Automated analysis of protein NMR assignments using methods from artificial intelligence

An expert system for determining resonance assignments from NMR spectra of proteins is described. Given the amino acid sequence, a two-dimensional 15N-1H heteronuclear correlation spectrum and seven to eight three-dimensional triple-resonance NMR spectra for seven proteins, AUTOASSIGN obtained an average of 98% of sequence-specific spin-system assignments with an error rate of less than 0.5%. Execution times on a Sparc 10 workstation varied from 16 seconds for smaller proteins with simple spectra to one to nine minutes for medium size proteins exhibiting numerous extra spin systems attributed to conformational isomerization. AUTOASSIGN combines symbolic constraint satisfaction methods with a domain-specific knowledge base to exploit the logical structure of the sequential assignment problem, the specific features of the various NMR experiments, and the expected chemical shift frequencies of different amino acids. The current implementation specializes in the analysis of data derived from the most sensitive of the currently available triple-resonance experiments. Potential extensions of the system for analysis of additional types of protein NMR data are also discussed.

Bone morphogenesis in implants of insoluble bone gelatin

Insoluble bone gelatin with inclusions of insoluble noncollagenous protein produces new bone when implanted in muscle in allogeneic rats. The implanted residue provides the milieu for expression of bone morphogenetic potential of migratory mesenchymal cells. Neutral buffer solutions activate endogenous enzymes that degrade components essential for cell interactions and differentiation of bone. Chloroform-methanol either denatures or extracts constituents responsible for degradation. Insoluble bone gelatin produces new bone after extraction at 2 degrees with neutral salts, 0.5 M EDTA, 0.1 M Tris.HCl, 4 M urea, 0.5 M hydroxylamine, and 10 M KCNS, as well as after limited digestion with pepsin or collagenase, but not after extraction with 5 M guanidine, 7 M urea, water saturated with phenol, or after alkali hydrolysis with 0.1 N NaOH. The specific activity of cell populations interacting with insoluble bone gelatin suggests that a chemical bond between collagen and a noncollagenous protein or part of a protein, cleaved by a neutral proteinase, controls the bone morphogenetic reaction.

Unintentional ingestion of over the counter medications in children less than 5 years old

OBJECTIVE

Childhood ingestion of medications remains a substantial problem. Medication available over the counter (OTC) is widely used and has significant toxicity. The present study aims to investigate the nature and extent of unintentional ingestion of OTC medication in children < 5 years old in Victoria, Australia, during the period 1996-2000, in order to highlight critical factors.

METHODS

Numbers of enquiries relating to unintentional ingestion of OTC medication in children < 5 years old and medication types were obtained from the Victorian Poisons Information Centre for 1998-2000. Emergency Department presentations involving poisoning of children < 5 years old, the medication types and subsequent admissions were obtained from the Victorian Emergency Minimum Dataset for 1996-2000.

RESULTS

Numbers of enquiries and Emergency Department attendances for poisoning were substantially higher for OTC medication than for prescription medication; however, a lower proportion of cases involving ingestion of OTC medication (24.8%) required hospital admission during the study period compared with cases involving ingestion of prescription medications (33.8%). Overall, the peak incidence was at 2 years of age, with a slight male over-representation. Paracetamol and cough/cold preparations were the most common agents.

CONCLUSIONS

The causes of unintentional ingestion of OTC medications by children might include lack of child-resistant closure (CRC), inadequate design of CRC, attitudes concerning the toxicity of OTC medications, or lack of vigilance by parents and carers in the storage and administration of OTC medications. Consideration should be given to restricting sales of toxic OTC medications to pharmacies, and increasing counselling of consumers concerning the toxicity and safe storage of OTC medications and the correct usage of CRC. The adequacy of CRC design and OTC medications warranting CRC should be reviewed by the relevant authorities.

Fetal behavioural state changes following maternal fluoxetine infusion in sheep

Clinical depression is diagnosed in 5-15% of women during pregnancy, increasing the risk of negative outcomes. Fluoxetine (FX), a selective serotonin reuptake inhibitor, is prescribed during pregnancy. In adults, FX alters sleep patterns with single doses decreasing total sleep time and rapid eye movement sleep. The effects of FX on sleep in the fetus are unknown. However, 5-hydroxytryptophan, the precursor of serotonin, has been reported to prolong high-voltage (HV) electrocortical (ECoG) activity and increase the incidence of fetal breathing movements (FBM) in the sheep fetus. We hypothesize that FX exposure will decrease the incidence of LV ECoG in the fetus. Twenty-one pregnant sheep were surgically prepared for chronic study of blood gases, ECoG activity, eye movements and FBM. After 3 days of recovery, ewes received a 70-mg bolus i.v. infusion of FX or sterile water followed by continuous infusion at a rate of 0.036 mg/min for 8 days. The incidence of low-voltage (LV) ECoG decreased from 54+/-4% on the preinfusion day to 45+/-5% on infusion day 1 in the FX group and remained decreased throughout the infusion period. In addition, the incidence of both eye movements and FBM was decreased on infusion day 1 compared to preinfusion day in the FX group. HV ECoG increased from 39+/-3% on preinfusion day to 68+/-14% on FX infusion day 1 and remained elevated throughout the infusion period. These data show that maternal FX administration alters fetal behavioural state.

A positive modulator of K Ca 2 and K Ca 3 channels, 4,5-dichloro-1,3-diethyl-1,3-dihydro-benzoimidazol-2-one (NS4591), inhibits bladder afferent firing in vitro and bladder overactivity in vivo

Calcium-activated potassium channels are attractive targets for the development of therapeutics for overactive bladder. In the current study, we addressed the role of calcium-activated potassium channels of small (SK; K(Ca)2) and intermediate (IK; K(Ca)3) conductance in bladder function pharmacologically. We identified and characterized a novel positive modulator of SK/IK channels, 4,5-dichloro-1,3-diethyl-1,3-dihydro-benzoimidazol-2-one (NS4591). In whole-cell patch-clamp experiments, NS4591 doubled IK-mediated currents at a concentration of 45 +/- 6 nM(n = 16), whereas 530 +/- 100 nM (n = 7) was required for doubling of SK3-mediated currents. In acutely dissociated bladder primary afferent neurons, the presence of SK channels was verified using apamin and 1-ethyl-2-benzimidazolinone. In these neurons, NS4591 (10 microM) inhibited the number of action potentials generated by suprathreshold depolarizing pulses. NS4591 also reduced carbachol-induced twitches in rat bladder detrusor rings in an apamin-sensitive manner. In vivo, NS4591 (30 mg/kg) inhibited bladder overactivity in rats and cats induced by capsaicin and acetic acid, respectively. In conclusion, the present study supports the involvement of calcium-activated potassium channels in bladder function and identifies NS4591 as a potent modulator of IK and SK channels that is effective in animal models of bladder overactivity.

Morphological, immunohistochemical and quantitative studies of murine brain mast cells after mating

The mast cell is one of the immune cells, and can be triggered behaviorally to increase in the CNS of the sexually active dove. In the present study, we used ICR mice to investigate the number of brain mast cells in mated (one male with three female mice), non-mated (housed with female mice, but no mating) and control (four male mice housed together in one cage) male mice. We found that at least 40% of mated male mice had significant more mast cells than the maximum value seen in the controls, and that a significant correlation existed between the distribution index of mast cells and the postcoitum date. These mast cells were especially numerous in the thalamus and velum interpositum (VIP). Morphological observations showed that the increased mast cells were ultrastructurally similar to those in the controls, and displayed gonadotropin-releasing hormone (GnRH)-like immunoreactivity. Based on the facts that the number of brain mast cells in the male mice increased significantly after mating and that the change in the distribution of mast cells in the VIP and the thalamic parenchyma correlated well with time postcoitum, we speculate that, after mating, mast cells may migrate from the VIP to the thalamic parenchyma along the vascular tree of the brain. These results strongly suggest that mast cells are involved in the interaction among the immune, endocrine, and nervous systems in the mated male mouse brain.

Study of EEG sleep characteristics in patients with anorexia nervosa before and after restoration of matched population mean weight consequent on ingestion of a "normal" diet

This experimental study confirms that insomnia and especially early morning waking is associated with low body weight in anorexia nervosa. It extends the view that there is a relationship between reduced nutritional intake and consequent change in weight and sleep disturbance. This relationship was studied by comparison of certain sleep EEG parameters in a group of hospitalized anorexia nervosa patients before and after a regime of re-feeding to matched population mean weight on a ‘normal’ diet. At low body weights, the patients had less sleep and more restlessness, especially in the last 4 hr of the night. After weight gain, there was a significant increase in length of sleep and REM sleep. The implications of these results are discussed with particular reference to an association between various anabolic profiles and differing need for REM sleep.

Taurine-sulfur assimilation and taurine-pyruvate aminotransferase activity in anaerobic bacteria

We demonstrated the ability of strictly fermentative, as well as facultatively fermentative, bacteria to assimilate sulfonate sulfur for growth. Taurine (2-aminoethanesulfonate) can be utilized by Clostridium pasteurianum C1 but does not support fermentative growth of two Klebsiella spp. and two different Clostridium spp. However, the latter are able to assimilate the sulfur of a variety of other sulfonates (e.g., cysteate, 3-sulfopyruvate, and 3-sulfolactate) anaerobically. A novel taurine-pyruvate aminotransferase activity was detected in cell extracts of C. pasteurianum C1 grown with taurine as the sole sulfur source. This activity was not detected in extracts of other bacteria examined, in C. pasteurianum C1 grown with sulfate or sulfite as the sulfur source, or in a Klebsiella isolate assimilating taurine-sulfur by aerobic respiration. More common aminotransferase activities (e.g., with aspartate or glutamate as the amino donor and pyruvate, oxalacetate, or (alpha)-ketoglutarate as the amino acceptor) were present, no matter what sulfur source was used for growth. Partial characterization of the taurine-pyruvate aminotransferase revealed an optimal temperature of 37(deg)C and a broad optimal pH range of 7.5 to 9.5.

HSI-II Gene Cluster of Pseudomonas syringae pv. tomato DC3000 Encodes a Functional Type VI Secretion System Required for Interbacterial Competition

The type VI secretion system (T6SS) is a widespread bacterial nanoweapon used for delivery of toxic proteins into cell targets and contributes to virulence, anti-inflammatory processes, and interbacterial competition. In the model phytopathogenic bacterium Pseudomonas syringae pv. tomato (Pst) DC3000, two T6SS gene clusters, HSI-I and HSI-II, were identified, but their functions remain unclear. We previously reported that hcp2, located in HSI-II, is involved in competition with enterobacteria and yeast. Here, we demonstrated that interbacterial competition of Pst DC3000 against several Gram-negative plant-associated bacteria requires mainly HSI-II activity. By means of a systematic approach using in-frame deletion mutants for each gene in the HSI-II cluster, we identified genes indispensable for Hcp2 expression, Hcp2 secretion and interbacterial competition ability. Deletion of PSPTO_5413 only affected growth in interbacterial competition assays but not Hcp2 secretion, which suggests that PSPTO_5413 might be a putative effector. Moreover, PSPTO_5424, encoding a putative σ⁵⁴-dependent transcriptional regulator, positively regulated the expression of all three operons in HSI-II. Our discovery that the HSI-II gene cluster gives Pst DC3000 the ability to compete with other plant-associated bacteria could help in understanding a possible mechanism of how phytopathogenic bacteria maintain their ecological niches.

The impact of antiseizure medications on polysomnographic parameters: a systematic review and meta-analysis

BACKGROUND

Oral antiseizure medications (ASMs) are first-line treatments for patients with epilepsy. However, ASMs may alter sleep architecture, adversely affecting patient outcomes. The meta-analysis aimed to elucidate the effect of ASMs on sleep architecture.

METHODS

PubMed, Embase, and Cochrane Central database (up to Febrary 2021) were searched for randomized control trials (RCT) with effects of ASMs on polysomnography parameters. A meta-analysis using a random-effects model was performed. We did not set limitation to the participants with underlying diagnosis of epilepsy.

RESULTS

Eighteen randomized-controlled trials fulfilled the eligibility criteria. The effects of five main groups of ASMs (sodium channel blockers, calcium channel blockers, GABA enhancers, synaptic vesicle glycoprotein 2A [SV2A] ligand, and broad-spetrum ASMs) on slow-wave sleep (SWS), rapid eye movement (REM) sleep, and sleep efficiency (SE) were analyzed. Compared with placebo, calcium channel blockers and GABA enhancers significantly increased SWS. GABA enhancers also decreased REM sleep percentage, whereas calcium channel blockers significantly increased SE. Sodium channel blockers, SV2A ligand and broad-spectrum ASMs did not affect SWS, REM sleep, or SE. The subgroup analysis revealed that gabapentin, pregabalin, and tiagabine increased the percentage of SWS. Tiagabine also decreased REM sleep, whereas pregabalin increased SE. Finally, levetiracetam did not affect SWS, REM sleep, and SE.

CONCLUSIONS

This meta-analysis indicated that ASMs can have a statistically significant effect on sleep parameters; the effect differs between ASMs.

MRI-Based Methods for Spinal Cord Atrophy Evaluation: A Comparison of Cervical Cord Cross-Sectional Area, Cervical Cord Volume, and Full Spinal Cord Volume in Patients with Aquaporin-4 Antibody Seropositive Neuromyelitis Optica Spectrum Disorders

BACKGROUND AND PURPOSE

Measures for spinal cord atrophy have become increasingly important as imaging biomarkers in the assessment of neuroinflammatory diseases, especially in neuromyelitis optica spectrum disorders. The most commonly used method, mean upper cervical cord area, is relatively easy to measure and can be performed on brain MRIs that capture cervical myelon. Measures of spinal cord volume (eg, cervical cord volume or total cord volume) require longer scanning and more complex analysis but are potentially better suited as spinal cord atrophy measures. This study investigated spinal cord atrophy measures in a cohort of healthy subjects and patients with aquaporin-4 antibody seropositive neuromyelitis optica spectrum disorders and evaluated the discriminatory performance of mean upper cervical cord cross-sectional area compared with cervical cord volume and total cord volume.

MATERIALS AND METHODS

Mean upper cervical cord area, cervical cord volume, and total cord volume were measured using 3T MRIs from healthy subjects (n = 19) and patients with neuromyelitis optica spectrum disorders (n = 30). Group comparison and receiver operating characteristic analyses between healthy controls and patients with neuromyelitis optica spectrum disorders were performed.

RESULTS

Mean upper cervical cord area, cervical cord volume, and total cord volume measures showed similar and highly significant group differences between healthy control subjects and patients with neuromyelitis optica spectrum disorders (P < .01 for all). All 3 measures showed similar receiver operating characteristic-area under the curve values (mean upper cervical cord area = 0.70, cervical cord volume = 0.75, total cord volume = 0.77) with no significant difference between them. No associations among mean upper cervical cord cross-sectional area, cervical cord volume, or total cord volume with disability measures were found.

CONCLUSIONS

All 3 measures showed similar discriminatory power between healthy control and neuromyelitis optica spectrum disorders groups. Mean upper cervical cord area is easier to obtain compared with cervical cord volume and total cord volume and can be regarded as an efficient representative measure of spinal cord atrophy in the neuromyelitis optica spectrum disorders context.

Induction of glutathione S-transferases activities in Drosophila melanogaster exposed to phenol

Studying the toxic effects of long-term exposing fruit flies to phenol is the object of this study. The induction of the glutathione S-transferases enzymatic activities, the change in the amount of mRNA related to phenol exposure, the change in survival rate of adult fruit flies, and the chemical interaction between phenol and benzene were the problems to be investigated. Glutathione S-transferases were separated by affinity chromatography and the mRNAs levels were quantified by reverse-transcription polymerase chain reaction. Long-term feeding phenol to wild type fruit flies had caused some toxic effects included increasing the resistance to phenol toxicity, lowering the benzene toxicity, and induction of glutathione S-transferases enzymatic activities. But no significant change in the amount of glutathione S-transferases GstD1 and GstD5 mRNAs had occurred. From these results, we concluded that fruit flies could develop resistance to phenol by decreasing its toxicity; phenol was a inducer of glutathione S-transferases; phenol could increase the glutathione S-transferases enzymatic activities by increasing the amount of proteins; phenol exposure could decrease the benzene toxicity; no new glutathione S-transferase isozyme subunit was induced; and the level of GstD1 and GstD5 mRNAs did not significantly increase in phenol-treated strain.

Nonhost resistance of tomato to the bean pathogen Pseudomonas syringae pv. syringae B728a is due to a defective E3 ubiquitin ligase domain in avrptobb728a

The bean pathogen Pseudomonas syringae pv. syringae B728a expresses homologs of the type III effectors AvrPto and AvrPtoB, either of which can trigger resistance in tomato cultivars expressing Pto and Prf genes. We found that strain B728a also elicits nonhost resistance in tomato cultivars VFNT Cherry and Moneymaker that lack Pto but express other members of the Pto family (e.g., SlFen and SlPtoC). Here, we show that the AvrPtoB homolog from B728a, termed AvrPtoBB728a (also known as HopAB1), is recognized by 'VFNT Cherry' and 'Moneymaker' when the effector is expressed in P. syringae pv. syringae 61, a strain lacking the avrPto or avrPtoB homolog. Using a gene-silencing approach, this recognition was shown to involve one or more Pto family members and Prf. AvrPtoBB728a interacted with SlFen, SlPtoC, and SlPtoD, in addition to Pto, in a yeast two-hybrid assay. In P. syringae pv. tomato DC3000, the C-terminal domain of AvrPtoB is an E3 ubiquitin ligase that ubiquitinates Fen, causing its degradation and leading to disease susceptibility. Although the C-terminal domain of AvrPtoBB728a shares 69% amino acid identity with that of AvrPtoB, we found that it has greatly reduced E3 ligase activity and is unable to ubiquitinate Fen in an in vitro ubiquitination assay. Thus, the nonhost resistance of 'VFNT Cherry' and 'Moneymaker' to B728a appears to be due to recognition of AvrPtoBB728 as a result of the effector's reduced E3 ligase activity, which prevents it from facilitating degradation of a Pto family member. We speculate that the primary plant host of B728a lacks a Fen-like protein and that, therefore, the E3 ligase of AvrPtoBB728 was unnecessary for pathogenicity and has diverged and become ineffective.

Mechanisms of bradykinin-mediated Ca(2+) signalling in canine cultured corneal epithelial cells

Experiments were designed to differentiate the mechanisms of bradykinin receptors mediating the changes in intracellular Ca(2+) concentration ([Ca(2+)](i)) in canine cultured corneal epithelial cells (CECs). Bradykinin and Lys-bradykinin caused an initial transient peak of [Ca(2+)](i) in a concentration-dependent manner, with half-maximal stimulation (pEC(50)) obtained at 6.9 and 7.1, respectively. Pretreatment of CECs with pertussis toxin (PTX) or cholera toxin (CTX) for 24 h did not affect the bradykinin-induced [Ca(2+)](i) changes. Application of Ca(2+) channel blockers, diltiazem and Ni(2+), inhibited the bradykinin-induced Ca(2+) mobilization, indicating that Ca(2+) influx was required for the bradykinin-induced responses. Addition of thapsigargin (TG), which is known to deplete intracellular Ca(2+) stores, transiently increased [Ca(2+)](i) in Ca(2+)-free buffer, and subsequently induced Ca(2+) influx when Ca(2+) was readded to this buffer. Pretreatment of CECs with TG completely abolished bradykinin-induced initial transient [Ca(2+)](i), but had slight effect on bradykinin-induced Ca(2+) influx. Pretreatment of CECs with 1-[beta-[3-(4-methoxyphenyl)propoxy]-4-methoxyphenethyl]-1H-imidazole (SKF96365) and 1-(6-((17beta-3-methoxyestra-1,3,5(10)-trien-17-yl)amino)hexyl)-1H-pyrrole-2,5-dione (U73122) inhibited the bradykinin-induced Ca(2+) release and Ca(2+) influx, consistent with the inhibition of receptor-gated Ca(2+) channels and phospholipase C (PLC) in CECs, respectively. These results demonstrate that bradykinin directly stimulates B(2) receptors and subsequently Ca(2+) mobilization via a PTX-insensitive G protein in canine CECs. These results suggest that bradykinin-induced Ca(2+) influx into the cells is not due to depletion of these Ca(2+) stores, as prior depletion of these pools by TG has no effect on the bradykinin-induced Ca(2+) influx that is dependent on extracellular Ca(2+) in CECs.