Independent Metabolic Pathways Research Articles

Bacteria use a catabolic patchwork pathway of apparently recent origin for degradation of the synthetic buffer compound TRIS.

The synthetic buffer compound TRIS (2-amino-2-(hydroxymethyl)propane-1,3-diol) is used in countless applications, and no detailed information on its degradation has been published so far. Herein, we describe the discovery of a complete bacterial degradation pathway for TRIS. By serendipity, a Pseudomonas strain was isolated from sewage sludge that was able to grow with TRIS as only carbon and nitrogen source. Genome and transcriptome analyses revealed two adjacent gene clusters embedded in a mobile genetic element on a conjugative plasmid to be involved in TRIS degradation. Heterologous gene expression revealed cluster I to encode a TRIS uptake protein, a TRIS alcohol dehydrogenase, and a TRIS aldehyde dehydrogenase, catalyzing the oxidation of TRIS into 2-hydroxymethylserine. Gene cluster II encodes a methylserine hydroxymethyltransferase (mSHMT) and a d-serine dehydratase that plausibly catalyze the conversion of 2-hydroxymethylserine into pyruvate. Conjugational plasmid transfer into Pseudomonas putida KT2440 enabled this strain to grow with TRIS and with 2-hydromethylserine, demonstrating that the complete TRIS degradation pathway can be transmitted by horizontal gene transfer. Subsequent enrichments from wastewater purification systems led to the isolation of further TRIS-degrading bacteria from the Pseudomonas and Shinella genera carrying highly similar TRIS degradation gene clusters. Our data indicate that TRIS degradation evolved recently via gene recruitment and enzyme adaptation from multiple independent metabolic pathways, and database searches suggest that the TRIS degradation pathway is now globally distributed. Overall, our study illustrates how engineered environments can enhance the emergence of new microbial metabolic pathways in short evolutionary time scales.

Mannose metabolism inhibition sensitizes acute myeloid leukaemia cells to therapy by driving ferroptotic cell death

Resistance to standard and novel therapies remains the main obstacle to cure in acute myeloid leukaemia (AML) and is often driven by metabolic adaptations which are therapeutically actionable. Here we identify inhibition of mannose-6-phosphate isomerase (MPI), the first enzyme in the mannose metabolism pathway, as a sensitizer to both cytarabine and FLT3 inhibitors across multiple AML models. Mechanistically, we identify a connection between mannose metabolism and fatty acid metabolism, that is mediated via preferential activation of the ATF6 arm of the unfolded protein response (UPR). This in turn leads to cellular accumulation of polyunsaturated fatty acids, lipid peroxidation and ferroptotic cell death in AML cells. Our findings provide further support to the role of rewired metabolism in AML therapy resistance, unveil a connection between two apparently independent metabolic pathways and support further efforts to achieve eradication of therapy-resistant AML cells by sensitizing them to ferroptotic cell death.

Regulations of myo-inositol homeostasis: Mechanisms, implications, and perspectives.

Phosphorylation is the most common module of cellular signalling pathways. The dynamic nature of phosphorylation, which is conferred by the balancing acts of kinases and phosphatases, allows this modification to finely control crucial cellular events such as growth, differentiation, and cell cycle progression. Although most research to date has focussed on protein phosphorylation, non-protein phosphorylation substrates also play vital roles in signal transduction. The most well-established substrate of non-protein phosphorylation is inositol, whose phosphorylation generates many important signalling molecules such as the second messenger IP3, a key factor in calcium signalling. A fundamental question to our understanding of inositol phosphorylation is how the levels of cellular inositol are controlled. While the availability of protein phosphorylation substrates is known to be readily controlled at the levels of transcription, translation, and/or protein degradation, the regulatory mechanisms that control the uptake, synthesis, and removal of inositol are underexplored. Potentially, such mechanisms serve as an important layer of regulation of cellular signal transduction pathways. There are two ways in which mammalian cells acquire inositol. The historic use of radioactive 3H-myo-inositol revealed that inositol is promptly imported from the extracellular environment by three specific symporters SMIT1/2, and HMIT, coupling sodium or proton entry, respectively. Inositol can also be synthesized de novo from glucose-6P, thanks to the enzymatic activity of ISYNA1. Intriguingly, emerging evidence suggests that in mammalian cells, de novo myo-inositol synthesis occurs irrespective of inositol availability in the environment, prompting the question of whether the two sources of inositol go through independent metabolic pathways, thus serving distinct functions. Furthermore, the metabolic stability of myo-inositol, coupled with the uptake and endogenous synthesis, determines that there must be exit pathways to remove this extraordinary sugar from the cells to maintain its homeostasis. This essay aims to review our current knowledge of myo-inositol homeostatic metabolism, since they are critical to the signalling events played by its phosphorylated forms.

SIRT1/PGC-1α/PPAR-γ Correlate With Hypoxia-Induced Chemoresistance in Non-Small Cell Lung Cancer.

Resistance is the major cause of treatment failure and disease progression in non-small cell lung cancer (NSCLC). There is evidence that hypoxia is a key microenvironmental stress associated with resistance to cisplatin, epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs), and immunotherapy in solid NSCLCs. Numerous studies have contributed to delineating the mechanisms underlying drug resistance in NSCLC; nevertheless, the mechanisms involved in the resistance associated with hypoxia-induced molecular metabolic adaptations in the microenvironment of NSCLC remain unclear. Studies have highlighted the importance of posttranslational regulation of molecular mediators in the control of mitochondrial function in response to hypoxia-induced metabolic adaptations. Hypoxia can upregulate the expression of sirtuin 1 (SIRT1) in a hypoxia-inducible factor (HIF)-dependent manner. SIRT1 is a stress-dependent metabolic sensor that can deacetylate some key transcriptional factors in both metabolism dependent and independent metabolic pathways such as HIF-1α, peroxisome proliferator-activated receptor gamma (PPAR-γ), and PPAR-gamma coactivator 1-alpha (PGC-1α) to affect mitochondrial function and biogenesis, which has a role in hypoxia-induced chemoresistance in NSCLC. Moreover, SIRT1 and HIF-1α can regulate both innate and adaptive immune responses through metabolism-dependent and -independent ways. The objective of this review is to delineate a possible SIRT1/PGC-1α/PPAR-γ signaling-related molecular metabolic mechanism underlying hypoxia-induced chemotherapy resistance in the NSCLC microenvironment. Targeting hypoxia-related metabolic adaptation may be an attractive therapeutic strategy for overcoming chemoresistance in NSCLC.

Caffeine protects against stress-induced murine depression through activation of PPAR\u03b3C1\u03b1-mediated restoration of the kynurenine pathway in the skeletal muscle

Exercise prevents depression through peroxisome proliferator-activated receptor-gamma coactivator 1α (PGC-1α)-mediated activation of a particular branch of the kynurenine pathway. From kynurenine (KYN), two independent metabolic pathways produce neurofunctionally different metabolites, mainly in somatic organs: neurotoxic intermediate metabolites via main pathway and neuroprotective end product, kynurenic acid (KYNA) via the branch. Elevated levels of KYN have been found in patients with depression. Herein, we investigated whether and how caffeine prevents depression, focusing on the kynurenine pathway. Mice exposed to chronic mild stress (CMS) exhibited depressive-like behaviours with an increase and decrease in plasma levels of pro-neurotoxic KYN and neuroprotective KYNA, respectively. However, caffeine rescued CMS-exposed mice from depressive-like behaviours and restored the plasma levels of KYN and KYNA. Concomitantly, caffeine induced a key enzyme converting KYN into KYNA, namely kynurenine aminotransferase-1 (KAT1), in murine skeletal muscle. Upon caffeine stimulation murine myotubes exhibited KAT1 induction and its upstream PGC-1α sustainment. Furthermore, a proteasome inhibitor, but not translational inhibitor, impeded caffeine sustainment of PGC-1α, suggesting that caffeine induced KAT1 by inhibiting proteasomal degradation of PGC-1α. Thus, caffeine protection against CMS-induced depression may be associated with sustainment of PGC-1α levels and the resultant KAT1 induction in skeletal muscle, and thereby consumption of pro-neurotoxic KYN.

Transcriptional and biochemical analyses of gibberellin expression and content in germinated barley grain.

Mobilization of reserves in germinated cereal grains is critical for early seedling vigour, global crop productivity, and hence food security. Gibberellins (GAs) are central to this process. We have developed a spatio-temporal model that describes the multifaceted mechanisms of GA regulation in germinated barley grain. The model was generated using RNA sequencing transcript data from tissues dissected from intact, germinated grain, which closely match measurements of GA hormones and their metabolites in those tissues. The data show that successful grain germination is underpinned by high concentrations of GA precursors in ungerminated grain, the use of independent metabolic pathways for the synthesis of several bioactive GAs during germination, and a capacity to abort bioactive GA biosynthesis. The most abundant bioactive form is GA1, which is synthesized in the scutellum as a glycosyl conjugate that diffuses to the aleurone, where it stimulates de novo synthesis of a GA3 conjugate and GA4. Synthesis of bioactive GAs in the aleurone provides a mechanism that ensures the hormonal signal is relayed from the scutellum to the distal tip of the grain. The transcript data set of 33 421 genes used to define GA metabolism is available as a resource to analyse other physiological processes in germinated grain.

Metabolomic biomarkers in cervicovaginal fluid for detecting endometrial cancer through nuclear magnetic resonance spectroscopy

Endometrial cancer (EC) is one of the most common gynecologic neoplasms in developed countries but lacks screening biomarkers. We aim to identify and validate metabolomic biomarkers in cervicovaginal fluid (CVF) for detecting EC through nuclear magnetic resonance (NMR) spectroscopy. We screened 100 women with suspicion of EC and benign gynecological conditions, and randomized them into the training and independent testing datasets using a 5:1 study design. CVF samples were analyzed using a 600-MHz NMR spectrometer equipped with a cryoprobe. Four machine learning algorithms-support vector machine (SVM), partial least squares discriminant analysis (PLS-DA), random forest (RF), and logistic regression (LR), were applied to develop the model for identifying metabolomic biomarkers in cervicovaginal fluid for EC detection. A total of 54 women were eligible for the final analysis, with 21 EC and 33 non-EC. From 29 identified metabolites in cervicovaginal fluid samples, the top-ranking metabolites chosen through SVM, RF and PLS-DA which existed in independent metabolic pathways, i.e. phosphocholine, malate, and asparagine, were selected to build the prediction model. The SVM, PLS-DA, RF, and LR methods all yielded area under the curve values between 0.88 and 0.92 in the training dataset. In the testing dataset, the SVM and RF methods yielded the highest accuracy of 0.78 and the specificity of 0.75 and 0.80, respectively. Phosphocholine, asparagine, and malate from cervicovaginal fluid, which were identified and independently validated through models built using machine learning algorithms, are promising metabolomic biomarkers for the detection of EC using NMR spectroscopy.

Characterisation of white and yellow eye colour mutant strains of house cricket, Acheta domesticus.

Two eye-colour mutant strains, white (W) and yellow (Y) of house cricket Acheta domesticus were established in our laboratory. We phenotyped and genotyped the mutants, performed genetic crossings and studied the eye structure and pigment composition using light and electron microscopy and biochemical analysis. We show that W and Y phenotypes are controlled by a single autosomal recessive allele, as both traits are metabolically independent. The analysis of the mutants`eye structure showed a reduced number of dark pigment granules while simultaneously, and an increased amount of light vacuoles in white eye mutants was observed. Significant differences in eye pigment composition between strains were also found. The Y mutant had a lower number of ommochromes, while the W mutant had a lower number of ommochromes and pteridines. This indicates that mutated genes are involved in two different, independent metabolic pathways regulating tryptophan metabolism enzymes, pigment transporter granules or pigment granule formation.

3008 Role of Interferon-gamma in Natural Clearance of Chlamydia trachomatis Infection in Women

OBJECTIVES/SPECIFIC AIMS: Chlamydia trachomatis (CT) infection can lead to reproductive morbidity in women. Animal models suggest that protection against CT is mediated through the cytokine interferon-gamma (IFN-γ), produced by CD4+ T-cells, which clears CT through intracellular tryptophan depletion. In humans, correlates of protection remain to be elucidated, which hinders chlamydia vaccine development. Natural clearance of CT infection (e.g., clearance before antibiotics) may be an immunological correlate of protection, evidenced by (1) CT clearance without antibiotics; and (2) a 4-fold reduced risk of CT reinfection within 6 months. We have identified women with and without natural clearance of CT infection. By comparing these two groups of women, the role of IFN-γ-mediated natural clearance of CT infection will be investigated. METHODS/STUDY POPULATION: Through collaboration with a cohort study of CT-infected women, we have access to stored specimens from women who naturally cleared CT or had persisting CT infection. Using peripheral blood mononuclear cell (PBMC), we will assess whether natural clearance of CT infection is associated with IFN-γ-producing CD4+ T-cells by stimulating PBMC ex vivo with CT antigens using intracellular cytokine staining. We will also use cervicovaginal lavage (CVL) and untargeted High-Performance Liquid Chromatography-Mass Spectrometry to assess for tryptophan-dependent and -independent metabolic pathways associated with natural clearance of CT infection. RESULTS/ANTICIPATED RESULTS:: To date, IFN-γ has been measured in 10 women who did not clear CT infection, demonstrating that <20% of these women produced significant levels of IFN-γ. Women who naturally cleared CT have yet to be studied. Untargeted HPLC-MS has been performed on 6 women (3 who cleared matched to 3 with persisting CT infection). To date, 11 pathways that are significantly associated with natural clearance have been identified. DISCUSSION/SIGNIFICANCE OF IMPACT: The outcome of natural clearance of CT infection is distinct from women with persisting chlamydia. These studies may inform whether IFN-γ, produced by CD4+ T-cells, or tryptophan-dependent or -independent metabolic pathways are associated with natural clearance, which may advance chlamydia vaccine development.

Studies on the metabolism, mode of action, and development of insecticides acting on the GABA receptor.

γ-BHC and dieldrin are legacy insecticides that were extensively used after the second World War. When they were banned, their modes of action and metabolism were not known. This article aims at providing a picture of the metabolism of γ-BHC and the modes of action of γ -BHC and dieldrin. γ-BHC is metabolized via two independent metabolic pathways. One is a glutathione conjugation pathway resulting in the formation of dichlorophenyl mercapturic acid and the other is an oxidative metabolism catalyzed by microsomes to mainly 2,4,6-trichlorophenol (TCP) and (36/45)-1,2,3,4,5,6-hexachlorocyclohex-1-ene (HCCHE). Other metabolites of this pathway are 2,4,5-TCP, 2,3,4,6-tetrachlorophenol (TeCP), (36/45)- and (346/5)-1,3,4,5,6-pentachlorocyclohex-1-enes (PCCHE). Nowadays, γ-BHC and dieldrin are very important reagents which are used to study the GABA receptor in insects and mammals. They were found to be noncompetitive GABA antagonists blocking the chloride ion selective pores in the GABA-gated chloride channels and leading to inhibition of chloride ion conductance. [3H]EBOB binding data showed that γ-BHC, its analogs, dieldrin, and other cyclodiene insecticides interact with the same site on GABA receptor as picrotoxinin. Only γ-BHC, among other BHC isomers, exhibits this binding characteristic. Milbemycin, currently widely used as an insecticide, acaricide and nematicide, has been found to open the GABA-gated chloride channel.

Extreme pathway analysis reveals the organizing rules of metabolic regulation.

Cellular systems shift metabolic states by adjusting gene expression and enzyme activities to adapt to physiological and environmental changes. Biochemical and genetic studies are identifying how metabolic regulation affects the selection of metabolic phenotypes. However, how metabolism influences its regulatory architecture still remains unexplored. We present a new method of extreme pathway analysis (the minimal set of conically independent metabolic pathways) to deduce regulatory structures from pure pathway information. Applying our method to metabolic networks of human red blood cells and Escherichia coli, we shed light on how metabolic regulation are organized by showing which reactions within metabolic networks are more prone to transcriptional or allosteric regulation. Applied to a human genome-scale metabolic system, our method detects disease-associated reactions. Thus, our study deepens the understanding of the organizing principle of cellular metabolic regulation and may contribute to metabolic engineering, synthetic biology, and disease treatment.

The Use of Transposon Insertion Sequencing to Interrogate the Core Functional Genome of the Legume Symbiont Rhizobium leguminosarum.

The free-living legume symbiont Rhizobium leguminosarum is of significant economic value because of its ability to provide fixed nitrogen to globally important leguminous food crops, such as peas and lentils. Discovery based research into the genetics and physiology of R. leguminosarum provides the foundational knowledge necessary for understanding the bacterium's complex lifestyle, necessary for augmenting its use in an agricultural setting. Transposon insertion sequencing (INSeq) facilitates high-throughput forward genetic screening at a genomic scale to identify individual genes required for growth in a specific environment. In this study we applied INSeq to screen the genome of R. leguminosarum bv. viciae strain 3841 (RLV3841) for genes required for growth on minimal mannitol containing medium. Results from this study were contrasted with a prior INSeq experiment screened on peptide rich media to identify a common set of functional genes necessary for basic physiology. Contrasting the two growth conditions indicated that approximately 10% of the chromosome was required for growth, under both growth conditions. Specific genes that were essential to singular growth conditions were also identified. Data from INSeq screening on mannitol as a sole carbon source were used to reconstruct a metabolic map summarizing growth impaired phenotypes observed in the Embden-Meyerhof-Parnas pathway, Entner-Doudoroff pathway, pentose phosphate pathway, and tricarboxylic acid cycle. This revealed the presence of mannitol dependent and independent metabolic pathways required for growth, along with identifying metabolic steps with isozymes or possible carbon flux by-passes. Additionally, genes were identified on plasmids pRL11 and pRL12 that are likely to encode functional activities important to the central physiology of RLV3841.

Science Rewritten to Accommodate its Origin

A ferroelectric phase transition in ice at ~72 K releases latent energy as λ ~ 4 μ infrared laser light, ‘ice light’, energizing selected targets. Polarized by multiple reflection[22], it photophosphorylated deoxynucleotides, turning tropical waters into a noodle soup of chiral DNA. tRNA analogues ‘transport DNAs’, tDNAs embedded in Alexander Oparin’s lightning-charged coacervates[23] formed H-bond lined pores. Absorbed ice light created an electric field, driving a ratchet mechanism which actively imported charged carrier-substrate complexes.
 All life descends from the first cell to replicate a tDNA and depends on the trace element requirements of 64 tDNA variants. They constitute life’s atomic alphabet, their substrate complexes its molecular vocabulary. The inviolable rules of active transport predate protein synthesis and enzyme catalysis. Medical, veterinary and pharmaceutical data are consistent with nine independent metabolic pathways. My account of water transport contradicts Peter Mitchell’s chemiosmotic hypothesis.[24] Trace element deficiencies disabling active transport cause most mental and physical maladies, supplements could prevent them.
 ‘Differentiation DNAs’, dDNAs selecting tDNAs control cells’ substrate uptake, c.f. mRNAs encode protein synthesis by selecting tRNAs. Barrels of α-helices[25] supplement tDNAs and tDNA genetics governs familial inheritance of metabolic disorders, a minion-based data base would facilitate their diagnosis. Trace element supplements would prevent heart attacks, strokes, cancers, diabetes, Alzheimer’s dementia and rarer conditions, improve health and reduce NHS expenditure.
 The 189*18 arrays of proton ordered H-bonds connecting amino acid ω-amines to DNA phosphates on ‘minions’ control metabolism, serve as biological clocks, memory stores and personality biased brain chips and are basis for reinterpreting scientific dogma. Nine parallel metabolic pathways reflecting their 9-fold symmetry control metabolism. Oscillating H-bonds accelerate protons along minion tunnels, driving molecular scale nuclear fusion. Trapping the γ-rays released at source could solve current energy and pollution crises. Computers and data-bases modelled on minions promise human-friendly artificial intelligence satisfying Turing’s criteria.[26]
 Comparing cybernetics, psychology and traditional wisdom suggested ‘minions’, the name connotes subservience. They comprise 189 anti-parallel β-sheet hairpins[27] with alternate neutral and basic amino acid residues and proline forming an asymmetric U-bend. They hold nine DNA base pairs flat, forming a nine-coil abacus. Evolved to pack DNA on chromosomes for efficient replication, they underpin philosophy and science, account for human intelligence and resolve many questions. My mutually consistent arguments contradict accepted dogma.

Natural product inspired antibacterial tetramic acid libraries with dual enzyme inhibition

The application of natural product inspired synthesis has identified novel antibacterial tetramic acids which exhibit wide ranging antibacterial activity, and which provide potential lead structures for antibacterial drug discovery. Their phenotypic activity appears to correlate with action at two enzymes, UPPS and RNAP, which operate in independent metabolic pathways. SAR maps and identification of their relevant binding sites by molecular modelling has been achieved, and characterisation of the most active compounds suggests that these systems offer potential for topical antibiotics but that for oral and injectable use further optimisation is required.

In Vitro Metabolism of Rivaroxaban, an Oral, Direct Factor Xa Inhibitor, in Liver Microsomes and Hepatocytes of Rats, Dogs, and Humans

The in vitro metabolism of rivaroxaban, a novel, oral, direct factor Xa inhibitor for the prevention and treatment of thromboembolic disorders, was investigated in several species, including humans. The objective of this study was to elucidate metabolite structures and identify the metabolic pathways to provide support for in vivo safety and clinical studies. [(14)C]Rivaroxaban was incubated with liver microsomes and hepatocytes of rats, dogs, and humans. The samples were analyzed by high-performance liquid chromatography-(14)C-tandem mass spectroscopy, to generate metabolite profiles and propose or confirm the structures of the metabolites formed. In vitro metabolite profiles showed no major differences between species. The main oxidative metabolic pathways identified for all species were hydroxylation at the morpholinone moiety (M-2, M-3, and M-8) and to a lesser extent at the oxazolidinone moiety (M-9). M-2 was the main metabolite in all microsomal incubations. M-1, a morpholinone ring-opened product formed by further oxidation of M-2, was the main metabolite in all hepatocyte incubations. Other pathways were amide hydrolysis at the morpholinone ring (M-7) and the chlorothiophene amide moiety (M-13 and M-15). In hepatocytes, M-13 was readily conjugated with glycine, leading to M-4. The metabolic fate of unlabeled M-15 was investigated separately. Incubations with human liver microsomes and hepatocytes showed that M-15 was first oxidized to the aldehyde intermediate M-16 and subsequently reduced to M-17 (alcohol) or oxidized to M-18 (carboxylic acid). No metabolism at the chlorothiophene moiety itself was found. Overall, rivaroxaban showed no species differences in metabolism, with different independent metabolic pathways and no formation of reactive metabolites.

Manganese cell labeling of murine hepatocytes using manganese(III)‐transferrin

Manganese(III)-transferrin [Mn(III)-Tf] was investigated as a way to accomplish manganese-labeling of murine hepatocytes for MRI contrast. It is postulated that Mn(III)-Tf can exploit the same transferrin-receptor-dependent and -independent metabolic pathways used by hepatocytes to transport the iron analog Fe(III)-Tf. More specifically, it was investigated whether manganese delivered by transferrin could give MRI contrast in hepatocytes. Comparison of the T1 and T2 relaxation times of Mn(III)-Tf and Fe(III)-Tf over the same concentration range showed that the r1 relaxivities of the two metalloproteins are the same in vitro, with little contribution from paramagnetic enhancement. The degree of manganese cell labeling following incubation for 2-7 h in 31.5 microm Mn(III)-Tf was comparable to that of hepatocytes incubated in 500 microm Mn2+ for 1 h. The intrinsic manganese tissue relaxivity between Mn(III)-Tf-labeled and Mn2+-labeled cells was found to be the same, consistent with Mn(III) being released from transferrin and reduced to Mn2+. For both treatment regimens, manganese uptake by hepatocytes appeared to saturate in the first 1-2 h of the incubation period and may explain why the efficiency of hepatocyte cell labeling by the two methods appeared to be comparable in spite of the approximately 16-fold difference in effective manganese concentration. Hepatocytes continuously released manganese, as detected by MRI, and this was the same for both Mn2+- and Mn(III)-Tf-labeled cells. Manganese release may be the result of normal hepatocyte function, much in the same way that hepatocytes excrete manganese into the bile in vivo. This approach exploits a biological process-namely receptor binding, endocytosis and endosomal acidification-to initiate the release of an MRI contrast agent, potentially conferring more specificity to the labeling process. The ubiquitous expression of transferrin receptors by eukaryotic cells should make Mn(III)-Tf particularly useful for manganese labeling of a wide variety of cells both in culture and in vivo.

Inhibition of hepatitis B virus replication by stably expressed shRNA

The major challenges for anti-hepatitis B Virus (HBV) therapy are the low efficacy of current drugs and the occurrence of drug resistant HBV mutations. A drug with new target sites or independent metabolic pathways may overcome these shortcomings. Small interfering RNA (siRNA) offers the possibility of developing a new anti-HBV therapy. Here we describe the almost complete inhibition of HBV replication by stably expressed 21-mer short hairpin RNAs (shRNA). Besides the conventional targets on HBV reverse-transcriptase, we also systemically targeted other sites of pregenomic RNA, including direct repeat (DR) elements, S, core, and X gene. Our results indicated that shRNAs can serve as efficient alternative anti-HBV agents. They can also be used in combination with chemotherapy, because they showed better effects on the inhibition of HBV replication due to different mechanisms of drug actions.

Enhanced biological phosphorus removal in an anaerobic-aerobic sequencing batch reactor: characteristics of carbon metabolism.

Carbon metabolism of activated sludge performing enhanced biological phosphorus removal (EBPR) was investigated in a sequencing batch reactor (SBR), where glucose and acetate were supplied as carbon sources. There have been reports that EBPR often failed because of outgrowth of G-bacteria, which are able to use glycogen (or glucose) alone instead of glycogen and polyphosphate as an internal energy storage pool for the anaerobic uptake and storage of acetate. However, in this experiment, complete EBPR was achieved without proliferation of G-bacteria despite the supply of glucose in addition to the acetate. Additional one-cycle SBR operation was carried out to investigate the detailed metabolism of glucose and acetate. Acetate-using, phosphorus-accumulating organisms (PAOs) could use glucose as a source for the anaerobic polyhydroxyalkanoate (PHA) synthesis from acetate. However, glucose and acetate were metabolized separately through independent metabolic pathways by respective microorganisms: acetate-using PAOs, lactate-producing organisms (LPOs), and lactate-using PAOs. Glucose was rapidly converted to lactic acid by LPOs before acetate-using PAOs used the glucose as an energy source for the anaerobic PHA synthesis from acetate and the lactateusing PAOs anaerobically synthesized PHA from lactate at the expense of polyphosphate. The EBPR was accomplished by acetate-using PAOs and lactate-using PAOs independently when glucose acetate were supplied together.

Mathematical modeling of growth and production of alcohol oxidase by Hansenula polymorpha grown on methanol–glucose mixtures

The modeling of growth and production of methanol oxidase (MOX) by Hansenula polymorpha CBS 4732 has been studied to provide a mathematical description of such production processes. Two kinds of mathematical models were constructed for growth on methanol and on mixtures of methanol and glucose. The model for growth on methanol as the sole carbon source consists of kinetics expressions, a limited number of key steps incorporating substrate and production inhibition. This model was used to predict and simulate the culture dynamics at the start-up, the most critical step in continuous cultivation. The growth on mixtures of methanol and glucose was modeled assuming virtually independent metabolic pathways. The induction and production of MOX could be described by adaptation of various repression equations for various data from the literature. The models describe both experimental data and literature data on growth of H. polymorpha CBS 4732 on glucose-methanol mixtures satisfactorily. All parameters for the induction-repression model for growth of H. polymorpha CBS 4732 on glucose-methanol mixtures yielded evidence that a similar induction-repression pattern is involved in MOX production. Catalase, however, is repressed by a different mechanism.

Chitosan-elicited synthesis of callose and of coumarin derivatives in parsley cell suspension cultures

In suspension cultured cells of parsley (Petroselinum crispum), chitosan elicited a rapid deposition of the 1,3-ß-glucan callose on the cell wall and a slower formation of coumarins. With cells remaining in conditioned growth medium, fully N-deacetylated chitosans and partially N-acetylated chitosans were about equally active, the potency increased with the degree of polymerization up to several thousand and addition of reduced glutathione increased the sensitivity of the cells. These results indicate common initial events in the induction of callose and coumarin synthesis although two fully independent metabolic pathways are involved. When the cells were suspended in fresh growth medium, less chitosan was required, and fully N-deacetylated chitosan became the best callose elicitor.