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PubMed2005

Molecular rationale for the pharmacological treatment of Alzheimer's disease.

Cerebral deposition of amyloid plaques containing amyloid beta-peptide (Abeta) has traditionally been considered the central feature of Alzheimer's disease (AD). Abeta is derived from amyloid precursor protein (APP), which is cleaved by several different proteases: alpha-, beta- and gamma-secretase. In the past decade, however, the molecular pathogenesis of AD has been shown to involve alterations in several neurotransmitter, inflammatory, oxidative, and hormonal pathways that represent potential targets for AD prevention and treatment. Much research has shown a direct link between cholinergic impairment and altered APP processing as a major pathogenetic event in AD. Three highly probable mechanisms of APP regulation through inhibition of acetylcholinesterase are thus current topics of investigation. Indeed, acetylcholinesterase inhibitors appear to cause selective muscarinic activation of alpha-secretase and to induce the translation of APP mRNA; they may also restrict amyloid fibre assembly. Activation of N-methyl-D-aspartate receptors is considered a probable cause of chronic neurodegeneration in AD, and memantine has been widely used in some countries in AD patients to block cerebral N-methyl-D-aspartate receptors that normally respond to glutamate. Further studies are needed to determine whether antioxidants such as vitamins C and E are effective, through various mechanisms, in patients with mild-to-moderate AD. Additional data are also required for non-steroidal anti-inflammatory drugs, some of which appear to possess experimental effects that may ultimately prove favourable in AD patients. Statins also warrant further investigation, since they have activated alpha-secretase and they reduced Abeta generation and amyloid accumulation in a transgenic mouse model. beta-Secretase would seem to be an ideal target for anti-amyloid therapy in AD, but potential clinical and pharmacological issues, such as ensuring selectivity of inhibition, stability, and ease of blood-brain barrier penetration and cellular uptake, remain to be addressed for beta-secretase inhibitors. gamma-Secretase is not an easy candidate for pharmacological manipulation. Immunotherapeutic strategies have targeted Abeta directly; however, intensive investigation of indirect approaches to the management of AD with immunotherapy is now underway.

Alzheimer Disease↗

PubMed2003

Novel destabilization of nucleotide binding by the gamma phosphate of ATP in the yeast SR protein kinase Sky1p.

SR protein kinases (SRPKs) regulate the temporal and cell-specific selection of alternative splice sites. These enzymes are highly unique members of the protein kinase family. SRPKs contain a large domain insert (approximately 200 residues) within the kinase core, do not require phosphorylation for regulation, have an extended helix insert near the nucleotide pocket, and possess unusual substrate specificity determinants. The yeast SRPK, Sky1p, rapidly phosphorylates its natural substrate Npl3 but binds ATP with a high K(m), suggesting that some of these distinctive structural features may be correlated with nucleotide binding [Aubol et al. (2002) Biochemistry 41, 10002-10009]. To address this issue, the nucleotide binding properties of Sky1p were studied using fluorescence spectroscopy. The affinities of several nucleotides (ATP, ADP, AMP, adenosine, and AMPPNP) to Sky1p and the prototype kinase, cAMP-dependent protein kinase, were compared in the absence and presence of the metal activator, Mg(2+), using a fluorescence-based displacement assay. The data indicate that Sky1p, unlike cAMP-dependent protein kinase, potently destabilizes the gamma phosphate of ATP. This novel finding suggests that rapid phosphoryl transfer may be facilitated by unique mechanisms in both protein kinases.

Adenosine Diphosphate↗

PubMed1994

Distinctive features of the gametes and reproductive tracts of the Asian musk shrew, Suncus murinus.

Insectivora are of special interest as the most primitive of the eutherian mammals, but essentially nothing is known of their gamete function. In this respect, the Asian musk shrew (Suncus murinus), investigated in the present study, displays many idiosyncrasies. In the epididymis, the giant acrosome undergoes further stabilization, its unusual resilience being especially evident in a "rim" created by a persistent close alignment of the outer acrosomal and overlying plasma membranes. However, until spermatozoa reached a gland on the vas deferens, no post-testicular change was demonstrable in the sperm head surface, the unusual nature of which was indicated by a dorso-ventral differentiation, by an inability to auto-agglutinate or to bind to the homologous zona pellucida, and by an insensitivity to anti-sperm immunoglobulin IgG in fresh serum. At mating, only about 1 x 10(6) spermatozoa are inseminated as far as the anterior vagina with plug formation. Within the small (6 mm) fallopian tube, the isthmus and ampulla are sharply delineated by their contractile activity and epithelial character; there is evidence of some sperm entry into isthmic crypts and a tendency for ipsilateral ovarian control of sperm transport to the tubal ampulla. The cumulus oophorus does not undergo preovulatory mucification and expansion, is characterized by persistent intercellular gap junctions, and is insensitive to hyaluronidase and trypsin. It is unclear how the compact cumulus is penetrated at fertilization. The giant acrosome contains acrosin and an unusually temperature-dependent cumulytic activity; it is intact in motile ampullary spermatozoa but appears to be discharged before reaching the zona pellucida. Since eggs were not penetrated in the presence of ampullary spermatozoa until 4-10 h after ovulation, Suncus spermatozoa spend a long period in the female before they can fertilize. The determinants of sperm function, including capacitation and the acrosome reaction (AR), may depend on a different set of controls in Suncus, perhaps as a legacy of the resilient giant acrosome. This possibility could be examined in other Crociduran and Soricine shrews selected according to acrosome size.

Acrosome↗

PubMed2005

Ab initio calculation of bowl, cage, and ring isomers of C20 and C20-.

High-level ab initio calculations have been carried out to reexamine relative stability of bowl, cage, and ring isomers of C(20) and C(20)(-). The total electronic energies of the three isomers show different energy orderings, strongly depending on the hybrid functionals selected. It is found that among three popular hybrid density-functional (DF) methods B3LYP, B3PW91, PBE1PBE, and a new hybrid-meta-DF method TPSSKCIS, only the PBE1PBE method (with cc-pVTZ basis set) gives qualitatively correct energy ordering as that predicted from ab initio CCSD(T)/cc-pVDZ [CCSD(T)-coupled-cluster method including singles, doubles, and noniterative perturbative triples; cc-pVDZ-correlation consistent polarized valence double zeta] as well as from MP4(SDQ)/cc-pVTZ [MP4-fourth-order Moller-Plesset; cc-pVTZ-correlation consistent polarized valence triple zeta] calculations. Both CCSD(T) and MP4 calculations indicate that the bowl is most likely the global minimum of neutral C(20) isomers, followed by the fullerene cage and ring. For the anionic counterparts, the PBE1PBE calculation also agrees with MP4/cc-pVTZ calculation, both predicting that the bowl is still the lowest-energy structure of C(20)(-) at T=0 K, followed by the ring and the cage. In contrast, both B3LYP/cc-pVTZ and B3PW91/cc-pVTZ calculations predict that the ring is the lowest-energy structure of C(20)(-). Apparently, this good reliability in predicting the energy ordering renders the hybrid PBE method a leading choice for predicting relative stability among large-sized carbon clusters and other carbon nanostructures (e.g., finite-size carbon nanotubes, nano-onions, or nanohorns). The relative stabilities derived from total energy with Gibbs free-energy corrections demonstrate a changing ordering in which ring becomes more favorable for both C(20) and C(20)(-) at high temperatures. Finally, photoelectron spectra (PES) for the anionic C(20)(-) isomers have been computed. With binding energies up to 7 eV, the simulated PES show ample spectral features to distinguish the three competitive C(20)(-) isomers.

Journal Article↗

PubMed2001

Type II protein secretion in gram-negative pathogenic bacteria: the study of the structure/secretion relationships of the cellulase Cel5 (formerly EGZ) from Erwinia chrysanthemi.

Erwinia chrysanthemi, a Gram-negative plant pathogen, secretes the cellulase Cel5 (formerly EGZ) via the type II secretion pathway (referred to as Out). Cel5 is composed of two domains, a large N-terminal catalytic domain (390 amino acid residues) and a small C-terminal cellulose-binding domain (62 amino acid residues) separated by a linker region. A combination of mutagenesis and structural analysis permitted us to investigate the structure/secretion relationships with respect to the catalytic domain of Cel5. The 3D structure of the catalytic domain was solved by molecular replacement at 2.3 A resolution. Cel5 exhibits the (beta/alpha)8 structural fold and two extra-barrel features. Our previous genetic study based upon tRNA-mediated suppression allowed us to predict positions of importance in the molecule in relation to structure and catalysis. Remarkably, all of the predictions proved to be correct when compared with the present structural information. Mutations of Arg57, which is located at the heart of the catalytic domain, allowed us to test the consequences of structural modifications on the secretion efficiency. The results revealed that secretability imposes remarkably strong constraints upon folding. In particular, an Arg-to-His mutation yielded a species that folded to a stable conformation close to, but distinct from the wild-type, which however was not secretable. We discuss the relationships between folding of a protein in the periplasm, en route to the cell exterior, and presentation of secretion information. We propose that different solutions have been selected for type II secreted exoproteins in order to meet the constraints imposed by their interaction with their respective secretion machineries. We propose that evolutionary pressure has led to the adaptation of different secretion motifs for different type II exoproteins.

Arginine↗

PubMed2004

Premature termination codons enhance mRNA decapping in human cells.

Nonsense-mediated mRNA decay (NMD) is a eukaryotic surveillance process that promotes selective degradation of imperfect messages containing premature translation termination codons (PTCs). In yeast, PTCs trigger both deadenylylation-independent mRNA decapping, thereby allowing their rapid degradation by a 5' to 3' exonuclease, and to a smaller extent accelerated deadenylylation. It is not clear to what extent this decay pathway is conserved in higher eukaryotes. We used a transcriptional pulse strategy relying on a tetracycline-regulated promoter to study the decay of a PTC- containing beta-globin mRNA in human cells. We show that a PTC destabilizes the mRNA and decreases its half-life from >16 h to 3 h. The deadenylylation rate is increased, but not sufficiently to account for the decreased half-life on its own. Using a circularization RT-PCR (cRT-PCR) strategy, we could detect decapped degradation intermediates and measure simultaneously their poly(A) tail length. This allowed us to show that a PTC enhances the rate of mRNA decapping and that decapped products have been deadenylylated to a certain extent. Thus the major feature of the NMD pathway, enhanced decapping, is conserved from yeast to man even though the kinetic details might differ between various mRNAs and/or species.

Codon, Nonsense↗

PubMed2001

Limited adhesion of biodegradable microspheres to E- and P-selectin under flow.

In a variety of disease settings the expression of the endothelial selectins E- and P-selectin appears to be increased. This feature makes these molecules attractive targets around which to design directed drug-delivery schemes. One possible approach for achieving such delivery is to use polymeric biodegradable microspheres bearing a humanized monoclonal antibody (MAb) for E- and P-selectin, MAb HuEP5C7.g2. Perhaps the simplest technique for "coupling" HuEP5C7.g2 to the microspheres is via nonspecific adsorption. Previous studies suggest, however, that the adsorption of proteins onto microspheres fabricated in the presence of a stabilizer such as poly(vinyl alcohol) (PVA) is limited. It is unclear to what extent this limited level of adsorbed HuEP5C7.g2 would be able to support adhesion to E- and P-selectin under flow conditions. To explore this issue, we prepared microspheres from the biodegradable polymer, poly(epsilon-caprolactone) (PCL), using a single emulsion process and PVA as a stabilizer. We then incubated the PCL microspheres with HuEP5C7.g2 and studied the adhesion of the resulting HuEP5C7.g2 microspheres to E- and P-selectin under in vitro flow conditions. We found that the HuEP5C7.g2 PCL microspheres exhibit specific adhesion to Chinese hamster ovary cells stably expressing P-selectin (CHO-P) and 4-h IL-1beta-activated human umbilical vein endothelial cells (HUVEC). In contrast, HuEP5C7.g2 PCL microspheres exhibit little adhesion to parental CHO cells or unactivated HUVEC. The attachment efficiency to the selectin substrates was quite low, with appreciable attachment occurring only at low shear (0.3 dyn/cm(2)). Other supporting data strongly suggest that the limited attachment efficiency is due to a low level of HuEP5C7.g2 adsorbed to the PCL microspheres. Although the attachment was limited, a significant percentage of the HuEP5C7.g2 PCL microspheres were able to remain adherent at relatively high shear (8 dyn/cm(2)). Combined, our data suggest that HuEP5C7.g2 PCL microspheres exhibit selective limited adhesion to cellular substrate expressing E- and P-selectin.

Adsorption↗

PubMed1998

Complete sequence of the IncPbeta plasmid R751: implications for evolution and organisation of the IncP backbone.

The broad host range IncP plasmids are of particular interest because of their ability to promote gene spread between diverse bacterial species. To facilitate study of these plasmids we have compiled the complete sequence of the IncPbeta plasmid R751. Comparison with the sequence of the IncPalpha plasmids confirms the conservation of the IncP backbone of replication, conjugative transfer and stable inheritance functions between the two branches of this family. As in the IncPalpha genome the DNA of this backbone appears to have been enriched for the GCCG/CGGC motifs characteristic of the genome of organisms with a high G+C content, such as P. aeruginosa, suggesting that IncPbeta plasmids have been subjected during their evolution to similar mutational and selective forces as IncPalpha plasmids and may have evolved in pseudomonad hosts. The IncP genome is consistently interrupted by insertion of phenotypic markers and/or transposable elements between oriV and trfA and between the tra and trb operons. The R751 genome reveals a family of repeated sequences in these regions which may form the basis of a hot spot for insertion of foreign DNA. Sequence analysis of the cryptic transposon Tn4321 revealed that it is not a member of the Tn21 family as we had proposed previously from an inspection of its ends. Rather it is a composite transposon defined by inverted repeats of a 1347 bp IS element belonging to a recently discovered family which is distributed throughout the prokaryotes. The central unique region of Tn4321 encodes two predicted proteins, one of which is a regulatory protein while the other is presumably responsible for an as yet unidentified phenotype. The most striking feature of the IncPalpha plasmids, the global regulation of replication and transfer by the KorA and KorB proteins encoded in the central control operon, is conserved between the two plasmids although there appear to be significant differences in the specificity of repressor-operator interactions. The importance of these global regulatory circuits is emphasised by the observation that the operator sequences for KorB are highly conserved even in contexts where the surrounding region, either a protein coding or intergenic sequence, has diverged considerably. There appears to be no equivalent of the parABCDE region which in the IncPalpha plasmids provides multimer resolution, lethality to plasmid-free segregants and active partitioning functions. However, we found that the continuous sector from co-ordinate 0 to 9100 bp, encoding the co-regulated klc and kle operons as well as the central control region, could confer a high degree of segregational stability on a low copy number test vector. Thus R751 appears to exhibit very clearly what was first revealed by study of the IncPalpha plasmids, namely a fully functional co-ordinately regulated set of replication, transfer and stable inheritance functions.

Amino Acid Sequence↗

PubMed2004

Oxyanion selectivity in sulfate and molybdate transport proteins: an ab initio/CDM study.

A striking feature of sulfate (SO(4)(2-)) and molybdate (MoO(4)(2-)) transport proteins, such as SBP and ModA, which specifically bind SO(4)(2-) and MoO(4)(2-), respectively, is their ability to discriminate very similar anions with the same net charge, geometry, and hydrogen-bonding properties. Here, we determine to what extent (1) oxyanion-solvent interactions, (2) oxyanion-amino acid interactions, and (3) the anion-binding pocket sizes of the cognate protein contribute to the anion selectivity process in SO(4)(2-) and MoO(4)(2-) transport proteins by computing the free energies for replacing SO(4)(2-) with MoO(4)(2)(-)/WO(4)(2-) in model SO(4)(2-)-binding sites of varying degrees of solvent exposure using a combined quantum mechanical/continuum dielectric approach. The calculations reveal that MoO(4)(2-) transport proteins, such as ModA, specifically bind MoO(4)(2-)/WO(4)(2-) but not SO(4)(2-), mainly because the desolvation penalty of MoO(4)(2-)/WO(4)(2-) is significantly less than that of SO(4)(2-) and, to a lesser extent, because the large and rigid cavity in these proteins attenuates ligand interactions with SO(4)(2-), as compared to MoO(4)(2-). On the other hand, SO(4)(2-) transport proteins prefer SO(4)(2-) to MoO(4)(2-)/WO(4)(2-) because the small anion-binding pocket characteristic of these proteins inhibits binding of the larger MoO(4)(2-) and WO(4)(2-) anions. The calculations also help to explain the absence of positively charged Lys/Arg side chains in the anion-binding sites of SBP and ModA. During evolution, these transport proteins may have excluded cationic ligands from their binding sites because, on one hand, Lys/Arg do not contribute to the selectivity of the binding pocket and, on the other, they substantially stabilize the complex between the oxyanion and protein ligands, which in turn would prohibit the rapid release of the bound oxyanion at a certain stage during the transport process.

Anions↗

PubMed1997

Influence of projected complication rates on estimated appropriate use rates for carotid endarterectomy. Appropriateness Project Investigators. Academic Medical Center Consortium.

OBJECTIVE: To examine specifically the influence of estimated perioperative mortality and stroke rate on the assessment of appropriateness of carotid endarterectomy. DATA SOURCES/STUDY SETTING: An expert panel convened to rate the appropriateness of a variety of potential indications for carotid endarterectomy based on various rates of perioperative complications. We then applied these ratings to the charts of 1,160 randomly selected patients who had carotid endarterectomy in one of the 12 participating academic medical centers. STUDY DESIGN: An expert panel evaluated indications for carotid endarterectomy using the modified Delphi approach. Charts of patients who received surgery were abstracted, and clinical indications for the procedure as well as perioperative complications were recorded. To examine the impact of surgical risk assessment on the rates of appropriateness, three different definitions of risk strata for combined perioperative death or stroke were used: Definition A, low risk < 3 percent; Definition B, low risk < 5 percent; and Definition C, low risk < 7 percent. PRINCIPAL FINDINGS: Overall hospital-specific mortality ranged from 0 percent to 4.0 percent and major complications, defined as death, stroke, intracranial hemorrhage, or myocardial infarction, varied from 2.0 percent to 11.1 percent. Most patients (72 percent) had surgery for transient ischemic attack or stroke; 24 percent of patients were asymptomatic. Most patients (82 percent) had surgery on the side of a high-grade stenosis (70-99 percent). When the thresholds for operative risk were placed at the values defined by the expert panel (Definition A), only 33.5 percent of 1,160 procedures were classified as "appropriate." When the definition of low risk was shifted upward, the proportion of cases categorized as appropriate increased to 58 percent and 81.5 percent for Definitions B and C, respectively. CONCLUSIONS: Despite the high proportion of procedures performed for symptomatic patients with a high degree of ipsilateral extracranial carotid artery stenosis and generally low rates of surgical complications at the participating institutions, the overall rate of "appropriateness" using a perioperative complication rate of < 3 percent was low. However, the rate of "appropriateness" was extremely sensitive to judgments about a single clinical feature, surgical risk. These data show that before applying such "appropriateness" ratings, it is crucial to perform sensitivity analyses in order to assess the stability of the results. Results that are robust to moderate in variation in surgical risk provide a much sounder basis for policy making than those that are not.

Academic Medical Centers↗

PubMed1986

Tryptic and chymotryptic cleavage sites in sequence of alpha-subunit of (Na+ + K+)-ATPase from outer medulla of mammalian kidney.

Localization of selective proteolytic splits in alpha-subunit of (Na+ + K+)-ATPase is important for understanding the mechanism of active Na+,K+-transport. Proteolytic fragments of alpha-subunit from pig kidney were purified by chromatography in NaDodSO4 on TSK 3000 SW columns. NH2-terminal amino acid sequences of fragments as determined in a gas phase sequenator were unambiguously located within the total sequence of alpha-subunit from sheep kidney (Shull, C.E., et al. (1985) Nature 316, 691-695) and pig kidney (Ovchinnikov, Y.A., et al. (1985) Proc. Acad. Sci. USSR 285, 1490-1495). The primary chymotryptic split in the E1-form is located between Leu-266 and Ala-267 while the tryptic cleavage site appears to be between Arg-262 and Ile-263 (Bond 3). Tryptic cleavage in the initial fast phase of inactivation of the E1-form is located between Lys-30 and Glu-31 (Bond 2). In the E2-form, primary tryptic cleavage is between Arg-438 and Ala-439 (Bond 1). Chymotryptic cleavage between Leu-266 and Ala-267 stabilizes the E1-form of the protein without affecting the sites for binding of cations or nucleotides. Titration of fluorescence responses demonstrates the importance of the NH2-terminal for E1-E2 transition. Protonation of His-13 facilitates transition from E1- to E2-forms of the protein. Removal of His-13 after cleavage of bond 2 can explain the increase in apparent affinity of the cleaved enzyme for Na+ and the shift in poise of E1-E2 equilibrium in direction of E1-forms. The NH2-terminal sequence in renal alpha-subunit is not conserved in alpha + from rat neurolemma or in alpha-subunit from Torpedo or brine shrimp. A regulatory function of the NH2-terminal part of the alpha-subunit may thus be a unique feature of the alpha-subunit in (Na+ + K+)-ATPase from mammalian kidney.

Amino Acid Sequence↗

PubMed2001

4'-Ethynyl nucleoside analogs: potent inhibitors of multidrug-resistant human immunodeficiency virus variants in vitro.

A series of 4'-ethynyl (4'-E) nucleoside analogs were designed, synthesized, and identified as being active against a wide spectrum of human immunodeficiency viruses (HIV), including a variety of laboratory strains of HIV-1, HIV-2, and primary clinical HIV-1 isolates. Among such analogs examined, 4'-E-2'-deoxycytidine (4'-E-dC), 4'-E-2'-deoxyadenosine (4'-E-dA), 4'-E-2'-deoxyribofuranosyl-2,6-diaminopurine, and 4'-E-2'-deoxyguanosine were the most potent and blocked HIV-1 replication with 50% effective concentrations ranging from 0.0003 to 0.01 microM in vitro with favorable cellular toxicity profiles (selectivity indices ranging 458 to 2,600). These 4'-E analogs also suppressed replication of various drug-resistant HIV-1 clones, including HIV-1(M41L/T215Y), HIV-1(K65R), HIV-1(L74V), HIV-1(M41L/T69S-S-G/T215Y), and HIV-1(A62V/V75I/F77L/F116Y/Q151M). Moreover, these analogs inhibited the replication of multidrug-resistant clinical HIV-1 strains carrying a variety of drug resistance-related amino acid substitutions isolated from HIV-1-infected individuals for whom 10 or 11 different anti-HIV-1 agents had failed. The 4'-E analogs also blocked the replication of a non-nucleoside reverse transcriptase inhibitor-resistant clone, HIV-1(Y181C), and showed an HIV-1 inhibition profile similar to that of zidovudine in time-of-drug-addition assays. The antiviral activity of 4'-E-thymidine and 4'-E-dC was blocked by the addition of thymidine and 2'-deoxycytidine, respectively, while that of 4'-E-dA was not affected by 2'-deoxyadenosine, similar to the antiviral activity reversion feature of 2',3'-dideoxynucleosides, strongly suggesting that 4'-E analogs belong to the family of nucleoside reverse transcriptase inhibitors. Further development of 4'-E analogs as potential therapeutics for infection with multidrug-resistant HIV-1 is warranted.

Anti-HIV Agents↗

PubMed2001

An open trial of divalproex sodium in autism spectrum disorders.

BACKGROUND: Autism spectrum disorders are characterized by core deficits in social interaction and speech/communication skills, repetitive behaviors, and restricted interests. Other abnormalities include seizures, electroencephalographic (EEG) abnormalities, affective instability, impulsivity, and aggression. Divalproex sodium is indicated as both an anticonvulsant in epilepsy and a mood stabilizer in bipolar illness and thus might be useful for these complicating symptoms in autism. METHOD: A retrospective pilot study was conducted to determine whether divalproex sodium was effective in treating core dimensions and associated features of autism. Fourteen patients who met DSM-IV criteria for autism, Asperger's disorder, or pervasive developmental disorder not otherwise specified, both with and without a history of seizure disorders or EEG abnormalities, were openly treated with divalproex sodium. Improvement was assessed via the Clinical Global Impressions-Improvement scale. RESULTS: Of 14 patients who completed a trial of divalproex sodium, 10 (71%) were rated as having sustained response to treatment. The mean dose of divalproex sodium was 768 mg/day (range, 125-2500 mg/day), and it was generally well tolerated. Improvement was noted in core symptoms of autism and associated features of affective instability, impulsivity, and aggression. CONCLUSION: Divalproex sodium may be beneficial to patients with autism spectrum disorders, particularly those with associated features of affective instability, impulsivity, and aggression as well as those with a history of EEG abnormalities or seizures. Of note, all patients with an abnormal EEG and/or seizure history were rated as responders. However, these findings must be interpreted with caution, given the open retrospective nature of the study. Controlled trials are needed to replicate these preliminary findings.

Adolescent↗

PubMed2004

The Sm-like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli.

In Escherichia coli, the post-transcriptional addition of poly(A) tails by poly(A) polymerase I (PAP I, pcnB) plays a significant role in cellular RNA metabolism. However, many important features of this system, including its regulation and the selection of polyadenylation sites, are still poorly understood. Here we show that the inactivation of Hfq (hfq), an abundant RNA-binding protein, leads to the reduction in the ability of PAP I to add poly(A) tails at the 3' termini of mRNAs containing Rho-independent transcription terminators even though PAP I protein levels remain unchanged. Those poly(A) tails that are synthesized in the absence of Hfq are shorter in length, even in the absence of polynucleotide phosphorylase (PNPase), RNase II and RNase E. In fact, the biosynthetic activity of PNPase in the hfq single mutant is enhanced and it becomes the primary polynucleotide polymerase, adding heteropolymeric tails almost exclusively to 3' truncated mRNAs. Surprisingly, both PNPase and Hfq co-purified with His-tagged PAP I under native conditions indicating a potential complex among these proteins. Immunoprecipitation experiments using PNPase- and Hfq-specific antibodies confirmed the protein-protein interactions among PAP I, PNPase and Hfq. Analysis of mRNA half-lives in hfq, deltapcnB and hfq deltapcnB mutants suggests that Hfq and PAP I function in the same mRNA decay pathway.

Base Sequence↗

PubMed1992

Ocular compensation for self-motion. Visual mechanisms.

In monkeys, there are several reflexes that generate eye movements to compensate for the observer's own movements. Two vestibuloocular reflexes compensate selectively for rotational (RVOR) and translational (TVOR) disturbances of the head, receiving their inputs from the semicircular canals and otolith organs, respectively. Two independent visual tracking systems that deal with residual disturbances of gaze are manifest in the two components of the optokinetic response: the indirect or delayed component (OKNd) and the direct or early component (OKNe). We hypothesize that OKNd--like the RVOR--is phylogenetically old, being found in all animals with mobile eyes, and that it evolved as a backup to the RVOR to compensate for rotational disturbances of gaze. Indeed, optically induced changes in the gain of the RVOR result in parallel changes in the gain of OKNd, consistent with the idea of shared pathways as well as shared functions. In contrast, OKNe--like the TVOR--seems to have evolved much more recently in frontal-eyed animals and, we suggest, acts as a backup to the TVOR to deal primarily with translational disturbances of gaze. Frontal-eyed animals with good binocular vision must be able to keep both eyes directed at the object of regard irrespective of proximity, and in order to achieve this during translational disturbances, the output of the TVOR is modulated inversely with the viewing distance. OKNe shares this sensitivity to absolute depth, consistent with the idea that it is synergistic with the TVOR and shares some of its central pathways. There is evidence that OKNe is also sensitive to relative depth cues such as motion parallax, which we suggest helps the system to segregate the object of regard from other elements in the scene. However, there are occasions when the global optic flow cannot be resolved into a single vector useful to the oculomotor system (e.g., when the moving observer looks towards the direction of heading). We suggest that on such occasions a third independent tracking mechanism, the smooth pursuit system, is deployed to stabilize gaze on the local feature of interest. In this scheme, the pursuit system has an attentional focusing mechanism that spatially filters the visual motion inputs driving the oculomotor system. The major distinguishing features of the 3 visual tracking mechanisms are summarized in Table 1.

Animals↗

PubMed1993

Multicopy STS1 restores both protein transport and ribosomal RNA stability in a new yeast sec23 mutant allele.

A thermosensitive mutant was selected on the basis of its resistance after a heat shock to the lethal effects of lomofungin, a drug that inhibits RNA synthesis. We demonstrate that the single mutation conferring thermosensitivity and lomofungin resistance is heteroallelic to sec23-1. This new allele of sec23 is designated sec23-11. The yeast SEC23 gene has previously been reported to function in protein transport from the endoplasmic reticulum (ER) to the Golgi apparatus. After a 1-min shift to elevated temperature, a sec23-1 mutant becomes defective in vesicle formation from the ER. We show here that upon a shift to high temperature, both sec23 alleles confer defects in ER-to-Golgi transport, and both mutants stop accumulating nascent RNA after 20 to 30 min. Transcription and early maturation of ribosomal RNA, the major RNA species, are normal in a sec23-11 mutant, but the matured ribosomal RNA is then degraded. This ribosomal RNA instability may reflect improper assembly of ribosomal subunits, due to failure to localize essential factors such as ribosomal proteins to the nucleus. In addition to the sec23 mutants, other ER-to-Golgi secretion mutants exhibit a strong RNA biosynthetic defect, and we conclude that continued post-ER protein transport, not just a functional SEC23 gene product (Sec23p), is required for ribosomal RNA stability. We also identified an extragenic multicopy suppressor of the sec23-11 mutant, the essential STS1 gene ("Sec Twenty-three Suppressor 1"). Besides restoring partial temperature resistance to the sec23-11 mutant, overexpression of STS1 also overcomes both the RNA synthesis and the protein transport blocks in this mutant. In contrast, multicopy STS1 exerts only small effects on the sec23-1 mutant. The predicted STS1 gene product (Sts1p) is a low-abundance protein of 36,500 daltons, with no signal peptide and no hydrophobic stretch of sufficient length to span a membrane. Like Sec23p, Sts1p is found in a cytosolic compartment. These features suggest that Sts1p may play a catalytic or regulatory role in conjunction with the more abundant Sec23p.

ATP-Binding Cassette Transporters↗

PubMed2001

Comparative biodistribution and metabolism of carbon-11-labeled N-[2-(dimethylamino)ethyl]acridine-4-carboxamide and DNA-intercalating analogues.

The tricyclic carboxamide N-[2-(dimethylamino)ethyl]acridine-4-carboxamide (DACA) is a DNA-intercalating agent capable of inhibiting both topoisomerases I and II and is currently in Phase II clinical trial. Many related analogues have been developed, but despite their potent in vitro cytotoxicities, they exhibit poor extravascular distribution. As part of an ongoing drug development program to obtain related "minimal intercalators" with lower DNA association constants, we have compared the biodistribution and metabolite profiles of the prototype compound, DACA, with three analogues to aid rational drug selection. All of these compounds share a common structural feature, N-dimethyl side chain, which was radiolabeled with the positron-emitting radioisotope, carbon-11. This strategy was selected because it allows promising candidates emerging from preclinical studies in animals to be evaluated rapidly in humans using positron emission tomography (PET). The acridine DACA, the phenazine SN 23490, the pyridoquinoline SN 23719, and the dibenzodioxin SN 23935 were found to be cytotoxic in in vitro assays with an IC50 of 1.4-1.8 microM, 0.4-0.6 microM, 1.3-1.6 microM, and 24-36 microM, respectively, in HT29, U87MG, and A375M cell lines. Ex vivo biodistribution studies with carbon-11 radiolabeled compounds in mice bearing human tumor xenografts showed rapid clearance of 11C-radioactivity (parent drug and metabolites) from blood and the major organs. Rapid hepatobiliary clearance and renal excretion were also observed. There was low [<5% of injected dose/gram (%ID/g)] and variable uptake of 11C-radioactivity in three tumor types for all of the compounds. Tumor (U87MG) to blood 11C-radioactivity for [11C]DACA, [11C](9-methoxyphenazine-1-carboxamide (SN 23490), [11C]2-(4-pyridyl)quinoline-8-carboxamide (SN 23719), and [11C]dibenzo[1,4]dioxin-1-carboxamide (SN 23935) at 30 min were 2.9 +/- 1.1, 2.3 +/- 0.6, 2.6 +/- 0.6, and 0.7 +/- 0.2, respectively. For SN 23719, the distribution of 11C-radioactivity in normal tissues and tumors determined ex vivo was in broad agreement with that determined in vivo by whole body PET scanning. [11C]DACA was rapidly and extensively metabolized to several plasma metabolites and a major tumor metabolite. In contrast, [11C]SN 23935, [11C]SN 23490, and [11C]SN 23719 showed less extensive metabolism. In the tumor samples, the parent [11C]DACA and [11C]SN 23935 represented between 0.3 and 1.5%ID/g, whereas [11C]SN 23490 and [11C]SN 23719 represented between 1.5 and 2.8%ID/g. In conclusion, by using a strategy with 11C-labeling, we have determined the tissue distribution and metabolic stability of novel tricyclic carboxamides with the view of selecting analogues with potentially better in vivo activity against solid tumors. SN 23490 and SN 23719 had more favorable distribution and metabolic stability compared with DACA and SN 23935 and may warrant further development. The radiolabeling strategy used allows ex vivo and in vivo evaluation of promising anticancer agents in animals and offers the potential of rapid translation to studies in humans using PET.

Acridines↗

PubMed1996

Meningeal carcinomatosis in patients with breast carcinoma. Clinical features, prognostic factors, and results of a high-dose intrathecal methotrexate regimen.

BACKGROUND: This retrospective study evaluates the results of a regimen of high-dose intrathecal methotrexate and the prognostic factors for the response in patients with meningeal from breast carcinoma. METHODS: From 1979 to 1994, 68 breast carcinoma patients were diagnosed with meningeal carcinomatosis at a mean age of 52 years. All but two had previous metastatic involvement. The proportion of lobular and ductal carcinomas was balanced. Malignant cells were present in cerebrospinal fluid (CSF) samples from 61 patients, whereas the 7 remaining patients had increased CSF protein associated with computerized tomographic scan evidence of meningeal metastases. From 1989, 41 of the patients received a regimen of high-dose intrathecal methotrexate with systemic folinic acid rescue (HD-MTX+FA): intrathecal MTX, 15 mg daily x 5 days, repeated every 2 weeks, and intrathecal hydrocortisone acetate, 125 mg on Day 1, and folinic acid, 10 mg intramuscularly 12 hours after each MTX injection. Systemic treatment and radiation therapy were usually associated. Patients treated before 1988 received intrathecal MTX in conventional doses (15 mg once a week). RESULTS: Clinical objective response, defined as a neurological improvement for at least one month, was achieved in 17 patients (41%) and stabilization in 14 (34%) treated with the HD-MTX+FA regimen. The response rate was significantly higher compared with that of the group treated with the conventional doses (P = 0.03). Median survival was 14 weeks for patients treated with the HD-MTX+FA regimen, compared with 7 weeks for patients who received conventional doses of MTX (P = 0.01). Grade 3 or 4 neutropenia was the main toxicity that occurred in 16 16 patients (39%) treated with the HD-MTX+FA regimen, and in 7 patients (33%) treated with conventional doses of MTX. In a univariate analysis, three parameters were singled out as having a favorable prognostic value for response to therapy; controlled systemic disease at diagnosis (P < 0.05), low initial CSF protein level (P < 0.05), and concomitant systemic chemotherapy during intrathecal therapy (P < 0.02). Multivariate analysis was not performed because the sample size was too small. CONCLUSIONS: Although this study was retrospective, the intrathecal HD-MTX+FA regimen appears to be a more efficient strategy than conventional doses of MTX to induce neurologic improvement and perhaps better survival. It should be recommended in combination with systemic chemotherapy for selected patients with meningeal carcinomatosis from breast carcinoma who are likely to benefit from intensive therapy, i.e., patients with a CSF protein level less than 5 g/L and in whom systemic disease has been controlled.

Adult↗