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Synthesis Pathway (synthesis + pathway)
Selected AbstractsIdentification of cyanobacteria and their toxigenicity in environmental samples by rapid molecular analysisENVIRONMENTAL TOXICOLOGY, Issue 6 2001Judith A. Baker Abstract We report molecular analyses which identify cyanobacterial strains present in environmental samples. These analyses do not require the isolation and culture of strains. Identification of cyanobacteria used the polymerase chain reaction (PCR), based on the phycocyanin operon. Differentiation was either by restriction endonuclease digestion (restriction fragment length polymorphisms) or sequencing of the PCR products. Identification was based on sequence homology of the intergenic spacer region (IGS) between the ,- and ,-phycocyanin subunits (PC-IGS) with database records. We have found that the length and sequence of the PC-IGS is capable of predicting the genus accurately, but not the species. Toxigenicity was determined with oligonucleotide probes for key steps in the microcystin toxin synthesis pathway. We have shown that it is possible to easily and routinely obtain PCR amplification products and differentiate the strains in bloom samples. The methods can detect even minor components in bloom samples, which may not be apparent on microscopic examination. Genetic probes for microcystin toxigenicity are effective on environmental samples, eliminating the need for isolation and culture of the organisms. The use of a suite of tests described here will allow water managers to determine the presence and the type of cyanobacteria and their microcystin toxigenicity. © 2001 John Wiley & Sons, Inc. Environ Toxicol 16: 472,482, 2001 [source] A novel role for polyamines in adult neurogenesis in rodent brainEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 2 2004Jordane Malaterre Abstract Although neurogenesis in the adult is known to be regulated by various internal cues such as hormones, growth factors and cell-adherence molecules, downstream elements underlying their action at the cellular level still remain unclear. We previously showed in an insect model that polyamines (putrescine, spermidine and spermine) play specific roles in adult brain neurogenesis. Here, we demonstrate their involvement in the regulation of secondary neurogenesis in the rodent brain. Using neurosphere assays, we show that putrescine addition stimulates neural progenitor proliferation. Furthermore, in vivo depletion of putrescine by specific and irreversible inhibition of ornithine decarboxylase, the first key enzyme of the polyamine synthesis pathway, induces a consistent decrease in neural progenitor cell proliferation in the two neurogenic areas, the dentate gyrus and the subventricular zone. The present study reveals common mechanisms underlying birth of new neurons in vertebrate and invertebrate species. [source] Nuclear factor TDP-43 can affect selected microRNA levelsFEBS JOURNAL, Issue 10 2010Emanuele Buratti TDP-43 has recently been described as the major component of the inclusions found in the brain of patients with a variety of neurodegenerative diseases, such as frontotemporal lobar degeneration and amyotrophic lateral sclerosis. TDP-43 is a ubiquitous protein whose specific functions are probably crucial to establishing its pathogenic role. Apart from its involvement in transcription, splicing and mRNA stability, TDP-43 has also been described as a Drosha-associated protein. However, our knowledge of the role of TDP-43 in the microRNA (miRNA) synthesis pathway is limited to the association mentioned above. Here we report for the first time which changes occur in the total miRNA population following TDP-43 knockdown in culture cells. In particular, we have observed that let-7b and miR-663 expression levels are down- and upregulated, respectively. Interestingly, both miRNAs are capable of binding directly to TDP-43 in different positions: within the miRNA sequence itself (let-7b) or in the hairpin precursor (miR-663). Using microarray data and real-time PCR we have also identified several candidate transcripts whose expression levels are selectively affected by these TDP-43,miRNA interactions. [source] Cover Picture: Synthesis of a Self-Assembled Hybrid of Ultrananocrystalline Diamond and Carbon Nanotubes (Adv. Mater.ADVANCED MATERIALS, Issue 12 200512/2005) Abstract The cover shows self-assembled hybrids of ultrananocrystalline diamond (UNCD) and carbon nanotubes (CNTs). These hybrids were successfully prepared by their simultaneous growth within an argon-rich Ar/CH4 plasma, in work reported on p.,1496 by Carlisle and co-workers. Various methods demonstrated the coexistence of UNCD and CNTs, and the capability of controlling the relative fraction and configuration of UNCD and CNTs in the hybrid material. This new synthesis pathway enables the development of new nanocarbons with unique mechanical, tribological, and electrochemical properties. [source] H, feedback-control theory in biochemical systemsINTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL, Issue 1 2008E. Gershon Abstract In this paper we study the possible optimality of biochemical pathways in the H, sense. We start by presenting simple linearized models of single enzymatic reaction systems, where we apply classical and modern tools of feedback-control theory. We then apply the results obtained by our analysis to a linearly unbranched enzyme pathway system, where we explore the effect of a negative feedback loop internally exerted on the system by a self-product of the pathway. We then probe the sensitivity of the enzymatic system to variations in certain variables and we deal with the problem of assessing the optimality of the static-output feedback control, in the H, sense, inherent to the closed-loop system. In this point we demonstrate the applicability of our results via a theoretical example that provides an open-loop and closed-loop analysis of a four-block enzymatic system. We then apply the various tools we developed to the optimal analysis of the Threonine synthesis pathway which is regulated by three feedback loops. We demonstrate that this pathway is optimal in the H, sense, in the face of considerable uncertainties in the various enzyme concentrations of the pathway. Copyright © 2007 John Wiley & Sons, Ltd. [source] An Integrative Analysis of the Effects of Auxin on Jasmonic Acid Biosynthesis in Arabidopsis thalianaJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 1 2006Jun Liu Abstract Auxin and jasmonic acid (JA) are two plant phytohormones that both participate in the regulation of many developmental processes. Jasmonic acid also plays important roles in plant stress response reactions. Although extensive investigations have been undertaken to study the biological functions of auxin and JA, little attention has been paid to the cross-talk between their regulated pathways. In the few available reports examining the effects of auxin on the expression of JA or JA-responsive genes, both synergetic and antagonistic results have been found. To further investigate the relationship between auxin and JA, we adopted an integrative method that combines microarray expression data with pathway information to study the behavior of the JA biosynthesis pathway under auxin treatment. Our results showed an overall down regulation of genes involved in JA biosynthesis, providing the first report of a relationship between auxin and the JA synthesis pathway in Arabidopsis seedlings. (Managing editor: Ya-Qin Han) [source] Gibberellins, jasmonate and abscisic acid modulate the sucrose-induced expression of anthocyanin biosynthetic genes in ArabidopsisNEW PHYTOLOGIST, Issue 4 2008Elena Loreti Summary ,,Anthocyanins are secondary metabolites, which play an important role in the physiology of plants. Both sucrose and hormones regulate anthocyanin synthesis. Here, the interplay between sucrose and plant hormones was investigated in the expression of sucrose-regulated genes coding for anthocyanin biosynthetic enzymes in Arabidopsis seedlings. ,,The expression pattern of 14 genes involved in the anthocyanin biosynthetic pathway, including two transcription factors (PAP1, PAP2), was analysed by real-time reverse transcriptase polymerase chain reaction (RT-PCR) in Arabidopsis seedlings treated with sucrose and plant hormones. ,,Sucrose-induction of the anthocyanin synthesis pathway was repressed by the addition of gibberellic acid (GA) whereas jasmonate (JA) and abscisic acid (ABA) had a synergic effect with sucrose. The gai mutant was less sensitive to GA-dependent repression of dihydroflavonol reductase. This would seem to prove that GAI signalling is involved in the crosstalk between sucrose and GA in wild-type Arabidopsis seedlings. Conversely, the inductive effect of sucrose was not strictly ABA mediated. Sucrose induction of anthocyanin genes required the COI1 gene, but not JAR1, which suggests a possible convergence of the jasmonate- and sucrose-signalling pathways. ,,The results suggest the existence of a crosstalk between the sucrose and hormone signalling pathways in the regulation of the anthocyanin biosynthetic pathway. [source] Expression of Genes in the Canine Pre-implantation Uterus and Embryo: Implications for an Active Role of the Embryo Before and During InvasionREPRODUCTION IN DOMESTIC ANIMALS, Issue 6 2008S Schäfer-Somi Contents The aim of the present study was to assess genes expressed in maternal uterine tissue and pre-implantation embryos which are presumably involved in maternal recognition and establishment of canine pregnancy. For this purpose, 10 pregnant bitches were ovariohysterectomized between days 10 and 12 after mating. Four non-pregnant bitches served as controls. Early pregnancy was verified by flushing the uterine horns with PBS solution. The collected embryos (n = 60) were stored deep-frozen (,80°C). Uterine tissue was excised, snaps frozen in liquid nitrogen and homogenized using TRI Reagent. All embryos from one litter were thawed together and also homogenized in TRI Reagent. RT-PCR was performed to prove mRNA expression of progesterone receptor, key enzymes of the prostaglandin synthesis pathway, selected growth factors, cytokines, immune cell receptors, major histocompatibility complex (MHC) and matrix-metalloproteinases (MMP). Only pregnant uteri revealed the presence of mRNA for interferon (IFN)-,, IL-4 and CD-8, which resembles the milieu in humans and other mammalians. Similarly, in day 10 embryos, mRNA for transforming growth factor-,, insulin-like growth factor-1,-2, hepatocyte growth factor, leukaemia inhibitor factor, tumour necrosis factor-,, interleukin-1,,-6,-8, cyclooxygenase-2, CD4+ cells, and MMP-2 and -9 were detected, but not MHC-I or -II. We therefore suppose that the canine embryo, like its human counterpart, actively initiates measures to prevent attacks from the maternal immune system to prepare its own adhesion, nidation, growth and further development. [source] Mapping of the bovine genes of the de novo AMP synthesis pathway,ANIMAL GENETICS, Issue 6 2004T. Bønsdorff Summary The purine nucleotides adenosine monophosphate (AMP) and guanosine monophosphate (GMP) are critical for energy metabolism, cell signalling and cell reproduction. Despite their essential function, little is known about the regulation and in vivo expression pattern of the genes involved in the de novo purine synthesis pathway. The complete coding region of the bovine phosphoribosylaminoimidazole carboxylase gene (PAICS), which catalyses steps 6 and 7 of the de novo purine biosynthesis pathway, as well as bovine genomic sequences of the six other genes in the pathway producing inosine monophosphate (IMP) and AMP [phosphoribosyl pyrophosphate amidotransferase (PPAT), phosphoribosylglycinamide formyltransferase (GART), phosphoribosylformylglycinamidine synthase (PFAS), adenylosuccinate lyase (ADSL), 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (ATIC) and adenylosuccinate synthase (ADSS)], were identified. The genes were mapped to segments of six different bovine chromosomes using a radiation hybrid (RH) cell panel. The gene PPAT, coding for the presumed rate-limiting enzyme of the purine de novo pathway was closely linked to PAICS on BTA6. These, and the other bovine locations i.e. GART at BTA1, PFAS at BTA19, ADSL at BTA5, ATIC at BTA2 and ADSS at BTA16, are in agreement with published comparative maps of cattle and man. PAICS and PPAT genes are known to be closely linked in human, rat and chicken. Previously, an expressed sequence fragment of PAICS (Bos taurus corpus luteum, BTCL9) was mapped to BTA13. By isolation and characterization of a BAC clone, we have now identified a PAICS processed pseudogene sequence (,PAICS) on BTA13. Processed pseudogene sequences of PAICS and other genes of the purine biosynthesis pathway were identified in several mammalian species, indicating that the genes of this pathway have been susceptible to retrotransposition. The seven bovine genes are expressed at a higher level in testicular and ovary tissues compared with skeletal muscle. [source] Protein preparation, crystallization and preliminary crystallographic studies of Bacillus subtilis glycinamide ribonucleotide transformylaseACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2009Yu-He Liang Glycinamide ribonucleotide transformylase (GART) catalyzes the transfer of a formyl group from formyl tetrahydrofolate (FTHF) to glycinamide ribonucleotide (GAR), which is an essential step in the de novo synthesis pathway of purines. In Bacillus subtilis, GART is encoded by the gene purN. In order to study the structure and function of B. subtilis GART, the purN gene was amplified, cloned into an expression vector and expressed in soluble form in Escherichia coli. The protein was purified to homogeneity and crystals suitable for X-ray data collection were obtained. These crystals diffracted to 2.5,Å resolution and belonged to space group P3121, with unit-cell parameters a = b = 95.5, c = 64.0,Å. [source] In silico genome-scale reconstruction and validation of the Corynebacterium glutamicum metabolic networkBIOTECHNOLOGY & BIOENGINEERING, Issue 2 2009Kjeld Raunkjær Kjeldsen Abstract A genome-scale metabolic model of the Gram-positive bacteria Corynebacterium glutamicum ATCC 13032 was constructed comprising 446 reactions and 411 metabolites, based on the annotated genome and available biochemical information. The network was analyzed using constraint based methods. The model was extensively validated against published flux data, and flux distribution values were found to correlate well between simulations and experiments. The split pathway of the lysine synthesis pathway of C. glutamicum was investigated, and it was found that the direct dehydrogenase variant gave a higher lysine yield than the alternative succinyl pathway at high lysine production rates. The NADPH demand of the network was not found to be critical for lysine production until lysine yields exceeded 55% (mmol,lysine,(mmol,glucose),1). The model was validated during growth on the organic acids acetate and lactate. Comparable flux values between in silico model and experimental values were seen, although some differences in the phenotypic behavior between the model and the experimental data were observed. Biotechnol. Bioeng. 2009;102: 583,597. © 2008 Wiley Periodicals, Inc. [source] COMMON EVOLUTIONARY ORIGIN OF STARCH BIOSYNTHETIC ENZYMES IN GREEN AND RED ALGAE,JOURNAL OF PHYCOLOGY, Issue 6 2005Nicola J. Patron Plastidic starch synthesis in green algae and plants occurs via ADP-glucose in likeness to prokaryotes from which plastids have evolved. In contrast, floridean starch synthesis in red algae proceeds via uridine diphosphate-glucose in semblance to eukaryotic glycogen synthesis and occurs in the cytosol rather than the plastid. Given the monophyletic origin of all plastids, we investigated the origin of the enzymes of the plastid and cytosolic starch synthetic pathways to determine whether their location reflects their origin,either from the cyanobacterial endosymbiont or from the eukaryotic host. We report that, despite the compartmentalization of starch synthesis differing in green and red lineages, all but one of the enzymes of the synthetic pathways shares a common origin. Overall, the pathway of starch synthesis in both lineages represents a chimera of the host and endosymbiont glycogen synthesis pathways. Moreover, host-derived proteins function in the plastid in green algae, whereas endosymbiont-derived proteins function in the cytosol in red algae. This complexity demonstrates the impacts of integrating pathways of host with those of both primary and secondary endosymbionts during plastid evolution. [source] Cerulenin Analogues as Inhibitors of Efflux Pumps in Drug-resistant Candida albicansARCHIV DER PHARMAZIE, Issue 3 2009Florian Diwischek Abstract Overexpression of the ABC transporters Cdr1 and Cdr2 or the major facilitator Mdr1 causes multidrug resistance in the human fungal pathogen Candida albicans. The fatty acid synthesis inhibitor cerulenin and the structurally unrelated Golgi transport inhibitor brefeldin A are substrates for both types of efflux pumps in Candida albicans. In an effort to overcome efflux pump-mediated drug resistance in Candida albicans, cerulenin analogues were generated using a variety of synthesis pathways. The so obtained cerulenin derivatives were tested on multidrug-resistant Candida albicans isolates which constitutively overexpress either Mdr1 or Cdr1 and Cdr2. Some of these compounds were found to decrease Mdr1-mediated resistance to brefeldin A up to eightfold compared to the control. [source] New roads lead to Rubisco in archaebacteriaBIOESSAYS, Issue 8 2007Oliver Mueller-Cajar The discovery of the CO2 -fixing enzyme Rubisco in the Archaebacteria has presented a conundrum in that they apparently lack the gene for phosphoribulokinase, which is required to generate Rubisco's substrate ribulose 1,5-bisphosphate (RuBP). However, two groups1, 2 have now demonstrated novel RuBP synthesis pathways, demystifying Rubisco's non-autotrophic and perhaps ancient role. A new CO2 fixing role for Rubisco, which is distinct from the globally dominant Calvin cycle, is providing important clues furthering our understanding of the evolution of autotrophy. This perspective is strengthened by the additional recognition in this commentary that some Rubisco-containing Archaea do also contain PRK and may represent an interesting autotrophic evolutionary transition. Supplementary material for this article can be found on the BioEssays website (http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html). BioEssays 29:722,724, 2007. © 2007 Wiley Periodicals, Inc. [source] In this issue: Biotechnology Journal 11/2009BIOTECHNOLOGY JOURNAL, Issue 11 2009Article first published online: 13 NOV 200 Forensic identification on chips Choi and Seo et al., Biotechnol. J. 2009, 4, 1530,1541 Short tandem repeat (STR) analysis can be used for genetic fingerprinting of individuals as it is done for forensic human identification. However, the current state-of-the-art STR genotyping processes and instruments are labor intensive, expensive, time consuming, and lack portability. Micro-total-analysis systems or lab-on-a-chip platforms based on microfabrication technologies have the capability to miniaturize and integrate bioanalysis steps in a single format and have already been successfully applied for forensic STR typing. Researchers from Daejeon, Korea, highlight up-to-date work on advanced microdevices for high-throughput STR genotyping, and a portable integrated microsystem for on-site forensic DNA analysis. Surface plasmon resonance on chips Maynard et al., Biotechnol. J. 2009, 4, 1542,1558 Technologies based on surface plasmon resonance (SPR) have allowed rapid, label-free characterization of protein-protein and protein-small molecule interactions. SPR has become the gold standard in industrial and academic settings, in which the interaction between a pair of soluble binding partners is characterized in detail or a library of molecules is screened for binding against a single soluble protein. In spite of these successes, SPR is only beginning to be adapted to the needs of membrane-bound proteins which are promising targets for drug and biomarker development. This team of authors from Austin, Minneapolis and Rochester (all USA) describe current SPR instrumentation and the potential for SPR nanopore arrays to enable quantitative, high-throughput screening of G-protein coupled receptor ligands and applications in cellular biology. Nucleotide immobilization on chips Sethi et al., Biotechnol. J. 2009, 4, 1513,1529 The development of oligonucleotide-based microarrays (biochips) is of major interest in science and biotechnology industry and has applications in a wide range of research areas including genomics, proteomics, computational biology and pharmaceuticals. Especially microarrays have proven to be a unique method for time and cost efficient analysis of thousands of genes at one. Authors from Delhi and Lucknow, India discuss currently used chemical strategies for immobilization of oligonucleotides and put a special emphasis on post-synthetic immobilization on glass surfaces. Recent advances on these synthesis pathways are presented in detail. [source] | ||||||||||||||||||||||