Applications of functional gene microarrays for profiling microbial communities

Functional gene arrays (FGAs) have been considered as a specific, sensitive, quantitative, and high throughput metagenomic tool to detect, monitor and characterize microbial communities. Especially GeoChips, the most comprehensive FGAs have been applied to analyze the functional diversity, composition, structure, and metabolic potential or activity of a variety of microbial communities from different habitats, such as aquatic ecosystems, soils, contaminated sites, extreme environments, and bioreactors. FGAs are able to address fundamental questions related to global change, bioremediation, land use, human health, and ecological theories, and link the microbial community structure to environmental properties and ecosystem functioning. This review focuses on applications of FGA technology for profiling microbial communities, including target preparation, hybridization and data processing, and data analysis. We also discuss challenges and future directions of FGA applications.     

Tardive dyskinesia risk with first‐ and second‐generation antipsychotics in comparative randomized controlled trials: a meta‐analysis

Tardive dyskinesia (TD) risk with D2/serotonin receptor antagonists or D2 receptor partial agonists (second‐generation antipsychotics, SGAs) is considered significantly lower than with D2 antagonists (first‐generation antipsychotics, FGAs). As some reports questioned this notion, we meta‐analyzed randomized controlled studies (RCTs) to estimate the risk ratio (RR) and annualized rate ratio (RaR) of TD comparing SGAs vs. FGAs and SGAs vs. SGAs. Additionally, we calculated raw and annualized pooled TD rates for each antipsychotic. Data from 57 head‐to‐head RCTs, including 32 FGA and 86 SGA arms, were meta‐analyzed, yielding 32 FGA‐SGA pairs and 35 SGA‐SGA pairs. The annualized TD incidence across FGA arms was 6.5% (95% CI: 5.3‐7.8%) vs. 2.6% (95% CI: 2.0‐3.1%) across SGA arms. TD risk and annualized rates were lower with SGAs vs. FGAs (RR=0.47, 95% CI: 0.39‐0.57, p<0.0001, k=28; RaR=0.35, 95% CI: 0.28‐0.45, p<0.0001, number‐needed‐to‐treat, NNT=20). Meta‐regression showed no FGA dose effect on FGA‐SGA comparisons (Z=?1.03, p=0.30). FGA‐SGA TD RaRs differed by SGA comparator (Q=21.8, df=7, p=0.003), with a significant advantage of olanzapine and aripiprazole over other non‐clozapine SGAs in exploratory pairwise comparisons. SGA‐SGA comparisons confirmed the olanzapine advantage vs. non‐clozapine SGAs (RaR=0.66, 95% CI: 0.49‐0.88, p=0.006, k=17, NNT=100). This meta‐analysis confirms a clinically meaningfully lower TD risk with SGAs vs. FGAs, which is not driven by high dose FGA comparators, and documents significant differences with respect to this risk between individual SGAs.     

Application of a Novel Functional Gene Microarray to Probe the Functional Ecology of Ammonia Oxidation in Nitrifying Activated Sludge

We report on the first study trialling a newly-developed, functional gene microarray (FGA) for characterising bacterial and archaeal ammonia oxidisers in activated sludge. Mixed liquor (ML) and media biofilm samples from a full-scale integrated fixed-film activated sludge (IFAS) plant were analysed with the FGA to profile the diversity and relative abundance of ammonia-oxidising archaea and bacteria (AOA and AOB respectively). FGA analyses of AOA and AOB communities revealed ubiquitous distribution of AOA across all samples – an important finding for these newly-discovered and poorly characterised organisms. Results also revealed striking differences in the functional ecology of attached versus suspended communities within the IFAS reactor. Quantitative assessment of AOB and AOA functional gene abundance revealed a dominance of AOB in the ML and approximately equal distribution of AOA and AOB in the media-attached biofilm. Subsequent correlations of functional gene abundance data with key water quality parameters suggested an important functional role for media-attached AOB in particular for IFAS reactor nitrification performance and indicate possible functional redundancy in some IFAS ammonia oxidiser communities. Results from this investigation demonstrate the capacity of the FGA to resolve subtle ecological shifts in key microbial communities in nitrifying activated sludge and indicate its value as a tool for better understanding the linkages between the ecology and performance of these engineered systems.     

基因芯片技术在环境微生物群落研究中的应用

基因芯片技术作为一种快速、敏感、高通量的检测技术,近几年来在环境微生物群落研究中的应用越来越广泛并且得到充分的发展.它不仅可以研究环境微生物群落的微生物分布、种类、功能、动力学变化,还能分析环境污染等环境因素改变对其微生物生态的影响.本文按照基因芯片探针的设计方法,将环境样品群落研究基因芯片分为系统寡核苷酸芯片、功能基因芯片、群落基因组芯片、宏基因组芯片,并简要综述了该技术在活性污泥、土壤、水等环境样品微生物群落研究上的应用,最后,本文展望了该技术的研究方向和在寻找不同环境微生物群落之间差异微生物、差异基因或差异表达基因研究中的应用前景.     

Premalignant Variations in Extracellular Matrix Composition in Chemically Induced Hepatocellular Carcinoma in Rats

Chemical composition of extracellular matrix (ECM) plays a pivotal role in cellular and tissue development, regeneration, and differentiation. It also plays a key role in pathogenesis of hepatocellular carcinoma (HCC). This study explored premalignant changes in the liver tissue content of collagen (as hydroxyproline, HP), total glycosaminoglycans (TGAGs), free glucosamine (FGA), total sialic acid (TSA), lysosomal membrane integrity variations (calculated as total and free cathepsin D activities), and liver histology. Serum alfa-fetoprotein (AFP) level was used as an early marker for HCC in two groups of Wistar rats. One group of rats served as control and was provided normal saline orally. The other group was provided trichloroacetic acid (TCA) as 0.5 g/kg/day for five consecutive days by oral gavage. Animals were killed before tumor development. The treatment revealed dysplastic changes in addition to microsteatosis (fatty changes). Both sinusoids and the portal vein among dysplastic cells were dilated and congested. These dysplastic foci are believed to be premalignant and may be precancerous lesions. The following things were observed: a highly significant increase in serum AFP (as a key marker for HCC), a significant decrease in HP and TSA, a significant increase in FGA, nonsignificant decrease in TGAGs, significant up-regulation of free cathepsin D, nonsignificant decrease in total cathepsin D activities, and destabilization of lysosomal membrane integrity. Down-regulation of HP, TSA, and TGAGs seems to be a prerequisite for cancer development. This might be stimulated by up-regulation of free cathepsin D activity. Perhaps tissue fibrosis is not a condition for developing HCC because collagen was significantly depressed. Up-regulated FGA could be assumed to be a defense mechanism against TCA-induced proteolysis of membrane proteins because it is frequently reported to be of value in cancer chemotherapy. Studied ECM perturbations can be assumed as preliminary changes during chemical hepatocarcinogenesis at the tissue level. Prospective studies on blood levels of cathepsins, TGAGs, and individual ECM variables such as TSA, FGA, and Hp in patients at risk for HCC, performed in parallel with assessments of AFP, may provide a cost-effective way to find new links between tissue changes and circulation that would permit early prediction of disease. It may also provide a way to monitor HCC and compensate for the missed peak AFP values.     

基因芯片及其在环境微生物研究中的应用

基因芯片因其具有高密度、高灵敏度、快速 (实时 )检测、经济、自动化和低背景水平等特点 ,而广泛应用于不同的研究领域。目前 ,应用于环境微生物研究的基因芯片主要有功能基因芯片 (FGAs)、系统发育的寡核苷酸芯片 (POAs)和群落基因组芯片 (CGAs)。综述了基因芯片在环境微生物研究中的应用 ,包括自然环境中微生物的基因表达分析、比较基因组分析和混合微生物群落的分析等。讨论了基因芯片面临的挑战和前景展望     

Punishment of Minor Female Genital Ritual Procedures: Is the Perfect the Enemy of the Good?

Female genital alteration (FGA) is any cutting, removal or destruction of any part of the external female genitalia. Various FGA practices are common throughout the world. While most frequent in Africa and Asia, transglobal migration has brought ritual FGA to Western nations. All forms of FGA are generally considered undesirable for medical and ethical reasons when performed on minors. One ritual FGA procedure is the vulvar nick (VN). This is a small laceration to the vulva that does not cause morphological changes. Besides being performed as a primary ritual procedure it has been proposed as a substitute for more extensive forms of FGA. Measures advocated or taken to reduce the burden of FGA can be punitive or non‐punitive. Even if it is unethical to perform VN, we argue that it also is unethical to attempt to suppress it through punishment. First, punishment of VN is likely to cause more harm than good overall, even to those ostensibly being protected. Second, punishment is likely to exceed legitimate retributive ends. We do not argue in favor of performing VN. Rather, we argue that non‐punitive strategies such as education and harm reduction should be employed.     

基于工业环境扰动的微生物适应性进化

合成生物学技术的快速发展极大提升了微生物细胞工厂的构建能力,为化学品的绿色高效生产提供了重要策略。然而,微生物细胞难以耐受高强度工业环境、抗逆性差,成为了限制其生产性能的关键因素。适应性进化是一种人为施加定向选择压力,使微生物经过长期或短期驯化,获得适应特定环境的表型或生理性能的重要方法。近年来,随着微流控、生物传感器、组学分析等技术的发展,适应性进化为提升微生物细胞在工业环境下的生产性能奠定了基础。本文论述了适应性进化的关键技术及在提高微生物细胞工厂环境耐受性和生产效率方面的重要应用,并展望了适应性进化实现微生物细胞工厂在工业环境下高效运行的重要前景。     

Differential effects of haloperidol and olanzapine on the expression of erythropoietin and its receptor in rat hippocampus and striatum

Compared with first-generation antipsychotics (FGAs), second-generation antipsychotics (SGAs) seem to be neuroprotective and trigger neuroplasticity. Because neuroplasticity is regulated by a variety of neurotrophic factors we studied differential effects of haloperidol (HAL, a FGA) and olanzapine (OLZ, a SGA) on temporal expression of erythropoietin (EPO), a potent neuroprotective factor and its receptor (EPOr) in rat brain. Rats (8-10/group) were treated with HAL or OLZ for 14 days (HAL-14 or OLZ-14) or 45 days (HAL-45 or OLZ-45). Animals were killed by decapitation or by perfusion to collect brains for immunoblotting and immunohistochemical analysis respectively. In hippocampus, the levels of both EPO and EPOr were significantly increased in HAL-14 (p < 0.001) and OLZ-14 (p < 0.001) groups. Their levels decreased in HAL-45 compared with levels in HAL-14 (EPO, p < 0.001; EPOr, p < 0.05), whereas the levels were further increased (EPO, p < 0.05) in OLZ-45 compared with OLZ-14. In striatum, the levels of both EPO and EPOr were unchanged in HAL-14 and EPO levels significantly decreased in HAL-45 (p < 0.05), whereas their levels were significantly increased in OLZ-14 and OLZ-45 compared with the vehicle-treated control (p < 0.001). Both EPO and EPOr were primarily expressed by neurons and endothelial cells. These data suggest that SGAs such as OLZ may have neuroprotective effects through expression of EPO that may be clinically relevant for long-term safe and beneficial management of psychotic patients.     

Improved Aerobic Colony Count Technique for Hydrophobic Grid Membrane Filters

The AOAC International official action procedure for performing aerobic colony counts on hydrophobic grid membrane filters (HGMFs) uses Trypticase soy-fast green FCF agar (FGA) incubated for 48 h. Microbial growths are various shades of green on a pale green background, which can cause problems for automated as well as manual counting. HGMFs which had been incubated 24 or 48 h at 35°C on Trypticase soy agar were flooded underneath with 1 to 2 ml of 0.1% triphenyltetrazolium chloride (TTC) solution by simply lifting one corner of the filter while it was still on the agar and adding the reagent. Microbial growths on HGMFs were counted after color had been allowed to develop for 15 min at room temperature. With representative foods, virtually all colonies stained pink to red. Automated electronic counts made by using the MI-100 HGMF Interpreter were easier and more reliable than control HGMF counts made by the AOAC International official action procedure. Manual counting was easier as well because of increased visibility of the microbial growths. Except in the case of dairy products, 24-h TTC counts did not differ significantly from 48-h FGA counts, whereas the FGA counts at 24 h were always significantly lower, indicating that for many food products the HGMF TTC flooding method permits aerobic colony counts to be made after 24 h.     

微生物药物学课程教学的改革与实践

微生物药物学是针对生命科学相关专业所开设的一门主干选修课。在生物技术高速发展的今天,如何有效建立合理的微生物药物学课程教学体系是教学工作者值得深思的课题。本文从微生物药物学教学内容及教学理念方面入手,简要阐述了作者对微生物药物学课程教学改革和实践所进行的一些有益的尝试和探索。     

Profiling plasma peptides for the identification of potential ageing biomarkers in Chinese Han adults

Advancing age is associated with cardiovascular disease, diabetes mellitus and cancer, and shows significant inter-individual variability. To identify ageing-related biomarkers we performed a proteomic analysis on 1890 Chinese Han individuals, 1136 males and 754 females, aged 18 to 82 years, using weak cation exchange magnetic bead based MALDI-TOF-MS analysis. The study identified 44 peptides which varied in concentration in different age groups. In particular, apolipoprotein A-I (ApoA1) concentration gradually increased between 18 to 50 years of age, the levels of fibrinogen alpha (FGA) decreased over the same age span, while albumin (ALB) was significantly degraded in middle-aged individuals. In addition, the plasma peptide profiles of FGA and four other unidentified proteins were found to be gender-dependent. Plasma proteins such as FGA, ALB and ApoA1 are significantly correlated with age in the Chinese Han population and could be employed as indicative ageing-related biomarkers.     

Filamentous green algae inhibit phytoplankton with enhanced effects when lakes get warmer

1. Filamentous green algae (FGA) may represent an alternative state in high‐nutrient shallow temperate lakes. Furthermore, a clear water state is sometimes associated with the dominance of FGA; however, the mechanisms involved remain uncertain. 2. We hypothesised that FGA may promote a clear water state by directly suppressing phytoplankton growth, mostly via the release of allelochemicals, and that this interaction may be affected by temperature. 3. We examined the relationships between FGA, phytoplanktonic chlorophyll a concentrations and zooplankton in a series of mesocosms (2.8 m³) mimicking enriched shallow ponds now and in a future warmer climate (0 and c. 5 °C above ambient temperatures). We then tested the potential allelopathic effects of FGA (Cladophora sp. and Spirogyra sp.) on phytoplankton using several short‐term microcosms and laboratory experiments. 4. Mesocosms with FGA evidenced lower phytoplanktonic chlorophyll a concentrations than those without. Zooplankton and zooplankton : phytoplankton biomass ratios did not differ between mesocosms with and without FGA, suggesting that grazing was not responsible for the negative effects on phytoplanktonic biomass (chlorophyll a). 5. Our field microcosm experiments demonstrated that FGA strongly suppressed the growth of natural phytoplankton at non‐limiting nutrient conditions and regardless of phytoplankton initial concentrations or micronutrients addition. Furthermore, we found that the negative effect of FGA on phytoplankton growth increased up to 49% under high incubation temperatures. The experiment performed using FGA filtrates confirmed that the inhibitory effect of FGA on phytoplankton may be attributed to allelochemicals. 6. Our results suggest that FGA control of phytoplankton growth may be an important mechanism for stabilising clear water in shallow temperate lakes dominated by FGA and that FGA may play a larger role when lakes get warmer.     

Development of a high-performance liquid chromatography-tandem mass spectrometry method for the determination of flurogestone acetate in ovine plasma

Flurogestone (FGA) is a synthetic progesterone, with a progestational action higher than that of progesterone itself. It is intended for vaginal use in large animals to induce oestrus synchronization. A quantitative method for the analysis of flurogestone acetate (FGA) in ovine plasma by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) has been developed. After the incorporation of megestrol acetate (MGA) as internal standard (IS) and followed by a liquid-liquid extraction from plasma, FGA and MGA were chromatographed using a reverse-phase HPLC column and detected by tandem mass spectrometry with a TurboIonSpray source. Multiple reaction-monitoring (MRM) mode was used for the quantitative determination of FGA in ovine plasma. The precursor ions [M+H](+) at m/z 407.2 and 385.1 for FGA and MGA, respectively, produced product ions at m/z 267.1/285.1 for FGA and m/z 267.1/224.0 for MGA. The validated concentration range was 0.2-5.0 ng/ml based on 500 microl plasma aliquots. The lower limit of quantitation was 0.2 ng/ml. Fully validated selectivity, accuracy, precision and reproducibility criteria for routine use in pharmacokinetic studies were demonstrated.     

Quantifying the Role of Adverse Events in the Mortality Difference between First and Second-Generation Antipsychotics in Older Adults: Systematic Review and Meta-Synthesis

Background

Observational studies have reported higher mortality among older adults treated with first-generation antipsychotics (FGAs) versus second-generation antipsychotics (SGAs). A few studies examined risk for medical events, including stroke, ventricular arrhythmia, venous thromboembolism, myocardial infarction, pneumonia, and hip fracture.

Objectives

1) Review robust epidemiologic evidence comparing mortality and medical event risk between FGAs and SGAs in older adults; 2) Quantify how much these medical events explain the observed mortality difference between FGAs and SGAs.

Data sources

Pubmed and Science Citation Index.

Study eligibility criteria, participants, and interventions

Studies of antipsychotic users that: 1) evaluated mortality or medical events specified above; 2) restricted to populations with a mean age of 65 years or older 3) compared FGAs to SGAs, or both to a non-user group; (4) employed a “new user” design; (5) adjusted for confounders assessed prior to antipsychotic initiation; (6) and did not require survival after antipsychotic initiation. A separate search was performed for mortality estimates associated with the specified medical events.

Study appraisal and synthesis methods

For each medical event, we used a non-parametric model to estimate lower and upper bounds for the proportion of the mortality difference—comparing FGAs to SGAs—mediated by their difference in risk for the medical event.

Results

We provide a brief, updated summary of the included studies and the biological plausibility of these mechanisms. Of the 1122 unique citations retrieved, we reviewed 20 observational cohort studies that reported 28 associations. We identified hip fracture, stroke, myocardial infarction, and ventricular arrhythmias as potential intermediaries on the causal pathway from antipsychotic type to death. However, these events did not appear to explain the entire mortality difference.

Conclusions

The current literature suggests that hip fracture, stroke, myocardial infarction, and ventricular arrhythmias partially explain the mortality difference between SGAs and FGAs.     

Astaxanthin production using Paracoccus carotinifaciens: a way forward?

Paracoccus carotinifaciens could be considered a key microbial factory for obtaining healthier natural products such as astaxanthin (AXT), thus contributing to a bioeconomy. Short cultivation time, high production titers, and thin cell wall are the main advantages that make this bacterium promising in the development of sustainable third-generation biorefineries.     

Realities and hopes in the application of microbial tools in agriculture

The use of microbial tools to sustainably increase agricultural production has received significant attention from researchers, industries and policymakers. Over the past decade, the market access and development of microbial products have been accelerated by (i) the recent advances in plant-associated microbiome science, (ii) the pressure from consumers and policymakers for increasing crop productivity and reducing the use of agrochemicals, (iii) the rising threats of biotic and abiotic stresses, (iv) the loss of efficacy of some agrochemicals and plant breeding programs and (v) the calls for agriculture to contribute towards mitigating climate change. Although the sector is still in its infancy, the path towards effective microbial products is taking shape and the global market of these products has increased faster than that of agrochemicals. Promising results from using microbes either as biofertilizers or biopesticides have been continually reported, fuelling optimism and high expectations for the sector. However, some limitations, often related to low efficacy and inconsistent performance in field conditions, urgently need to be addressed to promote a wider use of microbial tools. We propose that advances in in situ microbiome manipulation approaches, such as the use of products containing synthetic microbial communities and novel prebiotics, have great potential to overcome some of these current constraints. Much more progress is expected in the development of microbial inoculants as areas such as synthetic biology and nano-biotechnology advance. If key technical, translational and regulatory issues are addressed, microbial tools will not only play an important role in sustainably boosting agricultural production over the next few decades but also contribute towards other sustainable development goals, including job creation and mitigation of the impacts of climate change.     

Effects of FGA and PMSG on follicular growth and LH secretion in Suffolk ewes

The effects of fluorogestone acetate (FGA) and/or pregnant mare serum gonadotrophin (PMSG) on follicular growth and LH secretion in cyclic ewes were determined. Suffolk ewes (n = 40), previously synchronized with cloprostenol were divided into 4 experimental groups (n = 10 ewes per group). Group I served as the control, while groups II, III and IV received FGA, PMSG, FGA and PMSG respectively. Four ewes of each group underwent daily laparascopy for 17 d. All the ovarian follicles >/= 2 mm were measured, and their relative locations were recorded on an ovarian map in order to follow the sequential development of each individual follicle. Comparisons were made of the mean day of emergence and the mean number of small, medium and large follicles, the atresia rate and the ovulation rate. For each group, 3 waves of follicular growth and atresia were observed during the cycle. During luteal phase, FGA treatment accelerated the mechanisms of follicular growth but reduced the number of large follicles and increased the atresia rate. In the follicular phase, FGA treatment was detrimental to both the number of large follicles and the ovulation rate. By contrast, PMSG enhanced recruitment of small follicles and the ovulation rate. Serial blood samples were collected during the luteal and follicular phases to study LH secretion. None of the treatments had any effect on LH secretion patterns.