α-fur, an antisense RNA gene to fur in the extreme acidophile Acidithiobacillus ferrooxidans.

A large non-coding RNA, termed α-Fur, of ~1000 nt has been detected in the extreme acidophile Acidithiobacillus ferrooxidans encoded on the antisense strand to the iron-responsive master regulator fur (ferric uptake regulator) gene. A promoter for α-fur was predicted bioinformatically and validated using gene fusion experiments. The promoter is situated within the coding region and in the same sense as proB, potentially encoding a glutamate 5-kinase. The 3' termination site of the α-fur transcript was determined by 3' rapid amplification of cDNA ends to lie 7 nt downstream of the start of transcription of fur. Thus, α-fur is antisense to the complete coding region of fur, including its predicted ribosome-binding site. The genetic context of α-fur is conserved in several members of the genus Acidithiobacillus but not in all acidophiles, indicating that it is monophyletic but not niche specific. It is hypothesized that α-Fur regulates the cellular level of Fur. This is the fourth example of an antisense RNA to fur, although it is the first in an extreme acidophile, and underscores the growing importance of cis-encoded non-coding RNAs as potential regulators involved in the microbial iron-responsive stimulon.

SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences.

Single-exon coding sequences (CDSs), also known as 'single-exon genes' (SEGs), are defined as nuclear, protein-coding genes that lack introns in their CDSs. They have been studied not only to determine their origin and evolution but also because their expression has been linked to several types of human cancers and neurological/developmental disorders, and many exhibit tissue-specific transcription. We developed SinEx DB that houses DNA and protein sequence information of SEGs from 10 mammalian genomes including human. SinEx DB includes their functional predictions (KOG (euKaryotic Orthologous Groups)) and the relative distribution of these functions within species. Here, we report SinEx 2.0, a major update of SinEx DB that includes information of the occurrence, distribution and functional prediction of SEGs from 60 completely sequenced eukaryotic genomes, representing animals, fungi, protists and plants. The information is stored in a relational database built with MySQL Server 5.7, and the complete dataset of SEG sequences and their GO (Gene Ontology) functional assignations are available for downloading. SinEx DB 2.0 was built with a novel pipeline that helps disambiguate single-exon isoforms from SEGs. SinEx DB 2.0 is the largest available database for SEGs and provides a rich source of information for advancing our understanding of the evolution, function of SEGs and their associations with disorders including cancers and neurological and developmental diseases. Database URL: http://v2.sinex.cl/.

Chromosomal RNA: its properties.

We describe the properties of a special class of RNA associated with chromatin. We discuss why this RNA should be considered a distinct class of RNA and not an artifactual degradation product of either transfer or ribosomal RNA.

Sequence and expression of the rusticyanin structural gene from Thiobacillus ferrooxidans ATCC33020 strain.

The periplasmic blue copper protein rusticyanin is thought to play an important role in iron oxidation by Thiobacillus ferrooxidans. We present the sequence of the gene, rus, encoding rusticyanin together with about 1.4 kb of upstream and 0.3 kb of downstream DNA. The rus gene is unique to T. ferrooxidans. Evidence is presented that it is the last gene of an operon and that it can be transcribed from its own promoter. In ATCC33020 strain, rusticyanin is synthesized in ferrous iron but also in sulfur growth conditions suggesting that it could play a role in both energetic metabolisms. The rus gene transcribed from a vector promoter in Escherichia coli leads to the production of a processed aporusticyanin in the periplasmic space, indicating that its signal sequence is correctly recognized by the secretion machinery and the signal peptidase of E. coli.

Synthesis and structure-activity relationships of a series of penicillin-derived HIV proteinase inhibitors: heterocyclic ring systems containing P1' and P2' substituents.

As an extension of our earlier work based upon a single penicillin-derived thiazolidine moiety we have found that the decahydroisoquinoline grouping, also present in Ro 31-8959, is an effective replacement for one of the thiazolidine units in C2 symmetric penicillin-derived dimers. Reaction of racemic epoxide 6 with [3S-[3 alpha, 4a alpha, 8a alpha]]-decahydro-N-(1,1-dimethylethyl)-3- isoquinolinecarboxamide gave diasteroisomers 34a and 34b. The stereochemistry of the hydroxyl grouping of 34a was determined to be (S). Reaction of the amines derived from 34a and 34b with thiazolidine 8a gave 50 and 51, respectively. Compound 50 was a potent inhibitor of HIV proteinase (IC50 = 23 nM) with antiviral activity against HIV-1 in vitro (EC50 C8166 cells = 50 nM). However, a poor pharmacokinetic profile in the dog for compound 50 and its analogues, in keeping with earlier studies on penicillin-derived dimers in three species, precluded their development as potential antivirals.

Synthesis and structure-activity relationships of a series of penicillin-derived HIV proteinase inhibitors containing a stereochemically unique peptide isostere.

A series of HIV-1 proteinase inhibitors was synthesized based upon a single penicillin derived thiazolidine moiety. Reaction of the C-4 carboxyl group with (R)-phenylalaninol gave amide 10 which was a moderately potent inhibitor of HIV-1 proteinase (IC50 = 0.15 microM). Further modifications based on molecular modeling studies led to compound 48 which contained a stereochemically unique statine-based isostere. This was a potent competitive inhibitor (Ki = 0.25 nM) with antiviral activity against HIV-1 in vitro (5 microM). Neither modification to the benzyl group in an attempt to improve interaction with the S2' pocket, nor introduction of a hydrogen bond donating group to interact with residue Gly48' resulted in improved inhibitory or antiviral activity.

Construction and evaluation of a self-luminescent biosensor.

The genes encoding bioluminescence (lux genes), derived from the marine bacterium V. fischeri, have been fused next to the genes encoding mercury detoxification (mer genes), derived from a clinical isolate of S. marcescens. The fusion has been made so that the expression of the light genes comes under the control of the mer regulatory gene and promoter. These genetic elements activate the expression of the light genes in the presence of mercury. The light can readily be collected and quantitated, resulting in a biosensor for the detection of mercury.

Spontaneous abortion rate in ultrasonographically viable pregnancies.

In a prospective study of 500 patients who had an ultrasonically viable pregnancy at less than 12 weeks' gestation, the spontaneous abortion rate was 2% overall. In those women with a history of spontaneous abortion, the abortion rate increased tenfold. Spontaneous abortion at less than ten weeks' gestation was up to three times higher than that at greater than ten weeks' gestation; this may have implications when deciding on the timing of first-trimester diagnostic procedures.

IST1 insertional inactivation of the resB gene: implications for phenotypic switching in Thiobacillus ferrooxidans.

Thiobacillus ferroxidans ATCC 19859 undergoes rapid phenotypic switching between a wild-type state characterized by the ability to oxidize ferrous iron (FeII) and reduced sulfur compounds and a mutant state where it has lost the capacity to oxidize FeII but retains the ability to oxidize sulfur. The mutant has also gained the capacity to swarm. It is proposed that loss of FeII oxidation is due to the reversible transposition of the insertion sequence IST1 into resB encoding a putative cytochrome c-type biogenesis protein. Downstream from resB and co-transcribed with it is resC, encoding another putative cytochrome biogenesis protein. IST1 insertional inactivation of resB could result in the loss of activity of its target c-type cytochrome(s). This putative target cytochrome(s) is proposed to be essential for FeII oxidation but not for sulfur oxidation. Curiously, resB and resC pertain to the proposed system II cytochrome biogenesis pathway whereas gamma Proteobacteria, of which T. ferrooxidans is a member, normally use system I. This could represent an example of lateral gene transfer.

Influence of locus of control on interpersonal attraction and affective reactions in situations involving reward and punishment.

Ninety-six subjects with either high or low I-E Scale scores participated in individual discussions with an experimental who either (a) rewarded and then punished, (b) punished and then rewarded, or (c) gave no evaluative feedback after the subject's responses. Because previous research has suggested that internally controlled subjects attend primarily to rewards while externally controlled subjects attend primarily to punishments, it was hypothesized (a) that the internally controlled subjects, as compared to externally controlled subjects, would be more attracted to the experimenter in the conditions involving rewards and punishments regardless of the sequencing and (b) that the reverse would be true in the nonevaluative control condition. The prediction was consistently supported and subjects' feelings of anger and anxiety during the discussions generally complemented the attention and attraction hypotheses. The results indicate that individual differences influence attraction in situations involving rewards and punishments and they offer a prescription for developing interpersonal attraction and minimizing anger: Offer rewards to internally controlled persons and remain neutral with externally controlled persons.

Influence of denial (situation redefinition) and projection on anxiety associated with threat to self-esteem.

Subjects in a threat condition were informed that they had failed an important test while subjects in a nonthreat condition were not told that they had failed. To manipulate the use and timing of coping strategies for dealing with threat, subjects were told to (a) redefine the nature and importance of the test before receiving feedback, (b) redefine the nature and importance of the test after feedback, or (c) estimate the performance of their friends on the test (i.e., project) after receiving feedback. Repeated measures of subjective anxiety and pulse rate indicated that (a) the threat manipulation was effective in increasing stress, (b) redefinition occurring before the onset of threat was effective in eliminating stress, and (c) redefinition occuring after the onset of threat was ineffective in reducing stress. Projection reduced the report of subjective anxiety. The results revealed factors that influence coping strategy effectiveness and resolved conflicts in previous findings.

Expression of interpersonal aggression by angered and nonangered persons with the type A and type B behavior patterns.

Thirty-seven subjects with the Type A or the Type B behavior pattern were first either angered or not angered in a problem-solving task by a confederate who posed as another subject. In a subsequent bogus learning experiment, the Type A and Type B subjects had the opportunity to punish or reward the confederate. The effectiveness of the anger manipulation was attested to by the fact that angered subjects had reliably higher pulse rates, systolic blood pressure, and diastolic blood pressure. In the learning experiment, Type A subjects who had not been angered gave the confederate reliably higher levels of punishment than did Type B subjects, but there was not a difference in the levels of punishment given by Type A and Type B subjects who had been angered. There was not a difference between Type A and Type B subjects in the levels of reward they gave the confederate. The results provided behavioral evidence for aggression in persons with the Type A behavior pattern. The fact that the difference in aggression was limited to nonangered subjects was interpreted in terms of differences in attributions of responsibility.

Influence of aerobic exercise on depression.

Forty-three depressed women were randomly assigned to either (a) an aerobic exercise treatment condition in which they participated in strenuous exercise, (b) a placebo treatment condition in which they practiced relaxation exercises, or (c) a no-treatment condition. Aerobic capacity was assessed before and after the 10-week treatment period. Self-reported depression was assessed before, during, and after the treatment period. The results indicated that subjects in the aerobic exercise condition evidenced reliably greater improvements in aerobic capacity than did the subjects in either of the other conditions (p less than .002 in both cases) and that the subjects in the aerobic exercise condition evidenced reliably greater decreases in depression than did subjects in the placebo condition (p = .05) or subjects in the no-treatment condition (p = .001). These results provide the first controlled evidence concerning the effects of strenuous exercise on depression.

Control of respiration as a means of controlling responses to threat.

After a 30-minute rest period, (a) subjects in a respiration tracing condition began replicating their breathing patterns from the rest period; (b) subjects in an attention tracing condition participated in a comparable task that did not involve the control of respiration; and (c) subjects in a no-tracing condition were not assigned to perform any task. After the tracing manipulation was introduced, half of the subjects were assigned to a threat condition and informed that they would receive a series of painful electric shocks, whereas the other subjects were assigned to a no-threat condition and informed that they would receive red light stimulation. Analyses of heart rate and self-report data indicated that (a) the threat manipulation was effective; (b) controlling respiration did not reduce subjects' stress responses; and (c) subjects in the no-tracing condition were the only stressed subjects to show decreases in physiological arousal over time, an effect that may have been due to their use of a cognitive coping strategy (situation redefinition). These findings do not provide evidence that control of respiration is an effective strategy for controlling stress but do suggest that, when not interferred with, subjects can employ relatively effective, self-generated cognitive coping strategies.

Behavior control over aversive events: does control that requires effort reduce anxiety and physiological arousal?

Although it has been suggested that the ability to control (avoid) an aversive event will reduce arousal, it may be that the effort associated with exercising the control will offset the arousal reduction associated with avoidance. To determine whether the amount of effort required to control an aversive event influenced the amount of anxiety and physiological arousal associated with the aversive event, 89 subjects participated in a 3 (unavoidable threat, avoidable threat, no threat) X 2 (high-effort task performance, low-effort task performance) X 2 (anticipation period, performance period) factorial experiment. The results indicated that (a) the aversive event (threat of electrical shock) increased subjects' anxiety and physiological arousal; (b) exercising control was effective for decreasing subjects' anxiety to the non-threat level but only when low effort was required; (c) the prospect of control decreased subjects' physiological arousal to the no-threat level while the subjects were waiting to exercise control over the aversive event; however, (d) while actually exercising the control, subjects showed high physiological arousal like that of subjects who could not control the event. These findings impose important qualifications on the speculations concerning the influence of control.

Effects of paced respiration and expectations on physiological and psychological responses to threat.

While waiting to receive electric shocks, 105 males either (a) regulated their breathing at one half the normal rate, (b) regulated their breathing at the normal rate, or (c) did not regulate their breathing rate. Half of the subjects in each breathing condition were told that their breathing task would aid them in relaxing, whereas the other half were not given that expectation. Subjects in a no threat condition were not threatened with shocks, did not regulate their breathing, and were not provided with expectations. The results indicated that slowing respiration rate reduced physiological arousal as measured by skin resistance and finger pulse volume (but not heart rate) and reduced self-reports of anxiety. Expectations did not influence arousal. These data provide evidence for the effectiveness of paced respiration as a coping strategy, and they resolve the conflicting findings of previous investigations.

The timing of psychosocial transitions and changes in women's lives: an examination of women aged 45 to 60.

Sixty-four middle-class women from four cohorts aged 45, 50, 55, and 60 participated in a retrospective interview concerning psychosocial changes in their adult lives. Their responses provided self-report data relating to specific psychosocial changes, and judges who read the interview protocols provided independent ratings of major psychosocial transitions. The results indicated that major psychosocial transitions were more likely to be associated with phases of the family cycle than with chronological age; within the family cycle, transitions were more likely to occur during the preschool (28% of the women), launching (42% of the women), and postparental (33% of the women) phases than during the no children, school-age, or adolescent phases; transitions associated with the preschool and launching phases were characterized by dissatisfaction, personal disruption, marital unhappiness, and decreased personal development, whereas transitions associated with the postparental phase were characterized by personal mellowing and improved marital relations; and finally, numerous self-reported psychosocial changes were associated with family cycle phase, and a small number of changes was associated with chronological age.

The timing of psychosocial changes in women's lives: the years 25 to 45.

Sixty women, aged 30, 35, 40, and 45, participated in a retrospective interview concerning psychosocial changes in their adult lives. Subjects' responses provided self-report data concerning specific psychosocial changes, and judges who read the interview protocols provided independent ratings of major psychosocial transitions. The distributions of self-reported changes and rated transitions across both chronological age and family cycle phases were examined statistically. Rated transitions were found to be reliably related to chronological age but not to family cycle phase. Specifically, 78% of the subjects manifested a major transition commencing between ages 27 and 30. That transition was characterized initially by personal disruption, followed by reassessment and finally by increased psychological well-being. Both chronological age and family cycle phase were reliably related to a variety of self-reported changes. The implications for conceptions of adult developmental changes are discussed.

Effect of Transcendental Meditation versus resting on physiological and subjective arousal.

On four successive days, 10 highly trained and experienced meditators were asked to relax for 5 minutes, meditate for 20 minutes, and then relax for 5 minutes. In contrast, 10 other subjects who had no training or experience with meditation were asked to relax for 5 minutes, rest for 20 minutes, and then relax for 5 minutes. Physiological arousal (heart rate, skin resistance, respiration rate, systolic blood pressure, diastolic blood pressure) and subjective arousal (cognitive, somatic, relaxation) were measured throughout the experiment. Results indicated that (a) prior to meditating or resting, meditators tended to have higher heart rates and diastolic blood pressure than did nonmeditators, (b) meditation was associated with generally reduced arousal, but (c) while meditating, meditators did not evidence lower levels of arousal than nonmeditators did while resting. This investigation employed controls, which were not used in previous investigations, and the results place qualifications on previously reported results. The results have implications for the study of personality functioning, stress management, and psychotherapy.

Task-related arousal of type A and type B persons: level of challenge and response specificity.

To determine whether different levels of challenge had differential effects on the arousal levels of Type A and Type B persons, 30 Type A and 30 Type B male subjects worked on an intelligence test task (digits backwards recall) that was easy, moderately difficult, or extremely difficult. Arousal was measured in terms of systolic blood pressure, diastolic blood pressure, pulse rate, pulse volume, skin resistance, and subjective arousal. Results indicated that while working on the extremely difficult task, the Type A subjects evidenced reliably higher systolic blood pressure than did the Type B subjects (p = 0.1; difference = 7.52 mm of Hg) and that there were not reliable differences between the subjects in systolic blood pressure at other levels of challenge or on other measures of arousal.