Life Sciences Commons^™

Transforming Growth Factor Betas Induce Mmp-2 And Mmp-9 Secretion Via Smad-Dependent Signaling In Human Endometrial And Endometriotic Cells, Ezekiel O. Mecha, Cong Sui, Charles O.A . Omwandho, Hans-Rudolf Tinneberg, Lutz Konrad

Innovative Research Publications IRP India

Transforming growth factor-betas (TGF-βs) are elevated during menstruation and are involved in endometriosis. Similarly, matrix metalloproteinases like MMP-2 are also highly expressed in patients with endometriosis. Expression of gelatinases, MMP-2 and MMP-9, is increased by TGF-βs. TGF- βs bind and activate receptor-mediated Smad proteins to mediate gene expression, however, also non-Smad signaling pathways participate in signal transduction of the TGF-βs. In this study, we found that of MMP-2 and MMP-9 is higher in stromal cells especially in endometriotic cells compared to epithelial cells. Treatment of endometrial and endometriotic stromal and epithelial cells with TGF-β1 or TGF-β2 decreased cell numbers, induced …

Evaluation Of Effective Operational Cycle Time And Bioprocess Parameters In A Sequential Batch Reactor For Efficient Organic And Nutrient Removal From Domestic Sewage, Sandip S. Magdum, Siva Kumar Varigala, Yogesh N. Patil, Gauri P. Minde, Janardhan B. Bornare, V. Kalyanraman

Sandip S. Magdum

Anaerobic, anoxic and aerobic environment can be simulated in the single stage sequential batch reactor (SBR) . Various design conditions viz., combinations of different phase time and different cycle time, hydraulic residence time (HRT), substrate loading rate, sludge age (SRT) and aeration time were analyzed for optimum biological treatment. The pilot runs were evaluated with the design conditions of food/microbe ratio (F/M) 0.2 per day and MLSS of 4950 mg/L. For the given design conditions 4, 5 and 6 hours cycle lengths were analyzed for their efficient performance with 30-33% of decant volume for sewage containing C:N:P of 100:8:2. Studies …

The Complexity Of Molecular Interactions And Bindings Between Cyclic Peptide And Inhibit Polymerase A And B1 (Pac-Pb1n) H1n1, Arli A. Parikesit, Harry Noviardi Hn, Djati Kerami Dk, Usman Sumo Friend Tambunan Usft

Arli A Parikesit

The influenza/H1N1 virus has caused hazard in the public health of many countries. Hence, existing influenza drugs could not cope with H1N1 infection due to the high mutation rate of the virus. In this respect, new method to block the virus was devised. The polymerase pac-pb1n enzyme is responsible for the replication of H1N1 virus. Thus, novel inhibitors were developed to ward off the functionality of the enzyme. In this research, cyclic peptides has been chosen to inhibit PAc-PB1n due to its proven stability in reaching the drug target. Thus, computational method for elucidating the molecular interaction between cyclic peptides …

The In Silico Molecular Interaction Of Organoboron Compounds As Curative Measure Toward Cervical Cancer, Ridla Bakri Rb, Arli A. Parikesit, Cipta Prio Satryanto Cps, Djati Kerami Dk, Usman Sumo Friend Tambunan Usft

Arli A Parikesit

No abstract provided.

Experimental Demonstration Of Bindingless Signal Delivery In Human Cells Via Microfluidics, Fang-Tzu Chuang

Fang-Tzu Chuang

The cellular signal transduction is commonly believed to rely on the direct “contact” or “binding” of the participating molecule reaction that depends positively on the corresponding molecule concentrations. In living systems, however, it is somewhat difficult to precisely match the corresponding rapid “binding,” depending on the probability of molecular collision, existing in the cellular receptor-ligand interactions. Thus, a question arises that if there is another mechanism (i.e., bindingless) that could promote this signal communication. According to this hypothesis, we report a cellular model based on the examination of intracellular calcium concentration to explore whether the unidentified signal delivery in cells …

Biokimia Dan Teknologi Farmasi: Desain Obat Dan Vaksin Dengan Pendekatan Biomedis Molekular, Usman Sumo Friend Tambunan Usft, Arli A. Parikesit Aap

Arli A Parikesit

No abstract provided.

Modelling And Optimal Control Of A Time-Delayed Switched System In Fed-Batch Process, Chongyang Liu, Zhaohua Gong

Chongyang Liu

The main control goal of the fed-batch process is to maximize the yield of target product as well as to minimize the operation costs simultaneously. Considering the existence of time delay and the switching nature in the fed-batch process, a time-delayed switched system is proposed to formulate the 1,3-propanediol (1,3-PD) production process. Some important properties of the system are also discussed. Taking the switching instants and the terminal time as the control variables, a free terminal time delayed optimal control problem is then presented. Using a time-scaling transformation and parameterizing the switching instants into new parameters, an equivalently optimal control …

Enhanced Transmission Of Higher Order Plasmon Modes With Random Au Nanoparticles In Periodic Hole Arrays, Fang-Tzu Chuang

Fang-Tzu Chuang

The enhanced transmission of higher order plasmon modes with random gold nanoparticles embedded in periodic hole arrays using asymmetric pair aperture as a unit is investigated in the midinfrared regime. Different thicknesses of gold film were deposited inside holes and then annealed to form randomly sized and distributed nanoparticles. The holes deposited with thin gold film exhibit significantly enhanced transmission in higher order modes after thermal annealing. The enormous local electric field around the nanoparticles enhances the scattering effect that contributes to the enhanced infrared transmission. This unique design, which integrates localized and propagating surface plasmons, provides an easy way …

Screening Of Commercial Cyclic Peptides As Inhibitor Envelope Protein Dengue Virus (Denv) Through Molecular Docking And Molecular Dynamics, Arli A. Parikesit, Kinanty Kinanty, Usman Sumo F. Tambunan

Arli A Parikesit

Dengue virus (DENV) has spread throughout the world, especially in tropical climates. Effective treatment of DENV infection is not yet available although several candidate vaccines have been developed. Treatment at this time is only to reduce symptoms and reduce the risk of death. Therefore, antiviral treatment is much needed. Envelope protein is one of the structural proteins of DENV which is known and could be a target of antiviral inhibitors and plays a special role in the fusion process. The aim of this research is to screen the commercial cyclic peptides which are used as inhibitors of envelope protein DENV …

Bone Morphogenetic Protein 4 Inhibition Of Tgfβ-2 Induced Cross-Linked Actin Networks In Human Trabecular Meshwork Cells, Rafael A. Lima, Michela Montecchi-Palmer, Jaclyn Bermudez, Abbot F. Clark Phd, Robert J. Wordinger Phd

ral5@rice.edu

Bone Morphogenetic Protein 4 Inhibition of TGFβ-2 Induced Cross-Linked Actin Networks (CLANs) in Human Trabecular Meshwork Cells

RAFAEL A. LIMA1, MICHELA MONTECCHI-PALMER2,3, JACLYN BERMUDEZ2 ABBOT F. CLARK2, AND ROBERT J. WORDINGER2

1 Rice University, Houston, Texas, 2 Department of Cell Biology and Anatomy, North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, Texas, 3 Alcon Research, Ltd., Fort Worth, Texas

Background:

Primary open-angle glaucoma (POAG) is a degenerative eye disease characterized by irreversible loss of retinal ganglion cells. One of the most significant risk factors for POAG is increased intraocular pressure (IOP). Elevated IOP is …

Effect Of Paired Apertures In A Periodic Hole Array On Higher Order Plasmon Modes, Fang-Tzu Chuang

Fang-Tzu Chuang

We demonstrate that the transmission of higherorder surface plasmon modes in the mid-infrared range can be enhanced through rectangular hole array on the basis of paired apertures. Experiments prove that enhanced high-order transmission can be generated by either identical shapes or combinations of different hole shapes in pairs. The structure factor is adopted to explain the observed intensity of enhanced transmission. Numerical simulations of the enhanced secondorder mode verify a significant field enhancement in a unit cell of pairs. It is clarified that the separation between the paired apertures and the paired resonance is the key to determine certain higher-order …

Two Infrared Emission Modes With Different Wavelengths And Orthogonal Polarization In A Waveguide Thermal Emitter, Fang-Tzu Chuang

Fang-Tzu Chuang

This study investigates a Au/SiO2/Au waveguide thermal emitter incorporating a metallic grating embedded in the SiO2 layer. The metal grating acts as a beam splitter, dividing the device into two waveguide structures determined by the polarization of the waveguide modes. The thermal radiation spectrum exhibits two peaks with orthogonal polarization. The emitted wavelengths of the two waveguide modes can be adjusted by controlling the thickness of the SiO2 layers on both sides of the metallic grating during the fabrication process. The emission peaks have ratios of the full width at half maximum to the peak wavelength of 0.057 and 0.05 …

Nanoprojection Lithography Using Self-Assembled Interference Modules For Manufacturing Plasmonic Gratings, Fang-Tzu Chuang

Fang-Tzu Chuang

Abstract—A new nanoprojection lithography (NPL) is proposed to manufacture plasmonic nanogratings. Here, low-cost self-assembly elastomeric polydimethylsiloxane wavy structures are used as the interference modules, with their periods and amplitudes largely controlled by the applied mechanical strain in the synthesis process. Well defined plasmonic grating couplers with desired feature sizes and wavelengths of operation were obtained. This NPL may enable large-area and flash manufacturing of plasmonic nanogratings with tunable array periods.

Health Effects Of Trihalomethanes As Chlorinated Disinfection By Products: A Review Article, Mohammad Reza Mohammad Shafiee, Lobat Taghavi

Mohammad Reza Mohammad Shafiee

Trihalomethanes (THMs) were among the first disinfection byproducts to be discovered in chlorinated water. The substances form during a reaction between chlorine and organic matter in the water. Trihalomethanes are suspected to have negative effects on birth such as, low birth weight, intrauterine growth retardation in term births, as well as gestational age and preterm delivery. There are also some evidences showing these by-products to be mutagenic and carcinogenic, the greatest amount of evidence being related to the bladder cancer. However, there exist inconsistencies regarding such effects of THMs as different studies have provided different results in this regard. The …

Self-Assembled Rippling Structure Based On Metal-Elastomer Composite For Tunable Plasmonics, Fang-Tzu Chuang

Fang-Tzu Chuang

We demonstrate that a periodic metallic wavy-structure can be easily fabricated on elastomeric polydymethylsiloxane (PDMS) substrates. The metallic wavy-structures are self-assembly formed by thermal evaporation of Ag on PDMS without any lithography processes. The size of the PDMS substrate with an aspect ratio (the ratio of length to width) higher than 2 are found to be necessary to self-assemble the one-dimensional metallic wavy-structure. The period of the wavy-structure is controllable by varing the thickness of the deposited silver film. The elastomeric- gratings can excite surface plasmon on Ag/air interfaces; the resonant wavelength can be tuned to a range of 3.5% …

Localized Shape Resonance On Silver Film Perforated By H-Shaped And More Complex Shaped Hole Arrays, Fang-Tzu Chuang

Fang-Tzu Chuang

The experimental results of light transmission through periodic array of H-shaped hole and more complicated hole which is a combination of multiple U shape are demonstrated. The observations indicate that the localized shape resonance in the longest resonant length of unfolded U-shaped part of the hole always appears. However, localized modes resonant in smaller U-shaped length don't always appear. Localized mode with non-U-shaped resonant path cannot be seen in our sample. In addition, localized mode with different order and resonant path can be excited by different polarized light.

Evolution And Quantitative Comparison Of Genome-Wide Protein Domain Distributions, Arli A. Parikesit, Peter F. Stadler, Sonja J. Prohaska

Arli A Parikesit

The metabolic and regulatory capabilities of an organism are implicit in its protein content. This is often hard to estimate, however, due to ascertainment biases inherent in the available genome annotations. Its complement of recognizable functional protein domains and their combinations convey essentially the same information and at the same time are much more readily accessible, although protein domain models trained for one phylogenetic group frequently fail on distantly related sequences. Pooling related domain models based on their GO-annotation in combination with de novo gene prediction methods provides estimates that seem to be less affected by phylogenetic biases. We show …

Quantitative Comparison Of Genomic-Wide Protein Domain Distributions, Arli A. Parikesit, Peter F. Stadler, Sonja J. Prohaska

Arli A Parikesit

Investigations into the origins and evolution of regulatory mechanisms require quantitative estimates of the abundance and co-occurrence of functional protein domains among distantly related genomes. Currently available databases, such as the SUPERFAMILY, are not designed for quantitative comparisons since they are built upon transcript and protein annotations provided by the various different genome annotation projects. Large biases are introduced by the differences in genome annotation protocols, which strongly depend on the availability of transcript information and well-annotated closely related organisms. Here we show that the combination of de novo gene predictors and subsequent HMM-based annotation of SCOP domains in the …

Ethylene Receptors Function As Components Of High-Molecular-Mass Protein Complexes In Arabidopsis, Yi-Feng Chen, Zhiyong Gao, Robert J. Kerriss Iii, Wuyi Wang, Brad M. Binder, G. Eric Schaller

Brad M. Binder

The gaseous plant hormone ethylene is perceived in Arabidopsis thaliana by a five-member receptor family composed of ETR1, ERS1, ETR2, ERS2, and EIN4. Methodology/Principal Findings Gel-filtration analysis of ethylene receptors solubilized from Arabidopsis membranes demonstrates that the receptors exist as components of high-molecular-mass protein complexes. The ERS1 protein complex exhibits an ethylene-induced change in size consistent with ligand-mediated nucleation of protein-protein interactions. Deletion analysis supports the participation of multiple domains from ETR1 in formation of the protein complex, and also demonstrates that targeting to and retention of ETR1 at the endoplasmic reticulum only requires the first 147 amino acids of …

Genetic Effect Of The Dwarfing Genes On Some Culm Characteristics Associatcd With Lodging Resistance In Bread Wheat, Md. Mahbub Hasan

Md. Mahbub Hasan

Due to the challenge of screening traits related to lodging resistance under natural field conditions, selection for lodging resistant varieties in wheat breeding programs is difficult. The identification of easily measurable culm anatomical traits related to lodging resistance would simplify the selection process. The present study was conducted to determine the effect of dwarfing genes on culm anatomical traits related to lodging resistance in our of basal internode 1. Field and laboratory study was conducted in Shahjalal University of Science and Technology, Sylhet, Bangladesh with eight wheat genotypes having Rhr1, Rht2 dwarfing genes in them and a local land race …

Microproteomics: Analysis Of Protein Diversity In Small Samples, Howard B. Gutstein, Jeffrey S. Morris, Suresh P. Annangudi, Jonathan V. Sweedler

Jeffrey S. Morris

Proteomics, the large-scale study of protein expression in organisms, offers the potential to evaluate global changes in protein expression and their post-translational modifications that take place in response to normal or pathological stimuli. One challenge has been the requirement for substantial amounts of tissue in order to perform comprehensive proteomic characterization. In heterogeneous tissues, such as brain, this has limited the application of proteomic methodologies. Efforts to adapt standard methods of tissue sampling, protein extraction, arraying, and identification are reviewed, with an emphasis on those appropriate to smaller samples ranging in size from several microliters down to single cells. The …

A Kinetic Model For Growth And Biosynthesis Of Medium-Chain-Length Poly-(3-Hydroxyalkanoates) In Pseudomonas Putida, Irene Tan Kit Ping

Irene Tan Kit Ping

A kinetic model is presented giving a mathematical description of batch culture of Pseudomonas putida PGA1 grown using saponified palm kernel oil as carbon source and ammonium as the limiting nutrient. The growth of the micro-organism is well-described using. Tessier-type model which takes into account the inhibitory effect of ammonium at high concentrations. The ammonium consumption rate by the cells is related ill proportion to the rate of growth. The intracellular production of medium-chain-length poly(3-hydroxyalkanoates) (PHA(MCL)) by P. putida PGA1 cells is reasonably modeled by the modified Luedeking-Piret kinetics, which incorporate a function of product Synthesis inhibition (or reduction) by …

The Bible Closet: The Debate Over Same-Sex Marriage, Linsey L. Krauss

Linsey L Krauss

No abstract provided.

Ethylene Stimulates Nutations That Are Dependent On The Etr1 Receptor, Brad M. Binder, Ronan C. O'Malley, Wuyi Wang, Tobias C. Zutz, Anthony B. Bleeker

Brad M. Binder

Ethylene influences a number of processes in Arabidopsis (Arabidopsis thaliana) through the action of five receptors. In this study, we used high-resolution, time-lapse imaging to examine the long-term effects of ethylene on growing, etiolated Arabidopsis seedlings. These measurements revealed that ethylene stimulates nutations of the hypocotyls with an average delay in onset of over 6 h. The nutation response was constitutive in ctr1-2 mutants maintained in air, whereas ein2-1 mutants failed to nutate when treated with ethylene. Ethylene-stimulated nutations were also eliminated in etr1-7 loss-of-function mutants. Transformation of the etr1-7 mutant with a wild-type genomic ETR1 transgene rescued the nutation …

Soluble Fibrin Inhibits Monocyte Adherence And Cytotoxicity Against Tumor Cells: Implications For Cancer Metastasis, John Biggerstaff, Brandy Weidow, Jacqueline Vidosh, Judith Dexheimer, Shonak Patel, Pretesh Patel

John Biggerstaff

Background Soluble fibrin (sFn) is a marker for disseminated intravascular coagulation and may have prognostic significance, especially in metastasis. However, a role for sFn in the etiology of metastatic cancer growth has not been extensively studied. We have reported that sFn cross-linked platelet binding to tumor cells via the major platelet fibrin receptor αIIbβ3, and tumor cell CD54 (ICAM-1), which is the receptor for two of the leukocyte β2 integrins (αLβ2 and aMβ2). We hypothesized that sFn may also affect leukocyte adherence, recognition, and killing of tumor cells. Furthermore, in a rat experimental metastasis model sFn pre-treatment of tumor cells …

Farnesylated Lamins, Progeroid Syndromes And Farnesyl Transferase Inhibitors, Michael Sinensky, A. E. Rusinol

Michael Sinensky

Three mammalian nuclear lamin proteins, lamin B1, lamin B2 and the lamin A precursor, prelamin A, undergo canonical farnesylation and processing at CAAX motifs. In the case of prelamin A, there is an additional farnesylation-dependent endoproteolysis, which is defective in two congenital diseases: Hutchinson-Gilford progeria (HGPS) and restrictive dermopathy (RD). These two diseases arise respectively from defects in the prelamin A substrate and the enzyme (ZmpSte24) that processes it. Recent work has shed light on the roles of the lamin proteins and the enzymes involved in their farnesylation-dependent maturation. Other experimental work, including mouse model studies, have examined the possibility …

Dna Damage Responses In Progeroid Syndromes Arise From Defective Maturation Of Prelamin A, Michael Sinensky, Y. Liu, A. Rusinol, Y. Wang, Y. Zou

Michael Sinensky

The genetic diseases Hutchinson-Gilford progeria syndrome (HGPS) and restrictive dermopathy (RD) arise from accumulation of farnesylated prelamin A because of defects in the lamin A maturation pathway. Both of these diseases exhibit symptoms that can be viewed as accelerated aging. The mechanism by which accumulation of farnesylated prelamin A leads to these accelerated aging phenotypes is not understood. Here we present evidence that in HGPS and RD fibroblasts, DNA damage checkpoints are persistently activated because of the compromise in genomic integrity. Inactivation of checkpoint kinases Ataxia-telangiectasia-mutated (ATM) and ATR (ATM- and Rad3-related) in these patient cells can partially overcome their …

Molecular Characterization Of A Isoenzyme Of The Targeting Peptide Degrading Protease, Prep2- Catalysis, Subcellular Localization, Expression And Evolution, S. Bhushan, A. Stahl, S. Nilsson, B. Lefebvre, D. Mcwilliams, S.J. Wright, M. Seki, D.A. Liberles, K. Shinozaki, Barry D. Bruce, M. Boutry, E. Glaser

Barry D. Bruce

We have previously identified a zinc metalloprotease involved in the degradation of mitochondrial and chloroplast targeting peptides, the presequence protease (PreP). In the Arabidopsis thaliana genomic database, there are two genes that correspond to the protease, the zinc metalloprotease (AAL90904) and the putative zinc metalloprotease (AAG13049). We have named the corresponding proteins AtPreP1 and AtPreP2, respectively. AtPreP1 and AtPreP2 show significant differences in their targeting peptides and the proteins are predicted to be localized in different compartments. AtPreP1 was shown to degrade both mitochondrial and chloroplast targeting peptides and to be dual targeted to both organelles using an ambiguous targeting …

Reduced Macrophage Apoptosis Is Associated With Accelerated Atherosclerosis In Low-Denstiy Lipoprotein Receptor-Null Mice, Michael Sinensky, J. Liu, D. P. Thweke, Y. R. Su, M. F. Linton, S. Fazio

Michael Sinensky

Objective— The majority of apoptotic cells in atherosclerotic lesions are macrophages. However, the pathogenic role of macrophage apoptosis in the development of atherosclerosis remains unclear. Elevated expression of Bax, one of the pivotal proapoptotic proteins of the Bcl-2 family, has been found in human atherosclerotic plaques. Activation of Bax also occurs in free cholesterol-loaded and oxysterol-treated mouse macrophages. In this study, we examined the effect of Bax deficiency in bone marrow-derived leukocytes on the development of atherosclerosis in low-density lipoprotein receptor-null (LDLR−/−) mice. Methods and Results— Fourteen 8-week-old male LDLR−/− mice were lethally irradiated and reconstituted with either wild-type (WT) …

Towards A Systems Approach To Understanding Plant Cell Walls, Chris R. Somerville, Stefan Bauer, Ginger Brininstool, Michelle Facette, Thorsten Hamann, Jennifer Milne, Erin Osborne, Alex Paradez, Staffan Persson, Ted K. Raab, Sonja Vorwerk, Heather Youngs

Ted K. Raab

One of the defining features of plants is a body plan based on the physical properties of cell walls. Structural analyses of the polysaccharide components, combined with highresolution imaging, have provided the basis for much of the current understanding of cell walls. The application of genetic methods has begun to provide new insights into how walls are made, how they are controlled, and how they function. However, progress in integrating biophysical, developmental, and genetic information into a useful model will require a system-based approach.