Comparative genome‐wide analysis of small RNAs of major Gram‐positive pathogens: from identification to application

In the recent years, the number of drug- and multi-drug-resistant microbial strains has increased rapidly. Therefore, the need to identify innovative approaches for development of novel anti-infectives and new therapeutic targets is of high priority in global health care. The detection of small RNAs (sRNAs) in bacteria has attracted considerable attention as an emerging class of new gene expression regulators. Several experimental technologies to predict sRNA have been established for the Gram-negative model organism Escherichia coli. In many respects, sRNA screens in this model system have set a blueprint for the global and functional identification of sRNAs for Gram-positive microbes, but the functional role of sRNAs in colonization and pathogenicity for Listeria monocytogenes, Staphylococcus aureus, Streptococcus pyogenes, Enterococcus faecalis and Clostridium difficile is almost completely unknown. Here, we report the current knowledge about the sRNAs of these socioeconomically relevant Gram-positive pathogens, overview the state-of-the-art high-throughput sRNA screening methods and summarize bioinformatics approaches for genome-wide sRNA identification and target prediction. Finally, we discuss the use of modified peptide nucleic acids (PNAs) as a novel tool to inactivate potential sRNA and their applications in rapid and specific detection of pathogenic bacteria.     

Toxicological screening of chemical emissions from municipal solid waste landfills. application of a predictive framework to a state‐of‐the‐art facility

A screening‐level risk assessment was used to identify chemicals of potential health concern emitted during the normal operation of an hypothetical state‐of‐the‐art municipal solid waste landfill. Data on the amount of contaminants (carcinogens, non‐carcinogenic systemic toxicants, odorous compounds, and particulate‐bound metals) were obtained from existing facilities and used to estimate ground‐level air concentrations of airborne chemicals at the point of maximum impact (property line) and at year 20 (year of maximum emissions from the landfill). Concentrations of leachate components present in the corresponding underlying aquifer were also estimated. Intakes of chemicals experienced by a series of human receptors were then computed using either single‐media or multi‐media algorithms. Carcinogens of concern were selected as those contributing to a lifetime excess cancer risk (LECR) greater than 10^‐6; for non‐carcinogenic systemic toxicants and odorous volatiles an Exposure Ratio (ER=intake or concentration/RfD, RfC, odor threshold) greater than 0.1 was used as cut‐off. The results obtained identified a final set of air emission components (n = 25) constituted mainly of carcinogenic and odorous substances whereas 2 leachate components were retained. Additional analysis using more refined risk‐based approaches are necessary to verify the relevance of these projections.     

The season‐of‐birth paradox

Abstract

Vital statistics data show a remarkably consistent seasonality in U.S. birth patterns, with peaks in late summer and winter months, and a valley in the spring. An attitude survey of college students suggests that peaks in the actual birth distribution occur in unpopular months in which to give birth; the valley in the actual birth distribution occurs in popular months. This paradoxical finding is named the Season‐of‐Birth Paradox. Explanations to resolve the paradox include biological and psychological components. A psychological mechanism—named the Misinformed Reproducer Hypothesis—is tested using NSFG data from the 1973–75 and 1979–81 cycles. Results suggest that women stop contracepting with the expectation that they will get pregnant almost immediately. When it takes several months on the average for a successful conception to occur, the actual birth distribution is shifted away from the preferred birth distribution. These results suggest that psychological as well as biological mechanisms underlie the consistent seasonality patterns in U.S. births.     

Bioremediation of oil‐contaminated soil in Kuwait. I. landfarming to remediate oil‐contaminated soil

During the Gulf Crisis, the State of Kuwait was subjected to hazards caused by the oil well fires. The discharged oil formed over 300 oil lakes, covering land areas in excess of 49 km². In addition, deposits from aerial fallout covered massive areas of Kuwait's desert soil. It has been widely recognized that the heavily oil‐contaminated soil must be remediated in order to avoid total damage to the land, water ecosystems, and/or the eventual release of hazardous particulate compositions to the atmosphere. A large number of diverse technological options were being considered for the remediation of contaminated soil. Bioremediation techniques involving enhanced landfarming was selected and evaluated at pilot scale

The experiments were initiated in November 1992 at the Burgan oil field in which 16 landfarming plots of 120 m² each were constructed. The study continued for 18 months, during which time petroleum hydrocarbon concentration, polycyclic aromatic hydrocarbon (PAH), and heavy metals were monitored regularly. The result obtained showed that landfarming treatment resulted in more than 80% reduction of oil contamination within 15 months. The treatment also resulted in a substantial reduction of the PAHs concentrations.     

Photoanalogues of the Initiation Substrates of the RNA Polymerase II, 5‐Azido‐2‐Nitrobenzoyl Derivatives of the ATP γ‐Amidophosphate: The Possible Photoinduced Degradation of the Functional Group to an N‐Arylhydroxylamine

Photoanlogues of the initiation substrates of the RNA polymerase II, N₃Ar‐ NH(CH₂)_nNHpppA where N₃Ar is 5‐azido‐2‐nitrobenzoyl group (n = 2 or 4) were synthesized, allowing the preparation of photoreactive oligonucleotides in situ by RNA polymerase II for application as photolabels. Photolysis of p‐nitro‐substituted aromatic azide in aqueous medium was investigated. Using the azoxy‐coupling reaction it was possible to determine whether a nitrene or p‐nitrophenyl hydroxylamine azoxy compound is the trappable intermediate that is generated at ambient temperature in aqueous solution.     

Response of pest control by generalist predators to local‐scale plant diversity: a meta‐analysis

Disentangling the effects of plant diversity on the control of herbivores is important for understanding agricultural sustainability. Recent studies have investigated the relationships between plant diversity and arthropod communities at the landscape scale, but few have done so at the local scale. We conducted a meta‐analysis of 32 papers containing 175 independent measures of the relationship between plant diversity and arthropod communities. We found that generalist predators had a strong positive response to plant diversity, that is, their abundance increased as plant diversity increased. Herbivores, in contrast, had an overall weak and negative response to plant diversity. However, specialist and generalist herbivores differed in their response to plant diversity, that is, the response was negative for specialists and not significant for generalists. While the effects of scale remain unclear, the response to plant diversity tended to increase for specialist herbivores, but decrease for generalist herbivores as the scale increased. There was no clear effect of scale on the response of generalist predators to plant diversity. Our results suggest that the response of herbivores to plant diversity at the local scale is a balance between habitat and trophic effects that vary according to arthropod specialization and habitat type. Synthesis and applications. Positive effects of plant diversity on generalist predators confirm that, at the local scale, plant diversification of agroecosystems is a credible and promising option for increasing pest regulation. Results from our meta‐analysis suggest that natural control in plant‐diversified systems is more likely to occur for specialist than for generalist herbivores. In terms of pest management, our results indicate that small‐scale plant diversification (via the planting of cover crops or intercrops and reduced weed management) is likely to increase the control of specialist herbivores by generalist predators.     

Self‐Awareness of Impairment and the Decision to Drive after an Extended Period of Wakefulness

Fatigue is an increasingly noted factor in road accidents. The ability to predict and be aware of impairment in terms of driving capability is important for potential legal liability and road safety. However, to date, there have been few studies that have investigated the accuracy of individuals in predicting how safely they could drive during conditions of sleep loss. Research has demonstrated that individuals rate themselves as better than the population average in a number of domains, including driving‐related skills. Therefore, this study also aimed to investigate self‐ratings of predicted driving ability during extended wakefulness and compare them to ratings made of a hypothetical other person under the same conditions. Thirty‐two participants remained awake for a period of 40 h. Every 2 h, they completed the Psychomotor Vigilance Task (PVT) and rated on a seven‐point scale how well they thought they could drive safely, react quickly in an emergency, and stay in their own lane. They were also asked to assess how they thought someone else in their own position could drive. The participants rated their driving ability as becoming significantly poorer at the same time that their PVT performance became significantly slower. Self‐ratings indicating a qualitative assessment of poorer than neutral driving occurred at 03:00 h for both the “drive safely” and “react quickly” questions, after 19 h of continuous wakefulness (starting at 08:00 h). This occurred at 05:00 h for the “keep in my lane” question. Previous studies with a similar protocol demonstrated that under these conditions, individuals exhibit a performance decrements equivalent to someone with a blood alcohol concentration of 0.05% (the legal driving limit in Australia). Participants consistently rated the ability of others to drive as poorer than their own. The main implication from this study for road safety and legal liability is that it is reasonable to focus on a person's perception of the situation, as it does align with objective reality to a certain extent. A concern in terms of road safety is potential overconfidence, indicated by rating others consistently poorer than themselves.     

Effect of Time of Day on Aerobic Contribution to the 30‐s Wingate Test Performance

The purpose of this study was to evaluate the effects of time of day on aerobic contribution during high‐intensity exercise. A group of 11 male physical education students performed a Wingate test against a resistance of 0.087 kg · kg^?1 body mass. Two different times of day were chosen, corresponding to the minimum (06:00 h) and the maximum (18:00 h) levels of power. Oxygen uptake (V˙O₂) was recorded breath by breath during the test (30 sec). Blood lactate concentrations were measured at rest, just after the Wingate test, and again 5 min later. Oral temperature was measured before each test and on six separate occasions at 02:00, 06:00, 10:00, 14:00, 18:00, and 22:00 h. A significant circadian rhythm was found in body temperature with a circadian acrophase at 18:16±00:25 h as determined by cosinor analysis. Peak power (P_peak), mean power (P_mean), total work done, and V˙O₂ increased significantly from morning to afternoon during the Wingate Test. As a consequence, aerobic contribution recorded during the test increased from morning to afternoon. However, no difference in blood lactate concentrations was observed from morning to afternoon. Furthermore, power decrease was greater in the morning than afternoon. Altogether, these results indicate that the time‐of‐day effect on performances during the Wingate test is mainly due to better aerobic participation in energy production during the test in the afternoon than in the morning.     

Morning‐to‐Evening Differences in Oxygen Uptake Kinetics in Short‐Duration Cycling Exercise

This study analyzed diurnal variations in oxygen (O₂) uptake kinetics and efficiency during a moderate cycle ergometer exercise. Fourteen physically active diurnally active male subjects (age 23±5 yrs) not specifically trained at cycling first completed a test to determine their ventilatory threshold (T_vent) and maximal oxygen consumption (VO_2max); one week later, they completed four bouts of testing in the morning and evening in a random order, each separated by at least 24 h. For each period of the day (07:00–08:30 h and 19:00–20:30 h), subjects performed two bouts. Each bout was composed of a 5 min cycling exercise at 45 W, followed after 5 min rest by a 10 min cycling exercise at 80% of the power output associated with T_vent. Gas exchanges were analyzed breath‐by‐breath and fitted using a mono‐exponential function. During moderate exercise, the time constant and amplitude of VO₂ kinetics were significantly higher in the morning compared to the evening. The net efficiency increased from the morning to evening (17.3±4 vs. 20.5±2%; p<0.05), and the variability of cycling cadence was greater during the morning than evening (+34%; p<0.05). These findings suggest that VO₂ responses are affected by the time of day and could be related to variability in muscle activity pattern.     

Some aspects of the socio‐cultural adjustment of recent Soviet immigrants to the United States*

While Europe is unifying, it is also becoming more diverse, making multiculturalism one of the most hotly debated political issues in Western Europe. Minority citizens occupy an important place in the landscape of this challenging issue. Using the Eurobarometer 53 survey of European citizens, I look at the gap between Europeans who claim minority heritage and those who do not in support for multiculturalism in fifteen European Union member nations, taking into account percentage of extreme right-wing vote. This contextual factor has a persistent significant effect on the difference between minority and non-minority attitudes. High levels of support for extreme right-wing parties may have a polarizing effect, heightening awareness of personal heritage and making ethnic identity more salient in attitudes towards multiculturalism. This suggests an extension of group threat theory in which conceptions of what constitutes both a group and a threat can be created at the level of discourse.     

Adhesion of the marine fouling diatom amphora coffeaeformis to non‐solid gel surfaces

Diatom adhesion to different gel surfaces was tested under different shear conditions, using the fouling marine diatom Amphora coffeaeformis as test organism. Four polymers were selected to obtain a test matrix containing gels with different surface charge as well as different surface energies, viz. agarose, alginate, chitosan and chemically modified polyvinylalcohol (PVA‐SbQ). Three experimental systems were applied to obtain different shear rates. Experimental system 1 consisted of gels cast in a cell culturing well plate for comparing initial adhesion as well as long term biofilm development in the absence of shear. In experimental system 2, microscope slide based test surfaces were tested in aquaria under low shear conditions. A rotating annular biofilm reactor was used to obtain high and controlled shear rates. At high shear rates A. coffeaeformis cells adhered better to the charged polymer gels (alginate and chitosan) than to the low charged polymer gels (agarose and PVA‐SbQ). In the system where shear was absent A. coffeaeformis cells developed a biofilm on agarose equivalent to the charged polymer gels, while adhesion to PVA‐SbQ remained low at all shear rates. It is concluded that non‐solid surfaces did not represent an obstacle to settling and growth of this organism. As observed for solid surfaces, low charge density led to reduced attachment, particularly at high shear.     

Synthesis of (−)‐DAPD

A new synthesis of (?)‐DAPD, suitable for large scale development, is described.     

Use of meta‐analysis to predict degradation of carbaryl and malathion in freshwater for exposure assessment

Carbaryl (1‐naphthyl methylcarbamate) and malathion (diethyl mercaptosuccinate, S‐ester with O, O‐dimethyl phosphorodithioate) are insecticides used to control grasshopper infestations on rangeland. Insecticides used to control grasshopper infestations pose a hazard to aquatic organisms because although no‐spray buffer zones are observed around aquatic habitats, pesticide may be deposited by drift or mobilized from upland areas by runoff. A number of processes may affect the fate of carbaryl and malathion in the aquatic environment, but no method is available for estimating degradation over the range of conditions that occur in the field. We used results of published studies in meta‐analyses to estimate degradation models that predict half‐life of carbaryl and malathion in freshwater over temperature and pH ranges relevant to western grasshopper‐management programs. Estimated degradation models were:

In (half‐life carbaryl) = 24.3 ‐ 2.36(pH) ‐ 0.0788(t)

and In (half‐life malathion) = 5.98 + 2.84(pH) ‐ 0.326(pH ²) ‐ 0.202(t) + 0.00135(t ²)

where half‐life has units of hours, and temperature (t) has units °C. Both models accounted for a significant amount of total variation (P<0.0001) and had r²>0.97. Accuracy of these degradation models was evaluated by comparing predicted degradation of carbaryl and malathion to field and laboratory data. We suggest that use of these degradation models be restricted to conditions where water has 7 ≤. pH ≤. 10 for carbaryl, and 7 ≤ pH ≤ 8.2 for malathion.     

Using repeated winter surveys to estimate changes in abundance of seed‐eating passerines

Capsule Winter Atlas surveys of 16 species on lowland farmland revealed significant changes in count for four species.

Aims To estimate changes in abundance between the early 1980s and late 1990s, of wintering seed‐eating passerines, in ‘core’ areas of lowland Scotland.

Methods Ninety‐five Scottish 10‐km squares were selected that held high numbers of seed‐eating passerines in the 1981–84 Atlas of Wintering Birds in Britain and Ireland. The same survey methods were used to resurvey these in winters 1997/98 and 1998/99, and visits were matched as closely as possible for duration and date. Analyses compared counts between the two survey periods for 16 species of seed‐eating passerines and, for 12 of these, differences were also compared with national breeding population trend information for the same period.

Results Mean Corn Bunting Emberiza calandra count per visit declined by 62% between the early 1980s and late 1990s, a difference which was statistically significant (P = 0.026). Significant increases were recorded for Yellowhammer Emberiza citrinella (up 62%), Common Linnet Carduelis cannabina (up 3.4‐fold) and European Goldfinch Carduelis carduelis (up 13‐fold). For 12 species for which national breeding population trend data were available, trends were weakly positively correlated (r _s = 0.43, P = 0.08) with those from our results, but several species trends were more positive in our study. This difference was particularly marked for Eurasian Tree Sparrow Passer montanus, Goldfinch and Linnet.

Conclusion Repeating Winter Atlas surveys offers a useful additional method for assessing population trends. They are particularly useful in a region with low observer coverage and for species that are poorly covered by long‐term bird monitoring data sets. It would be valuable to validate this approach at a regional level, especially in a region for which detailed long‐term bird monitoring data are available.     

Correction to: Environmental life cycle implications of upscaling lithium‐ion battery production

The International Journal of Life Cycle Assessment -     

Alterations of the Characteristics of the Circadian Rest‐Activity Rhythm of Cancer In‐Patients

The aim of the present study was to evaluate the characteristics of the circadian rest‐activity rhythm of cancer patients. Thirty‐one in‐patients, consisting of 19 males and 12 females, were randomly selected from the Regional Cancer Center, Pandit Jawaharlal Nehru Medical College, Raipur, India. The rest‐activity rhythm was studied non‐invasively by wrist actigraphy, and compared with 35 age‐matched apparently healthy subjects (22 males and 13 females). All subjects wore an Actiwatch (AW64, Mini Mitter Co. Inc., USA) for at least 4–7 consecutive days. Fifteen‐second epoch length was selected for gathering actigraphy data. In addition, several sleep parameters, such as time in bed, assumed sleep, actual sleep time, actual wake time, sleep efficiency, sleep latency, sleep bouts, wake bouts, and fragmentation index, were also recorded. Data were analyzed using several statistical techniques, such as cosinor rhythmometry, spectral analysis, ANOVA, Duncan's multiple‐range test, and t‐test. Dichotomy index (I<O) and autocorrelation coefficient (r24) were also computed. The results validated a statistically significant circadian rhythm in rest‐activity with a prominent period of 24 h for most cancer patients and control subjects. Results of this study further revealed that cancer patients do experience a drastic alteration in the circadian rest‐activity rhythm parameters. Both the dichotomy index and r24 declined in the group of cancer patients. The occurrence of the peak (acrophase, Ø) of the rest‐activity rhythm was earlier (p<0.001) in cancer patients than age‐ and gender‐matched control subjects. Results of sleep parameters revealed that cancer patients spent longer time in bed, had longer assumed and actual sleep durations, and a greater number of sleep and wake bouts compared to control subjects. Further, nap frequency, total nap duration, average nap, and total nap duration per 1 h awake span were statistically significantly higher in cancer patients than control subjects. In conclusion, the results of the present study document the disruption of the circadian rhythm in rest‐activity of cancer in‐patients, with a dampening of amplitude, lowering of mean level of activity, and phase advancement. These alterations of the circadian rhythm characteristics could be attributed to disease, irrespective of variability due to gender, sites of cancer, and timings of therapies. These results might help in designing patient‐specific chronotherapeutic protocols.     

Origin of pre‐islamic architecture in West‐Africa

’Cultural theory’, launched by social anthropologist Mary Douglas, has been highly influential in the inter‐disciplinary field concerned with the study of risk perception and risk communication. The theory derives from the grid‐group analyses that Douglas developed in the 1970s. Cultural theory aims to explain universal ‘cultural bias’ by way of a general typology of group formation and a concomitant cosmology or world view. This article critically examines cultural theory and the study of hazards as culturally construed phenomena.