the whole herb of Swertia japonica that has been clinically used, its biological functions and applicat​ion in the foods have not been fully elucidated. Here, we showed that swertiajaponin efficiently blocked enzymatic browning in potatoes possibly by direct binding to and inactivating polyphenol oxidase. Furthermore, swertiajaponin showed potent antioxidant activity proven by markedly suppressed reactive oxygen species. Swertiajaponin significantly increased antioxidant properties of potato extract when it is added since it additively elevated total flavonoid content. Considering numerous beneficial effects of antioxidants, swertiajaponin may be used as a functional food additive to suppress enzymatic browning and elevate the antioxidant capacity of foods including beverages and soups by fortification of flavonoids. Copyright © 2018 Elsevier Ltd. All rights reserved.

System Integration - A Major Step toward Lab on a Chip

PubMed Central

2011-01-01

Microfluidics holds great promise to revolutionize various areas of biological engineering, such as single cell analysis, environmental monitoring, regenerative medicine, and point-of-care diagnostics. Despite the fact that intensive efforts have been devoted into the field in the past decades, microfluidics has not yet been adopted widely. It is increasingly realized that an effective system integration strategy that is low cost and broadly applicable to various biological engineering situations is required to fully realize the potential of microfluidics. In this article, we review several promising system integration approaches for microfluidics and discuss their advantages, limitations, and applications. Future advancements of these microfluidic strategies will lead toward translational lab-on-a-chip systems for a wide spectrum of biological engineering applications. PMID:21612614

The genus Pterocaulon (Asteraceae) - A review on traditional medicinal uses, chemical constituents and biological properties.

PubMed

Medeiros-Neves, Bruna; Teixeira, Helder Ferreira; von Poser, Gilsane Lino

2018-06-15

Species of the genus Pterocaulon (Asteraceae) are used in different parts of the world for mainly to treat skin and liver diseases, as well as disorders of the respiratory system, among others. This review aims to discuss the present state of the art concerning the ethnobotanical uses, secondary metabolites and biological effects of Pterocaulon species and their chemical components. The available information on the genus Pterocaulon was gathered from scientific databases (Web of Science, Pubmed, ScienceDirect, Scopus, ChemSpider, SciFinder ACS Publications, Wiley Online Library). Information was also obtained from local publications, M.Sc. and Ph.D. dissertations. All studies on the ethnobotany, phytochemistry, pharmacology and toxicology of the plants until December 2017 were included in this review. Approximately 40 coumarins and 30 flavonoids have been isolated from Pterocaulon species. Coumarins have been considered the chemotaxonomic markers in the genus and the most active components. Pharmacological studies carried out with extracts and isolated compounds revealed in vitro bioactivities that include antifungal, antiviral, and cytotoxicity. Most of the pharmacological investigations were not correlated with traditional uses of the plants. Pterocaulon species, a rich source of coumarins, have great ethnomedical potential. Nevertheless, further studies into the pharmacological activities are necessary since none of the purported effects of these plants was fully assessed. In-depth research regarding the toxicity are also required to ensure the safety of these medicinal plants. Copyright © 2018 Elsevier Ireland Ltd. All rights reserved.

Camouflage through an active choice of a resting spot and body orientation in moths.

PubMed

Kang, C-K; Moon, J-Y; Lee, S-I; Jablonski, P G

2012-09-01

Cryptic colour patterns in prey are classical examples of adaptations to avoid predation, but we still know little about behaviours that reinforce the match between animal body and the background. For example, moths avoid predators by matching their colour patterns with the background. Active choice of a species-specific body orientation has been suggested as an important function of body positioning behaviour performed by moths after landing on the bark. However, the contribution of this behaviour to moths' crypticity has not been directly measured. From observations of geometrid moths, Hypomecis roboraria and Jankowskia fuscaria, we determined that the positioning behaviour, which consists of walking and turning the body while repeatedly lifting and lowering the wings, resulted in new resting spots and body orientations in J. fuscaria and in new resting spots in H. roboraria. The body positioning behaviour of the two species significantly decreased the probability of visual detection by humans, who viewed photographs of the moths taken before and after the positioning behaviour. This implies that body positioning significantly increases the camouflage effect provided by moth's cryptic colour pattern regardless of whether the behaviour involves a new body orientation or not. Our study demonstrates that the evolution of morphological adaptations, such as colour pattern of moths, cannot be fully understood without taking into account a behavioural phenotype that coevolved with the morphology for increasing the adaptive value of the morphological trait. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

The Scorpion An ideal animal model to study long-term microgravity effects on circadian rhythms

NASA Astrophysics Data System (ADS)

Riewe, Pascal C.; Horn, Eberhard R.

2000-01-01

The temporal pattern of light and darkness is basic for the coordination of circadian rhythms and establishment of homoeostasis. The 24th frequency of zeitgebers is probably a function of the Earth's rotation. The only way to eliminate its influence on organisms is to study their behavior in space because the reduced day length during orbiting the Earth might disrupt synchronizing mechanisms based on the 24th rhythm. The stability of microgravity induced disturbances of synchronization as well as the extent of adaptation of different physiological processes to this novel environment can only be studied during long-term exposures to microgravity, i.e., on the International Space Station. Biological studies within the long-term domain on ISS demand the use of experimental models which can be exposed to automatic handling of measurements and which need less or no nutritional care. Scorpions offer these features. We describe a fully automatic recording device for the simultaneous collection of data regarding the sensorimotor system and homoeostatic mechanisms. In particular, we record sensitivity changes of the eyes, motor activity and heart beat and/or respiratory activity. The advantage of the scorpion model is supported by the fact that data can be recorded preflight, inflight and postflight from the same animal. With this animal model, basic insights will be obtained about the de-coupling of circadian rhythms of multiple oscillators and their adaptation to the entraining zeitgeber periodicity during exposure to microgravity for at least three biological parameters recorded simultaneously. .

Potential for pharmacological manipulation of human embryonic stem cells

PubMed Central

Atkinson, Stuart P; Lako, Majlinda; Armstrong, Lyle

2013-01-01

The therapeutic potential of human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) is vast, allowing disease modelling, drug discovery and testing and perhaps most importantly regenerative therapies. However, problems abound; techniques for cultivating self-renewing hESCs tend to give a heterogeneous population of self-renewing and partially differentiated cells and general include animal-derived products that can be cost-prohibitive for large-scale production, and effective lineage-specific differentiation protocols also still remain relatively undefined and are inefficient at producing large amounts of cells for therapeutic use. Furthermore, the mechanisms and signalling pathways that mediate pluripotency and differentiation are still to be fully appreciated. However, over the recent years, the development/discovery of a range of effective small molecule inhibitors/activators has had a huge impact in hESC biology. Large-scale screening techniques, coupled with greater knowledge of the pathways involved, have generated pharmacological agents that can boost hESC pluripotency/self-renewal and survival and has greatly increased the efficiency of various differentiation protocols, while also aiding the delineation of several important signalling pathways. Within this review, we hope to describe the current uses of small molecule inhibitors/activators in hESC biology and their potential uses in the future. LINKED ARTICLES This article is part of a themed section on Regenerative Medicine and Pharmacology: A Look to the Future. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2013.169.issue-2 PMID:22515554

Continuing progress toward controlled intracellular delivery of semiconductor quantum dots

PubMed Central

Breger, Joyce; Delehanty, James B; Medintz, Igor L

2015-01-01

The biological applications of luminescent semiconductor quantum dots (QDs) continue to grow at a nearly unabated pace. This growth is driven, in part, by their unique photophysical and physicochemical properties which have allowed them to be used in many different roles in cellular biology including: as superior fluorophores for a wide variety of cellular labeling applications; as active platforms for assembly of nanoscale sensors; and, more recently, as a powerful tool to understand the mechanisms of nanoparticle mediated drug delivery. Given that controlled cellular delivery is at the intersection of all these applications, the latest progress in delivering QDs to cells is examined here. A brief discussion of relevant considerations including the importance of materials preparation and bioconjugation along with the continuing issue of endosomal sequestration is initially provided for context. Methods for the cellular delivery of QDs are then highlighted including those based on passive exposure, facilitated strategies that utilize peptides or polymers and fully active modalities such as electroporation and other mechanically based methods. Following on this, the exciting advent of QD cellular delivery using multiple or combined mechanisms is then previewed. Several recent methods reporting endosomal escape of QD materials in cells are also examined in detail with a focus on the mechanisms by which access to the cytosol is achieved. The ongoing debate over QD cytotoxicity is also discussed along with a perspective on how this field will continue to evolve in the future. PMID:25154379

Development of an artificial sensor for hydrodynamic detection inspired by a seal's whisker array.

PubMed

Eberhardt, William C; Wakefield, Brendan F; Murphy, Christin T; Casey, Caroline; Shakhsheer, Yousef; Calhoun, Benton H; Reichmuth, Colleen

2016-08-31

Nature has shaped effective biological sensory systems to receive complex stimuli generated by organisms moving through water. Similar abilities have not yet been fully developed in artificial systems for underwater detection and monitoring, but such technology would enable valuable applications for military, commercial, and scientific use. We set out to design a fluid motion sensor array inspired by the searching performance of seals, which use their whiskers to find and follow underwater wakes. This sensor prototype, called the Wake Information Detection and Tracking System (WIDTS), features multiple whisker-like elements that respond to hydrodynamic disturbances encountered while moving through water. To develop and test this system, we trained a captive harbor seal (Phoca vitulina) to wear a blindfold while tracking a remote-controlled, propeller-driven submarine. After mastering the tracking task, the seal learned to carry the WIDTS adjacent to its own vibrissal array during active pursuit of the target. Data from the WIDTS sensors describe changes in the deflection angles of the whisker elements as they pass through the hydrodynamic trail left by the submarine. Video performance data show that these detections coincide temporally with WIDTS-wake intersections. Deployment of the sensors on an actively searching seal allowed for the direct comparison of our instrument to the ability of the biological sensory system in a proof-of-concept demonstration. The creation of the WIDTS provides a foundation for instrument development in the field of biomimetic fluid sensor technology.

Combined fluorimetric caspase 3/7 assay and bradford protein determination for assessment of polycation-mediated cytotoxicity.

PubMed

Larsen, Anna K; Hall, Arnaldur; Lundsgart, Henrik; Moghimi, S Moein

2013-01-01

Cationic polyplexes and lipoplexes are widely used as artificial systems for nucleic acid delivery into the cells, but they can also induce cell death. Mechanistic understanding of cell toxicity and biological side effects of these cationic entities is essential for optimization strategies and design of safe and efficient nucleic acid delivery systems. Numerous methods are presently available to detect and delineate cytotoxicity and cell death-mediated signals in cell cultures. Activation of caspases is part of the classical apoptosis program and increased caspase activity is therefore a well-established hallmark of programmed cell death. Additional methods to monitor cell death-related signals must, however, also be carried out to fully define the type of cell toxicity in play. These may include methods that detect plasma membrane damage, loss of mitochondrial membrane potential, phosphatidylserine exposure, and cell morphological changes (e.g., membrane blebbing, nuclear changes, cytoplasmic swelling, cell rounding). Here we describe a 96-well format protocol for detection of capsase-3/7 activity in cell lysates, based on a fluorescent caspase-3 assay, combined with a method to simultaneously determine relative protein contents in the individual wells.

Sweet smells prepare plants for future stress: airborne induction of plant disease immunity.

PubMed

Yi, Hwe-Su; Ryu, Choong-Min; Heil, Martin

2010-05-01

Plants require protection against a wide range of attackers such as insects and pathogens. The adequate plant defense responses are regulated via sophisticated signal cascades, which are activated following the perception of specific cues of the attackers. Plants might, however, gain a significant fitness advantage when pre-empting enemy attack before it actually occurs. Monitoring cues from attacked neighbors can permit plants to reach this goal. We have recently found airborne disease resistance against a bacterial pathogen in uninfected lima bean plants when these were located close to conspecific, resistance-expressing neighbors. The emitters could be chemically induced with benzothiadiazole or biologically with an avirulent pathogen. Unexpectedly, receiver plants, although expressing a functioning resistance, did not show reduced growth rates, which represent a common side-effect of directly induced pathogen resistance. Nonanal was identified as an active volatile and, rather than directly inducing full resistance, primed defense gene expression, which became fully activated only when the plants were subsequently challenged by a virulent pathogen. Priming by airborne signals allows for a more efficient and less costly preparation of plants for future attack and airborne signaling can affect resistance against both major groups of plant enemies: herbivores and pathogens.

Pinocembrin: A Novel Natural Compound with Versatile Pharmacological and Biological Activities

PubMed Central

Rasul, Azhar; Millimouno, Faya Martin; Ali Eltayb, Wafa; Ali, Muhammad; Li, Jiang; Li, Xiaomeng

2013-01-01

Pinocembrin (5,7-dihydroxyflavanone) is one of the primary flavonoids isolated from the variety of plants, mainly from Pinus heartwood, Eucalyptus, Populus, Euphorbia, and Sparattosperma leucanthum, in the diverse flora and purified by various chromatographic techniques. Pinocembrin is a major flavonoid molecule incorporated as multifunctional in the pharmaceutical industry. Its vast range of pharmacological activities has been well researched including antimicrobial, anti-inflammatory, antioxidant, and anticancer activities. In addition, pinocembrin can be used as neuroprotective against cerebral ischemic injury with a wide therapeutic time window, which may be attributed to its antiexcitotoxic effects. Pinocembrin exhibits pharmacological effects on almost all systems, and our aim is to review the pharmacological and therapeutic applications of pinocembrin with specific emphasis on mechanisms of actions. The design of new drugs based on the pharmacological effects of pinocembrin could be beneficial. This review suggests that pinocembrin is a potentially promising pharmacological candidate, but additional studies and clinical trials are required to determine its specific intracellular sites of action and derivative targets in order to fully understand the mechanism of its anti-inflammatory, anticancer, and apoptotic effects to further validate its medical applications. PMID:23984355

Crystal structure, molecular docking, and biological activity of the zinc complexes with 2-thenoyltrifluoroacetone and N-donor heterocyclic ligands

NASA Astrophysics Data System (ADS)

Eshaghi Malekshah, Rahime; Salehi, Mehdi; Kubicki, Maciej; Khaleghian, Ali

2017-12-01

Two novel mononuclear complexes, [Zn (TTA) (bipy)Cl] (1) and [Zn (TTA) (phen)Cl] (2) (TTA = 4,4,4-Trifluoro-1-(2-furyl)-1,3-butanedione, phen = 1,10-phenanthroline and bipy 2, 2ʹ-bipyridine), were synthesized and fully characterized by elemental analyses, 1H NMR, UV-Vis, FTIR spectroscopy, and conductivity measurements. The crystal structures of these two mono-nuclear zinc (II) complexes were determined by X-ray single-crystal diffraction. The result of X-ray diffraction analyses revealed that both complexes have distorted tetragonal-pyramid structures. In MTT cytotoxicity studies, these Zn (II) complexes exhibited antitumor activity against MCF-7 and MKN-45 cell lines. It was also found that the proliferation rate of MCF-7 and MKN-45 cells decreased after treatment with the above-mentioned complexes. In addition, the apoptosis-inducing activity was assessed by AO/EB (Acridine Orange/Ethidium bromide) staining assay and found that they have the potential to act as effective metal-based anticancer drugs. Finally, the molecular docking studies showed that complex 2 strongly binds through minor groove with DNA by relative binding energy -7.33 kcal mol-1.

Polyphenol Compound as a Transcription Factor Inhibitor.

PubMed

Park, Seyeon

2015-10-30

A target-based approach has been used to develop novel drugs in many therapeutic fields. In the final stage of intracellular signaling, transcription factor-DNA interactions are central to most biological processes and therefore represent a large and important class of targets for human therapeutics. Thus, we focused on the idea that the disruption of protein dimers and cognate DNA complexes could impair the transcriptional activation and cell transformation regulated by these proteins. Historically, natural products have been regarded as providing the primary leading compounds capable of modulating protein-protein or protein-DNA interactions. Although their mechanism of action is not fully defined, polyphenols including flavonoids were found to act mostly as site-directed small molecule inhibitors on signaling. There are many reports in the literature of screening initiatives suggesting improved drugs that can modulate the transcription factor interactions responsible for disease. In this review, we focus on polyphenol compound inhibitors against dimeric forms of transcription factor components of intracellular signaling pathways (for instance, c-jun/c-fos (Activator Protein-1; AP-1), c-myc/max, Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and β-catenin/T cell factor (Tcf)).

Bufadienolides from parotoid gland secretions of Cuban toad Peltophryne fustiger (Bufonidae): Inhibition of human kidney Na(+)/K(+)-ATPase activity.

PubMed

Perera Córdova, Wilmer H; Leitão, Suzana Guimarães; Cunha-Filho, Geraldino; Bosch, Roberto Alonso; Alonso, Isel Pascual; Pereda-Miranda, Rogelio; Gervou, Rodrigo; Touza, Natália Araújo; Quintas, Luis Eduardo M; Noël, François

2016-02-01

Parotoid gland secretions of toad species are a vast reservoir of bioactive molecules with a wide range of biological properties. Herein, for the first time, it is described the isolation by preparative reversed-phase HPLC and the structure elucidation by NMR spectroscopy and/or mass spectrometry of nine major bufadienolides from parotoid gland secretions of the Cuban endemic toad Peltophryne fustiger: ψ-bufarenogin, gamabufotalin, bufarenogin, arenobufagin, 3-(N-suberoylargininyl) marinobufagin, bufotalinin, telocinobufagin, marinobufagin and bufalin. In addition, the secretion was analyzed by UPLC-MS/MS which also allowed the identification of azelayl arginine. The effect of arenobufagin, bufalin and ψ-bufarenogin on Na(+)/K(+)-ATPase activity in a human kidney preparation was evaluated. These bufadienolides fully inhibited the Na(+)/K(+)-ATPase in a concentration-dependent manner, although arenobufagin (IC50 = 28.3 nM) and bufalin (IC50 = 28.7 nM) were 100 times more potent than ψ-bufarenogin (IC50 = 3020 nM). These results provided evidence about the importance of the hydroxylation at position C-14 in the bufadienolide skeleton for the inhibitory activity on the Na(+)/K(+)-ATPase. Published by Elsevier Ltd.

Estradiol and inflammatory markers in older men.

PubMed

Maggio, Marcello; Ceda, Gian Paolo; Lauretani, Fulvio; Bandinelli, Stefania; Metter, E Jeffrey; Artoni, Andrea; Gatti, Elisa; Ruggiero, Carmelinda; Guralnik, Jack M; Valenti, Giorgio; Ling, Shari M; Basaria, Shehzad; Ferrucci, Luigi

2009-02-01

Aging is characterized by a mild proinflammatory state. In older men, low testosterone levels have been associated with increasing levels of proinflammatory cytokines. It is still unclear whether estradiol (E2), which generally has biological activities complementary to testosterone, affects inflammation. We analyzed data obtained from 399 men aged 65-95 yr enrolled in the Invecchiare in Chianti study with complete data on body mass index (BMI), serum E2, testosterone, IL-6, soluble IL-6 receptor, TNF-alpha, IL-1 receptor antagonist, and C-reactive protein. The relationship between E2 and inflammatory markers was examined using multivariate linear models adjusted for age, BMI, smoking, physical activity, chronic disease, and total testosterone. In age-adjusted analysis, log (E2) was positively associated with log (IL-6) (r = 0.19; P = 0.047), and the relationship was statistically significant (P = 0.032) after adjustments for age, BMI, smoking, physical activity, chronic disease, and serum testosterone levels. Log (E2) was not significantly associated with log (C-reactive protein), log (soluble IL-6 receptor), or log (TNF-alpha) in both age-adjusted and fully adjusted analyses. In older men, E2 is weakly positively associated with IL-6, independent of testosterone and other confounders including BMI.

What is Proof of Concept Research and how does it Generate Epistemic and Ethical Categories for Future Scientific Practice?

PubMed

Kendig, Catherine Elizabeth

2016-06-01

"Proof of concept" is a phrase frequently used in descriptions of research sought in program announcements, in experimental studies, and in the marketing of new technologies. It is often coupled with either a short definition or none at all, its meaning assumed to be fully understood. This is problematic. As a phrase with potential implications for research and technology, its assumed meaning requires some analysis to avoid it becoming a descriptive category that refers to all things scientifically exciting. I provide a short analysis of proof of concept research and offer an example of it within synthetic biology. I suggest that not only are there activities that circumscribe new epistemological categories but there are also associated normative ethical categories or principles linked to the research. I examine these and provide an outline for an alternative ethical account to describe these activities that I refer to as "extended agency ethics". This view is used to explain how the type of research described as proof of concept also provides an attendant proof of principle that is the result of decision-making that extends across practitioners, their tools, techniques, and the problem solving activities of other research groups.

Review on the fate of organic micropollutants in wastewater treatment and water reuse with membranes.

PubMed

Siegrist, H; Joss, A

2012-01-01

A brief review of the fate of micropollutants in membrane-based wastewater treatment due to sorption, stripping, biological degradation/transformation and membrane separation is discussed, to give an overview of these technologies due to the growing importance for water reuse purposes. Compared with conventional activated sludge treatment (CAS) micropollutant removal in membrane bioreactor (MBR) is slightly improved due to complete suspended solids removal and increased sludge age. For discharge to sensitive receiving waters advanced treatment, such as post-ozonation or activated carbon adsorption, is recommended. In water reuse plants nanofiltration (NF) and reverse osmosis (RO) efficiently reject micropollutants due to size exclusions as well as electrostatic and hydrophobic effects reaching potable quality. To remove micropollutants fully, additionally post-ozone or the addition of powdered activated carbon (PAC) have to be applied, which in parallel also reduce NDMA precursors. The concentrate has to be treated if disposed to sensitive receiving waters due to its high micropollutant concentration and ecotoxicity potential. The present review summarizes principles and capabilities for the most important membrane-based applications for wastewater treatment, i.e. porous membranes in MBRs (micro- or ultrafiltration) and dense membrane applications (NF and RO) for water reuse.

Biochemical Effects of six Ti02 and four Ce02 Nanomaterials ...

EPA Pesticide Factsheets

Abstract The potential mammalian hepatotoxicity of nanomaterials were explored in dose-response and structure-activity studies with human hepatic HepG2 cells exposed to between 10 and 1000 ug/ml of six different TiO2 and four CeO2 nanomaterials for 3 days. Various biochemical parameters were then evaluated to study cytotoxicity, cell growth, hepatic function and oxidative stress. Few indications of cytotoxicity were observed between 10 and 100 ug/ml. In the 300 to 1000 ug/ml exposure range a moderate to substantial degree of cytotoxicity was observed. The percent of lactic dehydrogenase released from cells was the most sensitive cytotoxicity parameter. There were four major biochemical effects observed. By far decreased activities of glucose 6-phosphate dehydrogenase was the major finding of this enzymatic study with some significant decreases observed at 10 ug/ml. In the range of 100 to 1000 ug/ml, the activities of superoxide dismutase, glutathione reductase and glutathione peroxidase were decreased by many nanomaterials. There are six factors that contribute to substantial oxidative stress in cultured hepatocytes (decreased GSH content, and reduced G6PDH, GRD, GPX, SOD and altered catalase activities). Cytotoxicity per se did not seem to fully explain the patterns of biological responses observed. With respect to structure-activity, nanomaterials of CeO2 were more effective than TiO2 in reducing glutathione reductase and SOD activ

How, with whom and when: an overview of CD147-mediated regulatory networks influencing matrix metalloproteinase activity.

PubMed

Grass, G Daniel; Toole, Bryan P

2015-11-24

Matrix metalloproteinases (MMPs) comprise a family of 23 zinc-dependent enzymes involved in various pathologic and physiologic processes. In cancer, MMPs contribute to processes from tumour initiation to establishment of distant metastases. Complex signalling and protein transport networks regulate MMP synthesis, cell surface presentation and release. Earlier attempts to disrupt MMP activity in patients have proven to be intolerable and with underwhelming clinical efficacy; thus targeting ancillary proteins that regulate MMP activity may be a useful therapeutic approach. Extracellular matrix metalloproteinase inducer (EMMPRIN) was originally characterized as a factor present on lung cancer cells, which stimulated collagenase (MMP-1) production in fibroblasts. Subsequent studies demonstrated that EMMPRIN was identical with several other protein factors, including basigin (Bsg), all of which are now commonly termed CD147. CD147 modulates the synthesis and activity of soluble and membrane-bound [membrane-type MMPs (MT-MMPs)] in various contexts via homophilic/heterophilic cell interactions, vesicular shedding or cell-autonomous processes. CD147 also participates in inflammation, nutrient and drug transporter activity, microbial pathology and developmental processes. Despite the hundreds of manuscripts demonstrating CD147-mediated MMP regulation, the molecular underpinnings governing this process have not been fully elucidated. The present review summarizes our present knowledge of the complex regulatory systems influencing CD147 biology and provides a framework to understand how CD147 may influence MMP activity. © 2016 Authors.

How, with whom and when: an overview of CD147-mediated regulatory networks influencing matrix metalloproteinase activity

PubMed Central

Grass, G. Daniel; Toole, Bryan P.

2015-01-01

Matrix metalloproteinases (MMPs) comprise a family of 23 zinc-dependent enzymes involved in various pathologic and physiologic processes. In cancer, MMPs contribute to processes from tumour initiation to establishment of distant metastases. Complex signalling and protein transport networks regulate MMP synthesis, cell surface presentation and release. Earlier attempts to disrupt MMP activity in patients have proven to be intolerable and with underwhelming clinical efficacy; thus targeting ancillary proteins that regulate MMP activity may be a useful therapeutic approach. Extracellular matrix metalloproteinase inducer (EMMPRIN) was originally characterized as a factor present on lung cancer cells, which stimulated collagenase (MMP-1) production in fibroblasts. Subsequent studies demonstrated that EMMPRIN was identical with several other protein factors, including basigin (Bsg), all of which are now commonly termed CD147. CD147 modulates the synthesis and activity of soluble and membrane-bound [membrane-type MMPs (MT-MMPs)] in various contexts via homophilic/heterophilic cell interactions, vesicular shedding or cell-autonomous processes. CD147 also participates in inflammation, nutrient and drug transporter activity, microbial pathology and developmental processes. Despite the hundreds of manuscripts demonstrating CD147-mediated MMP regulation, the molecular underpinnings governing this process have not been fully elucidated. The present review summarizes our present knowledge of the complex regulatory systems influencing CD147 biology and provides a framework to understand how CD147 may influence MMP activity. PMID:26604323

Fostering Eroticism in Science Education to Promote Erotic Generosities for the Ocean-Other

ERIC Educational Resources Information Center

Luther, Rachel

2013-01-01

Despite the increase in marine science curriculum in secondary schools, marine science is not generally required curricula and has been largely deemphasized or ignored in relation to earth science, biology, chemistry, and physics. I call for the integration and implementation of marine science more fully in secondary science education through…

Quantum Monte Carlo Methods for First Principles Simulation of Liquid Water

ERIC Educational Resources Information Center

Gergely, John Robert

2009-01-01

Obtaining an accurate microscopic description of water structure and dynamics is of great interest to molecular biology researchers and in the physics and quantum chemistry simulation communities. This dissertation describes efforts to apply quantum Monte Carlo methods to this problem with the goal of making progress toward a fully "ab initio"…

Circadian Modulation of Short-Term Memory in "Drosophila"

ERIC Educational Resources Information Center

Lyons, Lisa C.; Roman, Gregg

2009-01-01

Endogenous biological clocks are widespread regulators of behavior and physiology, allowing for a more efficient allocation of efforts and resources over the course of a day. The extent that different processes are regulated by circadian oscillators, however, is not fully understood. We investigated the role of the circadian clock on short-term…

The Missing Discourse of Gender?

ERIC Educational Resources Information Center

Gilbert, Lucia Albino; Rader, Jill

2002-01-01

Gender theories provide a critical framework for considerations of heterosexual identity. Patriarchal power rests on the social meanings given to biological sex differences and to their reproduction as societal discourses regarding what it means to be a woman or a man. This is a crucial point and one that we believe is not fully recognized in the…

Evolution of Students' Ideas about Natural Selection through a Constructivist Framework

ERIC Educational Resources Information Center

Baumgartner, Erin; Duncan, Kanesa

2009-01-01

Educating students about the process of evolution through natural selection is vitally important because not only is it the unifying theory of biological science, it is also widely regarded as difficult for students to fully comprehend. Anderson and colleagues (2002) describe alternative ideas and misconceptions about natural selection as highly…

Evidence for polyphosphate accumulating organism (PAO)-mediated phosphorus cycling in stream biofilms under alternating aerobic/anaerobic conditions

USDA-ARS?s Scientific Manuscript database

Phosphorus (P) is often a limiting nutrient in freshwater ecosystems and excessive inputs can lead to eutrophication. In-stream cycling of P involves complex biological, chemical, and physical processes that are not fully understood. Microbial metabolisms are suspected to control oxygen-dependent up...

Determining Annealing Temperatures for Polymerase Chain Reaction

ERIC Educational Resources Information Center

Porta, Angela R.; Enners, Edward

2012-01-01

The polymerase chain reaction (PCR) is a common technique used in high school and undergraduate science teaching. Students often do not fully comprehend the underlying principles of the technique and how optimization of the protocol affects the outcome and analysis. In this molecular biology laboratory, students learn the steps of PCR with an…

Nested Neural Networks

NASA Technical Reports Server (NTRS)

Baram, Yoram

1992-01-01

Report presents analysis of nested neural networks, consisting of interconnected subnetworks. Analysis based on simplified mathematical models more appropriate for artificial electronic neural networks, partly applicable to biological neural networks. Nested structure allows for retrieval of individual subpatterns. Requires fewer wires and connection devices than fully connected networks, and allows for local reconstruction of damaged subnetworks without rewiring entire network.

Slide Set: Reproducible image analysis and batch processing with ImageJ.

PubMed

Nanes, Benjamin A

2015-11-01

Most imaging studies in the biological sciences rely on analyses that are relatively simple. However, manual repetition of analysis tasks across multiple regions in many images can complicate even the simplest analysis, making record keeping difficult, increasing the potential for error, and limiting reproducibility. While fully automated solutions are necessary for very large data sets, they are sometimes impractical for the small- and medium-sized data sets common in biology. Here we present the Slide Set plugin for ImageJ, which provides a framework for reproducible image analysis and batch processing. Slide Set organizes data into tables, associating image files with regions of interest and other relevant information. Analysis commands are automatically repeated over each image in the data set, and multiple commands can be chained together for more complex analysis tasks. All analysis parameters are saved, ensuring transparency and reproducibility. Slide Set includes a variety of built-in analysis commands and can be easily extended to automate other ImageJ plugins, reducing the manual repetition of image analysis without the set-up effort or programming expertise required for a fully automated solution.

Operation of the Australian Store.Synchrotron for macromolecular crystallography

PubMed Central

Meyer, Grischa R.; Aragão, David; Mudie, Nathan J.; Caradoc-Davies, Tom T.; McGowan, Sheena; Bertling, Philip J.; Groenewegen, David; Quenette, Stevan M.; Bond, Charles S.; Buckle, Ashley M.; Androulakis, Steve

2014-01-01

The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The service automatically receives and archives raw diffraction data, related metadata and preliminary results of automated data-processing workflows. Data are able to be shared with collaborators and opened to the public. In the nine months since its deployment in August 2013, the service has handled over 22.4 TB of raw data (∼1.7 million diffraction images). Several real examples from the Australian crystallographic community are described that illustrate the advantages of the approach, which include real-time online data access and fully redundant, secure storage. Discoveries in biological sciences increasingly require multidisciplinary approaches. With this in mind, Store.Synchrotron has been developed as a component within a greater service that can combine data from other instruments at the Australian Synchrotron, as well as instruments at the Australian neutron source ANSTO. It is therefore envisaged that this will serve as a model implementation of raw data archiving and dissemination within the structural biology research community. PMID:25286837

Operation of the Australian Store.Synchrotron for macromolecular crystallography.

PubMed

Meyer, Grischa R; Aragão, David; Mudie, Nathan J; Caradoc-Davies, Tom T; McGowan, Sheena; Bertling, Philip J; Groenewegen, David; Quenette, Stevan M; Bond, Charles S; Buckle, Ashley M; Androulakis, Steve

2014-10-01

The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The service automatically receives and archives raw diffraction data, related metadata and preliminary results of automated data-processing workflows. Data are able to be shared with collaborators and opened to the public. In the nine months since its deployment in August 2013, the service has handled over 22.4 TB of raw data (∼1.7 million diffraction images). Several real examples from the Australian crystallographic community are described that illustrate the advantages of the approach, which include real-time online data access and fully redundant, secure storage. Discoveries in biological sciences increasingly require multidisciplinary approaches. With this in mind, Store.Synchrotron has been developed as a component within a greater service that can combine data from other instruments at the Australian Synchrotron, as well as instruments at the Australian neutron source ANSTO. It is therefore envisaged that this will serve as a model implementation of raw data archiving and dissemination within the structural biology research community.

Epigenetics and environmental exposures.

PubMed

Stein, Richard A

2012-01-01

It is becoming increasingly apparent that genetic factors are inadequate to fully explain many processes that shape development and disease. For example, monozygotic twin pairs, despite sharing identical DNA sequences, are often discordant for many traits and diseases, indicating that the same genotype can give rise to distinct phenotypes. This points towards the involvement of additional factors that cannot be explained solely by the sequence of the genome. Epigenetic modifications, defined as heritable changes that do not alter the nucleotide sequence, emerge as key factors that regulate chromatin structure and gene expression and, together with genetic factors, provide the mechanistic basis to understand the biological effects of various classes of environmental exposures. Epigenetic mechanisms explain the ability of certain chemical compounds to initiate biological perturbations that can lead to malignancy, despite being weak mutagens or lacking mutagenic activity altogether-a view that challenges old beliefs and opens new avenues in public health. The field of epigenetics also explains the causal link between certain infectious diseases and cancer, a relationship that was first observed over a century ago and was initially discounted, then fell into oblivion and more recently re-emerged as an important concept in biology. A key feature that distinguishes epigenetic modifications from genetic changes is their reversible nature. This provides exciting prophylactic and therapeutic perspectives, some of which already materialised with the approval of the first drugs that modulate the epigenetic machinery, reinforcing the idea that our genes are not our destiny.

Embryogenesis and Larval Biology of the Cold-Water Coral Lophelia pertusa

PubMed Central

Strömberg, Susanna M.; Dahl, Mikael P.; Lundälv, Tomas; Brooke, Sandra

2014-01-01

Cold-water coral reefs form spectacular and highly diverse ecosystems in the deep sea but little is known about reproduction, and virtually nothing about the larval biology in these corals. This study is based on data from two locations of the North East Atlantic and documents the first observations of embryogenesis and larval development in Lophelia pertusa, the most common framework-building cold-water scleractinian. Embryos developed in a more or less organized radial cleavage pattern from ∼160 µm large neutral or negatively buoyant eggs, to 120–270 µm long ciliated planulae. Embryogenesis was slow with cleavage occurring at intervals of 6–8 hours up to the 64-cell stage. Genetically characterized larvae were sexually derived, with maternal and paternal alleles present. Larvae were active swimmers (0.5 mm s−1) initially residing in the upper part of the water column, with bottom probing behavior starting 3–5 weeks after fertilization. Nematocysts had developed by day 30, coinciding with peak bottom-probing behavior, and possibly an indication that larvae are fully competent to settle at this time. Planulae survived for eight weeks under laboratory conditions, and preliminary results indicate that these planulae are planktotrophic. The late onset of competency and larval longevity suggests a high dispersal potential. Understanding larval biology and behavior is of paramount importance for biophysical modeling of larval dispersal, which forms the basis for predictions of connectivity among populations. PMID:25028936

Treatment of table olive washing water using trickling filters, constructed wetlands and electrooxidation.

PubMed

Tatoulis, Triantafyllos; Stefanakis, Alexandros; Frontistis, Zacharias; Akratos, Christos S; Tekerlekopoulou, Athanasia G; Mantzavinos, Dionissios; Vayenas, Dimitrios V

2017-01-01

The production of table olives is a significant economic activity in Mediterranean countries. Table olive processing generates large volumes of rinsing water that are characterized by high organic matter and phenol contents. Due to these characteristics, a combination of more than one technology is imperative to ensure efficient treatment with low operational cost. Previously, biological filters were combined with electrooxidation to treat table olive washing water. Although this combination was successful in reducing pollutant loads, its cost could be further reduced. Constructed wetlands could be an eligible treatment method for integrated table olive washing water treatment as they have proved tolerant to high organic matter and phenol loads. Two pilot-scale horizontal subsurface constructed wetlands, one planted and one unplanted, were combined with a biological filter and electrooxidation over a boron-doped diamond anode to treat table olive washing water. In the biological filter inlet, chemical oxygen demand (COD) concentrations ranged from 5500 to 15,000 mg/L, while mean COD influent concentration in the constructed wetlands was 2800 mg/L. The wetlands proved to be an efficient intermediate treatment stage, since COD removal levels for the planted unit reached 99 % (mean 70 %), while the unplanted unit presented removal rates of around 65 %. Moreover, the concentration of phenols in the effluent was typically below 100 mg/L. The integrated trickling filter-constructed wetland-electrooxidation treatment system examined here could mineralize and decolorize table olive washing water and fully remove its phenolic content.

Food choice, appetite and physical activity.

PubMed

Bellisle, F

1999-09-01

Food choices and diet composition have been studied less often than energy intake in subjects with varying levels of physical activity. The reported effects of exercise on food choices are not fully consistent, especially on the short term. Type of exercise, intensity, duration can affect the results as well as subjects' characteristics (gender, age, previous training and fitness). A crucial role could also be played by psychological (chronic dieting, attitudes toward health and food, long-established food habits and preferences) and social (traditions, food availability, appropriate times and places) factors. In short-term intervention studies, where a meal is ingested a few minutes following a bout of exercise of varying duration and intensity, an increase in CHO intake is most often reported, while increased protein intake is an occasional observation. In long-term (several weeks) training interventions, intake is assessed from dietary records. Again CHO intake is augmented in exercised subjects as compared to controls, while that of saturated fats and cholesterol may also be affected. Epidemiological studies (without dietary or exercise intervention) often report that habitually active persons eat more and ingest more fruits and vegetables than less active peers. It is not known to what extent such food choices are driven by biological needs (e.g. replacement of glycogen) or elicited by social and psychological factors.

Regulation of Hepatic Cholesteryl Ester Transfer Protein Expression and Reverse Cholesterol Transport by Inhibition of DNA Topoisomerase II.

PubMed

Liu, Mengyang; Chen, Yuanli; Zhang, Ling; Wang, Qixue; Ma, Xingzhe; Li, Xiaoju; Xiang, Rong; Zhu, Yan; Qin, Shucun; Yu, Yang; Jiang, Xian-cheng; Duan, Yajun; Han, Jihong

2015-06-05

Cholesteryl ester transfer protein (CETP) transfers cholesteryl esters from high density lipoprotein to triglyceride-rich lipoproteins. CETP expression can be transcriptionally activated by liver X receptor (LXR). Etoposide and teniposide are DNA topoisomerase II (Topo II) inhibitors. Etoposide has been reported to inhibit atherosclerosis in rabbits with un-fully elucidated mechanisms. In this study we determined if Topo II activity can influence cholesterol metabolism by regulating hepatic CETP expression. Inhibition of Topo II by etoposide, teniposide, or Topo II siRNA increased CETP expression in human hepatic cell line, HepG2 cells, which was associated with increased CETP secretion and mRNA expression. Meanwhile, inhibition of LXR expression by LXR siRNA attenuated induction of CETP expression by etoposide and teniposide. Etoposide and teniposide induced LXRα expression and LXRα/β nuclear translocation while inhibiting expression of receptor interacting protein 140 (RIP140), an LXR co-repressor. In vivo, administration of teniposide moderately reduced serum lipid profiles, induced CETP expression in the liver, and activated reverse cholesterol transport in CETP transgenic mice. Our study demonstrates a novel function of Topo II inhibitors in cholesterol metabolism by activating hepatic CETP expression and reverse cholesterol transport. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

EF24 induces ROS-mediated apoptosis via targeting thioredoxin reductase 1 in gastric cancer cells

PubMed Central

Chen, Weiqian; Chen, Xi; Ying, Shilong; Feng, Zhiguo; Chen, Tongke; Ye, Qingqing; Wang, Zhe; Qiu, Chenyu; Yang, Shulin; Liang, Guang

2016-01-01

Gastric cancer (GC) is one of the leading causes of cancer mortality in the world, and finding novel agents for the treatment of advanced gastric cancer is of urgent need. Diphenyl difluoroketone (EF24), a molecule having structural similarity to curcumin, exhibits potent anti-tumor activities by arresting cell cycle and inducing apoptosis. Although EF24 demonstrates potent anticancer efficacy in numerous types of human cancer cells, the cellular targets of EF24 have not been fully defined. We report here that EF24 may interact with the thioredoxin reductase 1 (TrxR1), an important selenocysteine (Sec)-containing antioxidant enzyme, to induce reactive oxygen species (ROS)-mediated apoptosis in human gastric cancer cells. By inhibiting TrxR1 activity and increasing intracellular ROS levels, EF24 induces a lethal endoplasmic reticulum stress in human gastric cancer cells. Importantly, knockdown of TrxR1 sensitizes cells to EF24 treatment. In vivo, EF24 treatment markedly reduces the TrxR1 activity and tumor cell burden, and displays synergistic lethality with 5-FU against gastric cancer cells. Targeting TrxR1 with EF24 thus discloses a previously unrecognized mechanism underlying the biological activity of EF24, and reveals that TrxR1 is a good target for gastric cancer therapy. PMID:26919110

Anti-inflammatory effect of anthocyanins via modulation of nuclear factor-κB and mitogen-activated protein kinase signaling cascades.

PubMed

Vendrame, Stefano; Klimis-Zacas, Dorothy

2015-06-01

Anthocyanins are a group of bioactive compounds present in plant foods. Although they have consistently shown an anti-inflammatory effect both in vitro and in vivo, their mechanisms of action are not fully understood and have only recently begun to be elucidated. The aim of this review is to highlight the anti-inflammatory activity of anthocyanins, including their effect on the expression of several genes involved in inflammation. The available evidence suggests that their anti-inflammatory action can be attributed primarily to their antioxidant properties, which result in downregulation of the redox-sensitive nuclear factor-κB signaling pathway. Other pathways at least partly involved in the inflammatory response, particularly the mitogen-activated protein kinase pathways, also appear to play a role. A discussion is presented on the most effective dose of anthocyanins, the differential contribution of specific compounds, the comparative effects of anthocyanins versus other anti-inflammatory phenolic compounds, and the extent to which the observed biological activities are exerted by anthocyanins themselves or their metabolites. © The Author(s) 2015. Published by Oxford University Press on behalf of the International Life Sciences Institute. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Environmental Consequences of an Emerging Biosphere

NASA Technical Reports Server (NTRS)

DesMarais, David J.

2003-01-01

It seems feasible to detect biological signatures ("biosignatures") in other planetary systems using the tools of astronomy. There are at least two types of biosignatures; spectral and/or polarization features created by biological products, and electromagnetic signals created by technology. The latter example of a biosignature requires SETI-like searches. This presentation addresses only spectral signatures of biological products and properties of habitable planets. Spectral biosignatures are indeed promising targets for near-term exploration. They can arise from organic constituents (e.g., vegetation) and/or inorganic products (e.g., atmospheric O2). Features originating from a planet's surface are likely to be localized in specific regions, whereas gaseous biosignatures can become globally distributed by atmospheric circulation. Biosignatures should be most abundant within environments that are, or once were, habitable. We currently believe that habitable environments necessarily provide Liquid water and biochemically useful energy. However, we do not yet fully comprehend the diversity of features that might arise within these environments that are non-biological in origin, yet mimic biosignatures. For example, atmospheres reflect the events leading to their origins as well as a host of ongoing planetary processes that might include biological activity. We are persuaded that abundant atmospheric oxygen in an environment with abundant liquid water constitutes definitive evidence of life. However, our own early biosphere thrived for more than a billion years in the absence of abundant atmospheric oxygen. The production of other, more reduced, gaseous biomarkers of "young" and/or anaerobic biospheres has not been systematically studied. Biological gas production is strongly controlled by the structure and function of microbial ecosystems. Investigations of microbial ecosystems that are close analogs of ancient communities offer multiple benefits. Such studies can interpret the production of the most important biomarker gases, while simultaneously helping us to understand the formidable array of ecological processes that guided early biological evolution. Astrobiologists must recognize those aspects of biosignatures that truly reflect the most fundamental, and therefore universal, properties of life. We must learn how the environment can modify biosignatures, and how technology can enable an array of biosignatures to be detected remotely within realistic budgetary constraints

Biologically enhanced mineral weathering: what does it look like, can we model it?

NASA Astrophysics Data System (ADS)

Schulz, M. S.; Lawrence, C. R.; Harden, J. W.; White, A. F.

2011-12-01

The interaction between plants and minerals in soils is hugely important and poorly understood as it relates to the fate of soil carbon. Plant roots, fungi and bacteria inhabit the mineral soil and work symbiotically to extract nutrients, generally through low molecular weight exudates (organic acids, extracelluar polysachrides (EPS), siderophores, etc.). Up to 60% of photosynthetic carbon is allocated below ground as roots and exudates, both being important carbon sources in soils. Some exudates accelerate mineral weathering. To test whether plant exudates are incorporated into poorly crystalline secondary mineral phases during precipitation, we are investigating the biologic-mineral interface. We sampled 5 marine terraces along a soil chronosequence (60 to 225 ka), near Santa Cruz, CA. The effects of the biologic interactions with mineral surfaces were characterized through the use of Scanning Electron Microscopy (SEM). Morphologically, mycorrhizal fungi were observed fully surrounding minerals, fungal hyphae were shown to tunnel into primary silicate minerals and we have observed direct hyphal attachment to mineral surfaces. Fungal tunneling was seen in all 5 soils by SEM. Additionally, specific surface area (using a nitrogen BET method) of primary minerals was measured to determine if the effects of mineral tunneling are quantifiable in older soils. Results suggest that fungal tunneling is more extensive in the primary minerals of older soils. We have also examined the influence of organic acids on primary mineral weathering during soil development using a geochemical reactive transport model (CrunchFlow). Addition of organic acids in our models of soil development at Santa Cruz result in decreased activity of Fe and Al in soil pore water, which subsequently alters the spatial extent of primary mineral weathering and kaolinite precipitation. Overall, our preliminary modeling results suggest biological processes may be an important but underrepresented aspect of soil development in geochemical models.

Investigation of the impacts of thermal pretreatment on waste activated sludge and development of a pretreatment model.

PubMed

Burger, Gillian; Parker, Wayne

2013-09-15

This study investigated the impacts of high pressure thermal hydrolysis (HPTH) pretreatment on the distribution of chemical oxygen demand (COD) species in waste activated sludge (WAS). In the first phase of the project, WAS from a synthetically-fed biological reactor (BR) was fed to an aerobic digester (AD). In the second phase, WAS from the BR was pretreated by HPTH at 150 °C and 3 bars for 30 min prior to being fed to the AD. A range of physical, biochemical and biological properties were regularly measured in each process stream in both phases. The COD of the BR WAS consisted of storage products (XSTO), active heterotrophs (XH) and endogenous decay products (XE). Pretreatment did not increase the extent to which the BR WAS was aerobically digested and hence it was concluded that the unbiodegradable COD fraction, i.e. XE, was unchanged by pretreatment. However, pretreatment did increase the rate of degradation as it converted 36% of XH to readily biodegradable COD (SB) and the remaining XH to slowly biodegradable COD (XB). Furthermore, XSTO was fully converted to SB by pretreatment. Although pretreatment did not change the VSS concentration in the downstream aerobic digester, it did decrease the ISS concentration by 46 ± 11%. This reduced the total mass of solids produced by the digester by 21 ± 8%. A COD-based HPTH pretreatment model was developed and calibrated. When this model was integrated into BioWin 3.1(®), it was able to accurately simulate both the steady state performance of the overall system employed in this study as well as dynamic respirometry results. Copyright © 2013 Elsevier Ltd. All rights reserved.

Light at night alters daily patterns of cortisol and clock proteins in female Siberian hamsters.

PubMed

Bedrosian, T A; Galan, A; Vaughn, C A; Weil, Z M; Nelson, R J

2013-06-01

Humans and other organisms have adapted to a 24-h solar cycle in response to life on Earth. The rotation of the planet on its axis and its revolution around the sun cause predictable daily and seasonal patterns in day length. To successfully anticipate and adapt to these patterns in the environment, a variety of biological processes oscillate with a daily rhythm of approximately 24 h in length. These rhythms arise from hierarchally-coupled cellular clocks generated by positive and negative transcription factors of core circadian clock gene expression. From these endogenous cellular clocks, overt rhythms in activity and patterns in hormone secretion and other homeostatic processes emerge. These circadian rhythms in physiology and behaviour can be organised by a variety of cues, although they are most potently entrained by light. In recent history, there has been a major change from naturally-occurring light cycles set by the sun, to artificial and sometimes erratic light cycles determined by the use of electric lighting. Virtually every individual living in an industrialised country experiences light at night (LAN) but, despite its prevalence, the biological effects of such unnatural lighting have not been fully considered. Using female Siberian hamsters (Phodopus sungorus), we investigated the effects of chronic nightly exposure to dim light on daily rhythms in locomotor activity, serum cortisol concentrations and brain expression of circadian clock proteins (i.e. PER1, PER2, BMAL1). Although locomotor activity remained entrained to the light cycle, the diurnal fluctuation of cortisol concentrations was blunted and the expression patterns of clock proteins in the suprachiasmatic nucleus and hippocampus were altered. These results demonstrate that chronic exposure to dim LAN can dramatically affect fundamental cellular function and emergent physiology. © 2013 British Society for Neuroendocrinology.

Application of ecological criteria in selecting marine reserves and developing reserve networks

USGS Publications Warehouse

Roberts, Callum M.; Branch, George; Bustamante, Rodrigo H.; Castilla, Juan Carlos; Dugan, Jenifer; Halpern, Benjamin S.; Lafferty, Kevin D.; Leslie, Heather; McArdle, Deborah; Ruckelshaus, Mary; Warner, Robert R.

2003-01-01

Marine reserves are being established worldwide in response to a growing recognition of the conservation crisis that is building in the oceans. However, designation of reserves has been largely opportunistic, or protective measures have been implemented (often overlapping and sometimes in conflict) by different entities seeking to achieve different ends. This has created confusion among both users and enforcers, and the proliferation of different measures provides a false sense of protection where little is offered. This paper sets out a procedure grounded in current understanding of ecological processes, that allows the evaluation and selection of reserve sites in order to develop functional, interconnected networks of fully protected reserves that will fulfill multiple objectives. By fully protected we mean permanently closed to fishing and other resource extraction. We provide a framework that unifies the central aims of conservation and fishery management, while also meeting other human needs such as the provision of ecosystem services (e.g., maintenance of coastal water quality, shoreline protection, and recreational opportunities). In our scheme, candidate sites for reserves are evaluated against 12 criteria focused toward sustaining the biological integrity and productivity of marine systems at both local and regional scales. While a limited number of sites will be indispensable in a network, many will be of similar value as reserves, allowing the design of numerous alternative, biologically adequate networks. Devising multiple network designs will help ensure that ecological functionality is preserved throughout the socioeconomic evaluation process. Too often, socioeconomic criteria have dominated the process of reserve selection, potentially undermining their efficacy. We argue that application of biological criteria must precede and inform socioeconomic evaluation, since maintenance of ecosystem functioning is essential for meeting all of the goals for reserves. It is critical that stakeholders are fully involved throughout this process. Application of the proposed criteria will lead to networks whose multifunctionality will help unite the objectives of different management entities, so accelerating progress toward improved stewardship of the oceans.

Is chronic insomnia a precursor to major depression? Epidemiological and biological findings.

PubMed

Baglioni, Chiara; Riemann, Dieter

2012-10-01

Insomnia has been found to be a clinical predictor of subsequent depression. Nevertheless the biological processes underlying this causal relationship are yet not fully understood. Both conditions share a common imbalance of the arousal system. Patients with insomnia present fragmented REM sleep, which probably interferes with basal processes of emotion regulation. The interaction between the arousal and the affective system with the persistence of the disorder could slowly alter also the cognitive system and lead to depression. Although preliminary results seem to support this hypothesis, data are still too few to make valid conclusions.

Introductory science and mathematics education for 21st-Century biologists.

PubMed

Bialek, William; Botstein, David

2004-02-06

Galileo wrote that "the book of nature is written in the language of mathematics"; his quantitative approach to understanding the natural world arguably marks the beginning of modern science. Nearly 400 years later, the fragmented teaching of science in our universities still leaves biology outside the quantitative and mathematical culture that has come to define the physical sciences and engineering. This strikes us as particularly inopportune at a time when opportunities for quantitative thinking about biological systems are exploding. We propose that a way out of this dilemma is a unified introductory science curriculum that fully incorporates mathematics and quantitative thinking.

Larva and pupa of Megatoma (s. str.) undata (Linnaeus, 1758) with remarks on biology and economic importance (Coleoptera, Dermestidae)

PubMed Central

Kadej, Marcin

2017-01-01

Abstract An updated description of the final larval instar and pupa of Megatoma (s. str.) undata (Linnaeus, 1758) (Coleoptera: Dermestidae) is presented. Several morphological characteristics of M. undata larvae are documented and discussed: antenna, epipharynx, mandibula, maxilla, ligula with labial palpi, hastisetae, terga, and condition of the antecostal suture. The paper is fully illustrated and includes some important additions to extend notes on this species available in the references. Summarised data about biology, economic importance, and distribution of M. undata are also provided. PMID:29134022

Automated and miniaturized detection of biological threats with a centrifugal microfluidic system

NASA Astrophysics Data System (ADS)

Mark, D.; van Oordt, T.; Strohmeier, O.; Roth, G.; Drexler, J.; Eberhard, M.; Niedrig, M.; Patel, P.; Zgaga-Griesz, A.; Bessler, W.; Weidmann, M.; Hufert, F.; Zengerle, R.; von Stetten, F.

2012-06-01

The world's growing mobility, mass tourism, and the threat of terrorism increase the risk of the fast spread of infectious microorganisms and toxins. Today's procedures for pathogen detection involve complex stationary devices, and are often too time consuming for a rapid and effective response. Therefore a robust and mobile diagnostic system is required. We present a microstructured LabDisk which performs complex biochemical analyses together with a mobile centrifugal microfluidic device which processes the LabDisk. This portable system will allow fully automated and rapid detection of biological threats at the point-of-need.

Neutral Evolution in a Biological Population as Diffusion in Phenotype Space: Reproduction with Local Mutation but without Selection

NASA Astrophysics Data System (ADS)

Lawson, Daniel John; Jensen, Henrik Jeldtoft

2007-03-01

The process of “evolutionary diffusion,” i.e., reproduction with local mutation but without selection in a biological population, resembles standard diffusion in many ways. However, evolutionary diffusion allows the formation of localized peaks that undergo drift, even in the infinite population limit. We relate a microscopic evolution model to a stochastic model which we solve fully. This allows us to understand the large population limit, relates evolution to diffusion, and shows that independent local mutations act as a diffusion of interacting particles taking larger steps.

A functional approach to emotion in autonomous systems.

PubMed

Sanz, Ricardo; Hernández, Carlos; Gómez, Jaime; Hernando, Adolfo

2010-01-01

The construction of fully effective systems seems to pass through the proper exploitation of goal-centric self-evaluative capabilities that let the system teleologically self-manage. Emotions seem to provide this kind of functionality to biological systems and hence the interest in emotion for function sustainment in artificial systems performing in changing and uncertain environments; far beyond the media hullabaloo of displaying human-like emotion-laden faces in robots. This chapter provides a brief analysis of the scientific theories of emotion and presents an engineering approach for developing technology for robust autonomy by implementing functionality inspired in that of biological emotions.

Steroid hormonal bioactivities, culprit natural and synthetic hormones and other emerging contaminants in waste water measured using bioassays and UPLC-tQ-MS.

PubMed

Houtman, Corine J; Ten Broek, Rob; Brouwer, Abraham

2018-07-15

Emission of compounds with biological activities from waste water treatment plant (WWTP) effluents into surface waters is a topic of concern for ecology and drinking water quality. We investigated the occurrence of hormone-like activities in waste water sample extracts from four Dutch WWTPs and pursued to identify compounds responsible for them. To this aim, in vitro reporter gene bioassays for androgenic, anti-androgenic, estrogenic, glucocorticoid and progestogenic activity and a UPLC-tQ-MS target analysis method for 25 steroid hormones used in high volumes in pharmacy were applied. Principal component analysis of the data was performed to further characterize the detected activities and compounds. All five types of activities tested were observed in the WWTP samples. Androgenic and estrogenic activities were almost completely removed during WW treatment, anti-androgenic activity was only found in treated WW. Glucocorticoid and progestogenic activities persisted throughout the treatment. The androgenic activity in both influent could predominantly be attributed to the presence of androstenedione and testosterone. Anti-androgenic activity was explained by the presence of cyproterone acetate. The glucocorticoid activity in influent was fully explained by prednicarbate, triamcinolone acetonide, dexamethasone and amcinonide. In effluent however, detected hormones could only explain 10-32% of the activity, indicating the presence of unknown glucocorticoids or their metabolites in effluent. Progesterone and levonorgestrel could explain the observed progestogenic activity. The principle component analysis confirmed the way in which hormones fit in the spectrum of other emerging contaminants concerning occurrence and fate in WWTPs. Copyright © 2018 Elsevier B.V. All rights reserved.

Synthetic Biology: Applications in the Food Sector.

PubMed

Tyagi, Ashish; Kumar, Ashwani; Aparna, S V; Mallappa, Rashmi H; Grover, Sunita; Batish, Virender Kumar

2016-08-17

Synthetic biology also termed as "genomic alchemy" represents a powerful area of science that is based on the convergence of biological sciences with systems engineering. It has been fittingly described as "moving from reading the genetic code to writing it" as it focuses on building, modeling, designing and fabricating novel biological systems using customized gene components that result in artificially created genetic circuitry. The scientifically compelling idea of the technological manipulation of life has been advocated since long time. Realization of this idea has gained momentum with development of high speed automation and the falling cost of gene sequencing and synthesis following the completion of the human genome project. Synthetic biology will certainly be instrumental in shaping the development of varying areas ranging from biomedicine, biopharmaceuticals, chemical production, food and dairy quality monitoring, packaging, and storage of food and dairy products, bioremediation and bioenergy production, etc. However, potential dangers of using synthetic life forms have to be acknowledged and adoption of policies by the scientific community to ensure safe practice while making important advancements in the ever expanding field of synthetic biology is to be fully supported and implemented.

The genesis of craniofacial biology as a health science discipline.

PubMed

Sperber, G H; Sperber, S M

2014-06-01

The craniofacial complex encapsulates the brain and contains the organs for key functions of the body, including sight, hearing and balance, smell, taste, respiration and mastication. All these systems are intimately integrated within the head. The combination of these diverse systems into a new field was dictated by the dental profession's desire for a research branch of basic science devoted and attuned to its specific needs. The traditional subjects of genetics, embryology, anatomy, physiology, biochemistry, dental materials, odontology, molecular biology and palaeoanthropology pertaining to dentistry have been drawn together by many newly emerging technologies. These new technologies include gene sequencing, CAT scanning, MRI imaging, laser scanning, image analysis, ultrasonography, spectroscopy and visualosonics. A vibrant unitary discipline of investigation, craniofacial biology, has emerged that builds on the original concept of 'oral biology' that began in the 1960s. This paper reviews some of the developments that have led to the genesis of craniofacial biology as a fully-fledged health science discipline of significance in the advancement of clinical dental practice. Some of the key figures and milestones in craniofacial biology are identified. © 2014 Australian Dental Association.

Biological conversion system

DOEpatents

Scott, C.D.

A system for bioconversion of organic material comprises a primary bioreactor column wherein a biological active agent (zymomonas mobilis) converts the organic material (sugar) to a product (alcohol), a rejuvenator column wherein the biological activity of said biological active agent is enhanced, and means for circulating said biological active agent between said primary bioreactor column and said rejuvenator column.

A pharmacological appraisal of medicinal plants with antidiabetic potential

PubMed Central

Khan, Vasim; Najmi, Abul Kalam; Akhtar, Mohd.; Aqil, Mohd.; Mujeeb, Mohd.; Pillai, K. K.

2012-01-01

Diabetes mellitus is a complicated metabolic disorder that has gravely troubled the human health and quality of life. Conventional agents are being used to control diabetes along with lifestyle management. However, they are not entirely effective and no one has ever been reported to have fully recovered from diabetes. Numerous medicinal plants have been used for the management of diabetes mellitus in various traditional systems of medicine worldwide as they are a great source of biological constituents and many of them are known to be effective against diabetes. Medicinal plants with antihyperglycemic activities are being more desired, owing to lesser side-effects and low cost. This review focuses on the various plants that have been reported to be effective in diabetes. A record of various medicinal plants with their established antidiabetic and other health benefits has been reported. These include Allium sativa, Eugenia jambolana, Panax ginseng, Gymnema sylvestre, Momrodica charantia, Ocimum sanctum, Phyllanthus amarus, Pterocarpus marsupium, Trigonella foenum graecum and Tinospora cordifolia. All of them have shown a certain degree of antidiabetic activity by different mechanisms of action. PMID:22368396

High-power femtosecond-terahertz pulse induces a wound response in mouse skin

PubMed Central

Kim, Kyu-Tae; Park, Jaehun; Jo, Sung Jin; Jung, Seonghoon; Kwon, Oh Sang; Gallerano, Gian Piero; Park, Woong-Yang; Park, Gun-Sik

2013-01-01

Terahertz (THz) technology has emerged for biomedical applications such as scanning, molecular spectroscopy, and medical imaging. Although a thorough assessment to predict potential concerns has to precede before practical utilization of THz source, the biological effect of THz radiation is not yet fully understood with scant related investigations. Here, we applied a femtosecond-terahertz (fs-THz) pulse to mouse skin to evaluate non-thermal effects of THz radiation. Analysis of the genome-wide expression profile in fs-THz-irradiated skin indicated that wound responses were predominantly mediated by transforming growth factor-beta (TGF-β) signaling pathways. We validated NFκB1- and Smad3/4-mediated transcriptional activation in fs-THz-irradiated skin by chromatin immunoprecipitation assay. Repeated fs-THz radiation delayed the closure of mouse skin punch wounds due to up-regulation of TGF-β. These findings suggest that fs-THz radiation initiate a wound-like signal in skin with increased expression of TGF-β and activation of its downstream target genes, which perturbs the wound healing process in vivo. PMID:23907528

In vitro assembly of catalase.

PubMed

Baureder, Michael; Barane, Elisabeth; Hederstedt, Lars

2014-10-10

Most aerobic organisms contain catalase, which functions to decompose hydrogen peroxide. Typical catalases are structurally complex homo-tetrameric enzymes with one heme prosthetic group buried in each subunit. It is not known how catalase in the cell is assembled from its constituents. The bacterium Enterococcus faecalis cannot synthesize heme but can acquire it from the environment to form a cytoplasmic catalase. We have in E. faecalis monitored production of the enzyme polypeptide (KatA) depending on the availability of heme and used our findings to devise a procedure for the purification of preparative amounts of in vivo-synthesized apocatalase. We show that fully active catalase can be obtained in vitro by incubating isolated apoprotein with hemin. We have characterized features of the assembly process and describe a temperature-trapped hemylated intermediate of the enzyme maturation process. Hemylation of apocatalase does not require auxiliary cell components, but rapid assembly of active enzyme seemingly is assisted in the cell. Our findings provide insight about catalase assembly and offer new experimental possibilities for detailed studies of this process. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

A low cost, disposable cable-shaped Al-air battery for portable biosensors

NASA Astrophysics Data System (ADS)

Fotouhi, Gareth; Ogier, Caleb; Kim, Jong-Hoon; Kim, Sooyeun; Cao, Guozhong; Shen, Amy Q.; Kramlich, John; Chung, Jae-Hyun

2016-05-01

A disposable cable-shaped flexible battery is presented using a simple, low cost manufacturing process. The working principle of an aluminum-air galvanic cell is used for the cable-shaped battery to power portable and point-of-care medical devices. The battery is catalyzed with a carbon nanotube (CNT)-paper matrix. A scalable manufacturing process using a lathe is developed to wrap a paper layer and a CNT-paper matrix on an aluminum wire. The matrix is then wrapped with a silver-plated copper wire to form the battery cell. The battery is activated through absorption of electrolytes including phosphate-buffered saline, NaOH, urine, saliva, and blood into the CNT-paper matrix. The maximum electric power using a 10 mm-long battery cell is over 1.5 mW. As a demonstration, an LED is powered using two groups of four batteries in parallel connected in series. Considering the material composition and the cable-shaped configuration, the battery is fully disposable, flexible, and potentially compatible with portable biosensors through activation by either reagents or biological fluids.

Biodegradation of imidazolium ionic liquids by activated sludge microorganisms.

PubMed

Liwarska-Bizukojc, Ewa; Maton, Cedric; Stevens, Christian V

2015-11-01

Biological properties of ionic liquids (ILs) have been usually tested with the help of standard biodegradation or ecotoxicity tests. So far, several articles on the identification of intermediate metabolites of microbiological decay of ILs have been published. Simultaneously, the number of novel ILs with unrecognized characteristics regarding biodegradability and effect on organisms and environment is still increasing. In this work, seven imidazolium ionic liquids of different chemical structure were studied. Three of them are 1-alkyl-3-methyl-imidazolium bromides, while the other four are tetra- or completely substituted imidazolium iodides. This study focused on the identification of intermediate metabolites of the aforementioned ionic liquids subjected to biodegradation in a laboratory activated sludge system. Both fully substituted ionic liquids and 1-ethyl-3-methyl-imidazolium bromide were barely biodegradable. In the case of two of them, no biotransformation products were detected. The elongation of the alkyl side chain made the IL more susceptible for microbiological decomposition. 1-Decyl-3-methyl-imidazolium bromide was biotransformed most easily. Its primary biodegradation up to 100 % could be achieved. Nevertheless, the cleavage of the imidazolium ring has not been observed.

β-Lactam antibiotics. Spectroscopy and molecular orbital (MO) calculations . Part I: IR studies of complexation in penicillin-transition metal ion systems and semi-empirical PM3 calculations on simple model compounds

NASA Astrophysics Data System (ADS)

Kupka, Teobald

1997-12-01

IR studies were preformed to determine possible transition metal ion binding sites of penicillin. the observed changes in spectral position and shape of characteristic IR bands of cloxacillin in the presence of transition metal ions (both in solutions and in the solid state) indicate formation of M-L complexes with engagement of -COO - and/or -CONH- functional groups. The small shift of νCO towards higher frequencies rules out direct M-L interaction via β-lactam carbonyl. PM3 calculations on simple model compounds (substituted formamide, cyclic ketones, lactams and substituted monocyclic β-lactams) have been performed. All structures were fully optimized and the calculated bond lengths, angles, heats of formation and CO stretching frequencies were discussed to determine the β-lactam binding sites and to explain its susceptibility towards nucleophilic attack (hydrolysis in vitro) and biological activity. The relative changes of calculated values were critically compared with available experimental data and same correlation between structural parameters and in vivo activity was shown.

Microbubble-Assisted Ultrasound-Induced Transient Phosphatidylserine Translocation.

PubMed

Escoffre, Jean-Michel; Derieppe, Marc; Lammertink, Bart; Bos, Clemens; Moonen, Chrit

2017-04-01

Microbubble-assisted ultrasound (sonopermeabilization) results in reversible permeabilization of the plasma membrane of cells. This method is increasingly used in vivo because of its potential to deliver therapeutic molecules with limited cell damage. Nevertheless, the effects of sonopermeabilization on the plasma membrane remain not fully understood. We investigated the influence of sonopermeabilization on the transverse mobility of phospholipids, especially on phosphatidylserine (PS) externalization. We performed studies using optical imaging with Annexin V and FM1-43 probes to monitor PS externalization of rat glioma C6 cells. Sonopermeabilization induced transient membrane permeabilization, which is positively correlated with reversible PS externalization. This membrane disorganization was temporary and not associated with loss of cell viability. Sonopermeabilization did not induce PS externalization via activation of the scramblase. We hypothesize that acoustically induced membrane pores may provide a new pathway for PS migration between both membrane leaflets. During the membrane-resealing phase, PS asymmetry may be re-established by amino-phospholipid flippase activity and/or endocytosis, along with exocytosis processes. Copyright © 2016 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Opioid Receptor Probes Derived from Cycloaddition of the Hallucinogen Natural Product Salvinorin A†

PubMed Central

Lozama, Anthony; Cunningham, Christopher W.; Caspers, Michael J.; Douglas, Justin T.; Dersch, Christina M.; Rothman, Richard B.; Prisinzano, Thomas E.

2011-01-01

As part of our continuing efforts toward more fully understanding the structure-activity relationships of the neoclerodane diterpene salvinorin A, we report the synthesis and biological characterization of unique cycloadducts through [4+2] Diels-Alder cycloaddition. Microwave-assisted methods were developed and successfully employed, aiding in functionalizing the chemically sensitive salvinorin A scaffold. This demonstrates the first reported results for both cycloaddition of the furan ring and functionalization via microwave-assisted methodology of the salvinorin A skeleton. The cycloadducts yielded herein introduce electron-withdrawing substituents and bulky aromatic groups into the C-12 position. Kappa opioid (KOP) receptor space was explored through aromatization of the bent oxanorbornadiene system possessed by the cycloadducts to a planar phenyl ring system. Although dimethyl- and diethylcarboxylate analogues 5 and 6 retain some affinity and selectivity for KOP receptors and are full agonists, their aromatized counterparts 13 and 14 have reduced affinity for KOP receptors. The methods developed herein signify a novel approach toward rapidly probing the structure-activity relationships of furan containing natural products. PMID:21338114

Salinomycin, A Polyether Ionophoric Antibiotic, Inhibits Adipogenesis

PubMed Central

Szkudlarek-Mikho, Maria; Saunders, Rudel A.; Yap, Sook Fan; Ngeow, Yun Fong; Chin, Khew-Voon

2012-01-01

The polyether ionophoric antibiotics including monensin, salinomycin, and narasin, are widely used in veterinary medicine and as food additives and growth promoters in animal husbandry including poultry farming. Their effects on human health, however, are not fully understood. Recent studies showed that salinomycin is a cancer stem cell inhibitor. Since poultry consumption has risen sharply in the last three decades, we asked whether the consumption of meat tainted with growth promoting antibiotics might have effects on adipose cells. We showed in this report that the ionophoric antibiotics inhibit the differentiation of preadipocytes into adipocytes. The block of differentiation is not due to the induction of apoptosis nor the inhibition of cell proliferation. In addition, salinomycin also suppresses the transcriptional activity of the CCAAT/enhancer binding proteins and the peroxisome proliferator-activated receptor γ. These results suggest that the ionophoric antibiotics can be exploited as novel anti-obesity therapeutics and as pharmacological probes for the study of adipose biology. Further, the pharmacological effects of salinomycin could be a harbinger of its toxicity on the adipose tissue and other susceptible target cells in cancer therapy. PMID:23123626

Biological Mechanisms by Which Antiproliferative Actions of Resveratrol Are Minimized.

PubMed

Ho, Yih; Lin, Yu-Syuan; Liu, Hsuan-Liang; Shih, Ya-Jung; Lin, Shin-Ying; Shih, Ai; Chin, Yu-Tang; Chen, Yi-Ru; Lin, Hung-Yun; Davis, Paul J

2017-09-21

Preclinical and clinical studies have offered evidence for protective effects of various polyphenol-rich foods against cardiovascular diseases, neurodegenerative diseases, and cancers. Resveratrol is among the most widely studied polyphenols. However, the preventive and treatment effectiveness of resveratrol in cancer remain controversial because of certain limitations in existing studies. For example, studies of the activity of resveratrol against cancer cell lines in vitro have often been conducted at concentrations in the low μM to mM range, whereas dietary resveratrol or resveratrol-containing wine rarely achieve nM concentrations in the clinic. While the mechanisms underlying the failure of resveratrol to inhibit cancer growth in the intact organism are not fully understood, the interference by thyroid hormones with the anticancer activity of resveratrol have been well documented in both in vitro and xenograft studies. Thus, endogenous thyroid hormones may explain the failure of anticancer actions of resveratrol in intact animals, or in the clinic. In this review, mechanisms involved in resveratrol-induced antiproliferation and effects of thyroid hormones on these mechanisms are discussed.

Nitric Oxide Regulates Protein Methylation during Stress Responses in Plants.

PubMed

Hu, Jiliang; Yang, Huanjie; Mu, Jinye; Lu, Tiancong; Peng, Juli; Deng, Xian; Kong, Zhaosheng; Bao, Shilai; Cao, Xiaofeng; Zuo, Jianru

2017-08-17

Methylation and nitric oxide (NO)-based S-nitrosylation are highly conserved protein posttranslational modifications that regulate diverse biological processes. In higher eukaryotes, PRMT5 catalyzes Arg symmetric dimethylation, including key components of the spliceosome. The Arabidopsis prmt5 mutant shows severe developmental defects and impaired stress responses. However, little is known about the mechanisms regulating the PRMT5 activity. Here, we report that NO positively regulates the PRMT5 activity through S-nitrosylation at Cys-125 during stress responses. In prmt5-1 plants, a PRMT5 C125S transgene, carrying a non-nitrosylatable mutation at Cys-125, fully rescues the developmental defects, but not the stress hypersensitive phenotype and the responsiveness to NO during stress responses. Moreover, the salt-induced Arg symmetric dimethylation is abolished in PRMT5 C125S /prmt5-1 plants, correlated to aberrant splicing of pre-mRNA derived from a stress-related gene. These findings define a mechanism by which plants transduce stress-triggered NO signal to protein methylation machinery through S-nitrosylation of PRMT5 in response to environmental alterations. Copyright © 2017 Elsevier Inc. All rights reserved.

An organic water-gated ambipolar transistor with a bulk heterojunction active layer for stable and tunable photodetection

NASA Astrophysics Data System (ADS)

Xu, Haihua; Zhu, Qingqing; Wu, Tongyuan; Chen, Wenwen; Zhou, Guodong; Li, Jun; Zhang, Huisheng; Zhao, Ni

2016-11-01

Organic water-gated transistors (OWGTs) have emerged as promising sensing architectures for biomedical applications and environmental monitoring due to their ability of in-situ detection of biological substances with high sensitivity and low operation voltage, as well as compatibility with various read-out circuits. Tremendous progress has been made in the development of p-type OWGTs. However, achieving stable n-type operation in OWGTs due to the presence of solvated oxygen in water is still challenging. Here, we report an ambipolar OWGT based on a bulk heterojunction active layer, which exhibits a stable hole and electron transport when exposed to aqueous environment. The device can be used as a photodetector both in the hole and electron accumulation regions to yield a maximum responsivity of 0.87 A W-1. More importantly, the device exhibited stable static and dynamic photodetection even when operated in the n-type mode. These findings bring possibilities for the device to be adopted for future biosensing platforms, which are fully compatible with low-cost and low-power organic complementary circuits.

Linear fully dry polymer actuators

NASA Astrophysics Data System (ADS)

De Rossi, Danilo; Mazzoldi, Alberto

1999-05-01

In the last period, the interest in the development of devices that emulate the properties of the 'par excellence' biological actuator, the human muscle, is considerably grown. The recent advances in the field of conducting polymers open new interesting prospects in this direction: from this point of view polyaniline (PANi), since it is easily produced in fiber form, represents an interesting material. In this conference we report the development of a linear actuator prototype that makes use of PANi fiber. All fabrication steps (fiber extrusion, solid polymer electrolyte preparation, compound realization) and experimental set-up for the electromechanical characterization are described. Quantitative measurements of isotonic length changes and isometric stress generation during electrochemical stimulation are reported. An overall assessment of PANi fibers actuative properties in wet and dry conditions is reported and possible future developments are proposed. Finally, continuum and lumped parameter models formulated to describe passive and active contractile properties of conducting polymer actuators are briefly outlined.

Metabolic recycling of ammonia via glutamate dehydrogenase supports breast cancer biomass.

PubMed

Spinelli, Jessica B; Yoon, Haejin; Ringel, Alison E; Jeanfavre, Sarah; Clish, Clary B; Haigis, Marcia C

2017-11-17

Ammonia is a ubiquitous by-product of cellular metabolism; however, the biological consequences of ammonia production are not fully understood, especially in cancer. We found that ammonia is not merely a toxic waste product but is recycled into central amino acid metabolism to maximize nitrogen utilization. In our experiments, human breast cancer cells primarily assimilated ammonia through reductive amination catalyzed by glutamate dehydrogenase (GDH); secondary reactions enabled other amino acids, such as proline and aspartate, to directly acquire this nitrogen. Metabolic recycling of ammonia accelerated proliferation of breast cancer. In mice, ammonia accumulated in the tumor microenvironment and was used directly to generate amino acids through GDH activity. These data show that ammonia is not only a secreted waste product but also a fundamental nitrogen source that can support tumor biomass. Copyright © 2017, American Association for the Advancement of Science.

Dynamics of ligand substitution in labile cobalt complexes resolved by ultrafast T-jump

PubMed Central

Ma, Hairong; Wan, Chaozhi; Zewail, Ahmed H.

2008-01-01

Ligand exchange of hydrated metal complexes is common in chemical and biological systems. Using the ultrafast T-jump, we examined this process, specifically the transformation of aqua cobalt (II) complexes to their fully halogenated species. The results reveal a stepwise mechanism with time scales varying from hundreds of picoseconds to nanoseconds. The dynamics are significantly faster when the structure is retained but becomes rate-limited when the octahedral-to-tetrahedral structural change bottlenecks the transformation. Evidence is presented, from bimolecular kinetics and energetics (enthalpic and entropic), for a reaction in which the ligand assists the displacement of water molecules, with the retention of the entering ligand in the activated state. The reaction time scale deviates by one to two orders of magnitude from that of ionic diffusion, suggesting the involvement of a collisional barrier between the ion and the much larger complex. PMID:18725628

Mammalian Fe-S proteins: definition of a consensus motif recognized by the co-chaperone HSC20.

PubMed

Maio, N; Rouault, T A

2016-10-01

Iron-sulfur (Fe-S) clusters are inorganic cofactors that are fundamental to several biological processes in all three kingdoms of life. In most organisms, Fe-S clusters are initially assembled on a scaffold protein, ISCU, and subsequently transferred to target proteins or to intermediate carriers by a dedicated chaperone/co-chaperone system. The delivery of assembled Fe-S clusters to recipient proteins is a crucial step in the biogenesis of Fe-S proteins, and, in mammals, it relies on the activity of a multiprotein transfer complex that contains the chaperone HSPA9, the co-chaperone HSC20 and the scaffold ISCU. How the transfer complex efficiently engages recipient Fe-S target proteins involves specific protein interactions that are not fully understood. This mini review focuses on recent insights into the molecular mechanism of amino acid motif recognition and discrimination by the co-chaperone HSC20, which guides Fe-S cluster delivery.

4D blood flow mapping using SPIM-microPIV in the developing zebrafish heart

NASA Astrophysics Data System (ADS)

Zickus, Vytautas; Taylor, Jonathan M.

2018-02-01

Fluid-structure interaction in the developing heart is an active area of research in developmental biology. However, investigation of heart dynamics is mostly limited to computational uid dynamics simulations using heart wall structure information only, or single plane blood ow information - so there is a need for 3D + time resolved data to fully understand cardiac function. We present an imaging platform combining selective plane illumination microscopy (SPIM) with micro particle image velocimetry (μPIV) to enable 3D-resolved flow mapping in a microscopic environment, free from many of the sources of error and bias present in traditional epi uorescence-based μPIV systems. By using our new system in conjunction with optical heart beat synchronization, we demonstrate the ability obtain non-invasive 3D + time resolved blood flow measurements in the heart of a living zebrafish embryo.

Diabetes and Depression

PubMed Central

de Groot, Mary; Golden, Sherita Hill

2015-01-01

Diabetes and depression occur together approximately twice as frequently as would be predicted by chance alone. Comorbid diabetes and depression are a major clinical challenge as the outcomes of both conditions are worsened by the other. Although the psychological burden of diabetes may contribute to depression, this explanation does not fully explain the relationship between these 2 conditions. Both conditions may be driven by shared underlying biological and behavioral mechanisms, such as hypothalamic-pituitary-adrenal axis activation, inflammation, sleep disturbance, inactive lifestyle, poor dietary habits, and environmental and cultural risk factors. Depression is frequently missed in people with diabetes despite effective screening tools being available. Both psychological interventions and antidepressants are effective in treating depressive symptoms in people with diabetes but have mixed effects on glycemic control. Clear care pathways involving a multidisciplinary team are needed to obtain optimal medical and psychiatric outcomes for people with comorbid diabetes and depression. PMID:24743941

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

Sunden, Fanny; Peck, Ariana; Salzman, Julia

Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called ‘catalytic residues’ are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modesmore » of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes.« less

Chemerin as an independent predictor of cardiovascular event risk

PubMed Central

İnci, Sinan; Aksan, Gökhan; Doğan, Pınar

2016-01-01

Currently, coronary artery disease (CAD) is considered a major ailment in humans with widespread prevalence. CAD also accounts for high mortality rates around the world that involves several known risk factors. Chemerin is a novel adipokinine that is associated with inflammation and adipogenesis. Furthermore, experimental and clinical data indicate that localized as well as circulating chemerin expression and activation are elevated in numerous metabolic and inflammatory diseases including psoriasis, obesity, type 2 diabetes, metabolic syndrome and cardiovascular disease. Chemerin is accepted as being a strong marker because the serum chemerin levels are increased in a CAD condition. However, the chimeric characteristics of chemerin have not been fully investigated. Although chemerin is known to be responsible for CAD development among other factors, authors still investigate it at the marker level. This review focuses on chemerin expression, processing, biological function and relevance to human diseases, and on the role of chemerin in the maintenance of a cardiovascular disease. PMID:27092231

Construction of a Chassis for a Tripartite Protein-Based Molecular Motor.

PubMed

Small, Lara S R; Bruning, Marc; Thomson, Andrew R; Boyle, Aimee L; Davies, Roberta B; Curmi, Paul M G; Forde, Nancy R; Linke, Heiner; Woolfson, Derek N; Bromley, Elizabeth H C

2017-06-16

Improving our understanding of biological motors, both to fully comprehend their activities in vital processes, and to exploit their impressive abilities for use in bionanotechnology, is highly desirable. One means of understanding these systems is through the production of synthetic molecular motors. We demonstrate the use of orthogonal coiled-coil dimers (including both parallel and antiparallel coiled coils) as a hub for linking other components of a previously described synthetic molecular motor, the Tumbleweed. We use circular dichroism, analytical ultracentrifugation, dynamic light scattering, and disulfide rearrangement studies to demonstrate the ability of this six-peptide set to form the structure designed for the Tumbleweed motor. The successful formation of a suitable hub structure is both a test of the transferability of design rules for protein folding as well as an important step in the production of a synthetic protein-based molecular motor.

Bacteriocins from Lactobacillus plantarum - production, genetic organization and mode of action: produção, organização genética e modo de ação.

PubMed

Todorov, Svetoslav D

2009-04-01

Bacteriocins are biologically active proteins or protein complexes that display a bactericidal mode of action towards usually closely related species. Numerous strains of bacteriocin producing Lactobacillus plantarum have been isolated in the last two decades from different ecological niches including meat, fish, fruits, vegetables, and milk and cereal products. Several of these plantaricins have been characterized and the aminoacid sequence determined. Different aspects of the mode of action, fermentation optimization and genetic organization of the bacteriocin operon have been studied. However, numerous of bacteriocins produced by different Lactobacillus plantarum strains have not been fully characterized. In this article, a brief overview of the classification, genetics, characterization, including mode of action and production optimization for bacteriocins from Lactic Acid Bacteria in general, and where appropriate, with focus on bacteriocins produced by Lactobacillus plantarum, is presented.

[Comments on the seven clinical questions & answers in Japanese gastric treatment guidelines of the 4th edition].

PubMed

Xu, J M

2017-03-23

Japanese gastric cancer treatment guidelines of the 4th Edition proposed solutions to 7 clinically contentious questions. However, the solutions to question 1-3 are not complete and may cause ambiguity. In order to avoid the wrong choice of surgical resection, the solutions to question 1-3 should be clearly defined. For question 1-3, we suggest provisos be added such as patients with resectable M1 disease and without any other non-curable factors, after whose status and tumor biological behavior being fully understood and being fully discussed by a multidisciplinary team, can be recommended to receive comprehensive treatment including surgical resection.

Treatment of Orally Handicapped Edentulous Older Adults Using Dental Implants.

PubMed

Zahedi, Charles

2016-07-01

The oral handicap of complete edentulism is the terminal outcome of a multifactorial process involving biological factors and patient-related factors. Fully edentulous orally handicapped older adults have been neglected because removable acrylic dentures have been the classic therapy for complete edentulism but are only rehabilitative, not therapeutic. Not replacing missing teeth with stable dentures could prevent adequate food intake. Osseointegrated endosseous implants used as a therapeutic adjunct can reduce the problem of long-term bone resorption to less than 0.1 mm per year. Implant-borne prostheses substantially increase the overall health and quality of life of orally handicapped fully edentulous older adults. Copyright © 2016 Elsevier Inc. All rights reserved.

Online Interactive Teaching Modules Enhance Quantitative Proficiency of Introductory Biology Students

PubMed Central

Nelson, Kären C.; Marbach-Ad, Gili; Keller, Michael; Fagan, William F.

2010-01-01

There is widespread agreement within the scientific and education communities that undergraduate biology curricula fall short in providing students with the quantitative and interdisciplinary problem-solving skills they need to obtain a deep understanding of biological phenomena and be prepared fully to contribute to future scientific inquiry. MathBench Biology Modules were designed to address these needs through a series of interactive, Web-based modules that can be used to supplement existing course content across the biological sciences curriculum. The effect of the modules was assessed in an introductory biology course at the University of Maryland. Over the course of the semester, students showed significant increases in quantitative skills that were independent of previous math course work. Students also showed increased comfort with solving quantitative problems, whether or not they ultimately arrived at the correct answer. A survey of spring 2009 graduates indicated that those who had experienced MathBench in their course work had a greater appreciation for the role of mathematics in modern biology than those who had not used MathBench. MathBench modules allow students from diverse educational backgrounds to hone their quantitative skills, preparing them for more complex mathematical approaches in upper-division courses. PMID:20810959

Online interactive teaching modules enhance quantitative proficiency of introductory biology students.

PubMed

Thompson, Katerina V; Nelson, Kären C; Marbach-Ad, Gili; Keller, Michael; Fagan, William F

2010-01-01

There is widespread agreement within the scientific and education communities that undergraduate biology curricula fall short in providing students with the quantitative and interdisciplinary problem-solving skills they need to obtain a deep understanding of biological phenomena and be prepared fully to contribute to future scientific inquiry. MathBench Biology Modules were designed to address these needs through a series of interactive, Web-based modules that can be used to supplement existing course content across the biological sciences curriculum. The effect of the modules was assessed in an introductory biology course at the University of Maryland. Over the course of the semester, students showed significant increases in quantitative skills that were independent of previous math course work. Students also showed increased comfort with solving quantitative problems, whether or not they ultimately arrived at the correct answer. A survey of spring 2009 graduates indicated that those who had experienced MathBench in their course work had a greater appreciation for the role of mathematics in modern biology than those who had not used MathBench. MathBench modules allow students from diverse educational backgrounds to hone their quantitative skills, preparing them for more complex mathematical approaches in upper-division courses.

Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies.

PubMed

Martini, Paolo; Risso, Davide; Sales, Gabriele; Romualdi, Chiara; Lanfranchi, Gerolamo; Cagnin, Stefano

2011-04-11

In the last decades, microarray technology has spread, leading to a dramatic increase of publicly available datasets. The first statistical tools developed were focused on the identification of significant differentially expressed genes. Later, researchers moved toward the systematic integration of gene expression profiles with additional biological information, such as chromosomal location, ontological annotations or sequence features. The analysis of gene expression linked to physical location of genes on chromosomes allows the identification of transcriptionally imbalanced regions, while, Gene Set Analysis focuses on the detection of coordinated changes in transcriptional levels among sets of biologically related genes. In this field, meta-analysis offers the possibility to compare different studies, addressing the same biological question to fully exploit public gene expression datasets. We describe STEPath, a method that starts from gene expression profiles and integrates the analysis of imbalanced region as an a priori step before performing gene set analysis. The application of STEPath in individual studies produced gene set scores weighted by chromosomal activation. As a final step, we propose a way to compare these scores across different studies (meta-analysis) on related biological issues. One complication with meta-analysis is batch effects, which occur because molecular measurements are affected by laboratory conditions, reagent lots and personnel differences. Major problems occur when batch effects are correlated with an outcome of interest and lead to incorrect conclusions. We evaluated the power of combining chromosome mapping and gene set enrichment analysis, performing the analysis on a dataset of leukaemia (example of individual study) and on a dataset of skeletal muscle diseases (meta-analysis approach). In leukaemia, we identified the Hox gene set, a gene set closely related to the pathology that other algorithms of gene set analysis do not identify, while the meta-analysis approach on muscular disease discriminates between related pathologies and correlates similar ones from different studies. STEPath is a new method that integrates gene expression profiles, genomic co-expressed regions and the information about the biological function of genes. The usage of the STEPath-computed gene set scores overcomes batch effects in the meta-analysis approaches allowing the direct comparison of different pathologies and different studies on a gene set activation level.

Distinguishing friends, foes, and freeloaders in giant genomes.

PubMed

Bennetzen, Jeffrey L; Park, Minkyu

2018-04-01

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

Harnessing QbD, Programming Languages, and Automation for Reproducible Biology.

PubMed

Sadowski, Michael I; Grant, Chris; Fell, Tim S

2016-03-01

Building robust manufacturing processes from biological components is a task that is highly complex and requires sophisticated tools to describe processes, inputs, and measurements and administrate management of knowledge, data, and materials. We argue that for bioengineering to fully access biological potential, it will require application of statistically designed experiments to derive detailed empirical models of underlying systems. This requires execution of large-scale structured experimentation for which laboratory automation is necessary. This requires development of expressive, high-level languages that allow reusability of protocols, characterization of their reliability, and a change in focus from implementation details to functional properties. We review recent developments in these areas and identify what we believe is an exciting trend that promises to revolutionize biotechnology. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Designing Uniquely Addressable Bio-orthogonal Synthetic Scaffolds for DNA and RNA Origami.

PubMed

Kozyra, Jerzy; Ceccarelli, Alessandro; Torelli, Emanuela; Lopiccolo, Annunziata; Gu, Jing-Ying; Fellermann, Harold; Stimming, Ulrich; Krasnogor, Natalio

2017-07-21

Nanotechnology and synthetic biology are rapidly converging, with DNA origami being one of the leading bridging technologies. DNA origami was shown to work well in a wide array of biotic environments. However, the large majority of extant DNA origami scaffolds utilize bacteriophages or plasmid sequences thus severely limiting its future applicability as a bio-orthogonal nanotechnology platform. In this paper we present the design of biologically inert (i.e., "bio-orthogonal") origami scaffolds. The synthetic scaffolds have the additional advantage of being uniquely addressable (unlike biologically derived ones) and hence are better optimized for high-yield folding. We demonstrate our fully synthetic scaffold design with both DNA and RNA origamis and describe a protocol to produce these bio-orthogonal and uniquely addressable origami scaffolds.

Cardiac Muscle-cell Based Actuator and Self-stabilizing Biorobot - PART 1.

PubMed

Holley, Merrel T; Nagarajan, Neerajha; Danielson, Christian; Zorlutuna, Pinar; Park, Kidong

2017-07-11

Biological machines often referred to as biorobots, are living cell- or tissue-based devices that are powered solely by the contractile activity of living components. Due to their inherent advantages, biorobots are gaining interest as alternatives to traditional fully artificial robots. Various studies have focused on harnessing the power of biological actuators, but only recently studies have quantitatively characterized the performance of biorobots and studied their geometry to enhance functionality and efficiency. Here, we demonstrate the development of a self-stabilizing swimming biorobot that can maintain its pitch, depth, and roll without external intervention. The design and fabrication of the PDMS scaffold for the biological actuator and biorobot followed by the functionalization with fibronectin is described in this first part. In the second part of this two-part article, we detail the incorporation of cardiomyocytes and characterize the biological actuator and biorobot function. Both incorporate a base and tail (cantilever) which produce fin-based propulsion. The tail is constructed with soft lithography techniques using PDMS and laser engraving. After incorporating the tail with the device base, it is functionalized with a cell adhesive protein and seeded confluently with cardiomyocytes. The base of the biological actuator consists of a solid PDMS block with a central glass bead (acts as a weight). The base of the biorobot consists of two composite PDMS materials, Ni-PDMS and microballoon-PDMS (MB-PDMS). The nickel powder (in Ni-PDMS) allows magnetic control of the biorobot during cells seeding and stability during locomotion. Microballoons (in MB-PDMS) decrease the density of MB-PDMS, and enable the biorobot to float and swim steadily. The use of these two materials with different mass densities, enabled precise control over the weight distribution to ensure a positive restoration force at any angle of the biorobot. This technique produces a magnetically controlled self-stabilizing swimming biorobot.

Using Card Games to Simulate the Process of Natural Selection

ERIC Educational Resources Information Center

Grilliot, Matthew E.; Harden, Siegfried

2014-01-01

In 1858, Darwin published "On the Origin of Species by Means of Natural Selection." His explanation of evolution by natural selection has become the unifying theme of biology. We have found that many students do not fully comprehend the process of evolution by natural selection. We discuss a few simple games that incorporate hands-on…

Increases in Cognitive and Linguistic Processing Primarily Account for Increases in Speaking Rate with Age

ERIC Educational Resources Information Center

Nip, Ignatius S. B.; Green, Jordan R.

2013-01-01

Age-related increases of speaking rate are not fully understood, but have been attributed to gains in biologic factors and learned skills that support speech production. This study investigated developmental changes in speaking rate and articulatory kinematics of participants aged 4 ("N" = 7), 7 ("N" = 10), 10…

Postdoctoral Fellow | Center for Cancer Research

Cancer.gov

The Wolin laboratory has recently moved to the National Cancer Institute as part of a new initiative in RNA Biology. A fully funded postdoctoral position is available in the areas of noncoding RNA function, RNA surveillance pathways, and the mechanisms by which defects in RNA decay pathways contribute to diseases such as cancer and autoimmunity. We use mammalian cells and

From Trace Evidence to Bioinformatics: Putting Bryophytes into Molecular Biology Education

ERIC Educational Resources Information Center

Fuselier, Linda; Bougary, Azhar; Malott, Michelle

2011-01-01

Students benefit most from their science education when they participate fully in the process of science in the context of real-world problems. We describe a student-directed open-inquiry lab experience that has no predetermined outcomes and requires students to engage in all components of scientific inquiry from posing a question through…

In vivo effect of staphylococcal enterotoxin A on peripheral blood lymphocytes.

PubMed Central

Zehavi-Willner, T; Shenberg, E; Barnea, A

1984-01-01

Staphylococcal enterotoxin A (SEA) administration to monkeys produced an initial lymphocytic leukopenia lasting approximately 24 h. Lymphocytes isolated from blood circulation (PBL) during this stage had normal or decreased [3H]thymidine incorporating activity. After 48 h, however, a significant increase (five- to sixfold) in [3H]thymidine incorporating activity into PBL was apparent. The peak of incorporating activity (seven- to eightfold) was reached 3 to 4 days after SEA administration, followed by a gradual decline, reaching the baseline after 2 weeks. The increased levels of [3H] thymidine incorporation in PBL were concomitant with the conversion of lymphopenia into lymphocytosis, accompanied by the release of many immature cells into the circulation. Lymphocytes isolated 24 h after SEA administration in vivo did not respond to the mitogenic action of SEA in vitro. Lymphocytes isolated at later stages after SEA challenge were fully activated by toxin. From a series of studies, it was concluded that SEA administered to monkeys caused, during the initial 24 h, the removal of a great proportion of lymphocytes from the circulation, followed by the release of new immature cells with augmented DNA synthesis activity. The lymphocytic leukocytosis state declined gradually and reached normal levels between 3 and 4 weeks after the SEA challenge. The biological implications of the hematological changes occurring after SEA challenge in vivo are discussed. PMID:6715041

Systems analysis in Cellvibrio japonicus resolves predicted redundancy of β-glucosidases and determines essential physiological functions: Functional analysis of C. japonicus β-glucosidases

DOE PAGES

Nelson, Cassandra E.; Rogowski, Artur; Morland, Carl; ...

2017-02-28

Degradation of polysaccharides forms an essential arc in the carbon cycle, provides a percentage of our daily caloric intake, and is a major driver in the renewable chemical industry. Microorganisms proficient at degrading insoluble polysaccharides possess large numbers of carbohydrate active enzymes, many of which have been categorized as functionally redundant. Here we present data that suggests that carbohydrate active enzymes that have overlapping enzymatic activities can have unique, non-overlapping biological functions in the cell. Our comprehensive study to understand cellodextrin utilization in the soil saprophyte Cellvibrio japonicus found that only one of four predicted β-glucosidases is required in amore » physiological context. Gene deletion analysis indicated that only the cel3B gene product is essential for efficient cellodextrin utilization in C. japonicus and is constitutively expressed at high levels. Interestingly, expression of individual β-glucosidases in Escherichia coli K-12 enabled this non-cellulolytic bacterium to be fully capable of using cellobiose as a sole carbon source. Furthermore, enzyme kinetic studies indicated that the Cel3A enzyme is significantly more active than the Cel3B enzyme on the oligosaccharides but not disaccharides. Finally, our approach for parsing related carbohydrate active enzymes to determine actual physiological roles in the cell can be applied to other polysaccharide-degradation systems.« less

Genes Upregulated in Winter Wheat (Triticum aestivum L.) during Mild Freezing and Subsequent Thawing Suggest Sequential Activation of Multiple Response Mechanisms.

PubMed

Skinner, Daniel Z

2015-01-01

Exposing fully cold-acclimated wheat plants to a mild freeze-thaw cycle of -3 °C for 24h followed by +3 °C for 24 or 48 h results in dramatically improved tolerance of subsequent exposure to sub-freezing temperatures. Gene enrichment analysis of crown tissue from plants collected before or after the -3 °C freeze or after thawing at +3 °C for 24 or 48 h revealed that many biological processes and molecular functions were activated during the freeze-thaw cycle in an increasing cascade of responses such that over 150 processes or functions were significantly enhanced by the end of the 48 h, post-freeze thaw. Nearly 2,000 individual genes were upregulated more than 2-fold over the 72 h course of freezing and thawing, but more than 70% of these genes were upregulated during only one of the time periods examined, suggesting a series of genes and gene functions were involved in activation of the processes that led to enhanced freezing tolerance. This series of functions appeared to include extensive cell signaling, activation of stress response mechanisms and the phenylpropanoid biosynthetic pathway, extensive modification of secondary metabolites, and physical restructuring of cell membranes. By identifying plant lines that are especially able to activate these multiple mechanisms it may be possible to develop lines with enhanced winterhardiness.

A functional dual-coated (FDC) microtiter plate method to replace the botulinum toxin LD50 test.

PubMed

Liu, Yvonne Y B; Rigsby, Peter; Sesardic, Dorothea; Marks, James D; Jones, Russell G A

2012-06-01

Conventional capture ("Sandwich") ELISAs equally detect denatured inactive and native active botulinum type A toxin. Light chain endoprotease activity assays also fail to distinguish between various inactive molecules including partially denatured and fragmented material still retaining this protease activity. By co-coating microtiter plates with SNAP25 substrate and a monoclonal antibody specific for a conformational epitope of the toxin's Hc domain, it was possible to develop a highly sensitive (130 aM LoD), precise (1.4% GCV) new assay specific for the biologically active toxin molecule. Capture was performed in phosphate buffer with a fixed optimal concentration of chaotropic agent (e.g., 1.2 M urea) to differentially isolate functional toxin molecules. Addition of enzymatically favorable buffer containing zinc and DTT reduced the interchain disulfide bond releasing and activating the captured L-chain with subsequent specific cleavage of the SNAP25(1-206) substrate. A neoepitope antibody specific for the newly exposed Q(197) epitope was used to quantify the cleaved SNAP25(1-197). The assay's requirement for the intact toxin molecule was demonstrated with pre-reduced toxin (heavy and light chains), recombinant LHn fragments, and stressed samples containing partially or fully denatured material. This is the first known immunobiochemical assay that correlates with in vivo potency and provides a realistic alternative. Copyright © 2012 Elsevier Inc. All rights reserved.

Stabilization, Rolling, and Addition of Other Extracellular Matrix Proteins to Collagen Hydrogels Improve Regeneration in Chitosan Guides for Long Peripheral Nerve Gaps in Rats.

PubMed

Gonzalez-Perez, Francisco; Cobianchi, Stefano; Heimann, Claudia; Phillips, James B; Udina, Esther; Navarro, Xavier

2017-03-01

Autograft is still the gold standard technique for the repair of long peripheral nerve injuries. The addition of biologically active scaffolds into the lumen of conduits to mimic the endoneurium of peripheral nerves may increase the final outcome of artificial nerve devices. Furthermore, the control of the orientation of the collagen fibers may provide some longitudinal guidance architecture providing a higher level of mesoscale tissue structure. To evaluate the regenerative capabilities of chitosan conduits enriched with extracellular matrix-based scaffolds to bridge a critical gap of 15 mm in the rat sciatic nerve. The right sciatic nerve of female Wistar Hannover rats was repaired with chitosan tubes functionalized with extracellular matrix-based scaffolds fully hydrated or stabilized and rolled to bridge a 15 mm nerve gap. Recovery was evaluated by means of electrophysiology and algesimetry tests and histological analysis 4 months after injury. Stabilized constructs enhanced the success of regeneration compared with fully hydrated scaffolds. Moreover, fibronectin-enriched scaffolds increased muscle reinnervation and number of myelinated fibers compared with laminin-enriched constructs. A mixed combination of collagen and fibronectin may be a promising internal filler for neural conduits for the repair of peripheral nerve injuries, and their stabilization may increase the quality of regeneration over long gaps. Copyright © 2017 by the Congress of Neurological Surgeons

Catalytic and transport cycles of ABC exporters.

PubMed

Al-Shawi, Marwan K

2011-09-07

ABC (ATP-binding cassette) transporters are arguably the most important family of ATP-driven transporters in biology. Despite considerable effort and advances in determining the structures and physiology of these transporters, their fundamental molecular mechanisms remain elusive and highly controversial. How does ATP hydrolysis by ABC transporters drive their transport function? Part of the problem in answering this question appears to be a perceived need to formulate a universal mechanism. Although it has been generally hoped and assumed that the whole superfamily of ABC transporters would exhibit similar conserved mechanisms, this is proving not to be the case. Structural considerations alone suggest that there are three overall types of coupling mechanisms related to ABC exporters, small ABC importers and large ABC importers. Biochemical and biophysical characterization leads us to the conclusion that, even within these three classes, the catalytic and transport mechanisms are not fully conserved, but continue to evolve. ABC transporters also exhibit unusual characteristics not observed in other primary transporters, such as uncoupled basal ATPase activity, that severely complicate mechanistic studies by established methods. In this chapter, I review these issues as related to ABC exporters in particular. A consensus view has emerged that ABC exporters follow alternating-access switch transport mechanisms. However, some biochemical data suggest that alternating catalytic site transport mechanisms are more appropriate for fully symmetrical ABC exporters. Heterodimeric and asymmetrical ABC exporters appear to conform to simple alternating-access-type mechanisms.

Novel recombinant human lactoferrin: differential activation of oxidative stress related gene expression.

PubMed

Kruzel, Marian L; Actor, Jeffrey K; Zimecki, Michał; Wise, Jasen; Płoszaj, Paulina; Mirza, Shaper; Kruzel, Mark; Hwang, Shen-An; Ba, Xueqing; Boldogh, Istvan

2013-12-01

Lactoferrin, an iron-binding protein found in high concentrations in mammalian exocrine secretions, is an important component of the host defense system. It is also a major protein of the secondary granules of neutrophils from which is released upon activation. Due to its potential clinical utility, recombinant human lactoferrin (rhLF) has been produced in various eukaryotic expression systems; however, none of these are fully compatible with humans. Most of the biopharmaceuticals approved by the FDA for use in humans are produced in mammalian expression systems. The Chinese hamster ovary cells (CHO) have become the system of choice for proteins that require post-translational modifications, such as glycoproteins. The aim of this study was to scale-up expression and purification of rhLF in a CHO expression system, verify its glycan primary structure, and assess its biological properties in cell culture models. A stable CHO cell line producing >200mg/L of rhLF was developed and established. rhLF was purified by a single-step cation-exchange chromatography procedure. The highly homogenous rhLF has a molecular weight of approximately 80 kDa. MALDI-TOF mass spectrometric analysis revealed N-linked, partially sialylated glycans at two glycosylation sites, typical for human milk LF. This novel rhLF showed a protective effect against oxidative stress in a similar manner to its natural counterpart. In addition, rhLF revealed a modulatory effect on cellular redox via upregulation of key antioxidant enzymes. These data imply that the CHO-derived rhLF is fully compatible with the native molecule, thus it has promise for human therapeutic applications. Copyright © 2013 Elsevier B.V. All rights reserved.

Biochemical quantitation of the eIF5A hypusination in Arabidopsis thaliana uncovers ABA-dependent regulation

PubMed Central

Belda-Palazón, Borja; Nohales, María A.; Rambla, José L.; Aceña, José L.; Delgado, Oscar; Fustero, Santos; Martínez, M. Carmen; Granell, Antonio; Carbonell, Juan; Ferrando, Alejandro

2014-01-01

The eukaryotic translation elongation factor eIF5A is the only protein known to contain the unusual amino acid hypusine which is essential for its biological activity. This post-translational modification is achieved by the sequential action of the enzymes deoxyhypusine synthase (DHS) and deoxyhypusine hydroxylase (DOHH). The crucial molecular function of eIF5A during translation has been recently elucidated in yeast and it is expected to be fully conserved in every eukaryotic cell, however the functional description of this pathway in plants is still sparse. The genetic approaches with transgenic plants for either eIF5A overexpression or antisense have revealed some activities related to the control of cell death processes but the molecular details remain to be characterized. One important aspect of fully understanding this pathway is the biochemical description of the hypusine modification system. Here we have used recombinant eIF5A proteins either modified by hypusination or non-modified to establish a bi-dimensional electrophoresis (2D-E) profile for the three eIF5A protein isoforms and their hypusinated or unmodified proteoforms present in Arabidopsis thaliana. The combined use of the recombinant 2D-E profile together with 2D-E/western blot analysis from whole plant extracts has provided a quantitative approach to measure the hypusination status of eIF5A. We have used this information to demonstrate that treatment with the hormone abscisic acid produces an alteration of the hypusine modification system in Arabidopsis thaliana. Overall this study presents the first biochemical description of the post-translational modification of eIF5A by hypusination which will be functionally relevant for future studies related to the characterization of this pathway in Arabidopsis thaliana. PMID:24904603

Intravenous hemostats: challenges in translation to patients

NASA Astrophysics Data System (ADS)

Lashof-Sullivan, Margaret; Shoffstall, Andrew; Lavik, Erin

2013-10-01

Excessive bleeding and the resulting complications are a leading killer of young people globally. There are many successful methods to halt bleeding in the extremities, including compression, tourniquets, and dressings. However, current treatments for internal hemorrhage (including from head or truncal injuries), termed non-compressible bleeding, are inadequate. For these non-compressible injuries, blood transfusions are the current treatment standard. However, they must be refrigerated, may potentially transfer disease, and are of limited supply. In addition, time is of the essence for halting hemorrhage, since more than a third of civilian deaths due to hemorrhage from trauma occur before the patient even reaches the hospital. As a result, particles that can cross-link activated platelets through the glycoprotein IIb/IIIa receptor expressed on activated platelets are being investigated as an alternative treatment for non-compressible bleeding. Ideally, these particles would interact specifically with platelets to stabilize the platelet plug. Initial designs used biologically derived microparticles with red blood cell fragment or albumin cores decorated with RGD or fibrinogen, which bind to GPIIb/IIIa. More recently there has been research into the use of fully synthetic nanoparticles with liposomal or polymer cores that crosslink platelets through a targeting peptide bound to the surface. Some of the challenges for the development of these particles include appropriate sizing to prevent blocking the capillaries of the lungs, immune system evasion to prevent strong reactions and increase circulation time, and storage and resuspension so that first responders can easily use the particles. In addition, the effectiveness of the variety of animal bleeding models in predicting outcomes must be examined before test results can be fully understood. Progress has been made in the development of particles to combat hemorrhage, but issues of immune sensitivity and storage must be resolved before these types of particles can be translated for human use.

Impact of Learner's Characteristics and Learning Behaviour on Learning Performance during a Fully Online Course

ERIC Educational Resources Information Center

Nakayama, Minoru; Mutsuura, Kouichi; Yamamoto, Hiroh

2014-01-01

A fully online learning environment requires effective learning management in order to promote pro-active education. Since student's notes are a reflection of the progress of their education, analysis of notes taken can be used to track the learning process of students who participate in fully online courses. This paper presents the causal…

Purification of Oogonial Stem Cells From Adult Mouse and Human Ovaries: An Assessment of the Literature and a View Toward the Future

PubMed Central

Woods, Dori C.; White, Yvonne A. R.; Tilly, Jonathan L.

2013-01-01

Contemporary claims that mitotically active female germ line or oogonial stem cells (OSCs) exist and support oogenesis during postnatal life in mammals have been debated in the field of reproductive biology since March 2004, when a mouse study posed the first serious challenge to the dogma of a fixed pool of oocytes being endowed at birth in more than 50 years. Other studies have since been put forth that further question the validity of this dogma, including the isolation of OSCs from neonatal and adult mouse ovaries by 4 independent groups using multiple strategies. Two of these groups also reported that isolated mouse OSCs, once transplanted back into ovaries of adult female mice, differentiate into fully functional eggs that ovulate, fertilize, and produce healthy embryos and offspring. Arguably, one of the most significant advances in this emerging field was provided by a new research study published this year, which reported the successful isolation and functional characterization of OSCs from ovaries of reproductive age women. Two commentaries on this latest work, one cautiously supportive and one highly skeptical, were published soon afterward. This article evaluates the current literature regarding postnatal oogenesis in mammals and discusses important next steps for future work on OSC biology and function. PMID:23024060

Purification of oogonial stem cells from adult mouse and human ovaries: an assessment of the literature and a view toward the future.

PubMed

Woods, Dori C; White, Yvonne A R; Tilly, Jonathan L

2013-01-01

Contemporary claims that mitotically active female germ line or oogonial stem cells (OSCs) exist and support oogenesis during postnatal life in mammals have been debated in the field of reproductive biology since March 2004, when a mouse study posed the first serious challenge to the dogma of a fixed pool of oocytes being endowed at birth in more than 50 years. Other studies have since been put forth that further question the validity of this dogma, including the isolation of OSCs from neonatal and adult mouse ovaries by 4 independent groups using multiple strategies. Two of these groups also reported that isolated mouse OSCs, once transplanted back into ovaries of adult female mice, differentiate into fully functional eggs that ovulate, fertilize, and produce healthy embryos and offspring. Arguably, one of the most significant advances in this emerging field was provided by a new research study published this year, which reported the successful isolation and functional characterization of OSCs from ovaries of reproductive age women. Two commentaries on this latest work, one cautiously supportive and one highly skeptical, were published soon afterward. This article evaluates the current literature regarding postnatal oogenesis in mammals and discusses important next steps for future work on OSC biology and function.

Nitrous Oxide Production at a Fully Covered Wastewater Treatment Plant: Results of a Long-Term Online Monitoring Campaign.

PubMed

Kosonen, Heta; Heinonen, Mari; Mikola, Anna; Haimi, Henri; Mulas, Michela; Corona, Francesco; Vahala, Riku

2016-06-07

The nitrous oxide emissions of the Viikinmäki wastewater treatment plant were measured in a 12 month online monitoring campaign. The measurements, which were conducted with a continuous gas analyzer, covered all of the unit operations of the advanced wastewater-treatment process. The relation between the nitrous oxide emissions and certain process parameters, such as the wastewater temperature, influent biological oxygen demand, and ammonium nitrogen load, was investigated by applying online data obtained from the process-control system at 1 min intervals. Although seasonal variations in the measured nitrous oxide emissions were remarkable, the measurement data indicated no clear relationship between these emissions and seasonal changes in the wastewater temperature. The diurnal variations of the nitrous oxide emissions did, however, strongly correlate with the alternation of the influent biological oxygen demand and ammonium nitrogen load to the aerated zones of the activated sludge process. Overall, the annual nitrous oxide emissions of 168 g/PE/year and the emission factor of 1.9% of the influent nitrogen load are in the high range of values reported in the literature but in very good agreement with the results of other long-term online monitoring campaigns implemented at full-scale wastewater-treatment plants.

Fully Automated Sample Preparation for Ultrafast N-Glycosylation Analysis of Antibody Therapeutics.

PubMed

Szigeti, Marton; Lew, Clarence; Roby, Keith; Guttman, Andras

2016-04-01

There is a growing demand in the biopharmaceutical industry for high-throughput, large-scale N-glycosylation profiling of therapeutic antibodies in all phases of product development, but especially during clone selection when hundreds of samples should be analyzed in a short period of time to assure their glycosylation-based biological activity. Our group has recently developed a magnetic bead-based protocol for N-glycosylation analysis of glycoproteins to alleviate the hard-to-automate centrifugation and vacuum-centrifugation steps of the currently used protocols. Glycan release, fluorophore labeling, and cleanup were all optimized, resulting in a <4 h magnetic bead-based process with excellent yield and good repeatability. This article demonstrates the next level of this work by automating all steps of the optimized magnetic bead-based protocol from endoglycosidase digestion, through fluorophore labeling and cleanup with high-throughput sample processing in 96-well plate format, using an automated laboratory workstation. Capillary electrophoresis analysis of the fluorophore-labeled glycans was also optimized for rapid (<3 min) separation to accommodate the high-throughput processing of the automated sample preparation workflow. Ultrafast N-glycosylation analyses of several commercially relevant antibody therapeutics are also shown and compared to their biosimilar counterparts, addressing the biological significance of the differences. © 2015 Society for Laboratory Automation and Screening.

ÉquiNanos: innovative team for nanoparticle risk management.

PubMed

Nadeau, Sylvie; Bouchard, Michèle; Debia, Maximilien; DeMarcellis-Warin, Nathalie; Hallé, Stéphane; Songmene, Victor; Therrien, Marie-Christine; Wilkinson, Kevin; Ateme-Nguema, Barthélémy; Dufour, Geneviève; Dufresne, André; Fatisson, Julien; Haddad, Sami; Hadioui, Madjid; Kouam, Jules; Morency, François; Tardif, Robert; Viens, Martin; Weichenthal, Scott; Viau, Claude; Camus, Michel

2013-01-01

Interactions between nanoparticles (NP), humans and the environment are not fully understood yet. Moreover, frameworks aiming at protecting human health have not been adapted to NP but are nonetheless applied to NP-related activities. Consequently, business organizations currently have to deal with NP-related risks despite the lack of a proven effective method of risk-management. To respond to these concerns and fulfill the needs of populations and industries, ÉquiNanos was created as a largely interdisciplinary provincial research team in Canada. ÉquiNanos consists of eight platforms with different areas of action, from adaptive decision-aid tool to public and legal governance, while including biological monitoring. ÉquiNanos resources aim at responding to the concerns of the Quebec nanotechnology industry and public health authorities. Our mandate is to understand the impact of NP on human health in order to protect the population against all potential risks emerging from these high-priority and rapidly expanding innovative technologies. In this paper by Canadian authors an important framework is discussed with the goal of acquiring more detailed information and establishing an infrastructure to evaluate the interaction between nanoparticles and living organisms, with the ultimate goal of safety and risk management of the rapidly growing fields of nanotechnology-based biological applications. Copyright © 2013 Elsevier Inc. All rights reserved.

Microbial Growth in the Magnesium- Chloride - Sodium- Sulphate Ion System: Implications for Habitability in Terrestrial and Extraterrestrial Salts

NASA Astrophysics Data System (ADS)

Loudon, C. M.; Aka, S.; Cockell, C. S.

2017-12-01

Icy moons in the outer solar system are key targets in the search for extra-terrestrial life as there is evidence that they harbour subsurface oceans. Observational evidence of icy moons such as Europa suggest that these likely brine oceans should be composed of chloride and sulphate salts. The effects of the ions that compose these salts on biology and how the interactions between them can create geochemical and geophysical barriers to life are poorly understood. Here we present an in depth study of four microorganisms grown in solutions with varying combinations of the magnesium- chloride- sodium- sulphate ions. We find that the ion composition of the brine solution can have a large effect on growth. Whilst the water activity must be permissible for growth we found that this alone could not predict the effects of the ions on growth, chaotropic effects and ion specific effects influenced by the specific physiology of organisms are also evident. For this reason we conclude that simply knowing which salts are present on icy moons is not sufficient information to determine their potential habitibility. A full sample of any brine ocean would need to be studied to fully determine the potential for biology on these outer solar system satellites.

The therapeutic potential of CRTH2/DP2 beyond allergy and asthma.

PubMed

Jandl, Katharina; Heinemann, Akos

2017-11-01

Prostaglandin (PG) D 2 has been in the focus of research for quite a long time, but its biological effects and its roles in human disease are still not fully characterized. When in 2001 a second major PGD 2 receptor termed chemoattractant receptor homologue expressed on Th2 cells (CRTH2; alternative name DP2) was discovered, diverse investigations started to shed more light on the complex and often controversial actions of the prostaglandin. With various immunomodulating effects, such as induction of migration, activation, and cytokine release of leukocytes observed both in vivo and in vitro, CRTH2 has emerged as a promising target for the treatment of allergic diseases. However, with more and more research being performed on CRTH2, it has also become clear that its biological actions are far more diverse than expected at the beginning. In this review, we aim to summarize the roles that PGD 2 - and CRTH2 in particular - might play in diseases of the central nervous system, kidney, intestine, lung, hair and skin, bone and cartilage, and in cancer. Based on current data we propose that blocking CRTH2 might be a potential therapeutic approach to numerous conditions beyond classical allergic diseases and asthma. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Characterization of the stromatolite microbiome from Little Darby Island, The Bahamas using predictive and whole shotgun metagenomic analysis.

PubMed

Casaburi, Giorgio; Duscher, Alexandrea A; Reid, R Pamela; Foster, Jamie S

2016-05-01

Modern stromatolites represent ideal ecosystems to understand the biological processes required for the precipitation of carbonate due to their long evolutionary history and occurrence in a wide range of habitats. However, most of the prior molecular work on stromatolites has focused on understanding the taxonomic complexity and not fully elucidating the functional capabilities of these systems. Here, we begin to characterize the microbiome associated with stromatolites of Little Darby Island, The Bahamas using predictive metagenomics of the 16S rRNA gene coupled with direct whole shotgun sequencing. The metagenomic analysis of the Little Darby stromatolites revealed many shared taxa and core pathways associated with biologically induced carbonate precipitation, suggesting functional convergence within Bahamian stromatolites. A comparison of the Little Darby stromatolites with other lithifying microbial ecosystems also revealed that although factors, such as geographic location and salinity, do drive some differences within the population, there are extensive similarities within the microbial populations. These results suggest that for stromatolite formation, 'who' is in the community is not as critical as metabolic activities and environmental interactions. Together, these analyses help improve our understanding of the similarities among lithifying ecosystems and provide an important first step in characterizing the shared microbiome of modern stromatolites. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Understanding the spatiotemporal pattern of grazing cattle movement

NASA Astrophysics Data System (ADS)

Zhao, Kun; Jurdak, Raja

2016-08-01

Understanding the drivers of animal movement is significant for ecology and biology. Yet researchers have so far been unable to fully understand these drivers, largely due to low data resolution. In this study, we analyse a high-frequency movement dataset for a group of grazing cattle and investigate their spatiotemporal patterns using a simple two-state ‘stop-and-move’ mobility model. We find that the dispersal kernel in the moving state is best described by a mixture exponential distribution, indicating the hierarchical nature of the movement. On the other hand, the waiting time appears to be scale-invariant below a certain cut-off and is best described by a truncated power-law distribution, suggesting that the non-moving state is governed by time-varying dynamics. We explore possible explanations for the observed phenomena, covering factors that can play a role in the generation of mobility patterns, such as the context of grazing environment, the intrinsic decision-making mechanism or the energy status of different activities. In particular, we propose a new hypothesis that the underlying movement pattern can be attributed to the most probable observable energy status under the maximum entropy configuration. These results are not only valuable for modelling cattle movement but also provide new insights for understanding the underlying biological basis of grazing behaviour.

Characterization of the stromatolite microbiome from Little Darby Island, The Bahamas using predictive and whole shotgun metagenomic analysis

PubMed Central

Casaburi, Giorgio; Duscher, Alexandrea A.; Reid, R. Pamela; Foster, Jamie S.

2018-01-01

Summary Modern stromatolites represent ideal ecosystems to understand the biological processes required for the precipitation of carbonate due to their long evolutionary history and occurrence in a wide range of habitats. However, most of the prior molecular work on stromatolites has focused on understanding the taxonomic complexity and not fully elucidating the functional capabilities of these systems. Here, we begin to characterize the microbiome associated with stromatolites of Little Darby Island, The Bahamas using predictive metagenomics of the 16S rRNA gene coupled with direct whole shotgun sequencing. The metagenomic analysis of the Little Darby stromatolites revealed many shared taxa and core pathways associated with biologically induced carbonate precipitation, suggesting functional convergence within Bahamian stromatolites. A comparison of the Little Darby stromatolites with other lithifying microbial ecosystems also revealed that although factors, such as geographic location and salinity, do drive some differences within the population, there are extensive similarities within the microbial populations. These results suggest that for stromatolite formation, ‘who’ is in the community is not as critical as metabolic activities and environmental interactions. Together, these analyses help improve our understanding of the similarities among lithifying ecosystems and provide an important first step in characterizing the shared microbiome of modern stromatolites. PMID:26471001

Electrobioremediation of oil spills.

PubMed

Daghio, Matteo; Aulenta, Federico; Vaiopoulou, Eleni; Franzetti, Andrea; Arends, Jan B A; Sherry, Angela; Suárez-Suárez, Ana; Head, Ian M; Bestetti, Giuseppina; Rabaey, Korneel

2017-05-01

Annually, thousands of oil spills occur across the globe. As a result, petroleum substances and petrochemical compounds are widespread contaminants causing concern due to their toxicity and recalcitrance. Many remediation strategies have been developed using both physicochemical and biological approaches. Biological strategies are most benign, aiming to enhance microbial metabolic activities by supplying limiting inorganic nutrients, electron acceptors or donors, thus stimulating oxidation or reduction of contaminants. A key issue is controlling the supply of electron donors/acceptors. Bioelectrochemical systems (BES) have emerged, in which an electrical current serves as either electron donor or acceptor for oil spill bioremediation. BES are highly controllable and can possibly also serve as biosensors for real time monitoring of the degradation process. Despite being promising, multiple aspects need to be considered to make BES suitable for field applications including system design, electrode materials, operational parameters, mode of action and radius of influence. The microbiological processes, involved in bioelectrochemical contaminant degradation, are currently not fully understood, particularly in relation to electron transfer mechanisms. Especially in sulfate rich environments, the sulfur cycle appears pivotal during hydrocarbon oxidation. This review provides a comprehensive analysis of the research on bioelectrochemical remediation of oil spills and of the key parameters involved in the process. Copyright © 2017 Elsevier Ltd. All rights reserved.

Method for photo-altering a biological system to improve biological effect

DOEpatents

Hill, Richard A.; Doiron, Daniel R.; Crean, David H.

2000-08-01

Photodynamic therapy is a new adjunctive therapy for filtration surgery that does not use chemotherapy agents or radiation, but uses pharmacologically-active sensitizing compounds to produce a titratable, localized, transient, post operative avascular conjunctiva. A photosensitizing agent in a biological system is selectively activated by delivering the photosensitive agent to the biological system and laser activating only a spatially selected portion of the delivered photosensitive agent. The activated portion of the photosensitive agent reacts with the biological system to obtain a predetermined biological effect. As a result, an improved spatial disposition and effectuation of the biological effect by the photosensitive agent in the biological system is achieved.

Modeling microbial reaction rates in a submarine hydrothermal vent chimney wall

NASA Astrophysics Data System (ADS)

LaRowe, Douglas E.; Dale, Andrew W.; Aguilera, David R.; L'Heureux, Ivan; Amend, Jan P.; Regnier, Pierre

2014-01-01

The fluids emanating from active submarine hydrothermal vent chimneys provide a window into subseafloor processes and, through mixing with seawater, are responsible for steep thermal and compositional gradients that provide the energetic basis for diverse biological communities. Although several models have been developed to better understand the dynamic interplay of seawater, hydrothermal fluid, minerals and microorganisms inside chimney walls, none provide a fully integrated approach to quantifying the biogeochemistry of these hydrothermal systems. In an effort to remedy this, a fully coupled biogeochemical reaction-transport model of a hydrothermal vent chimney has been developed that explicitly quantifies the rates of microbial catalysis while taking into account geochemical processes such as fluid flow, solute transport and oxidation-reduction reactions associated with fluid mixing as a function of temperature. The metabolisms included in the reaction network are methanogenesis, aerobic oxidation of hydrogen, sulfide and methane and sulfate reduction by hydrogen and methane. Model results indicate that microbial catalysis is generally fastest in the hottest habitable portion of the vent chimney (77-102 °C), and methane and sulfide oxidation peak near the seawater-side of the chimney. The fastest metabolisms are aerobic oxidation of H2 and sulfide and reduction of sulfate by H2 with maximum rates of 140, 900 and 800 pmol cm-3 d-1, respectively. The maximum rate of hydrogenotrophic methanogenesis is just under 0.03 pmol cm-3 d-1, the slowest of the metabolisms considered. Due to thermodynamic inhibition, there is no anaerobic oxidation of methane by sulfate (AOM). These simulations are consistent with vent chimney metabolic activity inferred from phylogenetic data reported in the literature. The model developed here provides a quantitative approach to describing the rates of biogeochemical transformations in hydrothermal systems and can be used to constrain the role of microbial activity in the deep subsurface.

A Thermo-Poromechanics Finite Element Model for Predicting Arterial Tissue Fusion

NASA Astrophysics Data System (ADS)

Fankell, Douglas P.

This work provides modeling efforts and supplemental experimental work performed towards the ultimate goal of modeling heat transfer, mass transfer, and deformation occurring in biological tissue, in particular during arterial fusion and cutting. Developing accurate models of these processes accomplishes two goals. First, accurate models would enable engineers to design devices to be safer and less expensive. Second, the mechanisms behind tissue fusion and cutting are widely unknown; models with the ability to accurately predict physical phenomena occurring in the tissue will allow for insight into the underlying mechanisms of the processes. This work presents three aims and the efforts in achieving them, leading to an accurate model of tissue fusion and more broadly the thermo-poromechanics (TPM) occurring within biological tissue. Chapters 1 and 2 provide the motivation for developing accurate TPM models of biological tissue and an overview of previous modeling efforts. In Chapter 3, a coupled thermo-structural finite element (FE) model with the ability to predict arterial cutting is offered. From the work presented in Chapter 3, it became obvious a more detailed model was needed. Chapter 4 meets this need by presenting small strain TPM theory and its implementation in an FE code. The model is then used to simulate thermal tissue fusion. These simulations show the model's promise in predicting the water content and temperature of arterial wall tissue during the fusion process, but it is limited by its small deformation assumptions. Chapters 5-7 attempt to address this limitation by developing and implementing a large deformation TPM FE model. Chapters 5, 6, and 7 present a thermodynamically consistent, large deformation TPM FE model and its ability to simulate tissue fusion. Ultimately, this work provides several methods of simulating arterial tissue fusion and the thermo-poromechanics of biological tissue. It is the first work, to the author's knowledge, to simulate the fully coupled TPM of biological tissue and the first to present a fully coupled large deformation TPM FE model. In doing so, a stepping stone for more advanced modeling of biological tissue has been laid.

20 CFR 404.111 - When we consider a person fully insured based on World War II active military or naval service.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 20 Employees' Benefits 2 2014-04-01 2014-04-01 false When we consider a person fully insured based on World War II active military or naval service. 404.111 Section 404.111 Employees' Benefits SOCIAL... States during World War II; (b) The person died within three years after separation from service and...

20 CFR 404.111 - When we consider a person fully insured based on World War II active military or naval service.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 20 Employees' Benefits 2 2013-04-01 2013-04-01 false When we consider a person fully insured based on World War II active military or naval service. 404.111 Section 404.111 Employees' Benefits SOCIAL... States during World War II; (b) The person died within three years after separation from service and...

20 CFR 404.111 - When we consider a person fully insured based on World War II active military or naval service.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 20 Employees' Benefits 2 2012-04-01 2012-04-01 false When we consider a person fully insured based on World War II active military or naval service. 404.111 Section 404.111 Employees' Benefits SOCIAL... States during World War II; (b) The person died within three years after separation from service and...

Conformational Heterogeneity in a Fully Complementary DNA Three-Way Junction with a GC-Rich Branchpoint.

PubMed

Toulmin, Anita; Baltierra-Jasso, Laura E; Morten, Michael J; Sabir, Tara; McGlynn, Peter; Schröder, Gunnar F; Smith, Brian O; Magennis, Steven W

2017-09-19

DNA three-way junctions (3WJs) are branched structures that serve as important biological intermediates and as components in DNA nanostructures. We recently derived the global structure of a fully complementary 3WJ and found that it contained unpaired bases at the branchpoint, which is consistent with previous observations of branch flexibility and branchpoint reactivity. By combining high-resolution single-molecule Förster resonance energy transfer, molecular modeling, time-resolved ensemble fluorescence spectroscopy, and the first 19 F nuclear magnetic resonance observations of fully complementary 3WJs, we now show that the 3WJ structure can adopt multiple distinct conformations depending upon the sequence at the branchpoint. A 3WJ with a GC-rich branchpoint adopts an open conformation with unpaired bases at the branch and at least one additional conformation with an increased number of base interactions at the branchpoint. This structural diversity has implications for branch interactions and processing in vivo and for technological applications.

A novel fully-humanised 3D skin equivalent to model early melanoma invasion

PubMed Central

Hill, David S; Robinson, Neil D P; Caley, Matthew P; Chen, Mei; O’Toole, Edel A; Armstrong, Jane L; Przyborski, Stefan; Lovat, Penny E

2015-01-01

Metastatic melanoma remains incurable, emphasising the acute need for improved research models to investigate the underlying biological mechanisms mediating tumour invasion and metastasis, and to develop more effective targeted therapies to improve clinical outcome. Available animal models of melanoma do not accurately reflect human disease and current in vitro human skin equivalent models incorporating melanoma cells are not fully representative of the human skin microenvironment. We have developed a robust and reproducible, fully-humanised 3D skin equivalent comprising a stratified, terminally differentiated epidermis and a dermal compartment consisting of fibroblast-generated extracellular matrix. Melanoma cells incorporated into the epidermis were able to invade through the basement membrane and into the dermis, mirroring early tumour invasion in vivo. Comparison of our novel 3D melanoma skin equivalent with melanoma in situ and metastatic melanoma indicates this model accurately recreates features of disease pathology, making it a physiologically representative model of early radial and vertical growth phase melanoma invasion. PMID:26330548

Postinoculation PMPA Treatment, but Not Preinoculation Immunomodulatory Therapy, Protects against Development of Acute Disease Induced by the Unique Simian Immunodeficiency Virus SIVsmmPBj

PubMed Central

Hodge, Shekema; de Rosayro, Juliette; Glenn, Amanda; Ojukwu, Ifeoma C.; Dewhurst, Stephen; McClure, Harold M.; Bischofberger, Norbert; Anderson, Daniel C.; Klumpp, Sherry A.; Novembre, Francis J.

1999-01-01

The fatal disease induced by SIVsmmPBj4 clinically resembles endotoxic shock, with the development of severe gastrointestinal disease. While the exact mechanism of disease induction has not been fully elucidated, aspects of virus biology suggest that immune activation contributes to pathogenesis. These biological characteristics include induction of peripheral blood mononuclear cell (PBMC) proliferation, upregulation of activation markers and Fas ligand expression, and increased levels of apoptosis. To investigate the role of immune activation and viral replication on disease induction, animals infected with SIVsmmPBj14 were treated with one of two drugs: FK-506, a potent immunosuppressive agent, or PMPA, a potent antiretroviral agent. While PBMC proliferation was blocked in vitro with FK-506, pig-tailed macaques treated preinoculation with FK-506 were not protected from acutely lethal disease. However, these animals did show some evidence of modulation of immune activation, including reduced levels of CD25 antigen and FasL expression, as well as lower tissue viral loads. In contrast, macaques treated postinoculation with PMPA were completely protected from the development of acutely lethal disease. Treatment with PMPA beginning as late as 5 days postinfection was able to prevent the PBj syndrome. Plasma and cellular viral loads in PMPA-treated animals were significantly lower than those in untreated controls. Although PMPA-treated animals showed acute lymphopenia due to SIVsmmPBj14 infection, cell subset levels subsequently recovered and returned to normal. Based upon subsequent CD4+ cell counts, the results suggest that very early treatment following retroviral infection can have a significant effect on modifying the subsequent course of disease. These results also suggest that viral replication is an important factor involved in PBJ-induced disease. These studies reinforce the idea that the SIVsmmPBj model system is useful for therapy and vaccine testing. PMID:10482616

[6]-Shogaol attenuates inflammation, cell proliferation via modulate NF-κB and AP-1 oncogenic signaling in 7,12-dimethylbenz[a]anthracene induced oral carcinogenesis.

PubMed

Annamalai, Govindhan; Suresh, Kathiresan

2018-02-01

Nuclear factor-kappaB (NF-κB) and activator protein 1 (AP-1) is a major transcription factor which regulates many biological and pathological processes such as inflammation and cell proliferation, which are major implicates in cancer progression. [6]-Shogaol ([6]-SHO) is a major constituent of ginger, exhibits various biological properties such as anti-oxidants, anti-inflammation and anti-tumor. Recently, we proven that [6]-SHO prevents oral squamous cell carcinoma by activating proapoptotic factors in in vitro and in vivo experimental model. However, the preventive efficacy of [6]-SHO in 7,12-dimethylbenz[a]anthracene (DMBA) induced hamster buccal pouch carcinogenesis (HBP) has not been fully elucidated, so far. Hence, we aimed to investigate the effect of [6]-SHO on inflammation and cell proliferation by inhibiting the translocation of NF-κB and AP-1 in DMBA induced HBP carcinogenesis. In this study, we observed upregulation of inflammatory markers (COX-2, iNOS, TNF-α, interleukin-1 and -6), cell proliferative markers (Cyclin D1, PCNA and Ki-67) and aberrant activation of NF-κB, AP-1, IKKβ, c-jun, c-fos and decreased IκB-α in DMBA induced hamsters. Conversely, oral administration of [6]-SHO strongly inhibited constitutive phosphorylation and degradation of IκB and inhibit phosphorylation of c-jun, c-fos, resulting in inhibition of nuclear translocation of NF-κBp65 and AP-1. Thus, inhibition of NF-κB and AP-1 activation by [6]-SHO attenuates inflammation and cell proliferative response in DMBA induced hamsters. Our finding suggested that [6]-SHO is a novel functional agent capable of preventing DMBA induced inflammation and cell proliferation associated tumorigenesis by modulating multiple signalling molecules. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Knowledge Discovery from Biomedical Ontologies in Cross Domains.

PubMed

Shen, Feichen; Lee, Yugyung

2016-01-01

In recent years, there is an increasing demand for sharing and integration of medical data in biomedical research. In order to improve a health care system, it is required to support the integration of data by facilitating semantic interoperability systems and practices. Semantic interoperability is difficult to achieve in these systems as the conceptual models underlying datasets are not fully exploited. In this paper, we propose a semantic framework, called Medical Knowledge Discovery and Data Mining (MedKDD), that aims to build a topic hierarchy and serve the semantic interoperability between different ontologies. For the purpose, we fully focus on the discovery of semantic patterns about the association of relations in the heterogeneous information network representing different types of objects and relationships in multiple biological ontologies and the creation of a topic hierarchy through the analysis of the discovered patterns. These patterns are used to cluster heterogeneous information networks into a set of smaller topic graphs in a hierarchical manner and then to conduct cross domain knowledge discovery from the multiple biological ontologies. Thus, patterns made a greater contribution in the knowledge discovery across multiple ontologies. We have demonstrated the cross domain knowledge discovery in the MedKDD framework using a case study with 9 primary biological ontologies from Bio2RDF and compared it with the cross domain query processing approach, namely SLAP. We have confirmed the effectiveness of the MedKDD framework in knowledge discovery from multiple medical ontologies.

Knowledge Discovery from Biomedical Ontologies in Cross Domains

PubMed Central

Shen, Feichen; Lee, Yugyung

2016-01-01

In recent years, there is an increasing demand for sharing and integration of medical data in biomedical research. In order to improve a health care system, it is required to support the integration of data by facilitating semantic interoperability systems and practices. Semantic interoperability is difficult to achieve in these systems as the conceptual models underlying datasets are not fully exploited. In this paper, we propose a semantic framework, called Medical Knowledge Discovery and Data Mining (MedKDD), that aims to build a topic hierarchy and serve the semantic interoperability between different ontologies. For the purpose, we fully focus on the discovery of semantic patterns about the association of relations in the heterogeneous information network representing different types of objects and relationships in multiple biological ontologies and the creation of a topic hierarchy through the analysis of the discovered patterns. These patterns are used to cluster heterogeneous information networks into a set of smaller topic graphs in a hierarchical manner and then to conduct cross domain knowledge discovery from the multiple biological ontologies. Thus, patterns made a greater contribution in the knowledge discovery across multiple ontologies. We have demonstrated the cross domain knowledge discovery in the MedKDD framework using a case study with 9 primary biological ontologies from Bio2RDF and compared it with the cross domain query processing approach, namely SLAP. We have confirmed the effectiveness of the MedKDD framework in knowledge discovery from multiple medical ontologies. PMID:27548262

Isotopic studies of metabolic systems by mass spectrometry: using Pascal's triangle to produce biological standards with fully controlled labeling patterns.

PubMed

Millard, Pierre; Massou, Stéphane; Portais, Jean-Charles; Létisse, Fabien

2014-10-21

Mass spectrometry (MS) is widely used for isotopic studies of metabolism in which detailed information about biochemical processes is obtained from the analysis of isotope incorporation into metabolites. The biological value of such experiments is dependent on the accuracy of the isotopic measurements. Using MS, isotopologue distributions are measured from the quantitative analysis of isotopic clusters. These measurements are prone to various biases, which can occur during the experimental workflow and/or MS analysis. The lack of relevant standards limits investigations of the quality of the measured isotopologue distributions. To meet that need, we developed a complete theoretical and experimental framework for the biological production of metabolites with fully controlled and predictable labeling patterns. This strategy is valid for different isotopes and different types of metabolisms and organisms, and was applied to two model microorganisms, Pichia augusta and Escherichia coli, cultivated on (13)C-labeled methanol and acetate as sole carbon source, respectively. The isotopic composition of the substrates was designed to obtain samples in which the isotopologue distribution of all the metabolites should give the binomial coefficients found in Pascal's triangle. The strategy was validated on a liquid chromatography-tandem mass spectrometry (LC-MS/MS) platform by quantifying the complete isotopologue distributions of different intracellular metabolites, which were in close agreement with predictions. This strategy can be used to evaluate entire experimental workflows (from sampling to data processing) or different analytical platforms in the context of isotope labeling experiments.

Fully Integrated Microfluidic Device for Direct Sample-to-Answer Genetic Analysis

NASA Astrophysics Data System (ADS)

Liu, Robin H.; Grodzinski, Piotr

Integration of microfluidics technology with DNA microarrays enables building complete sample-to-answer systems that are useful in many applications such as clinic diagnostics. In this chapter, a fully integrated microfluidic device [1] that consists of microfluidic mixers, valves, pumps, channels, chambers, heaters, and a DNA microarray sensor to perform DNA analysis of complex biological sample solutions is present. This device can perform on-chip sample preparation (including magnetic bead-based cell capture, cell preconcentration and purification, and cell lysis) of complex biological sample solutions (such as whole blood), polymerase chain reaction, DNA hybridization, and electrochemical detection. A few novel microfluidic techniques were developed and employed. A micromix-ing technique based on a cavitation microstreaming principle was implemented to enhance target cell capture from whole blood samples using immunomagnetic beads. This technique was also employed to accelerate DNA hybridization reaction. Thermally actuated paraffin-based microvalves were developed to regulate flows. Electrochemical pumps and thermopneumatic pumps were integrated on the chip to provide pumping of liquid solutions. The device is completely self-contained: no external pressure sources, fluid storage, mechanical pumps, or valves are necessary for fluid manipulation, thus eliminating possible sample contamination and simplifying device operation. Pathogenic bacteria detection from ~mL whole blood samples and single-nucleotide polymorphism analysis directly from diluted blood were demonstrated. The device provides a cost-effective solution to direct sample-to-answer genetic analysis, and thus has a potential impact in the fields of point-of-care genetic analysis, environmental testing, and biological warfare agent detection.

In-Source Fragmentation and the Sources of Partially Tryptic Peptides in Shotgun Proteomics

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

Kim, Jong-Seo; Monroe, Matthew E.; Camp, David G.

2013-02-01

Partially tryptic peptides are often identified in shotgun proteomics using trypsin as the proteolytic enzyme; however, it has been controversial regarding the sources of such partially tryptic peptides. Herein we investigate the impact of in-source fragmentation on shotgun proteomics using three biological samples, including a standard protein mixture, a mouse brain tissue homogenate, and a mouse plasma sample. Since the in-source fragments of a peptide retain the same elution time with its parent fully tryptic peptide, the partially tryptic peptides from in-source fragmentation can be distinguished from the other partially tryptic peptides by plotting the observed retention times against themore » computationally predicted retention times. Most partially tryptic in-source fragmentation artifacts were misaligned from the linear distribution of fully tryptic peptides. The impact of in-source fragmentation on peptide identifications was clearly significant in a less complex sample such as a standard protein digest, where ~60 % of unique peptides were observed as partially tryptic peptides from in-source fragmentation. In mouse brain or mouse plasma samples, in-source fragmentation contributed to 1-3 % of all identified peptides. The other major source of partially tryptic peptides in complex biological samples is presumably proteolytic processing by endogenous proteases in the samples. By filtering out the in-source fragmentation artifacts from the identified partially tryptic or non-tryptic peptides, it is possible to directly survey in-vivo proteolytic processing in biological samples such as blood plasma.« less

Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium.

PubMed

Ellis, Matthew J; Gillette, Michael; Carr, Steven A; Paulovich, Amanda G; Smith, Richard D; Rodland, Karin K; Townsend, R Reid; Kinsinger, Christopher; Mesri, Mehdi; Rodriguez, Henry; Liebler, Daniel C

2013-10-01

The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium is applying the latest generation of proteomic technologies to genomically annotated tumors from The Cancer Genome Atlas (TCGA) program, a joint initiative of the NCI and the National Human Genome Research Institute. By providing a fully integrated accounting of DNA, RNA, and protein abnormalities in individual tumors, these datasets will illuminate the complex relationship between genomic abnormalities and cancer phenotypes, thus producing biologic insights as well as a wave of novel candidate biomarkers and therapeutic targets amenable to verification using targeted mass spectrometry methods. ©2013 AACR.

Some biological reflections on the concept of life.

PubMed

Pennazio, Sergio

2010-01-01

Life is the natural phenomenon that has always aroused the largest interest of philosophers, theologians and scientists, on which a new science--biology--was founded two century ago just for throwing light on its mechanisms. As the pre-Hellenic culture was not able to separate distinctly philosophy from science, life was interpreted as a spurious flurry of the activity of Nature, in which religion, magic and science were interlaced in an intricate way. The Hippocratic medicine constituted the first attempt to focus attention on life by collecting some biological knowledge in order to maintain man's health. All the subsequent physiologists (from the Hellenic to the Latin period) benefited from the precepts of the Corpus Hippocraticum as long as the Christian religion imposed its theological rules that favoured the question relative to soul ever more closely interlaced with the physiology of body. The concept of life became therefore subjected to a number of opposite theories with strong prevalence of metaphysical conjectures until the 19th century but, in spite of this imposition, splendid successes were achieved by physiologists and naturalists such as Harvey, Descartes, Haller, Malpighi, Spallanzani, Wolff, and others, who laid the foundation of a biology that has Lamarck as promoter. The importance of Lamarck's biology came from the release from metaphysics with the introduction of physical and structural concepts which permeated the experimental biology to come. Three main events characterised the biology of the 19th century: i) the interplay of the new chemistry with biology, ii) the cell theory, iii) the concept of metabolism. These events led biology to the 20th century, the era of biochemistry and molecular genetics. The discoveries relative to metabolism characterised the first half of this century, while the second half was witness to the internal mechanisms regulating the life of cells, perhaps the most advanced success of the biology of all time. Today, the cell is not only the centre of a metabolism that, on the whole, may be regarded as the material basis of life, but it is also the central control of communication in response to a great number of stimuli. May life be considered on the basis of biochemical and molecular genetical bases? The answer to this question depends on the credo of everybody. In any case, these mechanisms may explain "what" life is, whereas "why" life exists is still matter of philosophy, and then a fully open question.

Gamma oscillations in a nonlinear regime: a minimal model approach using heterogeneous integrate-and-fire networks.

PubMed

Bathellier, Brice; Carleton, Alan; Gerstner, Wulfram

2008-12-01

Fast oscillations and in particular gamma-band oscillation (20-80 Hz) are commonly observed during brain function and are at the center of several neural processing theories. In many cases, mathematical analysis of fast oscillations in neural networks has been focused on the transition between irregular and oscillatory firing viewed as an instability of the asynchronous activity. But in fact, brain slice experiments as well as detailed simulations of biological neural networks have produced a large corpus of results concerning the properties of fully developed oscillations that are far from this transition point. We propose here a mathematical approach to deal with nonlinear oscillations in a network of heterogeneous or noisy integrate-and-fire neurons connected by strong inhibition. This approach involves limited mathematical complexity and gives a good sense of the oscillation mechanism, making it an interesting tool to understand fast rhythmic activity in simulated or biological neural networks. A surprising result of our approach is that under some conditions, a change of the strength of inhibition only weakly influences the period of the oscillation. This is in contrast to standard theoretical and experimental models of interneuron network gamma oscillations (ING), where frequency tightly depends on inhibition strength, but it is similar to observations made in some in vitro preparations in the hippocampus and the olfactory bulb and in some detailed network models. This result is explained by the phenomenon of suppression that is known to occur in strongly coupled oscillating inhibitory networks but had not yet been related to the behavior of oscillation frequency.

The histone modifications governing TFF1 transcription mediated by estrogen receptor.

PubMed

Li, Yanyan; Sun, Luyang; Zhang, Yu; Wang, Dandan; Wang, Feng; Liang, Jing; Gui, Bin; Shang, Yongfeng

2011-04-22

Transcription regulation by histone modifications is a major contributing factor to the structural and functional diversity in biology. These modifications are encrypted as histone codes or histone languages and function to establish and maintain heritable epigenetic codes that define the identity and the fate of the cell. Despite recent advances revealing numerous histone modifications associated with transcription regulation, how such modifications dictate the process of transcription is not fully understood. Here we describe spatial and temporal analyses of the histone modifications that are introduced during estrogen receptor α (ERα)-activated transcription. We demonstrated that aborting RNA polymerase II caused a disruption of the histone modifications that are associated with transcription elongation but had a minimal effect on modifications deposited during transcription initiation. We also found that the histone H3S10 phosphorylation mark is catalyzed by mitogen- and stress-activated protein kinase 1 (MSK1) and is recognized by a 14-3-3ζ/14-3-3ε heterodimer through its interaction with H3K4 trimethyltransferase SMYD3 and the p52 subunit of TFIIH. We showed that H3S10 phosphorylation is a prerequisite for H3K4 trimethylation. In addition, we demonstrated that SET8/PR-Set7/KMT5A is required for ERα-regulated transcription and its catalyzed H4K20 monomethylation is implicated in both transcription initiation and elongation. Our experiments provide a relatively comprehensive analysis of histone modifications associated with ERα-regulated transcription and define the biological meaning of several key components of the histone code that governs ERα-regulated transcription.

The Complexity of Fungal β-Glucan in Health and Disease: Effects on the Mononuclear Phagocyte System

PubMed Central

Camilli, Giorgio; Tabouret, Guillaume; Quintin, Jessica

2018-01-01

β-glucan, the most abundant fungal cell wall polysaccharide, has gained much attention from the scientific community in the last few decades for its fascinating but not yet fully understood immunobiology. Study of this molecule has been motivated by its importance as a pathogen-associated molecular pattern upon fungal infection as well as by its promising clinical utility as biological response modifier for the treatment of cancer and infectious diseases. Its immune effect is attributed to the ability to bind to different receptors expressed on the cell surface of phagocytic and cytotoxic innate immune cells, including monocytes, macrophages, neutrophils, and natural killer cells. The characteristics of the immune responses generated depend on the cell types and receptors involved. Size and biochemical composition of β-glucans isolated from different sources affect their immunomodulatory properties. The variety of studies using crude extracts of fungal cell wall rather than purified β-glucans renders data difficult to interpret. A better understanding of the mechanisms of purified fungal β-glucan recognition, downstream signaling pathways, and subsequent immune regulation activated, is, therefore, essential not only to develop new antifungal therapy but also to evaluate β-glucan as a putative anti-infective and antitumor mediator. Here, we briefly review the complexity of interactions between fungal β-glucans and mononuclear phagocytes during fungal infections. Furthermore, we discuss and present available studies suggesting how different fungal β-glucans exhibit antitumor and antimicrobial activities by modulating the biologic responses of mononuclear phagocytes, which make them potential candidates as therapeutic agents. PMID:29755450

Extracellular matrix glycation and receptor for advanced glycation end-products activation: a missing piece in the puzzle of the association between diabetes and cancer.

PubMed

Rojas, Armando; Añazco, Carolina; González, Ileana; Araya, Paulina

2018-04-05

A growing body of epidemiologic evidence suggests that people with diabetes are at a significantly higher risk of many forms of cancer. However, the molecular mechanisms underlying this association are not fully understood. Cancer cells are surrounded by a complex milieu, also known as tumor microenvironment, which contributes to the development and metastasis of tumors. Of note, one of the major components of this niche is the extracellular matrix (ECM), which becomes highly disorganized during neoplastic progression, thereby stimulating cancer cell transformation, growth and spread. One of the consequences of chronic hyperglycemia, the most frequently observed sign of diabetes and the etiological source of diabetes complications, is the irreversible glycation and oxidation of proteins and lipids leading to the formation of the advanced glycation end-products (AGEs). These compounds may covalently crosslink and biochemically modify structure and functions of many proteins, and AGEs accumulation is particularly high in long-living proteins with low biological turnover, features that are shared by most, if not all, ECM proteins. AGEs-modified proteins are recognized by AGE-binding proteins, and thus glycated ECM components have the potential to trigger Receptor for advanced glycation end-products-dependent mechanisms. The biological consequence of receptor for advanced glycation end-products activation mechanisms seems to be connected, in different ways, to drive some hallmarks of cancer onset and tumor growth. The present review intends to highlight the potential impact of ECM glycation on tumor progression by triggering receptor for advanced glycation end-products-mediated mechanisms.

Retinoids and rexinoids in cancer prevention: from laboratory to clinic.

PubMed

Uray, Iván P; Dmitrovsky, Ethan; Brown, Powel H

2016-02-01

Early in the age of modern medicine the consequences of vitamin A deficiency drew attention to the fundamental link between retinoid-dependent homeostatic regulation and malignant hyperproliferative diseases. The term "retinoid" includes a handful of endogenous and a large group of synthetic derivatives of vitamin A. These multifunctional lipid-soluble compounds directly regulate target genes of specific biological functions and critical signaling pathways to orchestrate complex functions from vision to development, metabolism, and inflammation. Many of the retinoid activities on the cellular level have been well characterized and translated to the regulation of processes like differentiation and cell death, which play critical roles in the outcome of malignant transformation of tissues. In fact, retinoid-based differentiation therapy of acute promyelocytic leukemia was one of the first successful examples of molecularly targeted treatment strategies. The selectivity, high receptor binding affinity and the ability of retinoids to directly modulate gene expression programs present a distinct pharmacological opportunity for cancer treatment and prevention. However, to fully exploit their potential, the adverse effects of retinoids must be averted. In this review we provide an overview of the biology of retinoid (activated by nuclear retinoic acid receptors [RARs]) and rexinoid (engaged by nuclear retinoid X receptors [RXRs]) action concluded from a long line of preclinical studies, in relation to normal and transformed states of cells. We will also discuss the past and current uses of retinoids in the treatment of malignancies, the potential of rexinoids in the cancer prevention setting, both as single agents and in combinations. Copyright © 2016 Elsevier Inc. All rights reserved.

A characteristic chondroitin sulfate trisaccharide unit with a sulfated fucose branch exhibits neurite outgrowth-promoting activity: Novel biological roles of fucosylated chondroitin sulfates isolated from the sea cucumber Apostichopus japonicus.

PubMed

Shida, Miharu; Mikami, Tadahisa; Tamura, Jun-Ichi; Kitagawa, Hiroshi

2017-06-03

Chondroitin sulfate (CS) is a class of sulfated glycosaminoglycan (GAG) chains that consist of repeating disaccharide unit composed of glucuronic acid (GlcA) and N-acetylgalactosamine (GalNAc). CS chains are found throughout the pericellular and extracellular spaces and contribute to the formation of functional microenvironments for numerous biological events. However, their structure-function relations remain to be fully characterized. Here, a fucosylated CS (FCS) was isolated from the body wall of the sea cucumber Apostichopus japonicus. Its promotional effects on neurite outgrowth were assessed by using isolated polysaccharides and the chemically synthesized FCS trisaccharide β-D-GalNAc(4,6-O-disulfate) (1-4)[α-l-fucose (2,4-O-disulfate) (1-3)]-β-D-GlcA. FCS polysaccharides contained the E-type disaccharide unit GlcA-GalNAc(4,6-O-disulfate) as a CS major backbone structure and carried distinct sulfated fucose branches. Despite their relatively lower abundance of E unit, FCS polysaccharides exhibited neurite outgrowth-promoting activity comparable to squid cartilage-derived CS-E polysaccharides, which are characterized by their predominant E units, suggesting potential roles of the fucose branch in neurite outgrowth. Indeed, the chemically synthesized FCS trisaccharide was as effective as CS-E tetrasaccharide in stimulating neurite elongation in vitro. In conclusion, FCS trisaccharide units with 2,4-O-disulfated fucose branches may provide new insights into understanding the structure-function relations of CS chains. Copyright © 2017 Elsevier Inc. All rights reserved.

The Complexity of Fungal β-Glucan in Health and Disease: Effects on the Mononuclear Phagocyte System.

PubMed

Camilli, Giorgio; Tabouret, Guillaume; Quintin, Jessica

2018-01-01

β-glucan, the most abundant fungal cell wall polysaccharide, has gained much attention from the scientific community in the last few decades for its fascinating but not yet fully understood immunobiology. Study of this molecule has been motivated by its importance as a pathogen-associated molecular pattern upon fungal infection as well as by its promising clinical utility as biological response modifier for the treatment of cancer and infectious diseases. Its immune effect is attributed to the ability to bind to different receptors expressed on the cell surface of phagocytic and cytotoxic innate immune cells, including monocytes, macrophages, neutrophils, and natural killer cells. The characteristics of the immune responses generated depend on the cell types and receptors involved. Size and biochemical composition of β-glucans isolated from different sources affect their immunomodulatory properties. The variety of studies using crude extracts of fungal cell wall rather than purified β-glucans renders data difficult to interpret. A better understanding of the mechanisms of purified fungal β-glucan recognition, downstream signaling pathways, and subsequent immune regulation activated, is, therefore, essential not only to develop new antifungal therapy but also to evaluate β-glucan as a putative anti-infective and antitumor mediator. Here, we briefly review the complexity of interactions between fungal β-glucans and mononuclear phagocytes during fungal infections. Furthermore, we discuss and present available studies suggesting how different fungal β-glucans exhibit antitumor and antimicrobial activities by modulating the biologic responses of mononuclear phagocytes, which make them potential candidates as therapeutic agents.

Sustainable mechanical biological treatment of solid waste in urbanized areas with low recycling rates.

PubMed

Trulli, Ettore; Ferronato, Navarro; Torretta, Vincenzo; Piscitelli, Massimiliano; Masi, Salvatore; Mancini, Ignazio

2018-01-01

Landfill is still the main technological facility used to treat and dispose municipal solid waste (MSW) worldwide. In developing countries, final dumping is applied without environmental monitoring and soil protection since solid waste is mostly sent to open dump sites while, in Europe, landfilling is considered as the last option since reverse logistic approaches or energy recovery are generally encouraged. However, many regions within the European Union continue to dispose of MSW to landfill, since modern facilities have not been introduced owing to unreliable regulations or financial sustainability. In this paper, final disposal activities and pre-treatment operations in an area in southern Italy are discussed, where final disposal is still the main option for treating MSW and the recycling rate is still low. Mechanical biological treatment (MBT) facilities are examined in order to evaluate the organic stabilization practices applied for MSW and the efficiencies in refuse derived fuel production, organic waste stabilization and mass reduction. Implementing MBT before landfilling the environmental impact and waste mass are reduced, up to 30%, since organic fractions are stabilized resulting an oxygen uptake rate less than 1600 mgO 2  h -1  kg -1 VS , and inorganic materials are exploited. Based on experimental data, this work examines MBT application in contexts where recycling and recovery activities have not been fully developed. The evidence of this study led to state that the introduction of MBT facilities is recommended for developing regions with high putrescible waste production in order to decrease environmental pollution and enhance human healthy. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evolution in a fully constituted world: Charles Darwin's debts towards a static world in the Origin of Species (1859).

PubMed

Delisle, Richard G

2014-01-01

The Transformist Revolution was a long intellectual quest that has expanded from the 18th century to today. One area of inquiry after another has confronted the necessity of recasting its object of study under an evolutionary view: human history, geology, biology, astronomy, etc. No single scholar fully managed to make the transition from a static worldview to an evolutionary one during his or her own lifetime; Charles Darwin is no exception. Many versions of evolutionism were proposed during this revolution, versions offering all sorts of compromises between old and new views. Not sufficiently acknowledged in the historiography is the profoundness of Darwin's debts towards the old static view. As a dual child of the Scientific Revolution and natural theology, Darwin inherited key concepts such as stability, completeness, timelessness, unity, permanence, and uniformity. Darwin took these concepts into consideration while erecting his theory of biological evolution. Unsurprisingly, this theory was ill-equipped to embrace the directionality, historicity, and novelty that came along with a new evolutionary world. This paper analyses a fundamental idea at the heart of Darwin's Origins of Species (1859) inherited from a static, stable, and machine-like conception of the world: the notion of a fully constituted world. Although in principle antithetical to the very idea of evolution itself, Darwin found a way to 'loosen up' this notion so as to retain it in a way that allows for some kind of evolutionary change. Copyright © 2014 Elsevier Ltd. All rights reserved.

Fully automatic characterization and data collection from crystals of biological macromolecules

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

Svensson, Olof; Malbet-Monaco, Stéphanie; Popov, Alexander

A fully automatic system has been developed that performs X-ray centring and characterization of, and data collection from, large numbers of cryocooled crystals without human intervention. Considerable effort is dedicated to evaluating macromolecular crystals at synchrotron sources, even for well established and robust systems. Much of this work is repetitive, and the time spent could be better invested in the interpretation of the results. In order to decrease the need for manual intervention in the most repetitive steps of structural biology projects, initial screening and data collection, a fully automatic system has been developed to mount, locate, centre to themore » optimal diffraction volume, characterize and, if possible, collect data from multiple cryocooled crystals. Using the capabilities of pixel-array detectors, the system is as fast as a human operator, taking an average of 6 min per sample depending on the sample size and the level of characterization required. Using a fast X-ray-based routine, samples are located and centred systematically at the position of highest diffraction signal and important parameters for sample characterization, such as flux, beam size and crystal volume, are automatically taken into account, ensuring the calculation of optimal data-collection strategies. The system is now in operation at the new ESRF beamline MASSIF-1 and has been used by both industrial and academic users for many different sample types, including crystals of less than 20 µm in the smallest dimension. To date, over 8000 samples have been evaluated on MASSIF-1 without any human intervention.« less

Making evolutionary biology a basic science for medicine

PubMed Central

Nesse, Randolph M.; Bergstrom, Carl T.; Ellison, Peter T.; Flier, Jeffrey S.; Gluckman, Peter; Govindaraju, Diddahally R.; Niethammer, Dietrich; Omenn, Gilbert S.; Perlman, Robert L.; Schwartz, Mark D.; Thomas, Mark G.; Stearns, Stephen C.; Valle, David

2010-01-01

New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to use them fully. This article summarizes suggestions from several groups that have considered how evolutionary biology can be useful in medicine, what physicians should learn about it, and when and how they should learn it. Our general conclusion is that evolutionary biology is a crucial basic science for medicine. In addition to looking at established evolutionary methods and topics, such as population genetics and pathogen evolution, we highlight questions about why natural selection leaves bodies vulnerable to disease. Knowledge about evolution provides physicians with an integrative framework that links otherwise disparate bits of knowledge. It replaces the prevalent view of bodies as machines with a biological view of bodies shaped by evolutionary processes. Like other basic sciences, evolutionary biology needs to be taught both before and during medical school. Most introductory biology courses are insufficient to establish competency in evolutionary biology. Premedical students need evolution courses, possibly ones that emphasize medically relevant aspects. In medical school, evolutionary biology should be taught as one of the basic medical sciences. This will require a course that reviews basic principles and specific medical applications, followed by an integrated presentation of evolutionary aspects that apply to each disease and organ system. Evolutionary biology is not just another topic vying for inclusion in the curriculum; it is an essential foundation for a biological understanding of health and disease. PMID:19918069

Evolution in health and medicine Sackler colloquium: Making evolutionary biology a basic science for medicine.

PubMed

Nesse, Randolph M; Bergstrom, Carl T; Ellison, Peter T; Flier, Jeffrey S; Gluckman, Peter; Govindaraju, Diddahally R; Niethammer, Dietrich; Omenn, Gilbert S; Perlman, Robert L; Schwartz, Mark D; Thomas, Mark G; Stearns, Stephen C; Valle, David

2010-01-26

New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to use them fully. This article summarizes suggestions from several groups that have considered how evolutionary biology can be useful in medicine, what physicians should learn about it, and when and how they should learn it. Our general conclusion is that evolutionary biology is a crucial basic science for medicine. In addition to looking at established evolutionary methods and topics, such as population genetics and pathogen evolution, we highlight questions about why natural selection leaves bodies vulnerable to disease. Knowledge about evolution provides physicians with an integrative framework that links otherwise disparate bits of knowledge. It replaces the prevalent view of bodies as machines with a biological view of bodies shaped by evolutionary processes. Like other basic sciences, evolutionary biology needs to be taught both before and during medical school. Most introductory biology courses are insufficient to establish competency in evolutionary biology. Premedical students need evolution courses, possibly ones that emphasize medically relevant aspects. In medical school, evolutionary biology should be taught as one of the basic medical sciences. This will require a course that reviews basic principles and specific medical applications, followed by an integrated presentation of evolutionary aspects that apply to each disease and organ system. Evolutionary biology is not just another topic vying for inclusion in the curriculum; it is an essential foundation for a biological understanding of health and disease.

When Do Pictures Help Learning from Expository Text? Multimedia and Modality Effects in Primary Schools

ERIC Educational Resources Information Center

Herrlinger, Simone; Höffler, Tim N.; Opfermann, Maria; Leutner, Detlev

2017-01-01

Adding pictures to a text is very common in today's education and might be especially beneficial for elementary school children, whose abilities to read and understand pure text have not yet been fully developed. Our study examined whether adding pictures supports learning of a biology text in fourth grade and whether the text modality (spoken or…

Student Positions on the Relationship between Evolution and Creation: What Kinds of Changes Occur and for What Reasons?

ERIC Educational Resources Information Center

Yasri, Pratchayapong; Mancy, Rebecca

2016-01-01

Student positions on the relationship between biological evolution and divine creation have been examined in a range of contexts, and although there is evidence that students can change their position on the relationship over a period of study, these changes have not been well characterized or fully quantified. To investigate student changes in…

Enzyme dynamics and engineering: one step at a time.

PubMed

Tokuriki, Nobuhiko; Jackson, Colin J

2014-10-23

Although protein dynamics are accepted as being essential for enzyme function, their effects are not fully understood. In this issue of Chemistry and Biology, Gobeil and coworkers describe how engineered changes in the millisecond motions of a mutant TEM-1 β-lactamase do not significantly affect substrate turnover. This mutational robustness has implications for protein engineering and design strategies.

Distinct effects of thrombopoietin depending on a threshold level of activated Mpl in BaF-3 cells.

PubMed

Millot, Gaël A; Vainchenker, William; Duménil, Dominique; Svinarchuk, Fédor

2002-06-01

Thrombopoietin (TPO) plays a critical role in megakaryopoiesis through binding to its receptor Mpl. This involves activation of various intracellular signaling pathways, including phosphoinositide 3-kinase (PI3K) and the mitogen-activated protein kinase (MAPK) pathways. Their precise role in TPO-mediated proliferation, survival and differentiation is not fully understood. In the present study, we show that TPO induces different biological responses in Mpl-transduced BaF-3 cells, depending on the cell surface density of Mpl and the resulting activation level of signaling pathways. TPO mediates cell proliferation in cells expressing high levels of Mpl but only mediates survival without proliferation in cells expressing low levels of the receptor. By using the kinase inhibitors PD98059 and LY294002, we further showed that the activation level of the PI3K and MAPK p42/44 pathways is a determining factor for the proliferative effect. In cells expressing low levels of Mpl, the survival effect was strongly dependent on the activation level of the PI3K/AKT, but not the MAPK p42/44 pathway. Moreover, this effect was correlated with the phosphorylation level of BAD but not with the expression level of Bcl-X(L). However, PI3K pathway inhibition did not increase apoptosis when BaF-3 cells proliferated in response to TPO, indicating a compensating mechanism from other Mpl signaling pathways in this case.

Programmable Hydrogel Ionic Circuits for Biologically Matched Electronic Interfaces.

PubMed

Zhao, Siwei; Tseng, Peter; Grasman, Jonathan; Wang, Yu; Li, Wenyi; Napier, Bradley; Yavuz, Burcin; Chen, Ying; Howell, Laurel; Rincon, Javier; Omenetto, Fiorenzo G; Kaplan, David L

2018-06-01

The increased need for wearable and implantable medical devices has driven the demand for electronics that interface with living systems. Current bioelectronic systems have not fully resolved mismatches between engineered circuits and biological systems, including the resulting pain and damage to biological tissues. Here, salt/poly(ethylene glycol) (PEG) aqueous two-phase systems are utilized to generate programmable hydrogel ionic circuits. High-conductivity salt-solution patterns are stably encapsulated within PEG hydrogel matrices using salt/PEG phase separation, which route ionic current with high resolution and enable localized delivery of electrical stimulation. This strategy allows designer electronics that match biological systems, including transparency, stretchability, complete aqueous-based connective interface, distribution of ionic electrical signals between engineered and biological systems, and avoidance of tissue damage from electrical stimulation. The potential of such systems is demonstrated by generating light-emitting diode (LED)-based displays, skin-mounted electronics, and stimulators that deliver localized current to in vitro neuron cultures and muscles in vivo with reduced adverse effects. Such electronic platforms may form the basis of future biointegrated electronic systems. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Characterization of persistent colors and decolorization of effluent from biologically treated cellulosic ethanol production wastewater.

PubMed

Shan, Lili; Liu, Junfeng; Yu, Yanling; Ambuchi, John J; Feng, Yujie

2016-05-01

The high chroma of cellulosic ethanol production wastewater poses a serious environmental concern; however, color-causing compounds are still not fully clear. The characteristics of the color compounds and decolorization of biologically treated effluent by electro-catalytic oxidation were investigated in this study. Excitation-emission matrix (EEM), fourier transform infrared spectrometer (FTIR), UV-Vis spectra, and ultrafiltration (UF) fractionation were used to analyze color compounds. High chroma of wastewater largely comes from humic materials, which exhibited great fluorescence proportion (67.1 %) in the biologically treated effluent. Additionally, the color compounds were mainly distributed in the molecular weight fractions with 3-10 and 10-30 kDa, which contributed 53.5 and 34.6 % of the wastewater color, respectively. Further decolorization of biologically treated effluent by electro-catalytic oxidation was investigated, and 98.3 % of color removal accompanied with 97.3 % reduction of humic acid-like matter was achieved after 180 min. The results presented herein will facilitate the development of a well decolorization for cellulosic ethanol production wastewater and better understanding of the biological fermentation.

Exploration of the molecular basis of blast injury in a biofidelic model of traumatic brain injury

NASA Astrophysics Data System (ADS)

Thielen, P.; Mehoke, T.; Gleason, J.; Iwaskiw, A.; Paulson, J.; Merkle, A.; Wester, B.; Dymond, J.

2018-01-01

Biological response to blast overpressure is complex and results in various and potentially non-concomitant acute and long-term deficits to exposed individuals. Clinical links between blast severity and injury outcomes remain elusive and have yet to be fully described, resulting in a critical inability to develop associated protection and mitigation strategies. Further, experimental models frequently fail to reproduce observed physiological phenomena and/or introduce artifacts that confound analysis and reproducibility. New models are required that employ consistent mechanical inputs, scale with biological analogs and known clinical data, and permit high-throughput examination of biological responses for a range of environmental and battlefield- relevant exposures. Here we describe a novel, biofidelic headform capable of integrating complex biological samples for blast exposure studies. We additionally demonstrate its utility in detecting acute transcriptional responses in the model organism Caenorhabditis elegans after exposure to blast overpressure. This approach enables correlation between mechanical exposure and biological outcome, permitting both the enhancement of existing surrogate and computational models and the high-throughput biofidelic testing of current and future protection systems.

Design and implementation of an automated compound management system in support of lead optimization.

PubMed

Quintero, Catherine; Kariv, Ilona

2009-06-01

To meet the needs of the increasingly rapid and parallelized lead optimization process, a fully integrated local compound storage and liquid handling system was designed and implemented to automate the generation of assay-ready plates directly from newly submitted and cherry-picked compounds. A key feature of the system is the ability to create project- or assay-specific compound-handling methods, which provide flexibility for any combination of plate types, layouts, and plate bar-codes. Project-specific workflows can be created by linking methods for processing new and cherry-picked compounds and control additions to produce a complete compound set for both biological testing and local storage in one uninterrupted workflow. A flexible cherry-pick approach allows for multiple, user-defined strategies to select the most appropriate replicate of a compound for retesting. Examples of custom selection parameters include available volume, compound batch, and number of freeze/thaw cycles. This adaptable and integrated combination of software and hardware provides a basis for reducing cycle time, fully automating compound processing, and ultimately increasing the rate at which accurate, biologically relevant results can be produced for compounds of interest in the lead optimization process.

Hitchhiker's guide to multi-dimensional plant pathology.

PubMed

Saunders, Diane G O

2015-02-01

Filamentous pathogens pose a substantial threat to global food security. One central question in plant pathology is how pathogens cause infection and manage to evade or suppress plant immunity to promote disease. With many technological advances over the past decade, including DNA sequencing technology, an array of new tools has become embedded within the toolbox of next-generation plant pathologists. By employing a multidisciplinary approach plant pathologists can fully leverage these technical advances to answer key questions in plant pathology, aimed at achieving global food security. This review discusses the impact of: cell biology and genetics on progressing our understanding of infection structure formation on the leaf surface; biochemical and molecular analysis to study how pathogens subdue plant immunity and manipulate plant processes through effectors; genomics and DNA sequencing technologies on all areas of plant pathology; and new forms of collaboration on accelerating exploitation of big data. As we embark on the next phase in plant pathology, the integration of systems biology promises to provide a holistic perspective of plant–pathogen interactions from big data and only once we fully appreciate these complexities can we design truly sustainable solutions to preserve our resources.

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2.

PubMed

Mi, Huaiyu; Schreiber, Falk; Moodie, Stuart; Czauderna, Tobias; Demir, Emek; Haw, Robin; Luna, Augustin; Le Novère, Nicolas; Sorokin, Anatoly; Villéger, Alice

2015-09-04

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Activity Flow language represents the influences of activities among various entities within a network. Unlike SBGN PD and ER that focus on the entities and their relationships with others, SBGN AF puts the emphasis on the functions (or activities) performed by the entities, and their effects to the functions of the same or other entities. The nodes (elements) describe the biological activities of the entities, such as protein kinase activity, binding activity or receptor activity, which can be easily mapped to Gene Ontology molecular function terms. The edges (connections) provide descriptions of relationships (or influences) between the activities, e.g., positive influence and negative influence. Among all three languages of SBGN, AF is the closest to signaling pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

A biotherapy based on PSCs-in-3D spheroid-ameliorated biologics depletes in vivo cancer-sustaining stem cells

PubMed Central

Zhou, Tianlin; Li, Meng; Wen, Yanjun; Lin, Xiaojuan; Xiang, Rong; Chen, Xiancheng

2015-01-01

CSCs are able to survive routine anticancer procedures and peripheral-immune attack. Here we develop and detail a framework of CSC elimination governed by 3D-biologics. Pluripotent cells-engineered 3D-biologics (PMSB) and control non-3D-biologics were prepared from placenta-based somatic stem cells (PSCs) and inoculated respectively into senile hosts bearing progressive mammary, lung, colon carcinomas and melanoma. We demonstrate that PMSB evokes in vivo central-immune microenvironment with subsequent re-expression of thymosin-α1 ~ β4 in thymic cortex-medulla borderline for rapid MHC-unrestricted renewal of γδT-dominated immunocompetence. The post-renewal γδT-subsets could accurately bind and drive CSCs into apoptosis. Finally, with central/peripheral integral microenvironment renewal and TERT/Wnt/β-catenin pathway blockade, the CSC-subsets are fully depleted, leading to substantial cure of diverse tumors by PMSB inoculation (P < 0.01), yet not by non-3D-biologics. Thus, our study may contribute to open up a new avenue for tumor remission via pluripotent cells-engineered 3D-biologics addressing quick renewal of central-thymus and peripheral immune-microenvironment. PMID:26512920

Exploring the MACH Model’s Potential as a Metacognitive Tool to Help Undergraduate Students Monitor Their Explanations of Biological Mechanisms

PubMed Central

Trujillo, Caleb M.; Anderson, Trevor R.; Pelaez, Nancy J.

2016-01-01

When undergraduate biology students learn to explain biological mechanisms, they face many challenges and may overestimate their understanding of living systems. Previously, we developed the MACH model of four components used by expert biologists to explain mechanisms: Methods, Analogies, Context, and How. This study explores the implementation of the model in an undergraduate biology classroom as an educational tool to address some of the known challenges. To find out how well students’ written explanations represent components of the MACH model before and after they were taught about it and why students think the MACH model was useful, we conducted an exploratory multiple case study with four interview participants. We characterize how two students explained biological mechanisms before and after a teaching intervention that used the MACH components. Inductive analysis of written explanations and interviews showed that MACH acted as an effective metacognitive tool for all four students by helping them to monitor their understanding, communicate explanations, and identify explanatory gaps. Further research, though, is needed to more fully substantiate the general usefulness of MACH for promoting students’ metacognition about their understanding of biological mechanisms. PMID:27252295

Gromita: a fully integrated graphical user interface to gromacs 4.

PubMed

Sellis, Diamantis; Vlachakis, Dimitrios; Vlassi, Metaxia

2009-09-07

Gromita is a fully integrated and efficient graphical user interface (GUI) to the recently updated molecular dynamics suite Gromacs, version 4. Gromita is a cross-platform, perl/tcl-tk based, interactive front end designed to break the command line barrier and introduce a new user-friendly environment to run molecular dynamics simulations through Gromacs. Our GUI features a novel workflow interface that guides the user through each logical step of the molecular dynamics setup process, making it accessible to both advanced and novice users. This tool provides a seamless interface to the Gromacs package, while providing enhanced functionality by speeding up and simplifying the task of setting up molecular dynamics simulations of biological systems. Gromita can be freely downloaded from http://bio.demokritos.gr/gromita/.

A systems approach to bone pathophysiology.

PubMed

Weiss, Aaron J; Lipshtat, Azi; Mechanick, Jeffrey I

2010-11-01

With evolving interest in multiscalar biological systems one could assume that reductionist approaches may not fully describe biological complexity. Instead, tools such as mathematical modeling, network analysis, and other multiplexed clinical- and research-oriented tests enable rapid analyses of high-throughput data parsed at the genomic, proteomic, metabolomic, and physiomic levels. A physiomic-level approach allows for recursive horizontal and vertical integration of subsystem coupling across and within spatiotemporal scales. Additionally, this methodology recognizes previously ignored subsystems and the strong, nonintuitively obvious and indirect connections among physiological events that potentially account for the uncertainties in medicine. In this review, we flip the reductionist research paradigm and review the concept of systems biology and its applications to bone pathophysiology. Specifically, a bone-centric physiome model is presented that incorporates systemic-level processes with their respective therapeutic implications. © 2010 New York Academy of Sciences.

Catastrophe modelling in the biological sciences.

PubMed

Deakin, M A

1990-03-01

Catastrophe Theory was developed in an attempt to provide a form of Mathematics particularly apt for applications in the biological sciences. It was claimed that while it could be applied in the more conventional "physical" way, it could also be applied in a new "metaphysical" way, derived from the Structuralism of Saussure in Linguistics and Lévi-Strauss in Anthropology. Since those early beginnings there have been many attempts to apply Catastrophe Theory to Biology, but these hopes cannot be said to have been fully realised. This paper will document and classify the work that has been done. It will be argued that, like other applied Mathematics, applied Catastrophe Theory works best where the underlying laws are securely known and precisely quantified, requiring those same guarantees as does any other branch of Mathematics when it confronts a real-life situation.

Autonomy and Fear of Synthetic Biology: How Can Patients' Autonomy Be Enhanced in the Field of Synthetic Biology? A Qualitative Study with Stable Patients.

PubMed

Rakic, Milenko; Wienand, Isabelle; Shaw, David; Nast, Rebecca; Elger, Bernice S

2017-04-01

We analyzed stable patients' views regarding synthetic biology in general, the medical application of synthetic biology, and their potential participation in trials of synthetic biology in particular. The aim of the study was to find out whether patients' views and preferences change after receiving more detailed information about synthetic biology and its clinical applications. The qualitative study was carried out with a purposive sample of 36 stable patients, who suffered from diabetes or gout. Interviews were transcribed verbatim, translated and fully anonymized. Thematic analysis was applied in order to examine stable patients' attitudes towards synthetic biology, its medical application, and their participation in trials. When patients were asked about synthetic biology in general, most of them were anxious that something uncontrollable could be created. After a concrete example of possible future treatment options, patients started to see synthetic biology in a more positive way. Our study constitutes an important first empirical insight into stable patients' views on synthetic biology and into the kind of fears triggered by the term "synthetic biology." Our results show that clear and concrete information can change patients' initial negative feelings towards synthetic biology. Information should thus be transmitted with great accuracy and transparency in order to reduce irrational fears of patients and to minimize the risk that researchers present facts too positively for the purposes of persuading patients to participate in clinical trials. Potential participants need to be adequately informed in order to be able to autonomously decide whether to participate in human subject research involving synthetic biology.

Biological Mechanisms that Promote Weight Regain Following Weight Loss in Obese Humans

PubMed Central

Ochner, Christopher N.; Barrios, Dulce M.; Lee, Clement D.; Pi-Sunyer, F. Xavier

2013-01-01

Weight loss dieting remains the treatment of choice for the vast majority of obese individuals, despite the limited long-term success of behavioral weight loss interventions. The reasons for the near universal unsustainability of behavioral weight loss in [formerly] obese individuals have not been fully elucidated, relegating researchers to making educated guesses about how to improve obesity treatment, as opposed to developing interventions targeting the causes of weight regain. This article discusses research on several factors that may contribute to weight regain following weight loss achieved through behavioral interventions, including adipose cellularity, endocrine function, energy metabolism, neural responsivity, and addiction-like neural mechanisms. All of these mechanisms are engaged prior to weight loss, suggesting that so called “anti-starvation” mechanisms are activated via reductions in energy intake, rather than depletion of energy stores. Evidence suggests that these mechanisms are not necessarily part of a homeostatic feedback system designed to regulate body weight or even anti-starvation mechanisms per se. Though they may have evolved to prevent starvation, they appear to be more accurately described as anti-weight loss mechanisms, engaged with caloric restriction irrespective of the adequacy of energy stores. It is hypothesized that these factors may combine to create a biological disposition that fosters the maintenance of an elevated body weight and work to restore the highest sustained body weight, thus precluding the long-term success of behavioral weight loss. It may be necessary to develop interventions that attenuate these biological mechanisms in order to achieve long-term weight reduction in obese individuals. PMID:23911805

Recent advances in the understanding of brown spider venoms: From the biology of spiders to the molecular mechanisms of toxins.

PubMed

Gremski, Luiza Helena; Trevisan-Silva, Dilza; Ferrer, Valéria Pereira; Matsubara, Fernando Hitomi; Meissner, Gabriel Otto; Wille, Ana Carolina Martins; Vuitika, Larissa; Dias-Lopes, Camila; Ullah, Anwar; de Moraes, Fábio Rogério; Chávez-Olórtegui, Carlos; Barbaro, Katia Cristina; Murakami, Mario Tyago; Arni, Raghuvir Krishnaswamy; Senff-Ribeiro, Andrea; Chaim, Olga Meiri; Veiga, Silvio Sanches

2014-06-01

The Loxosceles genus spiders (the brown spiders) are encountered in all the continents, and the clinical manifestations following spider bites include skin necrosis with gravitational lesion spreading and occasional systemic manifestations, such as intravascular hemolysis, thrombocytopenia and acute renal failure. Brown spider venoms are complex mixtures of toxins especially enriched in three molecular families: the phospholipases D, astacin-like metalloproteases and Inhibitor Cystine Knot (ICK) peptides. Other toxins with low level of expression also present in the venom include the serine proteases, serine protease inhibitors, hyaluronidases, allergen factors and translationally controlled tumor protein (TCTP). The mechanisms by which the Loxosceles venoms act and exert their noxious effects are not fully understood. Except for the brown spider venom phospholipase D, which causes dermonecrosis, hemolysis, thrombocytopenia and renal failure, the pathological activities of the other venom toxins remain unclear. The objective of the present review is to provide insights into the brown spider venoms and loxoscelism based on recent results. These insights include the biology of brown spiders, the clinical features of loxoscelism and the diagnosis and therapy of brown spider bites. Regarding the brown spider venom, this review includes a description of the novel toxins revealed by molecular biology and proteomics techniques, the data regarding three-dimensional toxin structures, and the mechanism of action of these molecules. Finally, the biotechnological applications of the venom components, especially for those toxins reported as recombinant molecules, and the challenges for future study are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

Mechanisms for Induction of Pulmonary Capillary Hemorrhage by Diagnostic Ultrasound: Review and Consideration of Acoustical Radiation Surface Pressure.

PubMed

Miller, Douglas L

2016-12-01

Diagnostic ultrasound can induce pulmonary capillary hemorrhage (PCH) in rats and other mammals. This phenomenon represents the only clearly demonstrated biological effect of (non-contrast enhanced) diagnostic ultrasound and thus presents a uniquely important safety issue. However, the physical mechanism responsible for PCH remains uncertain more than 25 y after its discovery. Experimental research has indicated that neither heating nor acoustic cavitation, the predominant mechanisms for bioeffects of ultrasound, is responsible for PCH. Furthermore, proposed theoretical mechanisms based on gas-body activation, on alveolar resonance and on impulsive generation of liquid droplets all appear unlikely to be responsible for PCH, owing to unrealistic model assumptions. Here, a simple model based on the acoustical radiation surface pressure (ARSP) at a tissue-air interface is hypothesized as the mechanism for PCH. The ARSP model seems to explain some features of PCH, including the approximate frequency independence of PCH thresholds and the dependence of thresholds on biological factors. However, ARSP evaluated for experimental threshold conditions appear to be too weak to fully account for stress failure of pulmonary capillaries, gauging by known stresses for injurious physiologic conditions. Furthermore, consideration of bulk properties of lung tissue suggests substantial transmission of ultrasound through the pleura, with reduced ARSP and potential involvement of additional mechanisms within the pulmonary interior. Although these recent findings advance our knowledge, only a full understanding of PCH mechanisms will allow development of science-based safety assurance for pulmonary ultrasound. Copyright © 2016 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

A Quasi Experiment to Determine the Effectiveness of a "Partially Flipped" versus "Fully Flipped" Undergraduate Class in Genetics and Evolution

ERIC Educational Resources Information Center

Adams, Alison E. M.; Garcia, Jocelyn; Traustadóttir, Tinna

2016-01-01

Two sections of Genetics and Evolution were taught by one instructor. One group (the fully flipped section) had the entire class period devoted to active learning (with background material that had to be watched before class), and the other group (the partially flipped section) had just a portion of class time spent on active learning (with the…

A knowledge discovery object model API for Java

PubMed Central

Zuyderduyn, Scott D; Jones, Steven JM

2003-01-01

Background Biological data resources have become heterogeneous and derive from multiple sources. This introduces challenges in the management and utilization of this data in software development. Although efforts are underway to create a standard format for the transmission and storage of biological data, this objective has yet to be fully realized. Results This work describes an application programming interface (API) that provides a framework for developing an effective biological knowledge ontology for Java-based software projects. The API provides a robust framework for the data acquisition and management needs of an ontology implementation. In addition, the API contains classes to assist in creating GUIs to represent this data visually. Conclusions The Knowledge Discovery Object Model (KDOM) API is particularly useful for medium to large applications, or for a number of smaller software projects with common characteristics or objectives. KDOM can be coupled effectively with other biologically relevant APIs and classes. Source code, libraries, documentation and examples are available at . PMID:14583100

Biological and Psychosocial Predictors of Postpartum Depression: Systematic Review and Call for Integration

PubMed Central

Tanner Stapleton, Lynlee R.; Guardino, Christine M.; Hahn-Holbrook, Jennifer; Schetter, Christine Dunkel

2017-01-01

Postpartum depression (PPD) adversely affects the health and well being of many new mothers, their infants, and their families. A comprehensive understanding of biopsychosocial precursors to PPD is needed to solidify the current evidence base for best practices in translation. We conducted a systematic review of research published from 2000 through 2013 on biological and psychosocial factors associated with PPD and postpartum depressive symptoms. Two hundred fourteen publications based on 199 investigations of 151,651 women in the first postpartum year met inclusion criteria. The biological and psychosocial literatures are largely distinct, and few studies provide integrative analyses. The strongest PPD risk predictors among biological processes are hypothalamic-pituitary-adrenal dysregulation, inflammatory processes, and genetic vulnerabilities. Among psychosocial factors, the strongest predictors are severe life events, some forms of chronic strain, relationship quality, and support from partner and mother. Fully integrated biopsychosocial investigations with large samples are needed to advance our knowledge of PPD etiology. PMID:25822344

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways.

PubMed

Beltrame, Luca; Calura, Enrica; Popovici, Razvan R; Rizzetto, Lisa; Guedez, Damariz Rivero; Donato, Michele; Romualdi, Chiara; Draghici, Sorin; Cavalieri, Duccio

2011-08-01

Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions. The Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML is able to store multiple information, permitting a selective view of the pathway as it exists and/or behave in specific organisms, tissues and cells. Furthermore, BCML can be automatically converted into data formats suitable for analysis and into a fully SBGN-compliant graphical representation, making it an important tool that can be used by both computational biologists and 'wet lab' scientists. The XML schema and the BCML software suite are freely available under the LGPL for download at http://bcml.dc-atlas.net. They are implemented in Java and supported on MS Windows, Linux and OS X.

Prothrombin fragments in cardiovascular disease.

PubMed

Páramo, J A

2010-01-01

Prothrombin fragment 1+2 (F1+2), which comes from in vivo cleavage of prothrombin by factor Xa, is considered to be useful for diagnosis of thrombosis. Recognition of the central role of thrombosis in the pathogenesis ofcardiovascular disease has prompted growing interest in the association o F1+2 with cardiovascular clinical syndromes. Increased F1+2 levels have reported in venous thromboembolism, inflammation, cancer, sepsis, acute coronary syndromes, stroke, peripheral arterial disease, atrial fibrillation and during the postoperative period. However, a clear relationship with the appearance of thrombosis has not always been consistently demonstrated. Besides its potential prognostic and diagnostic value, it could also be usefu in assessing the impact of various therapies. However, it should be kept in mind that measurement of hemostasis activation markers has several important biological and methodological disadvantages. Activation markers reflect the presence of thrombosis in any vascular bed, so they are not specific. Furthermore, elevations occur not only in the presence of overt thrombosis but also during the hypercoagulable state. The cutoff level to be used for the definition of elevations is still largely unknown due to the use of different analytical methods, none of which have been standardized until know. Finally, the prognostic value of F1+2 and other markers of coagulation activation remains to be fully defined in future studies.

Use of the Endophytic Fungus Daldinia cf. concentrica and Its Volatiles as Bio-Control Agents

PubMed Central

Liarzi, Orna; Bar, Einat; Lewinsohn, Efraim; Ezra, David

2016-01-01

Endophytic fungi are organisms that spend most of their life cycle within plant tissues without causing any visible damage to the host plant. Many endophytes were found to secrete specialized metabolites and/or emit volatile organic compounds (VOCs), which may be biologically active and assist fungal survival inside the plant as well as benefit their hosts. We report on the isolation and characterization of a VOCs-emitting endophytic fungus, isolated from an olive tree (Olea europaea L.) growing in Israel; the isolate was identified as Daldinia cf. concentrica. We found that the emitted VOCs were active against various fungi from diverse phyla. Results from postharvest experiments demonstrated that D. cf. concentrica prevented development of molds on organic dried fruits, and eliminated Aspergillus niger infection in peanuts. Gas chromatography–mass spectrometry analysis of the volatiles led to identification of 27 VOCs. On the basis of these VOCs we prepared two mixtures that displayed a broad spectrum of antifungal activity. In postharvest experiments these mixtures prevented development of molds on wheat grains, and fully eliminated A. niger infection in peanuts. In light of these findings, we suggest use of D. cf. concentrica and/or its volatiles as an alternative approach to controlling phytopathogenic fungi in the food industry and in agriculture. PMID:27977739

Molecular dynamics simulations reveal the conformational dynamics of Arabidopsis thaliana BRI1 and BAK1 receptor-like kinases.

PubMed

Moffett, Alexander S; Bender, Kyle W; Huber, Steven C; Shukla, Diwakar

2017-07-28

The structural motifs responsible for activation and regulation of eukaryotic protein kinases in animals have been studied extensively in recent years, and a coherent picture of their activation mechanisms has begun to emerge. In contrast, non-animal eukaryotic protein kinases are not as well understood from a structural perspective, representing a large knowledge gap. To this end, we investigated the conformational dynamics of two key Arabidopsis thaliana receptor-like kinases, brassinosteroid-insensitive 1 (BRI1) and BRI1-associated kinase 1 (BAK1), through extensive molecular dynamics simulations of their fully phosphorylated kinase domains. Molecular dynamics simulations calculate the motion of each atom in a protein based on classical approximations of interatomic forces, giving researchers insight into protein function at unparalleled spatial and temporal resolutions. We found that in an otherwise "active" BAK1 the αC helix is highly disordered, a hallmark of deactivation, whereas the BRI1 αC helix is moderately disordered and displays swinging behavior similar to numerous animal kinases. An analysis of all known sequences in the A. thaliana kinome found that αC helix disorder may be a common feature of plant kinases. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Estradiol and Inflammatory Markers in Older Men

PubMed Central

Maggio, Marcello; Ceda, Gian Paolo; Lauretani, Fulvio; Bandinelli, Stefania; Metter, E. Jeffrey; Artoni, Andrea; Gatti, Elisa; Ruggiero, Carmelinda; Guralnik, Jack M.; Valenti, Giorgio; Ling, Shari M.; Basaria, Shehzad; Ferrucci, Luigi

2009-01-01

Background: Aging is characterized by a mild proinflammatory state. In older men, low testosterone levels have been associated with increasing levels of proinflammatory cytokines. It is still unclear whether estradiol (E2), which generally has biological activities complementary to testosterone, affects inflammation. Methods: We analyzed data obtained from 399 men aged 65–95 yr enrolled in the Invecchiare in Chianti study with complete data on body mass index (BMI), serum E2, testosterone, IL-6, soluble IL-6 receptor, TNF-α, IL-1 receptor antagonist, and C-reactive protein. The relationship between E2 and inflammatory markers was examined using multivariate linear models adjusted for age, BMI, smoking, physical activity, chronic disease, and total testosterone. Results: In age-adjusted analysis, log (E2) was positively associated with log (IL-6) (r = 0.19; P = 0.047), and the relationship was statistically significant (P = 0.032) after adjustments for age, BMI, smoking, physical activity, chronic disease, and serum testosterone levels. Log (E2) was not significantly associated with log (C-reactive protein), log (soluble IL-6 receptor), or log (TNF-α) in both age-adjusted and fully adjusted analyses. Conclusions: In older men, E2 is weakly positively associated with IL-6, independent of testosterone and other confounders including BMI. PMID:19050054

Sensors 2000! Program: Advanced Biosensor and Measurement Systems Technologies for Spaceflight Research and Concurrent, Earth-Based Applications

NASA Technical Reports Server (NTRS)

Hines, J.

1999-01-01

Sensors 2000! (S2K!) is a specialized, integrated projects team organized to provide focused, directed, advanced biosensor and bioinstrumentation systems technology support to NASA's spaceflight and ground-based research and development programs. Specific technology thrusts include telemetry-based sensor systems, chemical/ biological sensors, medical and physiological sensors, miniaturized instrumentation architectures, and data and signal processing systems. A concurrent objective is to promote the mutual use, application, and transition of developed technology by collaborating in academic-commercial-govemment leveraging, joint research, technology utilization and commercialization, and strategic partnering alliances. Sensors 2000! is organized around three primary program elements: Technology and Product Development, Technology infusion and Applications, and Collaborative Activities. Technology and Product Development involves development and demonstration of biosensor and biotelemetry systems for application to NASA Space Life Sciences Programs; production of fully certified spaceflight hardware and payload elements; and sensor/measurement systems development for NASA research and development activities. Technology Infusion and Applications provides technology and program agent support to identify available and applicable technologies from multiple sources for insertion into NASA's strategic enterprises and initiatives. Collaborative Activities involve leveraging of NASA technologies with those of other government agencies, academia, and industry to concurrently provide technology solutions and products of mutual benefit to participating members.

Multifaceted Role of Pneumolysin in the Pathogenesis of Myocardial Injury in Community-Acquired Pneumonia.

PubMed

Anderson, Ronald; Nel, Jan G; Feldman, Charles

2018-04-11

Pneumolysin (PLY), a member of the family of Gram-positive bacterial, cholesterol-dependent, β-barrel pore-forming cytolysins, is the major protein virulence factor of the dangerous respiratory pathogen, Streptococcus pneumoniae (pneumococcus). PLY plays a major role in the pathogenesis of community-acquired pneumonia (CAP), promoting colonization and invasion of the upper and lower respiratory tracts respectively, as well as extra-pulmonary dissemination of the pneumococcus. Notwithstanding its role in causing acute lung injury in severe CAP, PLY has also been implicated in the development of potentially fatal acute and delayed-onset cardiovascular events, which are now recognized as being fairly common complications of this condition. This review is focused firstly on updating mechanisms involved in the immunopathogenesis of PLY-mediated myocardial damage, specifically the direct cardiotoxic and immunosuppressive activities, as well as the indirect pro-inflammatory/pro-thrombotic activities of the toxin. Secondly, on PLY-targeted therapeutic strategies including, among others, macrolide antibiotics, natural product antagonists, cholesterol-containing liposomes, and fully humanized monoclonal antibodies, as well as on vaccine-based preventive strategies. These sections are preceded by overviews of CAP in general, the role of the pneumococcus as the causative pathogen, the occurrence and types of CAP-associated cardiac complication, and the structure and biological activities of PLY.

Activation of Peroxisome Proliferator-activated Receptor γ (PPARγ) and CD36 Protein Expression: THE DUAL PATHOPHYSIOLOGICAL ROLES OF PROGESTERONE.

PubMed

Yang, Xiaoxiao; Zhang, Wenwen; Chen, Yuanli; Li, Yan; Sun, Lei; Liu, Ying; Liu, Mengyang; Yu, Miao; Li, Xiaoju; Han, Jihong; Duan, Yajun

2016-07-15

Progesterone or its analog, one of components of hormone replacement therapy, may attenuate the cardioprotective effects of estrogen. However, the underlying mechanisms have not been fully elucidated. Expression of CD36, a receptor for oxidized LDL (oxLDL) that enhances macrophage/foam cell formation, is activated by the transcription factor peroxisome proliferator-activated receptor γ (PPARγ). CD36 also functions as a fatty acid transporter to influence fatty acid metabolism and the pathophysiological status of several diseases. In this study, we determined that progesterone induced macrophage CD36 expression, which is related to progesterone receptor (PR) activity. Progesterone enhanced cellular oxLDL uptake in a CD36-dependent manner. Mechanistically, progesterone increased PPARγ expression and PPARγ promoter activity in a PR-dependent manner and the binding of PR with the progesterone response element in the PPARγ promoter. Specific deletion of macrophage PPARγ (MφPPARγ KO) expression in mice abolished progesterone-induced macrophage CD36 expression and cellular oxLDL accumulation. We also determined that, associated with gestation and increased serum progesterone levels, CD36 and PPARγ expression in mouse adipose tissue, skeletal muscle, and peritoneal macrophages were substantially activated. Taken together, our study demonstrates that progesterone can play dual pathophysiological roles by activating PPARγ expression, in which progesterone increases macrophage CD36 expression and oxLDL accumulation, a negative effect on atherosclerosis, and enhances the PPARγ-CD36 pathway in adipose tissue and skeletal muscle, a protective effect on pregnancy. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Secretory sphingomyelinase (S-SMase) activity is elevated in patients with rheumatoid arthritis.

PubMed

Hanaoka, Beatriz Y; Ormseth, Michelle J; Michael Stein, C; Banerjee, Daipayan; Nikolova-Karakashian, Mariana; Crofford, Leslie J

2018-05-01

The goals of this study were to determine if secretory sphingomyelinase (S-SMase) activity is elevated in patients with rheumatoid arthritis (RA) compared to control subjects and to examine the relationships of S-SMase activity with functional status, quality of life, and RA disease activity measurements. We collected data on 33 patients who were diagnosed with RA and 17 non-RA controls who were comparable in terms of age, sex, and race. Demographic, clinical data and self-reported measures of fatigue, pain, and physical function were obtained directly from patients and controls. RA patients also completed quantitative joint assessment using a 28-joint count and functional status and quality of life assessment using the Modified Health Assessment Questionnaire (MHAQ). Archived serum samples were used to analyze retrospectively serum S-SMase activity in patients and controls. The mean serum S-SMase activity was 1.4-fold higher in patients with RA (RA 2.8 ± 1.0 nmol/ml/h vs. controls 2.0 ± 0.8 nmol/ml/h; p = 0.014). Spearman's rho correlations between S-SMase activity and oxidant activity, markers of inflammation and endothelial activation with the exception of P-selectin (rho = 0.40, p = 0.034), measures of disease activity, functional status, and quality of life were not statistically significant in patients with RA. We confirmed that S-SMase activity is higher among RA patients compared to controls, as in other acute and chronic inflammatory diseases. Future studies can build on the present findings to understand more fully the biologic role(s) of S-SMase activity in RA.

Glucose starvation increases V-ATPase assembly and activity in mammalian cells through AMP kinase and phosphatidylinositide 3-kinase/Akt signaling.

PubMed

McGuire, Christina M; Forgac, Michael

2018-06-08

The vacuolar H + -ATPase (V-ATPase) is an ATP-driven proton pump involved in many cellular processes. An important mechanism by which V-ATPase activity is controlled is the reversible assembly of its two domains, namely the peripheral V 1 domain and the integral V 0 domain. Although reversible assembly is conserved across all eukaryotic organisms, the signaling pathways controlling it have not been fully characterized. Here, we identify glucose starvation as a novel regulator of V-ATPase assembly in mammalian cells. During acute glucose starvation, the V-ATPase undergoes a rapid and reversible increase in assembly and activity as measured by lysosomal acidification. Because the V-ATPase has recently been implicated in the activation of AMP kinase (AMPK), a critical cellular energy sensor that is also activated upon glucose starvation, we compared the time course of AMPK activation and V-ATPase assembly upon glucose starvation. We observe that AMPK activation precedes increased V-ATPase activity. Moreover, the starvation-induced increase in V-ATPase activity and assembly are prevented by the AMPK inhibitor dorsomorphin. These results suggest that increased assembly and activity of the V-ATPase upon glucose starvation are dependent upon AMPK. We also find that the PI3K/Akt pathway, which has previously been implicated in controlling V-ATPase assembly in mammalian cells, also plays a role in the starvation-induced increase in V-ATPase assembly and activity. These studies thus identify a novel stimulus of V-ATPase assembly and a novel signaling pathway involved in regulating this process. The possible function of starvation-induced increase in lysosomal V-ATPase activity is discussed. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Systems Biology Approaches for Host–Fungal Interactions: An Expanding Multi-Omics Frontier

PubMed Central

Culibrk, Luka; Croft, Carys A.

2016-01-01

Abstract Opportunistic fungal infections are an increasing threat for global health, and for immunocompromised patients in particular. These infections are characterized by interaction between fungal pathogen and host cells. The exact mechanisms and the attendant variability in host and fungal pathogen interaction remain to be fully elucidated. The field of systems biology aims to characterize a biological system, and utilize this knowledge to predict the system's response to stimuli such as fungal exposures. A multi-omics approach, for example, combining data from genomics, proteomics, metabolomics, would allow a more comprehensive and pan-optic “two systems” biology of both the host and the fungal pathogen. In this review and literature analysis, we present highly specialized and nascent methods for analysis of multiple -omes of biological systems, in addition to emerging single-molecule visualization techniques that may assist in determining biological relevance of multi-omics data. We provide an overview of computational methods for modeling of gene regulatory networks, including some that have been applied towards the study of an interacting host and pathogen. In sum, comprehensive characterizations of host–fungal pathogen systems are now possible, and utilization of these cutting-edge multi-omics strategies may yield advances in better understanding of both host biology and fungal pathogens at a systems scale. PMID:26885725

Canadian regulatory requirements for recombinant fish vaccines.

PubMed

Sethi, M S; Gifford, G A; Samagh, B S

1997-01-01

In Canada, veterinary biological products derived by using conventional and new techniques of biotechnology are licensed and regulated under the Health of Animals Act and Regulations. Biological products include vaccines, bacterins, bacterin-toxoids and diagnostic kits which are used for the prevention, treatment or diagnosis of infectious diseases in all species of animals, including fish. Veterinary biologicals are licensed on the basis of fulfillment of four criteria: purity, potency, safety and efficacy. A risk-based approach is used to evaluate the safety of the product in target species, as well as non-target species, humans and the environment. On the basis of biological characteristics, biotechnology derived veterinary biologicals have been divided into two broad categories, high and low risk products. The paper describes the regulatory framework for the licensing of veterinary biologicals in Canada, with emphasis on the regulatory considerations for recombinant fish vaccines. Stages of movement of the product from research in a contained laboratory facility to a fully licensed product for free sale are discussed. The requirements for field testing and environmental assessment involved in these stages are highlighted. Manufacturers and researchers who intend to commercialize experimental vaccines are encouraged to consult with the Veterinary Biologics and Biotechnology Section early in the product development process so that the research data and quality assurance documentation are consistent with regulatory requirements.

The Active Role of the Ocean in the Temporal Evolution of Climate Sensitivity

DOE PAGES

Garuba, Oluwayemi A.; Lu, Jian; Liu, Fukai; ...

2017-11-30

Here, the temporal evolution of the effective climate sensitivity is shown to be influenced by the changing pattern of sea surface temperature (SST) and ocean heat uptake (OHU), which in turn have been attributed to ocean circulation changes. A set of novel experiments are performed to isolate the active role of the ocean by comparing a fully coupled CO 2 quadrupling community Earth System Model (CESM) simulation against a partially coupled one, where the effect of the ocean circulation change and its impact on surface fluxes are disabled. The active OHU is responsible for the reduced effective climate sensitivity andmore » weaker surface warming response in the fully coupled simulation. The passive OHU excites qualitatively similar feedbacks to CO 2 quadrupling in a slab ocean model configuration due to the similar SST spatial pattern response in both experiments. Additionally, the nonunitary forcing efficacy of the active OHU (1.7) explains the very different net feedback parameters in the fully and partially coupled responses.« less

The Active Role of the Ocean in the Temporal Evolution of Climate Sensitivity

NASA Astrophysics Data System (ADS)

Garuba, Oluwayemi A.; Lu, Jian; Liu, Fukai; Singh, Hansi A.

2018-01-01

The temporal evolution of the effective climate sensitivity is shown to be influenced by the changing pattern of sea surface temperature (SST) and ocean heat uptake (OHU), which in turn have been attributed to ocean circulation changes. A set of novel experiments are performed to isolate the active role of the ocean by comparing a fully coupled CO2 quadrupling community Earth System Model (CESM) simulation against a partially coupled one, where the effect of the ocean circulation change and its impact on surface fluxes are disabled. The active OHU is responsible for the reduced effective climate sensitivity and weaker surface warming response in the fully coupled simulation. The passive OHU excites qualitatively similar feedbacks to CO2 quadrupling in a slab ocean model configuration due to the similar SST spatial pattern response in both experiments. Additionally, the nonunitary forcing efficacy of the active OHU (1.7) explains the very different net feedback parameters in the fully and partially coupled responses.

The Active Role of the Ocean in the Temporal Evolution of Climate Sensitivity

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

Garuba, Oluwayemi A.; Lu, Jian; Liu, Fukai

Here, the temporal evolution of the effective climate sensitivity is shown to be influenced by the changing pattern of sea surface temperature (SST) and ocean heat uptake (OHU), which in turn have been attributed to ocean circulation changes. A set of novel experiments are performed to isolate the active role of the ocean by comparing a fully coupled CO 2 quadrupling community Earth System Model (CESM) simulation against a partially coupled one, where the effect of the ocean circulation change and its impact on surface fluxes are disabled. The active OHU is responsible for the reduced effective climate sensitivity andmore » weaker surface warming response in the fully coupled simulation. The passive OHU excites qualitatively similar feedbacks to CO 2 quadrupling in a slab ocean model configuration due to the similar SST spatial pattern response in both experiments. Additionally, the nonunitary forcing efficacy of the active OHU (1.7) explains the very different net feedback parameters in the fully and partially coupled responses.« less

Leukemia inhibitory factor: a novel bone-active cytokine.

PubMed

Reid, L R; Lowe, C; Cornish, J; Skinner, S J; Hilton, D J; Willson, T A; Gearing, D P; Martin, T J

1990-03-01

A number of cytokines have been found to be potent regulators of bone resorption and to share the properties originally attributed to osteoclast-activating factor. One such activity, differentiation-inducing factor (DIF, D-factor) from mouse spleen cells, shares a number of biological and biochemical properties with the recently characterized and cloned leukemia inhibitory factor (LIF). We have assessed the effects of recombinant LIF on bone resorption and other parameters in neonatal mouse calvaria. Both recombinant murine and human (h) LIFs stimulated 45Ca release from prelabeled calvaria in a dose-dependent manner. The increase in bone resorption was associated with an increase in the number of osteoclasts per mm2 bone. The osteolytic effect of hLIF were blocked by 10(-7) M indomethacin. hLIF also stimulated incorporation of [3H] thymidine into calvaria, but the dose-response relationship was distinct from that for bone resorption, and this effect was not blocked by indomethacin. Similarly, hLIF increased [3H]phenylalanine incorporation into calvaria, and this was also not inhibited by indomethacin. It is concluded that LIF stimulates bone resorption by a mechanism involving prostaglandin production, but that a distinct mechanism is responsible for its stimulation of DNA and protein synthesis. The primary structure of LIF differs from that of other fully characterized, bone-active cytokines, and it, thus, represents a novel factor which may be involved in the normal regulation of bone cell function.

EF24 induces ROS-mediated apoptosis via targeting thioredoxin reductase 1 in gastric cancer cells.

PubMed

Zou, Peng; Xia, Yiqun; Chen, Weiqian; Chen, Xi; Ying, Shilong; Feng, Zhiguo; Chen, Tongke; Ye, Qingqing; Wang, Zhe; Qiu, Chenyu; Yang, Shulin; Liang, Guang

2016-04-05

Gastric cancer (GC) is one of the leading causes of cancer mortality in the world, and finding novel agents for the treatment of advanced gastric cancer is of urgent need. Diphenyl difluoroketone (EF24), a molecule having structural similarity to curcumin, exhibits potent anti-tumor activities by arresting cell cycle and inducing apoptosis. Although EF24 demonstrates potent anticancer effïcacy in numerous types of human cancer cells, the cellular targets of EF24 have not been fully defined. We report here that EF24 may interact with the thioredoxin reductase 1 (TrxR1), an important selenocysteine (Sec)-containing antioxidant enzyme, to induce reactive oxygen species (ROS)-mediated apoptosis in human gastric cancer cells. By inhibiting TrxR1 activity and increasing intracellular ROS levels, EF24 induces a lethal endoplasmic reticulum stress in human gastric cancer cells. Importantly, knockdown of TrxR1 sensitizes cells to EF24 treatment. In vivo, EF24 treatment markedly reduces the TrxR1 activity and tumor cell burden, and displays synergistic lethality with 5-FU against gastric cancer cells. Targeting TrxR1 with EF24 thus discloses a previously unrecognized mechanism underlying the biological activity of EF24, and reveals that TrxR1 is a good target for gastric cancer therapy.

Clustering of 3D-Structure Similarity Based Network of Secondary Metabolites Reveals Their Relationships with Biological Activities.

PubMed

Ohtana, Yuki; Abdullah, Azian Azamimi; Altaf-Ul-Amin, Md; Huang, Ming; Ono, Naoaki; Sato, Tetsuo; Sugiura, Tadao; Horai, Hisayuki; Nakamura, Yukiko; Morita Hirai, Aki; Lange, Klaus W; Kibinge, Nelson K; Katsuragi, Tetsuo; Shirai, Tsuyoshi; Kanaya, Shigehiko

2014-12-01

Developing database systems connecting diverse species based on omics is the most important theme in big data biology. To attain this purpose, we have developed KNApSAcK Family Databases, which are utilized in a number of researches in metabolomics. In the present study, we have developed a network-based approach to analyze relationships between 3D structure and biological activity of metabolites consisting of four steps as follows: construction of a network of metabolites based on structural similarity (Step 1), classification of metabolites into structure groups (Step 2), assessment of statistically significant relations between structure groups and biological activities (Step 3), and 2-dimensional clustering of the constructed data matrix based on statistically significant relations between structure groups and biological activities (Step 4). Applying this method to a data set consisting of 2072 secondary metabolites and 140 biological activities reported in KNApSAcK Metabolite Activity DB, we obtained 983 statistically significant structure group-biological activity pairs. As a whole, we systematically analyzed the relationship between 3D-chemical structures of metabolites and biological activities. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Conceptual Framework for Organizing Active Learning Experiences in Biology Instruction

ERIC Educational Resources Information Center

Gardner, Joel; Belland, Brian R.

2012-01-01

Introductory biology courses form a cornerstone of undergraduate instruction. However, the predominantly used lecture approach fails to produce higher-order biology learning. Research shows that active learning strategies can increase student learning, yet few biology instructors use all identified active learning strategies. In this paper, we…

A Fully Automated Method to Detect and Segment a Manufactured Object in an Underwater Color Image

NASA Astrophysics Data System (ADS)

Barat, Christian; Phlypo, Ronald

2010-12-01

We propose a fully automated active contours-based method for the detection and the segmentation of a moored manufactured object in an underwater image. Detection of objects in underwater images is difficult due to the variable lighting conditions and shadows on the object. The proposed technique is based on the information contained in the color maps and uses the visual attention method, combined with a statistical approach for the detection and an active contour for the segmentation of the object to overcome the above problems. In the classical active contour method the region descriptor is fixed and the convergence of the method depends on the initialization. With our approach, this dependence is overcome with an initialization using the visual attention results and a criterion to select the best region descriptor. This approach improves the convergence and the processing time while providing the advantages of a fully automated method.

Polysaccharides from Traditional Chinese Medicines: Extraction, Purification, Modification, and Biological Activity.

PubMed

Chen, Yun; Yao, Fangke; Ming, Ke; Wang, Deyun; Hu, Yuanliang; Liu, Jiaguo

2016-12-13

Traditional Chinese Medicine (TCM) has been used to treat diseases in China for thousands of years. TCM compositions are complex, using as their various sources plants, animals, fungi, and minerals. Polysaccharides are one of the active and important ingredients of TCMs. Polysaccharides from TCMs exhibit a wide range of biological activities in terms of immunity- modifying, antiviral, anti-inflammatory, anti-oxidative, and anti-tumor properties. With their widespread biological activities, polysaccharides consistently attract scientist's interests, and the studies often concentrate on the extraction, purification, and biological activity of TCM polysaccharides. Currently, numerous studies have shown that the modification of polysaccharides can heighten or change the biological activities, which is a new angle of polysaccharide research. This review highlights the current knowledge of TCM polysaccharides, including their extraction, purification, modification, and biological activity, which will hopefully provide profound insights facilitating further research and development.

Human Cancer Models Initiative | Office of Cancer Genomics

Cancer.gov

The Human Cancer Models Initiative (HCMI) is an international consortium that is generating novel human tumor-derived culture models, which are annotated with genomic and clinical data. In an effort to advance cancer research and more fully understand how in vitro findings are related to clinical biology, HCMI-developed models and related data will be available as a community resource for cancer and other research.

Human Cancer Models Initiative | Office of Cancer Genomics

Cancer.gov

The Human Cancer Models Initiative (HCMI) is an international consortium that is generating novel human tumor-derived culture models, which are annotated with genomic and clinical data. In an effort to advance cancer research and more fully understand how in vitro findings are related to clinical biology, HCMI-developed models and related data will be available as a community resource for cancer research.

Mendelian Genetics as a Platform for Teaching about Nature of Science and Scientific Inquiry: The Value of Textbooks

ERIC Educational Resources Information Center

Campanile, Megan F.; Lederman, Norman G.; Kampourakis, Kostas

2015-01-01

The purpose of this study was to analyze seven widely used high school biology textbooks in order to assess the nature of science knowledge (NOS) and scientific inquiry (SI) aspects they, explicitly or implicitly, conveyed in the Mendelian genetics sections. Textbook excerpts that directly and/or fully matched our statements about NOS and SI were…

[The activity of prooxidant-antioxidant system in loach embryos under the action of microwave radiation].

PubMed

Iaremchuk, M M; Dyka, M V; Sanahurs'kyĭ, D I

2014-01-01

Electromagnetic radiation (EMR) affects biological organisms, primarily on the cellular level. However, the effects of EMR at low-intensity exposure on animals and state of metabolic systems are not fully defined yet. Thus, research of microwave radiation influence on the processes of lipid peroxidation and antioxidant protection system is important for understanding the mechanisms of EMR action on the cell, in particular, and organism development on the whole. The content of lipid peroxidation products--lipid hydroperoxides, thiobarbituric acid reactive substances and the activity of antioxidant enzymes--superoxide dismutase, glutathione peroxidase and catalase in loach embryos under the action of microwave radiation (GSM-900 MHz, SAR = 1.1 Vt/kg) lasting 1; 5; 10 and 20 min during early embryogenesis were studied. It has been found that content of lipid peroxidation products in germ cells undergoes significant changes under the action of low-intensity EMR. The effect of microwave radiation (1, 5, 10 min) leads to the increase of superoxide dismutase activity, nevertheless, 20 min exposure decreased this index to the level of control values as it is shown. It has been established that EMR at frequencies used for mobile communications reduce the activity of antioxidant protection system components, especially catalase and glutathione peroxidase. The growth of catalase activity at the 10-cell stage of blastomere division (P < 0.05) is an exception. The results of two-way analysis of variance attest that microwave radiation factor causes the large part of all observable modifications.

Antioxidant activity of various Mauritanian date palm (Phoenix dactylifera L.) fruits at two edible ripening stages

PubMed Central

Mohamed Lemine, Fouteye Mint; Mohamed Ahmed, Mohamed Vall O; Ben Mohamed Maoulainine, Lobna; Bouna, Zein el Abidine O; Samb, Abdoulaye; O Boukhary, Ali O Mohamed Salem

2014-01-01

The increasing interest in plant phenolics and flavonoids outlined the necessity of determining their contents and biological activity in Mauritanian date palm fruits. Methanolic extracts of fruit of six date palm cultivars commonly grown in Mauritania were screened for their antioxidant activity, total phenolics, and flavonoid content at two edible ripening stages. Polyphenols and flavonoids were higher in theBlah stage, corresponding toKhalal in the standard Iraqi Arabic nomenclature, compared to the fully matureTamr stage regardless the cultivar. The average of total phenolics atBlah andTamr stages were 728.5 and 558.9 mg gallic acid equivalents (GAE) per 100 g dry matter (DM), whereas the average flavonoid content was 119.6 and 67.3 mg quercetin equivalents (QE) per 100 g DM, respectively. TheBlah stage also exhibited the highest total antioxidant activity with a Trolox equivalents antioxidant capacity (TEAC) value of 129.3 μmol/100 g DM founded in Bou seker's Blah date, followed by Tijib cultivar with TEAC value of 114.3 μmol/100 g DM and an average TEAC value of 107.5 μmol/100 g DM. Furthermore, a high positive correlation was found between total phenolics inTamr (r = 0.92) andBlah (r = 0.87) stages and TEAC of fruit methanolic extracts compared to the flavonoids, suggesting that phenolics were the major contributor to the antioxidant activity. PMID:25493188