AutoFACT: AnAutomaticFunctionalAnnotation andClassificationTool

Background  

Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or more databases, an arduous process for large datasets.     

Furanocoumarins from Dorsteniafoetida

The linear furanocoumarins 5-(2,3-epoxy-3-methyl-butoxy)-chalepensin, 5-methoxy-3-(3-methyl-2,3-dihydroxybutyl)-psoralen-diacetate (7), 5-methoxy-3-[3-(β-d-glucopyranosyloxy)-2-acetyloxy-3-methyl-butyl]-psoralen and 5-(3-methyl-2,3-dihydroxybutyloxy)-3-[3-(β-d-glucopyranosyloxy)-2-hydroxy-3-methyl-butyl]-psoralen, and the coumarin derivative 7-hydroxy-5-methoxy-6-carboxymethyl-3-[3-(β-d-glucopyranosyloxy)-2-hydroxy-3-methyl-butyl]-coumarin were isolated from the leaves of Dorstenia foetida (Moraceae) along with the known compounds psoralen, bergapten, isopimpinellin, phellopterin, 5-methoxychalepensin and turbinatocoumarin. Further furanocoumarins were characterized by ESI-MS/MS investigations. The nonpolar extracts of D. foetida exhibit antifungal, antibacterial and cytotoxic activity, however, no anthelminthic activity.     

Regulation of nitrate uptake into Chara corallina cells via NH+4 stimulation of NO−3 efflux

Abstract. Net NO₃ uptake by NO⁻₃ deficient Chara cells was used to calculate [NO⁻₃]_c assuming that the cytoplasm occupies 10% total volume and that nitrate reduction and storage are negligible (i.e. maximum [NO⁻₃]_c was calculated). A linear relationship was found between NO⁻₃ efflux and [NO⁻₃]_c. There was an initial burst of NO⁻₃ efflux when NH⁺₄ was added, followed by a slower efflux rate which matched influx rate such that net NO⁻₃ uptake was zero. Over 50% of NO⁻₃ that had been taken up in 2 h was lost within the first 5 min of NH⁺₄ addition. The Nernst equation was used to predict the direction of the electrochemical driving force for NO⁻₃ entry. Under the experimental conditions used NO⁻₃ efflux is actively transported. The differential involvement of both NO⁻₃ influx and NO⁻₃ efflux in the regulation of NO⁻₃ uptake is discussed and a model is proposed to account for these results which envisages discrete NO⁻₃ influx and NO⁻₃ efflux carriers.     

Rapid invivo metabolism of Leukotriene C3 in the monkey, Macacairus

[5,6,8,9,11,12-³H₆] Leukotriene C₃ (5 μCi) was injected through a catheter into the right atrium of an anesthetized male monkey. Blood samples were drawn from the aorta via a second catheter. The concentration of tritium in blood decreased from 100 nCi/ml after 5 sec to 1 nCi/ml 15 min after injection, suggesting that leukotriene C₃ was rapidly eliminated from the circulation. Chromatographic analyses of radioactive material in blood collected before recirculation had occurred (15 sec after injection) demonstrated that 40% of the radioactive material had been converted into two less polar metabolites. These products had the same chromatographic properties as leukotrienes D₃ and E₃, respectively. The results indicate that leukotriene C₃ is rapidly transformed by monkey lung $\text{in}\text{vivo}$. Two minutes after injection, the component corresponding to leukotriene E₃ was the predominating metabolite in blood.     

Accelerated net efflux of 3-O-[14C]methylglucose in isolated fat cells

(1) A flow-tube apparatus suited for measurement of rapid efflux of sugars from adipocytes is described. (2) Due to heterogeneity of fat cell populations, a conventional analysis of the time-course of net efflux of $\text{3-O-}\text{methylglucose}$ based on the integrated rate equation can produce gross errors in estimates of kinetic parameters. (3) The half-saturation constant and maximum transport capacity for $\text{3-O-}\text{methylglucose}$ transport were found to be about 3-fold higher for net efflux than for equilibrium exchange flux, both in insulin-stimulated and non-stimulated adipocytes. This suggests asymmetric kinetic parameters for $\text{3-O-}\text{methylglucose}$ transport.     

catmap: Case-control And TDT Meta-Analysis Package

Background  

Risk for complex disease is thought to be controlled by multiple genetic risk factors, each with small individual effects. Meta-analyses of several independent studies may be helpful to increase the ability to detect association when effect sizes are modest. Although many software options are available for meta-analysis of genetic case-control data, no currently available software implements the method described by Kazeem and Farrall (2005), which combines data from independent family-based and case-control studies.     

Distribution of NO3− reduction between roots and shoots of peachtree seedlings as affected by NO3− uptake rate

The distribution of NO₃^? reduction between roots and shoots was studied in hydro-ponically-grown peach-tree seedlings (Prunus persica L.) during recovery from N starvation. Uptake, translocation and reduction of NO₃^?, together with transport through xylem and phloem of the newly reduced N were estimated, using ¹⁵N labellings, in intact plants supplied for 90 h with 0.5 mM NH₄⁺ and 0.5, 1.5 or 10 mM NO₃^?. Xylem transport of NO₃^? was further investigated by xylem sap analysis in a similar experiment. The roots were the main site of NO₃^? reduction at all 3 levels of NO₃^? nutrition. However, the contribution of the shoots to the whole plant NO₃^? reduction increased with increasing external NO₃^? availability. This contribution was estimated to be 20, 23 and 42% of the total assimilation at 0.5, 1.5 and 10 mM NO₃^?, respectively. Both ¹⁵N results and xylem sap analysis confirmed that this trend was due to an enhancement of NO₃^? translocation from roots to shoots. It is proposed that the lack of NO₃^? export to the shoots at low NO₃^? uptake rate resulted from a competition between NO₃^? reduction in the root epidermis/cortex and NO₃^? diffusion to the stele. On the other hand, net xylem transport of newly reduced N was very efficient since ca 70% of the amino acids synthesized in the roots were translocated to the shoots, regardless of the level of NO₃^? nutrition. This net xylem transport by far exceeded the net downward phloem transport of the reduced N assimilated in shoots. As a consequence, the reduced N resulting from NO₃^? assimilation, principally occurring in the roots, was mainly incorporated in the shoots.     

Structural studies on [Mo3S4] and [Mo3S4Cu] complexes with tripodal ligands providing various NxOy (x + Y = 3) donor sets

The interaction of 1,3,5-triamino-1,3,5-trideoxy-cis-inositol (taci) and its N-methylated derivative 1,3,5-trideoxy-1,3,5-tris(dimethylamino)-cis-inositol (tdci) with the incomplete [Mo₃S₄]⁴⁺ cube and the heterometallic [Mo₃S₄Cu]⁴⁺ cube have been investigated by X-ray analysis. The crystal structures of [Mo₃S₄(taci+ rmC₃H₆O-H₂O)₃-4H]·2OH₂O (1a, rhombohedral, space group R32, A = 15.964(3), C = 40.59(1) Å, Z = 6), [Mo₃S₄(tdci)₃]Br₄·9.5EtOH·5H₂O (2a, triclinic, space group

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and [CuBrMo₃S₄(tdci)₃]Br₃·11 H₂O·EtOH (3a, monoclinic, space group P2,/n, A = 14.887(3), B = 22.570(4), C = 21.974(5) Å, β = 98.54(2)°, Z = 4) revealed andN-N-O and an N-O-O coordination mode for taci and tdci, respectively. In 1a, taci is coordinated as an anion with deprotonated oxygen and nitrogen donors. In addition, the non-coordinating amino group reacted with one equivalent; of acetone, forming a Schiff base condensation product. For 2a, short Mo---O bonds and high pK_a values (compared to the aqua ion [Mo₃S₄(H₂O)₉]⁴⁺) indicate the formation of a zwitterionic form of the tdci ligand with coordinated alkoxo groups and peripheral dimethylammonium groups. No significant differences were found for the structural properties of the Mo-tdci fragment in 2a and 3a. The coordination modes of taci and tdci, as observed in the solid state, are in agreement with the previously reported solution structures, established by NMR spectroscopy. They are attributed to the specific steric requirements of the two ligands and to a pronounced preference of the [Mo₃(μS)₃(μ₃S)]⁴⁺ core to coordinate a nitrogen donor trans to μ₃S.     

Modulation of the Akt/Ras/Raf/MEK/ERK pathway by A3 adenosine receptor

Downstream A₃ receptor signalling plays an important role in the regulation of cell death and proliferation. Therefore, it is important to determine the molecular pathways involved through A₃ receptor stimulation. The phosphatidylinositide-3-OH kinase (PI3K)/Akt and the Raf/mitogen-activated protein kinase (MAPK/ERK) kinase (MEK)/mitogen-activated protein kinase (MAPK) pathways have central roles in the regulation of cell survival and proliferation. The crosstalk between these two pathways has also been investigated. The focus of this review centres on downstream mediators of A₃ adenosine receptor signalling.     

Distributions of H+,K+-ATPase and Cl–,HCO3–-ATPase in micromere-derived cells of sea urchin embryos

In cultured cells derived from isolated micromeres of sea urchin eggs, H+,K+-ATPase activity, which became detectable simultaneously with the initiation of spicule formation, was localized in the plasma membrane and the microsome fractions. Activities of marker enzymes for plasma membrane, 5'-nucleotidase, Na+,K+-ATPase, and adenylate cyclase, were found to be high in the plasma membrane fraction. Considerable activity of rotenone-insensitive NADPH-cytochrome c reductase, a marker enzyme for microsome, was detectable in the microsome fraction. These fractions exhibited barely any appreciable activity of markers for the other organellae. H+,K+-ATPase in plasma membrane probably mediates H+ release from the cells, in which H+ is produced in overall reaction to form CaCO3, the main component of spicules, from Ca2+, CO2 and H2O. Cl-,HCO3(-)-ATPase activity was also found in these two fractions before and after the initiation of spicule formation. After initiation, the skeletal vacuole fraction was obtained from subcellular structures containing spicules. Considerable activity of Cl-,HCO3(-)-ATPase was observed in this fraction, which exhibited a weak activity of UDP-galactose: N-acetylglucosamine galactosyltransferase, a marker enzyme for Golgi body. Cl-,HCO3(-)-ATPase in the skeletal vacuole membrane probably mediates HCO3- transport into the vacuoles to supply HCO3- for spicule formation.     

Mechanism of nitrate uptake into Chara corallina cells: lack of evidence for obligatory coupling to proton pump and a new NO3−/NO3− exchange model

Abstract. Nitrate uptake into Chara corallina cells at different external pH (pH_o) after different NO₃⁻ pretreatment conditions has been investigated. Following NO₃⁻ pretreatment (0.2 mol m⁻³ NO₃⁻) there was little effect of pH_o on subsequent net NO₃⁻ uptake into Chara cells. After N deprivation (2 mmol m⁻³ NO₃⁻) there was a pronounced effect of pH_o on nitrate uptake, the maximum rate occurring at pH_o 4.7. There was no consistent relationship between OH⁻ efflux and NO₃⁻ uptake in short term experiments (< 1 h). NO₃⁻ efflux was also sensitive to pH_o, the maximum rate occurring at ∼ pH_o 5.0. An inhibitor of the proton pump, DES, immediately stimulated NO₃⁻ uptake into cells pretreated with NO₃⁻ and prevented the time-dependent decrease in NO₃⁻, uptake into Chara cells that had been previously treated with low N (2 mmol m⁻³ NO₃⁻). NO₃⁻ efflux was found to be very sensitive to DES with K_i= 0.7 mmol m⁻³. At the optimum pH_o for NO₃⁻ uptake the effect of DES on membrane potential (ψ_m) were slight, and only apparent after 30 min. The results are interpreted in context of current models relating NO₃⁻ uptake and H⁺ pump activity. A new model for NO₃⁻ uptake is proposed which involves NO₃⁻/NO₃⁻ exchange at steady state.     

Promoter structure of mouse RANKL/TRANCE/OPGL/ODF gene

Receptor activator of NF-kappa B ligand (RANKL)/tumor necrosis factor-related activation induced cytokine (TRANCE)/osteoprotegerin ligand (OPGL)/osteoclast differentiation factor (ODF) is a membrane-bound signal transducer responsible for differentiation and maintenance of osteoclasts. To elucidate the mechanism regulating RANKL/TRANCE/OPGL/ODF gene expression, we cloned the 5'-flanking basic promoter region of the mouse RANKL/TRANCE/OPGL/ODF gene and characterized it by transient transfection studies and genomic Southern blot analysis. Inverted TATA- and CAAT-boxes and a putative Cbfa1/Osf2/AML3 binding domain constituted the basic promoter structure. The repeated half-sites for the vitamin D3 (VitD3) and glucocorticoid receptors were located at -935 and -640, respectively. Transient transfection studies revealed that short-term treatment with 1alpha,25(OH)2 VitD3 or dexamethasone increased luciferase activity up to 204% and 178%, respectively; on the other hand, treatment with dibutyryl cyclic AMP did not affect the promoter activity. Since the expression of Cbfa1/Osf2/AML3 is also regulated by VitD3, 1alpha,25(OH)2 VitD3 might affect RANKL/TRANCE/OPGL/ODF gene expression both directly and indirectly. CpG methylation was observed dominantly in mouse stromal cells, ST2, of a later passage which ceased to support in vitro osteoclastogenesis, suggesting that the methylation status of the CpG loci in the RANKL/TRANCE/OPGL/ODF gene promoter may be one of the influential cis-regulating factors.     

The synthesis of the tripodal phosphine CH3C{CH2P(m-CF3C6H4)2}3 and its rhodium coordination chemistry

The new tripodal phosphine CH₃C{CH₂P(m-CF₃C₆H₄)₂}₃, CF₃PPP, was prepared by reacting CH₃C(CH₂Br)₃ with Li⁺P(m-CF₃C₆H₄)₂⁻, the latter being best obtained by adding Li⁺NⁱPr₂⁻ to PH(m-CF₃C₆H₄)₂. The rhodium complexes [RhCl(CO)(CF₃PPP)], [Rh(LL)(CF₃PPP)](CF₃SO₃) (LL = 2 CO or NBD), [RhX₃(CF₃PPP)], [RhX(MeCN)₃(CF₃PPP)](CF₃SO₃)₂ (X = H and Cl), [RhCl₂(MeCN)(CF₃PPP)](CF₃SO₃) and [Rh(MeCN)₃(CF₃PPP)](CF₃SO₃)₃ were prepared and characterized. The X-ray crystal structure of [Rh(NBD)(CF₃PPP)](CF₃SO₃) is reported. The lower oxygen sensitivity of the CF₃PPP rhodium(I) complexes, relative to the corresponding species with the parent ligand CH₃C(CH₂PPh₂)₃, is attributed to the higher effective nuclear charge on the metal centers caused by the presence of the six CF₃ substituents on the terdentate phosphine. A similar effect may be responsible for the easier hydrolysis of the CF₃PPP-containing, cationic rhodium(III) complexes relative to the corresponding compounds of the parent ligand.     

Secretion of the STA3 heat-stable enterotoxin of Escherichia coli: extracellular delivery of Pro-STA is accomplished by either Pro or STA

The methanol-soluble, heat-stable enterotoxin of Escherichia coli is a protease-resistant extracellular peptide which is synthesized as a 72-amino-acid precursor Pre-Pro-STA3. The specific roles of Pre (19 amino acids), Pro (34 amino acids) and STA3 (19 amino acids) in the secretion process were studied by functionally deleting each of the three domains. Deletion of the Pre signal sequence resulted in a short-lived cell-associated molecule with an M(r) equivalent to that of Pro-STA3. Deletion of Pro (i.e., Pre-STA3) resulted in the rapid extracellular accumulation of STA3; the periplasmic intermediate found in the secretion of the wild-type toxin was undetected. Deletion of the STA3 domain resulted in a cell-associated Pre-Pro peptide; with time this form converted to periplasmic Pro which later became extracellular. When DNA encoding either STA3, by itself, or Pro-STA3 (lacking the signal peptide) was expressed, these peptides were degraded intracellularly, with no periplasmic or extracellular forms detected. The results presented demonstrate that the signal peptide (Pre) is essential even for the export of small peptides to the periplasm, and that its absence causes the STA3 domain to become susceptible to intracellular proteases. The rapid degradation of intracellular STA3 indicates that its proteolytic resistance is acquired in a compartment other than the cytoplasm. The results also show that after the Pre domain is proteolytically cleaved from Pre-STA3 and Pre-Pro, the STA3 and Pro peptides can exit to the culture supernatant.(ABSTRACT TRUNCATED AT 250 WORDS)     

Characterisation of 5-HT3C, 5-HT3D and 5-HT3E receptor subunits: evolution, distribution and function

The 5‐HT₃ receptor is a member of the ‘Cys‐loop’ family of ligand‐gated ion channels that mediate fast excitatory and inhibitory transmission in the nervous system. Current evidence points towards native 5‐HT₃ receptors originating from homomeric assemblies of 5‐HT_3A or heteromeric assembly of 5‐HT_3A and 5‐HT_3B. Novel genes encoding 5‐HT_3C, 5‐HT_3D, and 5‐HT_3E have recently been described but the functional importance of these proteins is unknown. In the present study, in silico analysis (confirmed by partial cloning) indicated that 5‐HT_3C, 5‐HT_3D, and 5‐HT_3E are not human–specific as previously reported: they are conserved in multiple mammalian species but are absent in rodents. Expression profiles of the novel human genes indicated high levels in the gastrointestinal tract but also in the brain, Dorsal Root Ganglion (DRG) and other tissues. Following the demonstration that these subunits are expressed at the cell membrane, the functional properties of the recombinant human subunits were investigated using patch clamp electrophysiology. 5‐HT_3C, 5‐HT_3D, and 5‐HT_3E were all non‐functional when expressed alone. Co‐transfection studies to determine potential novel heteromeric receptor interactions with 5‐HT_3A demonstrated that the expression or function of the receptor was modified by 5‐HT_3C and 5‐HT_3E, but not 5‐HT_3D. The lack of distinct effects on current rectification, kinetics or pharmacology of 5‐HT_3A receptors does not however provide unequivocal evidence to support a direct contribution of 5‐HT_3C or 5‐HT_3E to the lining of the ion channel pore of novel heteromeric receptors. The functional and pharmacological contributions of these novel subunits to human biology and diseases such as irritable bowel syndrome for which 5‐HT₃ receptor antagonists have major clinical usage, therefore remains to be fully determined.     

A comparison of NH4+ and NO3– net fluxes along roots of rice and maize

Net fluxes of NH₄⁺ and NO₃^– along adventitious roots of rice ( Oryza sativa L.) and the primary seminal root of maize ( Zea mays L.) were investigated under nonperturbing conditions using ion-selective microelectrodes. The roots of rice contained a layer of sclerenchymatous fibres on the external side of the cortex, whereas this structure was absent in maize. Net uptake of NH₄⁺ was faster than that of NO₃^– at 1 mm behind the apex of both rice and maize roots when these ions were supplied together, each at 0·1 mol m^–3. In rice, NH₄⁺ net uptake declined in the more basal regions, whereas NO₃^– net uptake increased to a maximum at 21 mm behind the apex and then it also declined. Similar patterns of net uptake were observed when NH₄⁺ or NO₃^– was the sole nitrogen source, although the rates of NO₃^– net uptake were faster in the absence of NH₄⁺. In contrast to rice, rates of NH₄⁺ and NO₃^– net uptake in the more basal regions of maize roots were similar to those near the root apex. Hence, the layer of sclerenchymatous fibres may have limited ion absorption in the older regions of rice roots.     

Antibodies Recognising the GABAA/Benzodiazepine Receptor Including Its Regulatory Sites

Polyclonal antibodies have been raised against the GABA/benzodiazepine receptor purified to homogeneity from bovine cerebral cortex in deoxycholate and Triton X-100 media. Radioimmunoassay was applied to measure specific antibody production using the 125I-labelled gamma-aminobutyric acid (GABA)/benzodiazepine receptor as antigen. The antibodies specifically immunoprecipitated the binding sites for [3H]muscimol and for [3H]flunitrazepam from purified preparations. In addition, when a 3-[(3-cholamidopropyl)dimethylammonio] 1-propanesulphonate (CHAPS) extract of bovine brain membranes was treated with the antibodies, those sites as well as the [3H]propyl-beta-carboline-3-carboxylate binding, the [35S]t-butylbicyclophosphorothionate binding (TBPS), the barbiturate-enhanced [3H]flunitrazepam binding, and the GABA-enhanced [3H]flunitrazepam binding were all removed together into the immunoprecipitate. Western blot experiments showed that these antibodies recognise the alpha-subunit of the purified GABA/benzodiazepine receptor. These results further support the existence in the brain of a single protein, the GABAA receptor, containing a set of regulatory binding sites for benzodiazepines and chloride channel modulators.     

Sarcoid granulomas metabolize 25-hydroxyvitamin D3invitro

Sarcoid granulomas metabolized 25-hydroxyvitamin D₃ to two unidentified metabolites during $\text{in}\text{vitro}$ incubation. A two-step high pressure liquid chromatography system revealed two unique elution positions of these sarcoid-derived metabolites that exactly comigrated with the elution positions of 5(Z)-19-nor-10-oxo-25(OH)D₃ and 5(E)-19-nor-10-oxo-25(OH)D₃, respectively. These unique metabolites did not bind specifically to a protein receptor for 1,25(OH)₂D₃.     

IN VITRO INCORPORATION OF 3H-THYMIDINE, 3H-URIDINE, 3H-LEUCINE AND 3H-MELPHALAN BY PLASMACYTOMA PLASMA CELLS

Bone marrow plasma cells from fifteen cases of multiple myeloma, immunologically typed, were incubated with different tritiated compounds. The labelling index with tritiated thymidine is generally low, while the mean grain count is fairly normal in the active cells. The labelling index of ³H-uridine and ³H-leucine was very high, while the mean grain count per cell lies within the normal range. The results obtained with ³H-phenylalanine-mustard (melphalan), which is a drug used in the treatment of the plasmacytoma, show also incorporation values roughly comparable to those of ³H-leucine. The present data seem to support the clinical use of melphalan as a compound that is actively incorporated into the plasma cells of plasmacytoma although inhibition of protein synthesis due to specific binding to protein was not demonstrated.     

mCCG methylation in angiosperms

Two different methods were used to investigate the abundance of cytosine methylation at the outer (5′) position in 5′-CCG-3′ trinucleotides in angiosperm genomes. Mspl is unable to cut its target site if the outer cytosine is methylated (5′-^mCCGG-3′). Using Mspl restriction analysis, it was shown that 5′-^mCCG-3′ is present in all angiosperm genomes examined, and that the amount of cytosine methylation at this site varies between species. Subsequently, direct measurements were made of the amount of methylation at both cytosines in a subset of 5′-CCG-3′ trinucleotides in the Arabidopsis thaliana genome. Based upon these analyses, it was estimated that approximately 20–30% of 5′-CCG-3′ trinucleotides in A. thaliana are methylated at the outer cytosine. Approximately 20% of the 5′-CCG-3′ trinucleotides contain 5-methyl-cytosine at the inner cytosine position, which corresponds to a previous determination of 5′-^mCG-3′ methylation in A. thaliana. The implications of 5′-^mCCG-3′ methylation are discussed.