Aerobic Growth of Escherichia coli Is Reduced,and ATP Synthesis Is Selectively Inhibited when Five C-terminal Residues Are Deleted from the ? Subunit of ATP Synthase

F-type ATP synthases are rotary nanomotor enzymes involved in cellular energy metabolism in eukaryotes and eubacteria. The ATP synthase from Gram-positive and -negative model bacteria can be autoinhibited by the C-terminal domain of its ϵ subunit (ϵCTD), but the importance of ϵ inhibition in vivo is unclear. Functional rotation is thought to be blocked by insertion of the latter half of the ϵCTD into the central cavity of the catalytic complex (F₁). In the inhibited state of the Escherichia coli enzyme, the final segment of ϵCTD is deeply buried but has few specific interactions with other subunits. This region of the ϵCTD is variable or absent in other bacteria that exhibit strong ϵ-inhibition in vitro. Here, genetically deleting the last five residues of the ϵCTD (ϵΔ5) caused a greater defect in respiratory growth than did the complete absence of the ϵCTD. Isolated membranes with ϵΔ5 generated proton-motive force by respiration as effectively as with wild-type ϵ but showed a nearly 3-fold decrease in ATP synthesis rate. In contrast, the ϵΔ5 truncation did not change the intrinsic rate of ATP hydrolysis with membranes. Further, the ϵΔ5 subunit retained high affinity for isolated F₁ but reduced the maximal inhibition of F₁-ATPase by ϵ from >90% to ∼20%. The results suggest that the ϵCTD has distinct regulatory interactions with F₁ when rotary catalysis operates in opposite directions for the hydrolysis or synthesis of ATP.     

Polymorphic analysis of the three MHC-linked HSP70 genes

Three genes encoding members of the M _r 70 000 heat shock protein family (HSP70) are known to lie in the class III region of the human major histocompatibility complex. IN order to determine whether these genes or their protein products exhibit any polymorphism the three genes have been specifically amplified from genomic DNA and sequenced. The HSP70-1 and HSP70-2 genes encode the major heat-inducible HSP70. A comparison of the nucleotide sequences of these genes from B8, SC01, DR3, B18, F1C30, DR3, and B7, SC30, DR2 haplotypes has revelad only very limited sequence variation which is not associated with any amino acid polymorphism. The HSP70-Hom gene encodes a protein that is highly related to HSP70-1, but which is not heat-inducible. Nucleotide sequence analysis of this gene from different haplotypes has revealed a Met Thr amino acid substitution at residue 493 in a number of the haplotypes tested. This variable amino acid lies in the proposed peptide-binding site of the HSP70-Hom protein. Address correspondence and offprint requests to: R. D. Campbell.     

Pinocytosis in the rat visceral yolk sac effects of temperature, metabolic inhibitors and some other modifiers

Low temperature, 2,4-dinitrophenol and moniodoacetate could each completely abolish the pinocytic uptake of ¹²⁵I-labelled polyvinylpyrrolidone, ¹²⁵I-labelled bovine serum albumin or colloidal ¹⁹⁸Au by 17.5-day rat visceral yolk sac cultured in vitro. Cytochalasin B and colchicine caused a partial and dose-dependent inhibition. It is concluded that the mechanism of pinocytic uptake of these substrates is not micropinocytosis as conventionally defined. Removal of extracellular calcium or the oresence of theophylline inhibited liquid-phase pinocytosis by the rat yolk sac, whereas addition of ouabain caused a biphasic response: a slight stimulation of pinosome formation at a low concentration, and an inhibitory effect at a higher concentration.     

The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic–anoxic interphases

Faecalibacterium prausnitzii is one of the most abundant bacteria in the human gut ecosystem and it is an important supplier of butyrate to the colonic epithelium. Low numbers of faecalibacteria have been associated with inflammatory bowel disease. Despite being extremely oxygen sensitive, F. prausnitzii is found adherent to the gut mucosa where oxygen diffuses from epithelial cells. This paradox is now explained on the basis of gas tube experiments, flavin-dependent reduction of 5,5′-dithiobis-2-nitrobenzoate and microbial fuel cell experiments. The results show that F. prausnitzii employs an extracellular electron shuttle of flavins and thiols to transfer electrons to oxygen. Both compounds are present in the healthy human gut. Our observations may have important implications for the treatment of patients with Crohn''s disease, for example, with flavin- or antioxidant rich diets, and they provide a novel key insight in host–microbe interactions at the gut barrier.     

Landscape structure influences pollinator movements and directly affects plant reproductive success

Pollinators play a key role within most terrestrial communities in maintaining plant populations, as well as pollinating many agricultural crops for seed and fruit production. The mobility of pollinating animals is significant to their importance but we know little about how landscape structure influences pollinator movements. Linear landscape features such as hedgerows and embankments are conspicuous features of agricultural landscape structure and are important artificial habitats in their own right. However, there has been some debate as to the function of these landscape elements as corridors between larger expanses of semi‐natural habitat separated by urban and agricultural habitats. Few studies have specifically studied insect flight responses to linear landscape elements. By observing bumblebee flight behaviour along hedgerows and, by creating a medium‐scale experimental array of flower patches using an artificial linear feature, we examined whether such structures can elicit an oriented flight response along them and therefore facilitate insect movement through the landscape. We found that both hedgerows and artificial linear landscape features can influence the flight directions of bumblebees (Bombus spp. Hymenoptera, Apidae), one of Europe's most important groups of pollinators. A bioassay experiment in which Salvia pratensis (Lamiaceae) was planted into landscape patches with differing numbers of connecting hedgerows showed that this directional response can have a profound effect on plant reproductive success – plants had increased pollinator activity, pollen receipt and subsequent seed set in patches with more connections. The overall hedgerow connectedness of a landscape is therefore important both to bumblebee movement and to those plants which depend on bumblebees for pollination services.     

Automated High-Throughput RNAi Screening in Human Cells Combined with Reporter mRNA Transfection to Identify Novel Regulators of Translation

Proteins that promote angiogenesis, such as vascular endothelial growth factor (VEGF), are major targets for cancer therapy. Accordingly, proteins that specifically activate expression of factors like VEGF are potential alternative therapeutic targets and may help to combat evasive resistance to angiogenesis inhibitors. VEGF mRNA contains two internal ribosome entry sites (IRESs) that enable selective activation of VEGF protein synthesis under hypoxic conditions that trigger angiogenesis. To identify novel regulators of VEGF IRES-driven translation in human cells, we have developed a high-throughput screening approach that combines siRNA treatment with transfection of a VEGF-IRES reporter mRNA. We identified the kinase MAPK3 as a novel positive regulator of VEGF IRES-driven translation and have validated its regulatory effect on endogenous VEGF. Our automated method is scalable and readily adapted for use with other mRNA regulatory elements. Consequently, it should be a generally useful approach for high-throughput identification of novel regulators of mRNA translation.     

A framework for estimating the sensitivity of eDNA surveys

Imperfect sensitivity, or imperfect detection, is a feature of all survey methods that needs to be accounted for when interpreting survey results. Detection of environmental DNA (eDNA) is increasingly being used to infer species distributions, yet the sensitivity of the technique has not been fully evaluated. Sensitivity, or the probability of detecting target DNA given it is present at a site, will depend on both the survey method and the concentration and dispersion of target DNA molecules at a site. We present a model to estimate target DNA concentration and dispersion at survey sites and to estimate the sensitivity of an eDNA survey method. We fitted this model to data from a species‐specific eDNA survey for Oriental weatherloach, Misgurnus anguillicaudatus, at three sites sampled in both autumn and spring. The concentration of target DNA molecules was similar at all three sites in autumn but much higher at two sites in spring. Our analysis showed the survey method had ≥95% sensitivity at sites where target DNA concentrations were ≥11 molecules per litre. We show how these data can be used to compare sampling schemes that differ in the number of field samples collected per site and number of PCR replicates per sample to achieve ≥95% sensitivity at a given target DNA concentration. These models allow researchers to quantify the sensitivity of eDNA survey methods to optimize the probability of detecting target species, and to compare DNA concentrations spatially and temporarily.     

A two-stage model for multiple time series data of counts

We propose a two-stage model for time series data of counts from multiple locations. This method fits first-stage model(s) using the technique of iteratively weighted filtered least squares (IWFLS) to obtain location-specific intercepts and slopes, with possible lagged effects via polynomial distributed lag modeling. These slopes and/or intercepts are then taken to a second-stage mixed-effects meta-regression model in order to stabilize results from various locations. The representation of the models from the stages into a combined mixed-effects model, issues of inference and choices of the parameters in modeling the lag structure are discussed. We illustrate this proposed model via detailed analysis on the effect of air pollution on school absenteeism based on data from the Southern California Children's Health Study.