The role of the amino terminus of Bacillus subtilis sigmaK in transcription initiation

The sigma (σ) subunit of eubacterial RNA polymerase (RNAP) is required for specific recognition of promoter DNA sequences and transcription initiation. Regulation of bacterial gene expression can be achieved by modulating a factor activity. The Bacillus subtilis sporulation a σ factor, σ K, controls gene expression of the late sporulation regulon. σ K is synthesized as an inactive precursor protein, pro-σ K, with a 20 amino acid pro sequence. Proteolytic processing of the pro sequence produces the active form, σK, which is able to bind to the core subunits of RNAP to direct gene expression. Thus, the pro sequence renders σK inactive in vivo. After processing, the amino terminus of σK consists of region 1.2, which is conserved among various σ factors. To understand the role of the amino terminus of σK, namely the pro sequence and region 1.2, mutagenesis of both regions was pursued. NH 2-terminal truncations of pro-σK were constructed to address how the pro sequence silences σK activity. The work described here shows that the pro sequence inhibits the ability of σ K to associate with the core subunits and that a deletion of only six amino acids of the pro sequence is sufficient to activate pro-σ K for DNA binding and transcription initiation to levels similar to σ K. Additionally, site directed mutagenesis was used to obtain single amino acid substitutions in region 1.2 to address the role of region 1.2 in σ K transcriptional activity. Two mutations were isolated, converting a lysine (K) to an alanine (A) at position three, and an asparagine (N) to a tyrosine (Y) at position five, both of which alter the efficiency of transcription initiation by RNAP containing the mutant σKs. Surprisingly, σ KK3A increased transcript production when compared to wild type. This increase is due to improvement in DNA affinity and increased stability of RNAP-DNA promoter open complexes. σKN5Y showed a decrease in transcription activity that is related to defects in the ability of RNAP to make the transition from the closed to open RNAP-DNA complex. Results of both the pro sequence and region 1.2 analyses indicate that the amino terminus of σK is important for transcription activity and this work adds to the increasing body of evidence that the amino termini of many σ factors modulate transcription initiation by RNAP. ^

Determinants of Acidobacteria activity inferred from the relative abundances of 16S rRNA transcripts in German grassland and forest soils

16S rRNA genes and transcripts of Acidobacteria were investigated in 57 grassland and forest soils of three different geographic regions. Acidobacteria contributed 9-31% of bacterial 16S rRNA genes whereas the relative abundances of the respective transcripts were 4-16%. The specific cellular 16S rRNA content (determined as molar ratio of rRNA:rRNA genes) ranged between 3 and 80, indicating a low in situ growth rate. Correlations with flagellate numbers, vascular plant diversity and soil respiration suggest that biotic interactions are important determinants of Acidobacteria 16S rRNA transcript abundances in soils. While the phylogenetic composition of Acidobacteria differed significantly between grassland and forest soils, high throughput denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism fingerprinting detected 16S rRNA transcripts of most phylotypes in situ. Partial least squares regression suggested that chemical soil conditions such as pH, total nitrogen, C:N ratio, ammonia concentrations and total phosphorus affect the composition of this active fraction of Acidobacteria. Transcript abundance for individual Acidobacteria phylotypes was found to correlate with particular physicochemical (pH, temperature, nitrogen or phosphorus) and, most notably, biological parameters (respiration rates, abundances of ciliates or amoebae, vascular plant diversity), providing culture-independent evidence for a distinct niche specialization of different Acidobacteria even from the same subdivision.

The Jewish law of marriage and divorce in ancient and modern times and its relation to the law of the State

by M. Mielziner

On the stratigraphic integrity of leaf-wax biomarkers in loess paleosols

Paleoenvironmental and paleoclimate reconstructions based on molecular proxies, such as those derived from leaf-wax biomarkers, in loess-paleosol sequences represent a promising line of investigation in Quaternary research. The main premise of such reconstructions is the synsedimentary deposition of biomarkers and dust, which has become a debated subject in recent years. This study uses two independent approaches to test the stratigraphic integrity of leaf-wax biomarkers: (i) long-chain n-alkanes and fatty acids are quantified in two sediment-depth profiles in glacial till on the Swiss Plateau, consisting of a Holocene topsoil and the underlying B and C horizons. Since glacial sediments are initially very poor in organic matter, significant amounts of leaf-wax biomarkers in the B and C horizons of those profiles would reflect postsedimentary root-derived or microbial contributions. (ii) Compound-specific radiocarbon measurements are conducted on n-alkanes and n-alkanoic (fatty) acids from several depth intervals in the loess section "Crvenka", Serbia, and the results are compared to independent estimates of sediment age. We find extremely low concentrations of plant-wax n-alkanes and fatty acids in the B and C horizons below the topsoils in the sediment profiles. Moreover, compound-specific radiocarbon analysis yields plant-wax 14C ages that agree well with published luminescence ages and stratigraphy of the Serbian loess deposit. Both approaches confirm that postsedimentary, root-derived or microbial contributions are negligible in the two investigated systems. The good agreement between the ages of odd and even homologues also indicates that reworking and incorporation of fossil leaf waxes is not particularly relevant either.

The reporting quality of randomized controlled trials in orthodontics.

OBJECTIVES Accurate trial reporting facilitates evaluation and better use of study results. The objective of this article is to investigate the quality of reporting of randomized controlled trials (RCTs) in leading orthodontic journals, and to explore potential predictors of improved reporting. METHODS The 50 most recent issues of 4 leading orthodontic journals until November 2013 were electronically searched. Reporting quality assessment was conducted using the modified CONSORT statement checklist. The relationship between potential predictors and the modified CONSORT score was assessed using linear regression modeling. RESULTS 128 RCTs were identified with a mean modified CONSORT score of 68.97% (SD = 11.09). The Journal of Orthodontics (JO) ranked first in terms of completeness of reporting (modified CONSORT score 76.21%, SD = 10.1), followed by American Journal of Orthodontics and Dentofacial Orthopedics (AJODO) (73.05%, SD = 10.1). Journal of publication (AJODO: β = 10.08, 95% CI: 5.78, 14.38; JO: β = 16.82, 95% CI: 11.70, 21.94; EJO: β = 7.21, 95% CI: 2.69, 11.72 compared to Angle), year of publication (β = 0.98, 95% CI: 0.28, 1.67 for each additional year), region of authorship (Europe: β = 5.19, 95% CI: 1.30, 9.09 compared to Asia/other), statistical significance (significant: β = 3.10, 95% CI: 0.11, 6.10 compared to non-significant) and methodologist involvement (involvement: β = 5.60, 95% CI: 1.66, 9.54 compared to non-involvement) were all significant predictors of improved modified CONSORT scores in the multivariable model. Additionally, median overall Jadad score was 2 (IQR = 2) across journals, with JO (median = 3, IQR = 1) and AJODO (median = 3, IQR = 2) presenting the highest score values. CONCLUSION The reporting quality of RCTs published in leading orthodontic journals is considered suboptimal in various CONSORT areas. This may have a bearing in trial result interpretation and use in clinical decision making and evidence- based orthodontic treatment interventions.

Assessment of the excretion time of electronic capsules placed in the intestinal lumen of cows with cecal dilatation-dislocation, healthy control cows, and cows with left displacement of the abomasum

OBJECTIVE To analyze the transit time from various locations in the intestines of cows with cecal dilatation-dislocation (CDD), healthy control cows, and cows with left displacement of the abomasum (LDA). ANIMALS 15 cows with naturally occurring CDD (group 1), 14 healthy control cows (group 2), and 18 cows with LDA (group 3). PROCEDURES 5 electronic transmitters were encased in capsules and placed in the lumen of the ileum, cecum, proximal portion of the colon, and 2 locations in the spiral colon (colon 1 and colon 2) and used to measure the transit time (ie, time between placement in the lumen and excretion of the capsules from the rectum). Excretion time of the capsules from each intestinal segment was compared among groups. RESULTS Cows recovered well from surgery, except for 1 cow with relapse of CDD 4 days after surgery and 2 cows with incisional infection. High variability in capsule excretion times was observed for all examined intestinal segments in all groups. Significant differences were detected for the excretion time from the colon (greater in cows with CDD than in healthy control cows) and cecum (less in cows with LDA than in cows of the other 2 groups). CONCLUSIONS AND CLINICAL RELEVANCE The technique developed to measure excretion time of capsules from bovine intestines was safe and reliable; however, the large variability observed for all intestinal segments and all groups would appear to be a limitation for its use in assessment of intestinal transit time of cattle in future studies.

Within the pale : the true story of anti-semitic persecution in Russia

by Michael Davitt

The longitudinal course of gross motor activity in schizophrenia - within and between episodes

Schizophrenia is associated with heterogeneous course of positive and negative symptoms. In addition, reduced motor activity as measured by wrist actigraphy has been reported. However, longitudinal studies of spontaneous motor activity are missing. We aimed to explore whether activity levels were stable within and between psychotic episodes. Furthermore, we investigated the association with the course of negative symptoms. In 45 medicated patients, we investigated motor behavior within a psychotic episode. In addition, we followed 18 medicated patients across 2 episodes. Wrist actigraphy and psychopathological ratings were applied. Within an episode symptoms changed but activity levels did not vary systematically. Activity at baseline predicted the course of negative symptoms. Between two episodes activity recordings were much more stable. Again, activity at the index episode predicted the outcome of negative symptoms. In sum, spontaneous motor activity shares trait and state characteristics, the latter are associated with negative symptom course. Actigraphy may therefore become an important ambulatory instrument to monitor negative symptoms and treatment outcome in schizophrenia.

Elucidating the internal structure of psychophysical timing performance in the sub-second and second range by utilizing confirmatory factor analysis

The most influential theoretical account in time psychophysics assumes the existence of a unitary internal clock based on neural counting. The distinct timing hypothesis, on the other hand, suggests an automatic timing mechanism for processing of durations in the sub-second range and a cognitively controlled timing mechanism for processing of durations in the range of seconds. Although several psychophysical approaches can be applied for identifying the internal structure of interval timing in the second and sub-second range, the existing data provide a puzzling picture of rather inconsistent results. In the present chapter, we introduce confirmatory factor analysis (CFA) to further elucidate the internal structure of interval timing performance in the sub-second and second range. More specifically, we investigated whether CFA would rather support the notion of a unitary timing mechanism or of distinct timing mechanisms underlying interval timing in the sub-second and second range, respectively. The assumption of two distinct timing mechanisms which are completely independent of each other was not supported by our data. The model assuming a unitary timing mechanism underlying interval timing in both the sub-second and second range fitted the empirical data much better. Eventually, we also tested a third model assuming two distinct, but functionally related mechanisms. The correlation between the two latent variables representing the hypothesized timing mechanisms was rather high and comparison of fit indices indicated that the assumption of two associated timing mechanisms described the observed data better than only one latent variable. Models are discussed in the light of the existing psychophysical and neurophysiological data.

The dominant role of semi-arid ecosystems in the trend and variability of the land CO2 sink

The growth rate of atmospheric carbondioxide(CO2) concentrations since industrialization is characterized by large interannual variability, mostly resulting from variability in CO 2 uptake by terrestrial ecosystems (typically termed carbon sink). However, the contributions of regional ecosystems to that variability are not well known. Using an ensemble of ecosystem and land-surface models and an empirical observation-based product of global gross primary production, we show that the mean sink, trend, and interannual variability in CO2 uptake by terrestrial ecosystems are dominated by distinct biogeographic regions. Whereas the mean sink is dominated by highly productive lands (mainly tropical forests), the trend and interannual variability of the sink are dominated by semi-arid ecosystems whose carbon balance is strongly associated with circulation-driven variations in both precipitation and temperature.