Light-induced carotenogenesis in Myxococcus xanthus: light-dependent membrane sequestration of ECF sigma factor CarQ by anti-sigma factor CarR

Light-induced carotenogenesis in Myxococcus xanthus is under the control of the carQRS operon. CarQ, a proposed extracytoplasmic (ECF) RNA polymerase sigma factor, is required for expression of the operon and the carC gene that encodes phytoene dehydrogenase. CarR, an inner membrane protein in Escherichia coli, is essential for carQRS promoter inactivation in the dark. CarS is required for the light-dependent expression of the promoter of the carB gene cluster that encodes the rest of the structural genes for carotenogenesis. Regulation of carQRS is dependent on the stoichiometry of CarQ and CarR. Increasing the copy number of carQ over carR led to constitutive carotenogenesis, as did loss of translational coupling between carQ and carR. The severity of the constitutive phenotype depended on the distance between the uncoupled genes. When expressed in M. xanthus, a CarR:β-galactosidase fusion protein disappeared in the light. We propose that anti-sigma factor CarR sequesters CarQ to the membrane in the dark, but, in the light, loss of CarR leads to release of the sigma factor.     

Disentangling natural and anthropogenic drivers of changes in a shallow lake using palaeolimnology and historical archives

Shallow lakes are susceptible to catastrophic regime shifts characterised by the presence or absence or macrophytes. However, the long-term controls on macrophyte succession in shallow lakes are incompletely understood. To investigate this, we analysed multiple sediment proxies in Lake Rotcze (Eastern Poland), a small, shallow and densely macrophyte-covered lake to (1) reconstruct the ‘reference conditions’ (sensu WFD) and development of the lake in recent centuries, (2) compare historical evidence with the sedimentary record, and (3) identify the natural and anthropogenic drivers of macrophyte succession. Before the twentieth century, conditions in the lake may be referred to as ‘reference conditions’. Subsequently forest clearance in the catchment resulted in lower water transparency, but concurrent catchment drainage lowered water levels and increased macrophyte development. Since 1950 elevated nutrient supply and climatically driven increases in water levels led to the deterioration of water transparency and partial macrophyte withdrawal. At the end of the twentieth century lake-level drawdown led to low phytoplankton biomass and clear water creating a novel ecosystem where macrophytes invade the whole lake. These patterns suggest that both natural and anthropogenically induced water level fluctuations have been critical drivers of macrophyte development.     

Sleep quality,chronotype and social jetlag differentially associate with symptoms of attention deficit hyperactivity disorder in adults

Attention deficit hyperactivity disorder (ADHD) is a common neurobehavioural disorder which has been associated with sleep and circadian rhythm disturbances. Numerous studies have linked evening circadian typology with traits and behaviours associated with the disorder, although a precise reason for this relationship has not been clarified. The current study examines ADHD symptoms, impulsivity, cognitive failures, sleep quality and chronotype in a cohort of healthy young adults (N = 396). Results show significant, small magnitude associations between mid-point of sleep on free days, social jetlag (SJL) and ADHD symptoms and impulsivity, although not with cognitive failures. Similarly, sleep quality is also associated with ADHD symptoms and impulsivity. Group-wise approaches show that higher SJL is associated with significantly more ADHD symptoms and impulsivity, and later mid-sleep on free days is also associated with more ADHD symptoms. Stepwise multiple linear regression reveals that, when controlling for age and sex, SJL but not mid-sleep on free days is a significant predictor of ADHD symptoms and impulsivity. These results indicate that SJL may be an important factor to consider when exploring circadian rhythm associations with ADHD symptoms.     

Interactive Data Visualization for HIV Cohorts: Leveraging Data Exchange Standards to Share and Reuse Research Tools

Objective

To develop and disseminate tools for interactive visualization of HIV cohort data.

Design and Methods

If a picture is worth a thousand words, then an interactive video, composed of a long string of pictures, can produce an even richer presentation of HIV population dynamics. We developed an HIV cohort data visualization tool using open-source software (R statistical language). The tool requires that the data structure conform to the HIV Cohort Data Exchange Protocol (HICDEP), and our implementation utilized Caribbean, Central and South America network (CCASAnet) data.

Results

This tool currently presents patient-level data in three classes of plots: (1) Longitudinal plots showing changes in measurements viewed alongside event probability curves allowing for simultaneous inspection of outcomes by relevant patient classes. (2) Bubble plots showing changes in indicators over time allowing for observation of group level dynamics. (3) Heat maps of levels of indicators changing over time allowing for observation of spatial-temporal dynamics. Examples of each class of plot are given using CCASAnet data investigating trends in CD4 count and AIDS at antiretroviral therapy (ART) initiation, CD4 trajectories after ART initiation, and mortality.

Conclusions

We invite researchers interested in this data visualization effort to use these tools and to suggest new classes of data visualization. We aim to contribute additional shareable tools in the spirit of open scientific collaboration and hope that these tools further the participation in open data standards like HICDEP by the HIV research community.     

Uncertainty in identifying local extinctions: the distribution of missing data and its effects on biodiversity measures

Identifying local extinctions is integral to estimating species richness and geographic range changes and informing extinction risk assessments. However, the species occurrence records underpinning these estimates are frequently compromised by a lack of recorded species absences making it impossible to distinguish between local extinction and lack of survey effort—for a rigorously compiled database of European and Asian Galliformes, approximately 40% of half-degree cells contain records from before but not after 1980. We investigate the distribution of these cells, finding differences between the Palaearctic (forests, low mean human influence index (HII), outside protected areas (PAs)) and Indo-Malaya (grassland, high mean HII, outside PAs). Such cells also occur more in less peaceful countries. We show that different interpretations of these cells can lead to large over/under-estimations of species richness and extent of occurrences, potentially misleading prioritization and extinction risk assessment schemes. To avoid mistakes, local extinctions inferred from sightings records need to account for the history of survey effort in a locality.     

Correlation of thrombin-induced glycoprotein V hydrolysis and platelet activation

To assess the possibility that hydrolysis of the platelet surface thrombin substrate, glycoprotein V, is a necessary step in thrombin-induced platelet activation, thrombin-catalyzed hydrolysis of glycoprotein V was correlated with thrombin-induced platelet activation. Hydrolysis of tritium-labeled glycoprotein V on washed human platelets was measured by the appearance of a labeled supernatant fragment, and platelet activation was measured as secretion of ATP. Hydrolysis of glycoprotein V was linear with respect to both thrombin concentration and time of incubation. The extent of platelet activation was correlated with the rate of hydrolysis but not with the amount hydrolyzed. Maximum platelet activation could be obtained with thrombin treatments resulting in hydrolysis of as little as 4% of glycoprotein V per min. Glycoprotein V was partially removed from platelets by pretreatment with either platelet calcium-dependent protease or chymotrypsin. The rate of thrombin-catalyzed hydrolysis of the remaining glycoprotein V from these pretreated platelets was as little as 1.5% the rate from control platelets, but there was no impairment of the extent of platelet activation. Thus, these protease-pretreated platelets compared with control platelets showed a different correlation of glycoprotein V hydrolysis with platelet activation. Glycoprotein V was also partially removed by pretreatment of prostacyclin-inhibited platelets with thrombin. After removal of thrombin and prostacyclin, these platelets were desensitized to subsequent activation by thrombin. Incubation of desensitized platelets with nonsaturating levels of thrombin led to less than 25% of the activation seen with control platelets but to a slightly greater hydrolysis of glycoprotein V. Thus, the desensitization to thrombin was not due to loss of ability of the activating thrombin to hydrolyze glycoprotein V. These results do not exclude a role for glycoprotein V as a component of the platelet thrombin receptor, but they indicate that there is no simple relationship between thrombin-induced hydrolysis of glycoprotein V and platelet activation.     

Depression of follicle stimulating hormone in bulls injected with follicular fluid

Eight bulls were divided into two groups and injected with either charcoal-extracted steer blood serum or charcoal-extracted bovine follicular fluid (bFF). Ten-milliliter injections were given subcutaneous every 12 h for 4 wk. Jugular blood collected before, during and after the injection period was analyzed for follicle-stimulating hormone (FSH) and luteinizing hormone (LH) by radioimmunoassay. All bulls were exposed to restrained, estrual heifers for 15 min every 2 wk for 16 wk starting 4 wk before the first injection. The number of mounts and services by each bull was recorded. Semen was collected with an artificial vagina and evaluated on alternate weeks during the same period. The concentration of FSH in serum decreased (P < 0.05) by 12 h after the first injection and remained 61% lower than that of serum-injected bulls during the injection period. The concentration of FSH increased (P < 0.05) by 3 d after the last injection. Injections of bFF did not affect the concentration of LH in serum. Bovine follicular fluid injections significantly depressed FSH; however, libido, serving capacity, and semen characteristics were unchanged.