High ethanol titers from cellulose by using metabolically engineered thermophilic, anaerobic microbes

This work describes novel genetic tools for use in Clostridium thermocellum that allow creation of unmarked mutations while using a replicating plasmid. The strategy employed counter-selections developed from the native C. thermocellum hpt gene and the Thermoanaerobacterium saccharolyticum tdk gene and was used to delete the genes for both lactate dehydrogenase (Ldh) and phosphotransacetylase (Pta). The Δldh Δpta mutant was evolved for 2,000 h, resulting in a stable strain with 40:1 ethanol selectivity and a 4.2-fold increase in ethanol yield over the wild-type strain. Ethanol production from cellulose was investigated with an engineered coculture of organic acid-deficient engineered strains of both C. thermocellum and T. saccharolyticum. Fermentation of 92 g/liter Avicel by this coculture resulted in 38 g/liter ethanol, with acetic and lactic acids below detection limits, in 146 h. These results demonstrate that ethanol production by thermophilic, cellulolytic microbes is amenable to substantial improvement by metabolic engineering.     

The Effect of Increasing Water Temperatures on Schistosoma mansoni Transmission and Biomphalaria pfeifferi Population Dynamics: An Agent-Based Modelling Study

Introduction

There is increasing interest in the control and elimination of schistosomiasis. Little is known, however, about the likely effects of increasing water-body temperatures on transmission.

Methods

We have developed an agent-based model of the temperature-sensitive stages of the Schistosoma and intermediate host snail life-cycles, parameterised using data from S. mansoni and Biomphalaria pfeifferi laboratory and field-based observations. Infection risk is calculated as the number of cercariae in the model, adjusted for their probability of causing infection.

Results

The number of snails in the model is approximately constant between 15–31°C. Outside this range, snail numbers drop sharply, and the snail population cannot survive outside the range 14–32°C. Mean snail generation time decreases with increasing temperature from 176 days at 14°C to 46 days at 26°C. Human infection risk is highest between 16–18°C and 1 pm and 6–10 pm in calm water, and 20–25°C and 12–4 pm in flowing water. Infection risk increases sharply when temperatures increase above the minimum necessary for sustained transmission.

Conclusions

The model suggests that, in areas where S. mansoni is already endemic, warming of the water at transmission sites will have differential effects on both snails and parasites depending on abiotic properties of the water-body. Snail generation times will decrease in most areas, meaning that snail populations will recover faster from natural population reductions and from snail-control efforts. We suggest a link between the ecological properties of transmission sites and infection risk which could significantly affect the outcomes of interventions designed to alter water contact behaviour – proposing that such interventions are more likely to reduce infection levels at river locations than lakes, where infection risk remains high for longer. In cooler areas where snails are currently found, increasing temperatures may significantly increase infection risk, potentially leading to new, high-intensity foci of infection.     

Oxytocin and Vasopressin Receptor Gene Variation as a Proximate Base for Inter- and Intraspecific Behavioral Differences in Bonobos and Chimpanzees

Recent literature has revealed the importance of variation in neuropeptide receptor gene sequences in the regulation of behavioral phenotypic variation. Here we focus on polymorphisms in the oxytocin receptor gene (OXTR) and vasopressin receptor gene 1a (Avpr1a) in chimpanzees and bonobos. In humans, a single nucleotide polymorphism (SNP) in the third intron of OXTR (rs53576 SNP (A/G)) is linked with social behavior, with the risk allele (A) carriers showing reduced levels of empathy and prosociality. Bonobos and chimpanzees differ in these same traits, therefore we hypothesized that these differences might be reflected in variation at the rs53576 position. We sequenced a 320 bp region surrounding rs53576 but found no indications of this SNP in the genus Pan. However, we identified previously unreported SNP variation in the chimpanzee OXTR sequence that differs from both humans and bonobos. Humans and bonobos have previously been shown to have a more similar 5′ promoter region of Avpr1a when compared to chimpanzees, who are polymorphic for the deletion of ∼360 bp in this region (+/− DupB) which includes a microsatellite (RS3). RS3 has been linked with variation in levels of social bonding, potentially explaining part of the interspecies behavioral differences found in bonobos, chimpanzees and humans. To date, results for bonobos have been based on small sample sizes. Our results confirmed that there is no DupB deletion in bonobos with a sample size comprising approximately 90% of the captive founder population, whereas in chimpanzees the deletion of DupB had the highest frequency. Because of the higher frequency of DupB alleles in our bonobo population, we suggest that the presence of this microsatellite may partly reflect documented differences in levels of sociability found in bonobos and chimpanzees.     

Competitive interactions between grass and succulent shrubs at the ecotone between an arid grassland and succulent shrubland in the Karoo

Nearest-neighbour analysis was used to examine the competitive interactions between Stipagrostis brevifolia, a C₄ perennial grass, and two leaf succulent shrubs, Ruschia robusta and Leipoldtia pauciflora, at the ecotone between semi-arid grassland and succulent shrubland in the Karoo. The root distribution in the soil was also compared to assess the degree of overlap in the potential use of soil resources. Regressions between the combined sizes of interspecific, nearest-neighbour species and the distance between them showed significant positive correlations for S. brevifolia and R. robusta, which suggest the presence of competition. We infer from individual species regressions that the grass exerted a stronger competitive force on the shrub R. robusta than R. robusta on the grass. There was also evidence for strong intraspecific competitive relationships within S. brevifolia and R. robusta. There was no evidence of competition between S. brevifolia and L. pauciflora or among L. pauciflora individuals. S. brevifolia had the deepest root system, and was recorded at depths of 70 cm. Most of this root mass occurred between 10 and 40 cm. Ruschia robusta roots were recorded as deep as 55 cm, but more than 90% was found in the top 20 cm of the soil, creating a degree of overlap with the vertical root distribution of S. brevifolia. A clear separation in rooting depths occurred between S. brevifolia, and L. pauciflora which had only 3% of the total root mass below 10 cm. The partial overlap in the vertical root distribution between S. brevifolia and R. robusta may account for the observed competitive relationship, but each species dominates in a different layer, potentially minimising the net competition between S. brevifolia and R. robusta. Our findings demonstrate the possibility of a two-layer water-obtaining strategy in a semi-desert ecosystem, where the succulent shrubs seem to be playing the typical “grass” role described in most models of water partitioning between grass and woody plants. The stronger competitive effect of S. brevifolia on R. robusta at all the sites is of significance to species dynamics, and might be related to winter/summer rainfall dynamics at the climatic transition.     

The inflammatory microenvironment in colorectal neoplasia

Colorectal cancer (CRC) is a major cause of mortality and morbidity worldwide. Inflammatory activity within the stroma of invasive colorectal tumours is known to be a key predictor of disease activity with type, density and location of immune cells impacting on patient prognosis. To date, there has been no report of inflammatory phenotype within pre-malignant human colonic adenomas. Assessing the stromal microenvironment and particularly, inflammatory activity within colorectal neoplastic lesions is central to understanding early colorectal carcinogenesis. Inflammatory cell infiltrate was assessed by immunohistochemistry in paired colonic adenoma and adjacent normal colonic mucosa samples, and adenomas exhibiting increasing degrees of epithelial cell dysplasia. Macrophage phenotype was assessed using double stain immunohistochemistry incorporating expression of an intracellular enzyme of function. A targeted array of inflammatory cytokine and receptor genes, validated by RT-PCR, was used to assess inflammatory gene expression. Inflammatory cell infiltrates are a key feature of sporadic adenomatous colonic polyps with increased macrophage, neutrophil and T cell (specifically helper and activated subsets) infiltration in adenomatous colonic polyps, that increases in association with characteristics of high malignant potential, namely, increasing degree of cell dysplasia and adenoma size. Macrophages within adenomas express iNOS, suggestive of a pro-inflammatory phenotype. Several inflammatory cytokine genes (CXCL1, CXCL2, CXCL3, CCL20, IL8, CCL23, CCL19, CCL21, CCL5) are dysregulated in adenomas. This study has provided evidence of increased inflammation within pre-malignant colonic adenomas. This may allow potential mechanistic pathways in the initiation and promotion of early colorectal carcinogenesis to be identified.     

Lack of association between the rs2294008 polymorphism in the prostate stem cell antigen gene and colorectal neoplasia: a case-control and immunohistochemical study

ABSTRACT: BACKGROUND: Prostate stem cell antigen (PSCA) has been implicated in the pathogenesis of several solid tumours, either due to changes in protein expression, or through association with the rs2294008 polymorphism in the PSCA gene. To our knowledge, the role of PSCA in the development of colorectal neoplasia has not been explored. We performed a genotyping study to assess for associations between the rs2294008 polymorphism and risk of adenomatous polyps and colorectal cancer. DNA samples were available from 388 individuals with colorectal neoplasia and 496 controls, all of whom had undergone screening colonoscopy. In addition, we performed immunohistochemical staining for PSCA in colonic tissue representing all stages of the adenoma-carcinoma sequence. RESULTS: No genotypic associations were found between the rs2294008 polymorphism and the risk of colorectal adenomata or cancer. Immunohistochemical staining did not reveal any alteration in PSCA expression accompanying the adenoma-carcinoma sequence. CONCLUSION: From these data it seems unlikely that PSCA has a role in the initiation or progression of colorectal neoplasia.     

The relationship between impulsive choice and impulsive action: a cross-species translational study

Maladaptive impulsivity is a core symptom in various psychiatric disorders. However, there is only limited evidence available on whether different measures of impulsivity represent largely unrelated aspects or a unitary construct. In a cross-species translational study, thirty rats were trained in impulsive choice (delayed reward task) and impulsive action (five-choice serial reaction time task) paradigms. The correlation between those measures was assessed during baseline performance and after pharmacological manipulations with the psychostimulant amphetamine and the norepinephrine reuptake inhibitor atomoxetine. In parallel, to validate the animal data, 101 human subjects performed analogous measures of impulsive choice (delay discounting task, DDT) and impulsive action (immediate and delayed memory task, IMT/DMT). Moreover, all subjects completed the Stop Signal Task (SST, as an additional measure of impulsive action) and filled out the Barratt impulsiveness scale (BIS-11). Correlations between DDT and IMT/DMT were determined and a principal component analysis was performed on all human measures of impulsivity. In both rats and humans measures of impulsive choice and impulsive action did not correlate. In rats the within-subject pharmacological effects of amphetamine and atomoxetine did not correlate between tasks, suggesting distinct underlying neural correlates. Furthermore, in humans, principal component analysis identified three independent factors: (1) self-reported impulsivity (BIS-11); (2) impulsive action (IMT/DMT and SST); (3) impulsive choice (DDT). This is the first study directly comparing aspects of impulsivity using a cross-species translational approach. The present data reveal the non-unitary nature of impulsivity on a behavioral and pharmacological level. Collectively, this warrants a stronger focus on the relative contribution of distinct forms of impulsivity in psychopathology.     

The effects of care bundles on patient outcomes: a systematic review and meta-analysis

Background

Care bundles are a set of three to five evidence-informed practices performed collectively and reliably to improve the quality of care. Care bundles are used widely across healthcare settings with the aim of preventing and managing different health conditions. This is the first systematic review designed to determine the effects of care bundles on patient outcomes and the behaviour of healthcare workers in relation to fidelity with care bundles.

Methods

This systematic review is reported in line with the PRISMA statement for reporting systematic reviews and meta-analyses. A total of 5796 abstracts were retrieved through a systematic search for articles published between January 1, 2001, to February 4, 2017, in the Cochrane Central Register for Controlled Trials, MEDLINE, EMBASE, British Nursing Index, CINAHL, PsychInfo, British Library, Conference Proceeding Citation Index, OpenGrey trials (including cluster-randomised trials) and non-randomised studies (comprising controlled before-after studies, interrupted time series, cohort studies) of care bundles for any health condition and any healthcare settings were considered. Following the removal of duplicated studies, two reviewers independently screen 3134 records. Three authors performed data extraction independently. We compared the care bundles with usual care to evaluate the effects of care bundles on the risk of negative patient outcomes. Random-effect models were used to further explore the effects of subgroups.

Results

In total, 37 studies (6 randomised trials, 31 controlled before-after studies) were eligible for inclusion. The effect of care bundles on patient outcomes is uncertain. For randomised trial data, the pooled relative risk of negative effects between care bundle and control groups was 0.97 [95% CI 0.71 to 1.34; 2049 participants]. The relative risk of negative patient outcomes from controlled before-after studies favoured the care bundle treated groups (0.66 [95% CI 0.59 to 0.75; 119,178 participants]). However, using GRADE, we assessed the certainty of all of the evidence to be very low (downgraded for risk of bias, inconsistency, indirectness).

Conclusions

Very low quality evidence from controlled before-after studies suggests that care bundles may reduce the risk of negative outcomes when compared with usual care. By contrast, the better quality evidence from six randomised trials is more uncertain.

Trial registration

PROSPERO, CRD42016033175