In emotional learning tasks, sex differences, stress effects and an interaction of these two moderators have often been observed. The sex hormones estradiol (E2) and progesterone (P4) vary over the menstrual cycle. We tested groups with different sex hormone status: 39 men, 30 women in the luteal phase (LU, high E2+P4) and 29 women taking oral contraceptives (OC, low E2+P4). They received either 30 mg cortisol or placebo prior to instructed differential fear conditioning consisting of neutral conditioned stimuli (CS) and an electrical stimulation (unconditioned stimulus; UCS). One figure (CS+) was paired with the UCS, the other figure (CS-) never. During extinction, no electrical stimulation was administered. Regarding fear acquisition, results showed higher skin conductance and higher brain responses to the CS+ compared to the CS- in several structures that were not modulated by cortisol or sex hormones. However, OC women exhibited higher CS+/CS- differentiations than men and LU women in the amygdala, thalamus, anterior cingulate and ventromedial prefrontal cortex during extinction. The suppression of endogenous sex hormones by OC seems to alter neuronal correlates of extinction. The observation that extinction is influenced by the current sex hormone availability is relevant for future studies and might also be clinically important.

IGF-II is a mitogenic peptide that has been implicated in hepatocellular oncogenesis. Since the silencing of gene expression is frequently associated with cytosine methylation at cytosine-guanine (CpG) dinucleotides, we designed a methylated oligonucleotide (MON1) complementary to a region encompassing IGF2 promoter P4 in an attempt to induce DNA methylation at that locus and diminish IGF2 mRNA levels. MON1 specifically inhibited IGF2 mRNA accumulation in vitro, whereas an oligonucleotide (ON1) with the same sequence but with nonmethylated cytosines had no effect on IGF2 mRNA abundance. MON1 treatment led to the specific induction of de novo DNA methylation in the region of IGF2 promoter hP4. Cells from a human hepatocellular carcinoma (HCC) cell line, Hep 3B, were implanted into the livers of nude mice, resulting in the growth of large tumors. Animals treated with MON1 had markedly prolonged survival as compared with those animals treated with saline or a truncated methylated oligonucleotide that did not alter IGF2 mRNA levels in vitro. This study demonstrates that a methylated sense oligonucleotide can be used to induce epigenetic changes in the IGF2 gene and that inhibition of IGF2 mRNA accumulation may lead to enhanced survival in a model of HCC.

Our understanding of RNA functions in the cell is evolving rapidly. As for proteins, the detailed three-dimensional (3D) structure of RNA is often key to understanding its function. Although crystallography and nuclear magnetic resonance (NMR) can determine the atomic coordinates of some RNA structures, many 3D structures present technical challenges that make these methods difficult to apply. The great flexibility of RNA, its charged backbone, dearth of specific surface features, and propensity for kinetic traps all conspire with its long folding time, to challenge in silico methods for physics-based folding. On the other hand, base-pairing interactions (either in runs to form helices or isolated tertiary contacts) and motifs are often available from relatively low-cost experiments or informatics analyses. We present RNABuilder, a novel code that uses internal coordinate mechanics to satisfy user-specified base pairing and steric forces under chemical constraints. The code recapitulates the topology and characteristic L-shape of tRNA and obtains an accurate noncrystallographic structure of the Tetrahymena ribozyme P4/P6 domain. The algorithm scales nearly linearly with molecule size, opening the door to the modeling of significantly larger structures.

To gain insight into the physiological function of phosphoinositide 3-kinase (PI 3-kinase) lipid products, this study examines the interactions of the D-3 phosphoinositides with profilin and the consequent effects on actin dynamics and phosphoinositide turnover. Profilin, a ubiquitous actin-regulating protein, plays a putative role in regulating actin assembly and PLC-gamma 1 signaling in light of its unique interactions with actin and phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2]. Here we raise evidence that the affinity of profilin with the D-3 phosphoinositides is substantially higher than that of PtdIns(4,5)P2. The dissociation constants (Kd) are estimated to be 1.1 microM, 5.7 microM, and 11 microM for phosphatidylinositol 3,4-bisphosphate [PtdIns(3,4)P2], phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5)P3], and PtdIns(4,5)P2, respectively. Spectroscopic data show that while all these phosphoinositides alter the tryptophan fluorescence of profilin in a similar fashion, the respective conformational effect on profilin is vastly different. Based on CD data, the alpha-helical contents of profilin in the presence of 8 molar equiv of PtdIns(4,5)P2, PtdIns(3,4,5)P3, and PtdIns(3,4)P2 are 17.4%, 11.5%, and 1.4%, respectively, vis-a-vis 9.4% for profilin alone. In contrast, no appreciable change in the fluorescence and CD spectra is observed when related inositol phosphates such as Ins(1,4,5)P3, Ins(1,3,4,5)P4, or Ins(1,3,4)P3 at comparable concentrations are tested. Evidence suggests that this differential recognition bears functional significance concerning the intricate roles of profilin and inositol lipids in modulating actin polymerization and PtdIns(4,5)P2 turnover. The relative potency of individual phosphoinositides in offsetting the inhibitory effect of profilin on actin assembly is PtdIns(3,4)P2>> PtdIns(3,4,5)P3>> PtdIns(4,5)P2, consistent with their relative binding affinity with profilin. Moreover, the inhibitory effect of profilin on PLC-gamma 1-mediated PtdIns(4,5)P2 hydrolysis is overcome by PtdIns(3,4)P2 and PtdIns(3,4,5)P3 through a combined effect of PLC-gamma 1 activation and preferential profilin binding. This D-3 phosphoinositide-mediated regulation may represent a new mechanism for controlling PtdIns(4,5)P2 turnover by PLC-gamma 1.

Osmoregulation, inhibitory neurotransmission and pH balance depend on chloride ion (Cl-) flux. In intestinal epithelial cells, apical Cl- channels control salt and fluid secretion and are, in turn, regulated by agonists acting through cyclic nucleotides and internal calcium ion concentration ([Ca2+]i). Recently, we found that muscarinic pretreatment prevents [Ca2+]i increases from eliciting Cl- secretion in T84 colonic epithelial cells. By studying concomitant inositol phosphate metabolism, we have now identified D-myo-inositol 3,4,5,6-tetrakisphosphate (Ins(3,4,5,6)P4), as the inositol phosphate most likely to mediate this uncoupling. A novel, membrane-permeant ester prepared by total synthesis delivers Ins(3,4,5,6)P4 intracellularly and confirms that this emerging messenger does inhibit Cl- flux resulting from thapsigargin- or histamine-induced [Ca2+]i elevations.

Botulinum neurotoxins (BoNTs) are zinc proteases that cleave SNARE proteins to elicit flaccid paralysis by inhibiting neurotransmitter-carrying vesicle fusion to the plasma membrane of peripheral neurons. Unlike other zinc proteases, BoNTs recognize extended regions of SNAP25 for cleavage; however, the molecular basis for this extended substrate recognition is unclear. Here, we define a multistep mechanism for recognition and cleavage of SNAP25 by BoNT/A. SNAP25 initially binds along the belt region of BoNT/A, which aligns the P5 residue to the S5 pocket at the periphery of the active site. Although the exact order of each step of recognition of SNAP25 by BoNT/A at the active site is not clear, the initial binding could subsequently orient the P4'-residue of SNAP25 to form a salt bridge with the S4'-residue, which opens the active site allowing the P1'-residue access to the S1'-pocket. Subsequent hydrophobic interactions between the P3 residue of SNAP25 and the S3 pocket optimize alignment of the scissile bond for cleavage. This explains how the BoNTs recognize and cleave specific coiled SNARE substrates and provides insight into the development of inhibitors to prevent botulism.

Epidemiological evidence in human fetuses links inflammation during development with white matter damage. Breakdown of the blood-brain barrier has been proposed as a possible mechanism. This was investigated in the present study by inducing a prolonged inflammatory response in newborn rats, with intraperitoneal injections of lipopolysaccharide (LPS; 0.2 mg/kg) given at postnatal (P) day 0, P2, P4, P6 and P8. An acute phase response was present over the whole period of injections. Changes in blood-brain barrier permeability were determined for small (sucrose and inulin) and large (protein) molecules. During and immediately after the inflammatory response, plasma proteins were detected in the brain only within white matter tracts, indicating an increased permeability of the blood-brain barrier to protein during this period. The alteration in permeability to protein was transient. In contrast, the permeability of the blood-brain barrier to 14C-sucrose and 14C-inulin was significantly higher in adult animals that had received serial LPS injections during development. Adult animals receiving a single 1 mg/kg LPS injection at P0 showed no alteration in blood-brain barrier permeability to either small or larger molecules. A significant decrease in the volume of CNPase immunoreactive presumptive white matter tracts occurred in the external capsule and corpus callosum at P9. These results demonstrate that a prolonged systemic inflammatory response in the early postnatal period in rats causes size selective increases in blood-brain barrier permeability at different stages of brain development and results in changes in white matter volume.

The amino acid sequence of a 90-residue segment of human pregnancy zone protein containing its bait region has been determined. Human alpha 2-macroglobulin, human pregnancy zone protein, and rat alpha 1-macroglobulin, alpha 2-macroglobulin, and alpha 1-inhibitor 3 variants 1 and 2 constitute a group of homologous proteins; but the sequences of their bait regions are not related, and they differ in length (32-53 residues). The alpha-macroglobulin bait region is located equivalently with residues 666-706 in human alpha 2-macroglobulin. In view of the extreme sequence variation of the bait regions, the evolutionary constraints for these regions are likely to differ from those of the remainder of the alpha-macroglobulin structure. The sites of specific limited proteolysis in the bait regions of human pregnancy zone protein and rat alpha 1-macroglobulin, alpha 2-macroglobulin, and alpha 1-inhibitor 3 variants 1 and 2 by a variety of proteinases differing in specificity have been determined and compared with those identified earlier in human alpha 2-macroglobulin. The sites of cleavage generally conform to the substrate specificity of the proteinase in question, but the positions and nature of the P4-P4' sites differ. Most cleavages occur in two relatively small segments spaced by 6-10 residues; and in each case, bait region cleavage leads to alpha-macroglobulin-proteinase complex formation. The rate at which a given proteinase cleaves alpha-macroglobulin bait regions is likely to show great variation. Possible structural features of the widely different bait regions and their role in the mechanism of activation are discussed.

BACKGROUND

Female athletes suffer a higher incidence of anterior cruciate ligament injuries compared to their male counterparts, and they appear to be at increased risk for these injuries when they have increased anterior-posterior knee laxity and at specific phases of the menstrual cycle. Although the mechanism by which these factors combine to increase injury risk is unclear, studies suggest that cyclic variations in joint laxity produced by hormone fluctuation during the menstrual cycle predispose an athlete to increased risk of ligamentous injury. Little is known about whether joint laxity varies cyclically during the menstrual cycle and if so, whether it is modulated by cyclic variations of estradiol (E2) and progesterone (P4).

OBJECTIVE

Increased serum estradiol (E2) and progesterone (P4) levels are associated with increased ankle and knee joint laxity.

METHODS

Cohort study. Level of evidence, 2.

METHODS

Ankle laxity, anterior-posterior knee laxity, and serum concentrations of estradiol (E2) and progesterone (P4) were measured during the menstrual cycle in women and at corresponding time intervals in men (controls). Ankle laxity was measured from stress radiographs and included anterior talar translation relative to the tibia and talar tilt relative to the tibia; anterior-posterior knee laxity was measured with the KT-1000 arthrometer.

RESULTS

Women had greater knee and ankle laxity values compared to men. There was, however, no change in knee and ankle laxity over the normal menstrual cycle in women and no change over time in men. There was no relationship between estradiol and progesterone fluctuation and ankle and knee joint laxity.

CONCLUSIONS

Knee and ankle joint laxities are greater for women compared to men; however, the cyclic estradiol and progesterone fluctuations that occur during the menstrual cycle do not produce cyclic fluctuations of joint laxity. Studies using joint laxity to identify a subject at risk for ligamentous injury need only consider making measurements at a specific point in time, such as during a preseason screening evaluation.

Physiological evidence suggests that SK-type Ca2+-activated K+ channels participate in ACh-induced hyperpolarization of OHCs (outer hair cells). Based on the sequences published by Kohler et al. [(1996), Science, 273: 1709), we designed degenerated primers recognizing cDNA subunits of rSK1, rSK2 and rSK3. Using this consensus set of primers, we probed by PCR a rat organ of Corti cDNA library. Two PCR products of 707 base pairs with sequence identical to rSK3 and rSK2 were obtained and cloned to generate RNA probes for in situ hybridization in the rat cochlea. The subunit rSK2 showed hybridization in the organ of Corti, at the location of the OHCs. The expression of rSK2 by OHCs was confirmed by probing with PCR a poly(A) amplified OHC cDNA library. During development, rSK2 hybridization in the organ of Corti was negative at embryonic days E16, E18 and at P0, weak at P4 and stronger from P8 to adulthood. The subunit rSK2 could also be detected in the spiral ganglion from P4 to the adult stage. Contrary to rSK2, the subunit rSK3 did not show specific hybridization in the organ of Corti at the adult stage (P120) and only a weak expression was observed at P10 and P21. Our study demonstrates expression of rSK2 in OHCs. These potassium channels are good candidates to underlie the ACh-activated K+ currents recorded during patch-clamp recordings in isolated OHCs. The expression of rSK2 in the cochlear ganglion at the adult stage suggests that SK Ca2+-activated K+ channels may also participate in the repolarization of the auditory neurons after the action potential and may influence their firing patterns.

Previous studies suggest that sex differences in morphine antinociception in rodents might be attributed to the activational effects of gonadal hormones. The present study determined whether hormonal modulation of opioid antinociception in adult rats extends to opioids other than the prototypic mu agonist morphine. Male and female rats were sham-gonadectomized (sham-GDX) or gonadectomized (GDX) and replaced with no hormone, estradiol (E2, females), progesterone (P4, females), E2+P4 (females), or testosterone (males). Approximately 28 days later, nociception was evaluated on the 50 degrees C hot plate and warm water tail withdrawal tests before and after subcutaneous administration of hydromorphone, buprenorphine, U50,488, or SNC 80. In sham-GDX (gonadally intact) rats, the mu agonists and U50,488 were less effective in females than in males in at least one nociceptive test, and the delta agonist SNC 80 was less effective in males than in females. In males, gonadectomy tended to decrease, and testosterone tended to increase antinociception produced by 3 of the 4 agonists. In females, gonadectomy and hormone treatment had more variable effects, although E2 tended to decrease mu opioid antinociception. The present results suggest that activational effects of gonadal hormones are relatively modest and somewhat inconsistent on antinociception produced by various opioid agonists in the adult rat.

CONCLUSIONS

This study demonstrates that reproductive hormones such as testosterone in males and estradiol in females do not consistently modulate sensitivity to the analgesic effects of opioids in the adult organism.

The cerebellar cortex is histologically uniform by conventional staining techniques, but contains an elaborate topography. In particular, on the efferent side the cerebellar cortex can be subdivided into multiple parasagittal compartments based upon the selective expression by Purkinje cell subsets of various molecules, for example the polypeptide antigens zebrin I and II, and on the afferent side many mossy fibers terminate as parasagittal bands of terminals. The relationships between mossy fiber terminal fields and Purkinje cell compartments are important for a full understanding of cerebellar structure and function. In this study the locations of spino- and cuneocerebellar mossy fiber terminal fields in lobules II and III of the rat cerebellum are compared to the compartmentation of the Purkinje cells as revealed by using zebrin II immunocytochemistry. Wheat germ agglutinin-horseradish peroxidase was injected at three different levels in the spinal cord and in the external cuneate nucleus, and the terminal field distributions in lobules II and III of the cerebellar cortex were compared with the Purkinje cell compartmentation. In the anterior lobe, zebrin II immunocytochemistry reveals three prominent, narrow immunoreactive bands of Purkinje cells, P1+ at the midline and P2+ laterally at each side. These are separated and flanked by wide zebrin- compartments (P1- and P2-). There are also less strongly stained P3+ and P4+ bands more laterally. The spinocerebellar terminals in the granular layer are distributed as parasagittally oriented bands. Projections from the lumbar region of the spinal cord terminate in five bands, one at the midline (L1), a second with its medial border midway across P1- and its lateral border at the P2+/P2- interface (L2), and a third extending laterally from midway across P2-. The lateral edge of L3 may align with the P3+/P3- border. The terminal fields labeled by a tracer injection into the thoracic region give a very similar distribution (T1, T2 and T3). The only systematic difference is in T2, which statistical analysis suggests may be broader than L2. In contrast, anterograde tracer injections into the cervical region label synaptic glomeruli scattered throughout the lobule with much weaker or no evidence of banding. The terminal fields of the cuneocerebellar projection have a complementary distribution to those of thoracic and lumbar spinocerebellar terminals. There are two lateral bands, Cu2 and Cu3. Cu2 lies within the Purkinje cell P1-compartment, abutting L1/T1 medially and L2/T2 laterally. Cu3 lies between L2 and L3 within the P2- Purkinje cell compartment. The medial edge of Cu3 is tightly aligned with the P2+/P2- border.(ABSTRACT TRUNCATED AT 400 WORDS)

We used repetitive, rapid-rate transcranial magnetic stimulation (rTMS) for the noninvasive study of visual attention in humans. Six right-handed volunteers completed eight blocks of 20 single- and 10 double-visual-stimulus trials. The visual stimulus was a single asterisk on the right or left side of a computer screen or two asterisks presented simultaneously. The subject had to respond to the stimulus by pressing the right or left response key or both keys simultaneously. During six of the blocks, we applied focal rTMS in trains of five pulses at 25 Hz and 115% of the subject's motor threshold intensity to scalp positions O1, O2, P3, P4, T5, or T6. Occipital rTMS led to a large number of misses of the contralateral asterisk regardless of whether a single or double stimulus was presented. Parietal rTMS did not induce misses of single stimuli but led to a large number of misses of the contralateral asterisk in the double-stimulus condition. The effects of temporal rTMS were inconsistent. We conclude that rTMS to the occipital lobe causes a sensory detection block, whereas rTMS to the parietal lobe can induce selective extinction of contralateral visual stimuli during a simultaneous double stimulus.

The development and application of systems strategies to biology and disease are transforming medical research and clinical practice in an unprecedented rate. In the foreseeable future, clinicians, medical researchers, and ultimately the consumers and patients will be increasingly equipped with a deluge of personal health information, e.g., whole genome sequences, molecular profiling of diseased tissues, and periodic multi-analyte blood testing of biomarker panels for disease and wellness. The convergence of these practices will enable accurate prediction of disease susceptibility and early diagnosis for actionable preventive schema and personalized treatment regimes tailored to each individual. It will also entail proactive participation from all major stakeholders in the health care system. We are at the dawn of predictive, preventive, personalized, and participatory (P4) medicine, the fully implementation of which requires marrying basic and clinical researches through advanced systems thinking and the employment of high-throughput technologies in genomics, proteomics, nanofluidics, single-cell analysis, and computation strategies in a highly-orchestrated discipline we termed translational systems medicine.

A hybrid bacteriophage, P4P4 and a 3.6-kilobase derivative of plasmid ColE1. In Escherichia coli, the plasmid-phage hybrid can exist as a stable plasmid or can be packaged into infective bacteriophage particles. Replication of P4P4P4P4, replication was dependent on DNA polymerase I and was sensitive to rifampicin. The presence of a resident ColE1 plasmid in the infected cells resulted in an inhibition of the replication of the incoming P4P4 bacteriophage for coupling bacteriophage properties to a plasmid replicon.

LPS and lipid A initiated enhanced hydrolysis of PIP2 in macrophages. When murine peritoneal macrophages were labeled with [2-3H]myoinositol and stimulated with either LPS or lipid A, a rapid (within 10 sec) rise in Ins(1,4,5)P3 was observed. The breakdown pattern of Ins(1,4,5)P3 was complex; this included breakdown of Ins(1,4,5)P3 and formation of Ins(1,3,4,5)P4 (approximately 10 to 30 sec), and ultimately formation of Ins(1,3,4)P3 (approximately 60 sec). Within 10 sec after treatment, LPS caused an average increase of about fourfold to fivefold in Ins(1,4,5)P3, which declined over 5 min. When the total isomers of InsP3 were measured, levels rose about twofold in response to LPS or to lipid A and remained elevated for as long as 5 min. Lipid A, in the concentration range of 0.1 to 10 micrograms/ml, induced elevated intracellular levels of Ca2+ as quantified by fluorescence with Quin 2 or with Fura 2. When single, adherent Fura 2-loaded macrophages were treated with lipid A, basal levels of calcium rose over 10 sec from approximately 55 nM to almost 600 nM. LPS, paradoxically, did not cause such substantial increases in intracellular calcium (i.e., increases of approximately 26 nM) when judged by Fura 2 fluorescence. LPS treatment led to enhanced phosphorylation of a characteristic set of proteins, similar to those induced by stimulating protein kinase C (PKC) with phorbol myristate acetate as previously reported. The enhanced phosphorylation of pp28, pp33, and pp67 in macrophages was evident by 15 min and optimal by 30 min. Taken together, these observations indicate that LPS and lipid A cause increased breakdown of phosphatidylinositol 4,5-bisphosphate, which led to enhanced intracellular levels of calcium and also to enhanced protein phosphorylation, presumably mediated by PKC. The data thus suggest that one major intracellular signal transduction mechanism, initiated by LPS and lipid A in macrophages, is the rapid breakdown of PIP2.

Fifteen subjects were presented with series of tones. Any one tone was either loud or soft, and in any one series the probability of one tone intensity was either 0.9 or 0.1. Subjects were instructed to count the frequent tones or to count the rare tones. The stimuli were also presented while the subjects were solving a word-puzzle. Event-related potentials (ERPs) were recorded from 9 scalp locations (F3, C3, P3, FZ, CZ, PZ, F4, C4, P4) referred to linked mastoids. ERP components were measured with a Principal Components analysis and the relations between these measures and the independent variables were evaluated with the ANOVA procedure. This paradigm allowed an evaluation of the effect of stimulus probability, stimulus relevance, and task relevance on the waveform of the ERPs. We conclude that the P350 component is enhanced whenever the eliciting stimulus is both rare and in some sense relevant to the subject's task and the degree of enhancement is greatest when the rare--relevant tone is loud. A "slow wave" component which follows P350 is related to the same variables but has a scalp distribution quite different from that of P350. The slow wave shows a progressive shift in polarity from negative to positive from the frontal to the parietal sites, while the P350 is of nearly equal amplitude (and positive) at the central and parietal sites and has a smaller (positive) and amplitude at FZ. A third prominent component, negative in polarity, peaking at about 210 msec, is most pronounced following rare stimuli, whether or not they were task relevant. The amplitude of N210 tended to be largest at the frontal electrode. This study then demonstrates that when suitable measurement techniques are used, multiple endogenous ERP components can be observed, each related to distinct aspects of cognitive behavior.

The late genes of bacteriophage P2 are clustered into four transcription units. We have reported the transcription initiation sites for two of the late messenger RNAs, encoding genes QP and ONMLKRS. We have now located the 5' ends of the two remaining late mRNAs. The first gene in the VJHG transcription unit has been located by DNA sequence determination of the single nucleotide change in a V amber mutant. Location of the first gene in the FETUD transcription unit has been inferred from the DNA sequence. The 5' ends of the mRNAs for these two transcription units were located by protection of end-labeled restriction fragments in RNA-DNA hybrids from digestion with nuclease S1. Similar protection of hybrids using RNA that had been 5' end-labeled with [alpha-32P]GTP and guanylyl transferase confirmed that these 5' termini resulted from initiation of transcription. The DNA sequences preceding the P2 late transcription starts are different from the Escherichia coli promoter consensus sequences at -10 and -35, consistent with the apparent requirement for phage-encoded proteins in the regulation of P2 late gene expression. The four P2 late promoters do share sequence homologies in the -10 and -35 regions, however, and several additional homologies further upstream. P2 late gene expression also appears to involve negative regulation by a product of the ONMLKRS gene cluster. When cells are infected with P2 polar O amber mutants, a marked increase in the levels of proteins encoded by the other three gene clusters is observed. This increase is reflected in the amounts of late mRNAs, suggesting that RNA synthesis is normally repressed or that late mRNAs are more labile in the presence of a gene product from the ONMLKRS transcription unit. Satellite phage P4 induced P2 late gene expression without the usual requirement for P2 DNA replication. The 5' ends of the P2 late mRNAs are the same during P4 transactivation as during normal P2 late gene expression. Thus, the regulation of P2 late gene expression by P4 does not involve altered promoter selection.

We present a simple approach to locate sites that undergo conformational changes upon crystallization by comparative structural mapping of the same RNA in three different environments. As a proof of principle, we probed the readily crystallized P4-P6DeltaC209 domain from the Tetrahymena thermophila group I intron in a native solution, in a solution mimicking the crystallization drop, and in crystals. We chose the selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry, which monitors the flexibility and the conformation of each nucleotide. First, SHAPE successfully revealed the structural changes that occur during the crystallization process. Specifically, 64% of the nucleotides implicated in packing contacts and present in the portion of the molecule analyzed were identified. Second, reactivity differences for some of these nucleotides were already observed in the crystallization solution, suggesting that the crystallization buffer locked down a particular structure that was favorable to crystal formation. Third, the probing of a known structure extends our understanding of the structural basis for the SHAPE reaction by suggesting that reactivity is enhanced by a C2'-endo sugar pucker. Furthermore, by identifying local conformational changes of the RNA that take place during crystallization, SHAPE could be combined with the in vitro selection of stable mutants to rationalize the design of RNA candidates for crystallization.

1. The characterization of a radioreceptor assay for determining Ins(1,4,5)P3 concentration in tissue extracts is described which utilizes the binding of [3H]Ins(1,4,5)P3 to an adrenal-cortex membrane fraction. 2. Analysis of [3H]Ins(1,4,5)P3 binding by isotope dilution demonstrated an apparent single population of binding sites (KD 3.65 +/- 0.18 nM, Bmax. 872 +/- 70 fmol/mg of protein). Specific binding of [3H]Ins(1,4,5)P3 was enhanced at alkaline pH values (maximum at pH 8.5), with complete loss of specific binding at pH less than 6. These binding sites displayed strict stereo- and positional specificity for Ins(1,4,5)P3, with L-Ins(1,4,5)P3, Ins(1,3,4)P3 and DL-Ins(1,3,4,5)P4 causing 50% displacement of specific [3H]Ins(1,4,5)P3 binding (IC50 values) at concentrations of 14 +/- 3 microM, 3.0 +/- 0.3 microM and 0.53 +/- 0.03 microM respectively. 3. Kinetic analysis of binding data, however, revealed a high-affinity [3H]Ins(1,4,5)P3 binding site (KD 0.052 nM) in addition to the lower-affinity site (KD 2.53 nM) already demonstrated in displacement studies. 4. It is shown that the presence of the high-affinity site can be exploited to increase the sensitivity of the [3H]Ins(1,4,5)P3 radioreceptor assay, allowing accurate detection of 20 fmol of Ins(1,4,5)P3 in 300 microliters of tissue extract. 5. Further validation of the specificity of the above assay for Ins(1,4,5)P3 was provided by incubating tissue extracts with either a 5-phosphatase or 3-kinase preparation. It was shown that identical loss occurred of both Ins(1,4,5)P3 mass and [3H]Ins(1,4,5)P3, added to parallel incubations. 6. The ability of the assay to measure basal and agonist-stimulated increases in Ins(1,4,5)P3 concentration has been demonstrated with rat cerebral cortex and bovine tracheal smooth-muscle slices and a range of cultured and isolated cell preparations.

Maturation of pro-von Willebrand factor (vWF) to its active form requires proteolytic processing after a pair of dibasic amino acids (-LysArg-) at residue 763. By coexpression of vWF and various propeptide processing enzymes in COS-1 cells, we here demonstrate that vWF is preferentially processed by the paired dibasic amino acid-cleaving enzyme PACE (furin). Processing of vWF by the yeast homologue of PACE, Kex2, was inefficient and not specific for the authentic site. Two additional recently identified mammalian propeptide-processing enzymes PC2 and PC3 had no detectable vWF-processing activity. The inability of PC2 and PC3 to cleave vWF was apparently not due to the absence of a transmembrane domain, since deletion of the transmembrane domain from PACE resulted in a secreted form which retained its propeptide processing activity within the secretory apparatus. The inability of PC2 and PC3 to process wild-type vWF or any of the vWF mutants described suggests different members of subtilisin-related propeptide-processing enzyme family have evolved to selectively recognize and cleave specific sets of substrates. In addition to paired dibasic residues at the propeptide cleavage site, many proteins, including vWF, also contain an arginine at the P4 position. We have generated mutant vWFs with substitutions at the P2 lysine and/or the P4 arginine to investigate their significance in substrate specificity. A conservative substitution of the P4 arginine by lysine resulted in a decrease in vWF processing by PACE, as did a nonconservative substitution to alanine. Substitution of the P2 lysine to aspartic acid decreased processing and little or no processing was detected when both the P4 and P2 were mutated to lysine and aspartic acid, respectively. These data indicate that both the P4 arginine and the P2 lysine play an important role in substrate recognition by PACE.

Comparative genomic analysis of important signaling pathways in Caenorhabditis briggsae and Caenorhabditis elegans reveals both conserved features and also differences. To build a framework to address the significance of these features we determined the C. briggsae embryonic cell lineage, using the tools StarryNite and AceTree. We traced both cell divisions and cell positions for all cells through all but the last round of cell division and for selected cells through the final round. We found the lineage to be remarkably similar to that of C. elegans. Not only did the founder cells give rise to similar numbers of progeny, the relative cell division timing and positions were largely maintained. These lineage similarities appear to give rise to similar cell fates as judged both by the positions of lineally equivalent cells and by the patterns of cell deaths in both species. However, some reproducible differences were seen, e.g., the P4 cell cycle length is more than 40% longer in C. briggsae than that in C. elegans (p<0.01). The extensive conservation of embryonic development between such divergent species suggests that substantial evolutionary distance between these two species has not altered these early developmental cellular events, although the developmental defects of transpecies hybrids suggest that the details of the underlying molecular pathways have diverged sufficiently so as to not be interchangeable.

Divalent metal ions are essential for the folding and catalytic activities of many RNAs. A commonly employed biochemical technique to identify metal-binding sites in RNA is the rescue of Rp alpha-phosphorothioate (PS) interference by the addition of soft divalent metal ions. To access the ability of such experiments to accurately identify metal-ion coordinations within a complex RNA fold, we report metal-rescue results from the Tetrahymena group I intron P4-P6 domain, where the location and coordination of five divalent metal ions have been determined by X-ray crystallography [J.H. Cate et al., Nat Struct Biol, 1997, 4:553]. We used a native gel mobility-shift to assay for P4-P6 folding in the presence of various divalent metal ions, and found that even moderate concentrations of Mn2+ >> or =0.5 mM) can rescue PS interference at sites that do not coordinate metal ions within the P4-P6 crystal structure. To control for such effects, 2'-deoxynucleotide interference was used to titrate the Mn2+ concentration to a level that produces metal-ion-specific rescue (0.3 mM). This concentration of Mn2+ specifically rescued four of the six metal-dependent phosphorothioate effects within the RNA domain, including PS interference resulting from outer-sphere coordination to the metals. Both sites that were not specifically rescued make inner-sphere metal-ion coordinations. Cd2+ and Zn2+ afforded rescue at a smaller subset of the six metal-specific PS sites, though again phosphates making outer-sphere coordinations to metal ions were rescued preferentially. These data on P4-P6 domain folding reinforce the need for caution when interpreting metal-rescue experiments.