Characterization of the regulatory and expression context of an alternative oxidase gene provides insights into cyanide-insensitive respiration during growth and development

Alternative oxidase (AOX) is encoded in small multigene families in plants. Functional analysis of the Arabidopsis (Arabidopsis thaliana) alternative oxidase 1c (AtAOX1c) promoter, an AOX gene not induced by oxidative stress, indicated that regulation of expression was complex, with the upstream promoter region containing positive and negative response regions. Comparison to the promoter region of soybean (Glycine max) alternative oxidase 2b (GmAOX2b), another AOX gene not induced by oxidative stress, revealed that they contained seven sequence elements in common. All elements were active in the promoter region of AtAOX1c in suspension cells and in leaf tissue from Columbia and mutant plants, where a mitochondrial protein import receptor was inactivated. Analysis of coexpressed and putatively coregulated genes, the latter defined as containing five or more sequence elements functional in AtAOX1c, indicated that AtAOX1c was coregulated with components involved with cell division and growth. Consistent with this analysis, we demonstrated that site II elements, previously shown to regulate the proliferating cell nuclear antigen, are present in the upstream promoter region of AtAOX1c and were strong negative regulators of AtAOX1c expression. It was demonstrated that NDB4, a gene encoding an external NAD(P)H dehydrogenase, displayed strong coexpression with AtAOX1c. Overall, these results indicate that AtAOX1c is regulated by growth and developmental signals.     

What is a schizophrenic mouse?

In this issue of Neuron, Clapcote et al. examine mice containing missense mutations of the DISC1 gene, a locus associated with major mental illness in at least one large Scottish family. Genetic manipulation of mouse homologs of genes implicated in the etiology of psychiatric disorders is a promising avenue of research, but also one that is fraught with interpretative difficulties.     

Cell interaction knowledgebase: an online database for innate immune cells, cytokines and chemokines

The innate immune system is fundamental to the recognition of pathogens, triggering of immune-inflammatory response and host defense. Recent advance in this area has resulted in enormous amount of data, which are stored across different databases. Integrating relevant information from these different data sources is difficult because of their heterogeneous nature and dispersed physical location. We present here a single portal system, Cell Interaction Knowledgebase, with focus on the innate immunity. In particular, the knowledgebase houses comprehensive information on innate immune cells and cytokines/chemokines which are the principal mediators of communication among the immune cells. Currently the knowledgebase consists of extensive information on 2 major innate immune cell types (Macrophages and Dendritic cells) and 7 6 cytokines/chemokines for both human and mouse. In addition, intra-cellular molecular interactions and inter-cellular interactions involved in the innate immunity are curated and presented in an interactive and dynamic manner by animated pathways and query-driven cell-interaction map respectively. This is one of the first databases that houses extensive phenotypic, signaling, genomic, proteomic and knockout data on both the innate immune cells and their attendant cytokines/chemokines, and is aimed to evolve as a one-stop-shop for immunologists. The first version of database is available at http://cell-interaction.bii.a-star.edu.sg/.     

Options for In Situ Remediation of Soil Contaminated with a Mixture of Perchlorinated Compounds

Environments contaminated with mixtures of chlorinated hydrocarbons represent a formidable challenge for bioremediation because biodegradation of all components of the mixture must be demonstrated. In this study a soil site contaminated with hexachloro-1,3-butadiene (HCBD), hexachlorobenzene (HCB), and perchloroethene (PCE) was investigated. Environmental parameters (including toxicity) and microbial community composition were characterized. The lack of scientific literature on HCBD biodegradation led to attempts to develop HCBD-respiring enrichment cultures and to test the hypothesis that known PCE-degrading cultures could dechlorinate HCBD. No HCBD dechlorination was observed. An alternative approach, using electron shuttles to degrade the mixture of chlorinated hydrocarbons, was compared with the activity of zero-valent iron. The authors conclude that electron shuttles offer promise for the in situ treatment of mixtures of chlorinated hydrocarbons.     

Disentangling olfactory and visual information used by field foraging birds

Foraging strategies of birds can influence trophic plant–insect networks with impacts on primary plant production. Recent experiments show that some forest insectivorous birds can use herbivore‐induced plant volatiles (HIPVs) to locate herbivore‐infested trees, but it is unclear how birds combine or prioritize visual and olfactory information when making foraging decisions. Here, we investigated attraction of ground‐foraging birds to HIPVs and visible prey in short vegetation on farmland in a series of foraging choice experiments. Birds showed an initial preference for HIPVs when visual information was the same for all choice options (i.e., one experimental setup had all options with visible prey, another setup with hidden prey). However, if the alternatives within an experimental setup included visible prey (without HIPV) in competition with HIPV‐only, then birds preferred the visual option over HIPVs. Our results show that olfactory cues can play an important role in birds’ foraging choices when visual information contains little variation; however, visual cues are preferred when variation is present. This suggests certain aspects of bird foraging decisions in agricultural habitats are mediated by olfactory interaction mechanisms between birds and plants. We also found that birds from variety of dietary food guilds were attracted to HIPVs; hence, the ability of birds to use plant cues is probably more general than previously thought, and may influence the biological pest control potential of birds on farmland.     

Expression of IGF system genes during T-antigen driven pituitary tumorigenesis.

Expression of IGF-I, IGF-II, the Type-I IGF receptor and six IGF binding proteins were examined in three different T-ag-driven mouse tumors. Unlike the widespread expression of IGF-II in pancreatic beta-cell tumors, IGF-II was not widely expressed in the two different pituitary tumors examined indicating that a mechanism independent of focal IGF-II expression can also drive T-antigen tumorigenesis. In addition, multiple IGF binding proteins were expressed in all three tumor types. This expression, however, was generally heterogeneous with no specific changes to indicate a required role for any IGF binding protein in T-antigen tumorigenesis.     

A Predictive Model of the Extent of Listerial Contamination Within Damaged Silage Bales

A computer simulation model which describes the spatial and temporal variation in the extent of listerial contamination within a damaged silage bale is presented. The silage bale is assumed to be split into a number of distinct sites and these sites are represented by a two dimensional lattice structure. Each site is classified in relation to its listerial composition. This classification results in three states which are dormant, active and unpopulated. Sites change state as a result of the movement of oxygen through the bale. This movement is initiated when a hole is punched in the plastic covering of the bale. The model is stochastic in nature and at any time following damage, the proportion of the bale which is contaminated is calculated. Furthermore, the spatial distribution of contaminated sites is predicted. The models are a first attempt at introducing structure into the selection process for feeding silage. We highlight areas of future research which will be invaluable for validation and practical use of the model.     

The impact of removing financial incentives and/or audit and feedback on chlamydia testing in general practice: A cluster randomised controlled trial (ACCEPt-able)

BackgroundFinancial incentives and audit/feedback are widely used in primary care to influence clinician behaviour and increase quality of care. While observational data suggest a decline in quality when these interventions are stopped, their removal has not been evaluated in a randomised controlled trial (RCT), to our knowledge. This trial aimed to determine whether chlamydia testing in general practice is sustained when financial incentives and/or audit/feedback are removed.Methods and findingsWe undertook a 2 × 2 factorial cluster RCT in 60 general practices in 4 Australian states targeting 49,525 patients aged 16–29 years for annual chlamydia testing. Clinics were recruited between July 2014 and September 2015 and were followed for up to 2 years or until 31 December 2016. Clinics were eligible if they were in the intervention group of a previous cluster RCT where general practitioners (GPs) received financial incentives (AU$5–AU$8) for each chlamydia test and quarterly audit/feedback reports of their chlamydia testing rates. Clinics were randomised into 1 of 4 groups: incentives removed but audit/feedback retained (group A), audit/feedback removed but incentives retained (group B), both removed (group C), or both retained (group D). The primary outcome was the annual chlamydia testing rate among 16- to 29-year-old patients, where the numerator was the number who had at least 1 chlamydia test within 12 months and the denominator was the number who had at least 1 consultation during the same 12 months. We undertook a factorial analysis in which we investigated the effects of removal versus retention of incentives (groups A + C versus groups B + D) and the effects of removal versus retention of audit/feedback (group B + C versus groups A + D) separately. Of 60 clinics, 59 were randomised and 55 (91.7%) provided data (group A: 15 clinics, 11,196 patients; group B: 14, 11,944; group C: 13, 11,566; group D: 13, 14,819). Annual testing decreased from 20.2% to 11.7% (difference −8.8%; 95% CI −10.5% to −7.0%) in clinics with incentives removed and decreased from 20.6% to 14.3% (difference −7.1%; 95% CI −9.6% to −4.7%) where incentives were retained. The adjusted absolute difference in treatment effect was −0.9% (95% CI −3.5% to 1.7%; p = 0.2267). Annual testing decreased from 21.0% to 11.6% (difference −9.5%; 95% CI −11.7% to −7.4%) in clinics where audit/feedback was removed and decreased from 19.9% to 14.5% (difference −6.4%; 95% CI −8.6% to −4.2%) where audit/feedback was retained. The adjusted absolute difference in treatment effect was −2.6% (95% CI −5.4% to −0.1%; p = 0.0336). Study limitations included an unexpected reduction in testing across all groups impacting statistical power, loss of 4 clinics after randomisation, and inclusion of rural clinics only.ConclusionsAudit/feedback is more effective than financial incentives of AU$5–AU$8 per chlamydia test at sustaining GP chlamydia testing practices over time in Australian general practice.Trial registrationAustralian New Zealand Clinical Trials Registry ACTRN12614000595617

In a cluster randomized trial, Jane S Hocking and colleagues investigate the impact of removing financial incentives and/or audit and feedback on chlamydia testing in general practice in Australia.     

Mutational alteration of Bacillus subtilis DNA polymerase 3 to hydroxyphenylazopyrimidine resistance: polymerase 3 is necessary for DNA replication

A spontaneous mutant of $\text{Bacillus}\text{subtilis}$ resistant to killing by two hydroxyphenylazopyrimidines has been isolated. The DNA polymerase III of this mutant is resistant to inhibition by these drugs. The K_i for 6-(p-hydroxyphenylazo)-uracil (HPUra) is 20 μM, about 40 times higher than the K_i of the wild-type enzyme. The mutant and wild-type polymerases behave similarly during purification, are sensitive to N-ethylmaleimide and to 0.1 M KCl, and have the same K_m for dGTP (0.5 μM). The HPUra inhibition of both enzymes is attenuated competitively by dGTP. We conclude that polymerase III is the target for hydroxyphenylazopyrimidines $\text{in}\text{vivo}$, and since the drugs specifically inhibit replicative DNA synthesis, polymerase III is necessary for DNA replication.