High correlation between genotypes and phenotypes of environmental bacteria Comamonas testosteroni strains

Background

Members of Comamonas testosteroni are environmental microorganisms that are usually found in polluted environment samples. They utilize steroids and aromatic compounds but rarely sugars, and show resistance to multiple heavy metals and multiple drugs. However, comprehensive genomic analysis among the C. testosteroni strains is lacked.

Results

To understand the genome bases of the features of C. testosteroni, we sequenced 10 strains of this species and analyzed them together with other related published genome sequences. The results revealed that: 1) the strains of C. testosteroni have genome sizes ranging from 5.1 to 6.0 Mb and G + C contents ranging from 61.1% to 61.8%. The pan-genome contained 10,165 gene families and the core genome contained 3,599 gene families. Heap’s law analysis indicated that the pan-genome of C. testosteroni may be open (α = 0.639); 2) by analyzing 31 phenotypes of 11 available C. testosteroni strains, 99.4% of the genotypes (putative genes) were found to be correlated to the phenotypes, indicating a high correlation between phenotypes and genotypes; 3) gene clusters for nitrate reduction, steroids degradation and metal and multi-drug resistance were found and were highly conserved among all the genomes of this species; 4) the genome similarity of C. testosteroni may be related to the geographical distances.

Conclusions

This work provided an overview on the genomes of C. testosteroni and new genome resources that would accelerate the further investigations of this species. Importantly, this work focused on the analysis of potential genetic determinants for the typical characters and found high correlation between the phenotypes and their corresponding genotypes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1314-x) contains supplementary material, which is available to authorized users.     

Beta2-adrenoceptor polymorphisms: relation between in vitro and in vivo phenotypes

Beta2-adrenoceptors are expressed in many cell types throughout the body and play a pivotal role in the regulation of the cardiac, pulmonary, vascular, endocrine and central nervous system. Recent studies have discovered that Beta2-adrenoceptor are polymorphic. Three common polymorphisms appear to influence receptor function: Arg16Gly, Gln27Glu, and Thr164Ile. In vitro studies of agonist-stimulation have shown that the Gly16 Beta2-adrenoceptors demonstrate enhanced agonist-promoted down-regulation, while Glu27 variants seem to be resistant. The Ile164 variant, on the other hand, demonstrates decreased responsiveness to agonist stimulation in vitro. However, the functional relevance and phenotypic consequence of such Beta2-adrenoceptor variants in vivo is still unclear. The aim of this review is therefore to provide an overview about the somewhat controversy in vitro, ex vivo and in vivo studies.     

Mouse mutants and phenotypes: accessing information for the study of mammalian gene function

Recent advances in high-throughput gene targeting and conditional mutagenesis are creating new and powerful resources to study the in vivo function of mammalian genes using the mouse as an experimental model. Mutant ES cells and mice are being generated at a rapid rate to study the molecular and phenotypic consequences of genetic mutations, and to correlate these study results with human disease conditions. Likewise, classical genetics approaches to identify mutations in the mouse genome that cause specific phenotypes have become more effective. Here, we describe methods to quickly obtain information on what mutant ES cells and mice are available, including recombinase driver lines for the generation of conditional mutants. Further, we describe means to access genetic and phenotypic data that identify mouse models for specific human diseases.     

In vivo functions of mitogen-activated protein kinases: conclusions from knock-in and knock-out mice

Multicellular organisms achieve intercellular communication by means of signalling molecules whose effect on the target cell is mediated by signal transduction pathways. Such pathways relay, amplify and integrate signals to elicit appropriate biological responses. Protein kinases form crucial intermediate components of numerous signalling pathways. One group of protein kinases, the mitogen-activated protein kinases (MAP kinases) are kinases involved in signalling pathways that respond primarily to mitogens and stress stimuli. In vitro studies revealed that the MAP kinases are implicated in several cellular processes, including cell division, differentiation, cell survival/apoptosis, gene expression, motility and metabolism. As such, dysfunction of specific MAP kinases is associated with diseases such as cancer and immunological disorders. However, the genuine in vivo functions of many MAP kinases remain elusive. Genetically modified mouse models deficient in a specific MAP kinase or expressing a constitutive active or a dominant negative variant of a particular MAP kinase offer valuable tools for elucidating the biological role of these protein kinases. In this review, we focus on the current status of MAP kinase knock-in and knock-out mouse models and their phenotypes. Moreover, examples of the application of MAP kinase transgenic mice for validating therapeutic properties of specific MAP kinase inhibitors, and for investigating the role of MAP kinase in pathogen-host interactions will be discussed.     

Genetically engineered mice and their use in aging research

Genetically engineered animal models have been and will continue to be invaluable for exploring the basic mechanisms involved in the aging process as well as in extending our understanding of diseases found to be more prevalent in the older human population. Continued development of such in vivo systems will allow scientists to further dissect the role genetic and environmental factors play in aging and in age-related disease states and to enhance our understanding of these processes. In this article we discuss techniques involved in the development of such models and review some examples of laboratory mouse strains that have been used to study either normal aging or select diseases associated with aging.     

Genetically modified mice to unravel physiological and pathophysiological roles played by NCX isoforms

Since the discovery of the three isoforms of the Na⁺/Ca²⁺ exchanger, NCX1, NCX2 and NCX3 in 1990s, many studies have been devoted to identifying their specific roles in different tissues under several physiological or pathophysiological conditions. In particular, several seminal experimental works laid the foundation for better understanding gene and protein structures, tissue distribution, and regulatory functions of each antiporter isoform. On the other hand, despite the efforts in the development of specific compounds selectively targeting NCX1, NCX2 or NCX3 to test their physiological or pathophysiological roles, several drawbacks hampered the achievement of these goals. In fact, at present no isoform-specific compounds have been yet identified. Moreover, these compounds, despite their potency, possess some nonspecific actions against other ion antiporters, ion channels, and channel receptors. As a result, it is difficult to discriminate direct effects of inhibition/activation of NCX isoforms from the inhibitory or stimulatory effects exerted on other antiporters, channels, receptors, or enzymes. To overcome these difficulties, some research groups used transgenic, knock-out and knock-in mice for NCX isoforms as the most straightforward and fruitful strategy to characterize the biological role exerted by each antiporter isoform. The present review will survey the techniques used to study the roles of NCXs and the current knowledge obtained from these genetic modified mice focusing on the advantages obtained with these strategies in understanding the contribution exerted by each isoform.     

A conceptual review on systems biology in health and diseases: from biological networks to modern therapeutics

Human physiology is an ensemble of various biological processes spanning from intracellular molecular interactions to the whole body phenotypic response. Systems biology endures to decipher these multi-scale biological networks and bridge the link between genotype to phenotype. The structure and dynamic properties of these networks are responsible for controlling and deciding the phenotypic state of a cell. Several cells and various tissues coordinate together to generate an organ level response which further regulates the ultimate physiological state. The overall network embeds a hierarchical regulatory structure, which when unusually perturbed can lead to undesirable physiological state termed as disease. Here, we treat a disease diagnosis problem analogous to a fault diagnosis problem in engineering systems. Accordingly we review the application of engineering methodologies to address human diseases from systems biological perspective. The review highlights potential networks and modeling approaches used for analyzing human diseases. The application of such analysis is illustrated in the case of cancer and diabetes. We put forth a concept of cell-to-human framework comprising of five modules (data mining, networking, modeling, experimental and validation) for addressing human physiology and diseases based on a paradigm of system level analysis. The review overtly emphasizes on the importance of multi-scale biological networks and subsequent modeling and analysis for drug target identification and designing efficient therapies.     

Heterogeneity in disease resistance and the impact of antibiotics in the US

We hypothesize that the impact of antibiotics is moderated by a population’s inherent (genetic) resistance to infectious disease. Using the introduction of sulfa drugs in 1937, we show that US states that are more genetically susceptible to infectious disease saw larger declines in their bacterial mortality rates following the introduction of sulfa drugs in 1937. This suggests area-level genetic endowments of disease resistance and the discovery of medical technologies have acted as substitutes in determining levels of health across the US. We also document immediate effects of sulfa drug exposure to the age of the workforce and cumulative effects on educational attainment for cohorts exposed to sulfa drugs in early life.     

Variation, natural selection, and information content--a simulation

In Neo-Darwinism, variation and natural selection are the two evolutionary mechanisms that propel biological evolution. Variation implies changes in the gene pool of a population, enlarging the genetic variability from which natural selection can choose. But in the absence of natural selection, variation causes dissipation and randomization. Natural selection, in contrast, constrains this variability by decreasing the survival and fertility of the less-adapted organisms. The objective of this study is to propose a highly simplified simulation of variation and natural selection, and to relate the observed evolutionary changes in a population to its information content. The model involves an imaginary population of individuals. A quantifiable character allows the individuals to be categorized into bins. The distribution of bins (a histogram) was assumed to be Gaussian. The content of each bin was calculated after one to twelve cycles, each cycle spanning N generations (N being undefined). In a first study, selection was simulated in the absence of variation. This was modeled by assuming a differential fertility factor F that increased linearly from the lower bins (F<1.00) to the higher bins (F>1.00). The fertility factor was applied as a multiplication factor during each cycle. Several ranges of fertility were investigated. The resulting histograms became skewed to the right. In a second study, variation was simulated in the absence of selection. This was modeled by assuming that during each cycle each bin lost a fixed percentage of its content (variation factor Y) to its two adjacent bins. The resulting histograms became broader and flatter, while retaining their bilateral symmetry. Different values of Y were monitored. In a third study, various values of F and Y were combined. Our model allows the straightforward application of Shannon's equation and the calculation of a Shannon-entropy (SE) values for each histogram. Natural selection was, thus, shown to result in a progressive decrease in SE as a function of F. In other words, natural selection, when acting alone, progressively increased the information content of the population. In contrast, variation resulted in a progressive increase in SE as a function of Y. In other words, variation acting alone progressively decreased the information content of a population. When both factors, F and Y, were applied simultaneously, their relative weight determined the progressive change in SE.     

Design and baseline characteristics of the Food4Me study: a web-based randomised controlled trial of personalised nutrition in seven European countries

Improving lifestyle behaviours has considerable potential for reducing the global burden of non-communicable diseases, promoting better health across the life-course and increasing well-being. However, realising this potential will require the development, testing and implementation of much more effective behaviour change interventions than are used conventionally. Therefore, the aim of this study was to conduct a multi-centre, web-based, proof-of-principle study of personalised nutrition (PN) to determine whether providing more personalised dietary advice leads to greater improvements in eating patterns and health outcomes compared to conventional population-based advice. A total of 5,562 volunteers were screened across seven European countries; the first 1,607 participants who fulfilled the inclusion criteria were recruited into the trial. Participants were randomly assigned to one of the following intervention groups for a 6-month period: Level 0—control group—receiving conventional, non-PN advice; Level 1—receiving PN advice based on dietary intake data alone; Level 2—receiving PN advice based on dietary intake and phenotypic data; and Level 3—receiving PN advice based on dietary intake, phenotypic and genotypic data. A total of 1,607 participants had a mean age of 39.8 years (ranging from 18 to 79 years). Of these participants, 60.9 % were women and 96.7 % were from white-European background. The mean BMI for all randomised participants was 25.5 kg m⁻², and 44.8 % of the participants had a BMI ≥ 25.0 kg m⁻². Food4Me is the first large multi-centre RCT of web-based PN. The main outcomes from the Food4Me study will be submitted for publication during 2015.

Electronic supplementary material

The online version of this article (doi:10.1007/s12263-014-0450-2) contains supplementary material, which is available to authorized users.     

The neurological presentations of childhood and adult mitochondrial disease: established syndromes and phenotypic variations

Mitochondrial disorders are caused by mutations of nuclear or mitochondrial DNA encoded genes involved in oxidative phosphorylation (OXPHOS). Mutations in these critical genes are associated with specific clinical syndromes with diverse presentations (DiMauro and Schon, 2003. NEJM 348, 2656; Hart et al., 2002. Mitochondrial Disorders in Neurology). Since mitochondria are present in many of our organs and play a key role in energy metabolism, mitochondrial encephalomyopathies often present as multisystem disorders which may manifest with neurologic, cardiac, endocrine, gastrointestinal, hepatic, renal and/or hematologic involvement (DiMauro and Bonilla, 1997. The Molecular and Genetic Basis of Neurological Disease; Vu et al., 2002. Neurol. Clin. N. Am. 20, 809). This chapter will address adult and childhood onset mitochondrial DNA encephalomyopathies, characteristic clinical presentations, as well as their molecular characterization.     

Genetics and cardiovascular system: influence of human genetic variants on vascular function

Candidate gene association studies in cardiovascular diseases have provided evidence on the molecular basis of phenotypic differences between individuals. The comprehension of how inherited genetic variants are able to affect protein functions has increased the knowledge of how genes interact with environment in order to modulate a particular phenotype. Although it is known that the human genome contains more than 10 million SNPs, only a minor part of them are supposed to be functional. A causative SNP in a particular gene may confer a small to moderate effect in complex phenotypes, such as functions important to cardiovascular homeostasis. This paper is a selective review of the literature on the evidence for interactions between vascular function and naturally occurring genetic variants in endothelial nitric oxide synthase (eNOS) and beta-2 adrenergic receptor (ADRB2), two genes among those influencing vascular phenotype and examples for which there is a strong evidence base. eNOS and ADRB2 will be characterized, as well as the mechanisms by which the enzyme and the receptor work to control vascular responses will be described. Understanding the molecular mechanisms underlying gene-mediated vascular function and their modification by genetic variants is expected to result in a better comprehension about individual's phenotypic differences.     

Magel2 knockout mice manifest altered social phenotypes and a deficit in preference for social novelty

MAGEL2 is one of five protein‐coding, maternally imprinted, paternally expressed genes in the Prader–Willi syndrome (PWS)‐critical domain on chromosome 15q11‐q13. Truncating pathogenic variants of MAGEL2 cause Schaaf‐Yang syndrome (SHFYNG) (OMIM #615547), a neurodevelopmental disorder related to PWS. Affected individuals manifest a spectrum of neurocognitive and behavioral phenotypes, including intellectual disability and autism spectrum disorder (ASD). Magel2 knockout mice carrying a maternally inherited, imprinted wild‐type (WT) allele and a paternally inherited Magel2‐lacZ knock‐in allele, which abolishes endogenous Magel2 gene function, exhibit several features reminiscent of the human Prader–Willi phenotypes, including neonatal growth retardation, excessive weight gain after weaning and increased adiposity in adulthood. They were shown to have altered circadian rhythm, reduced motor activity and reduced fertility. An extensive assessment for autism‐like behaviors in this mouse model was warranted, because of the high prevalence of ASD in human patients. The behavior of Magel2 knockout mice and their WT littermates were assayed via open field, elevated plus maze, tube, three‐chamber and partition tests. Our studies confirm decreased horizontal activity of male and female mice and increased vertical activity of females, in the open field. Both sexes spent more time in the open arm of the elevated plus maze, suggestive of reductions in anxiety. Both sexes displayed a lack of preference for social novelty, via a lack of discrimination between known and novel partners in the partition test. The in‐depth investigation of behavioral profiles caused by Magel2 loss‐of‐function helps to elucidate the etiology of behavioral phenotypes both for SHFYNG and PWS in general.     

玉溪市大肠埃希菌O157菌株的流行率、表型与毒力因子特征

目的:检测并分析大肠埃希菌O157(Escherichia coli O157)在玉溪市奶牛、猪、鸡和腹泻病人中的带菌率及其特征,为E.coli O157感染症的防治和该菌分离鉴定技术的建立提供科学依据.方法:将玉溪市最大的一个奶牛场、1个猪屠宰场、2个生禽市场和市医院检验科作为监测点,采集牛、猪、鸡、腹泻病人粪便标本数分别为70、250、350和400例,用免疫磁性分离法和免疫色层技术进行E.coli O157菌株的分离培养,纯化菌株经3种鉴别培养基培养以及法国生物梅里埃公司全自动微生物鉴定系统VITEK 32 GNI 或肠杆菌科鉴定系统API 20 E试条、血清学、噬菌体型、亚碲酸盐抗性、聚合酶链反应等检测与分析.结果:牛、猪、鸡、腹泻病人E.coli O157的带菌率分别为1.4%、2.0%、0和1.2%,分离到4株E.coli O157∶H7、6株E.coli O157∶Hund和1株E.coli O157∶HNM,认识了11株E.coli O157的形态学、生物化学、血清学、噬菌体型、亚碲酸盐抗性、毒力因子等特征.结论:单一动物群或人群可同时携带多株E.coli O157,甚至同一个体也会携带2株E.coli O157;E.coli O157菌株间的表型与毒力因子特征存在一定差异,基因指纹技术可确认并证实菌株间的差异性.     

Differences in growth,pigment composition and photosynthetic rates of two phenotypes Microcystis aeruginosa strains under high and low iron conditions

This paper provided insight into the influence of iron on the growth of Microcystis aeruginosa strains related to different phenotypes of this species. In this research it was intended to compare the growth, pigment composition, photosynthetic efficiency and extracellular polysaccharides production of unicellular and colonial strains of M. aeruginosa. A significantly growth inhibition under iron-limited condition on unicellular M. aeruginosa was noted, whereas the colonial strain could maintain a steady growth along with the culture time. This observation was reconfirmed by the content of chlorophyll a. Compared with unicellular strain; the colonial strain exhibited a higher PSII maximum light energy transformation, photosynthetic oxygen evolution and extracellular polysaccharides (EPS) production in iron-limited condition. Further, in order to gain more information about the accessibility of iron in the two phenotypic Microcystis, we found the two strains could produce hydroxamate-type siderophores, the content of siderophores produced by the colonial strain was more than those in unicellular strain under the iron-limited condition. It was interpreted as an adaptation to the dilute environment. Our results demonstrated that the colonial phenotypes possessed stronger ability to endure iron-limited condition than unicellular strain by higher pigment contents, higher photosynthetic activities, higher EPS production and higher siderophores secretion. It might elucidate that the colonial M. aeruginosa bloom can sustain in eutrophic reservoirs and lakes.     

Behavioural food anticipation in clock genes deficient mice: confirming old phenotypes,describing new phenotypes

Animals fed daily at the same time exhibit circadian food‐anticipatory activity (FAA), which has been suggested to be driven by one or several food‐entrainable oscillators (FEOs). FAA is altered in mice lacking some circadian genes essential for timekeeping in the main suprachiasmatic clock (SCN). Here, we confirmed that single mutations of clock genes Per1^?/? and Per2^Brdm1 alter FAA expression in constant darkness (DD) or under a light–dark cycle (LD). Furthermore, we found that Per1^?/?;Per2^Brdm1 and Per2^Brdm1;Cry1^?/? double mutant animals did not display a stable and significant FAA either in DD or LD. Interestingly, rescued behavioural rhythms in Per2^Brdm1;Cry2^?/? mice in DD were totally entrained to feeding time and re‐synchronized after phase‐shifts of mealtime, indicating a higher SCN sensitivity to feeding cues. However, under an LD cycle and restricted feeding at midday, FAA in double Per2^Brdm1;Cry2^?/? mutant mice was absent. These results indicate that shutting down one or two clock genes results in altered circadian meal anticipation. Moreover, we show that in a genetically rescued SCN clock (Per2^Brdm1;Cry2^?/?), food is a powerful zeitgeber to entrain behavioural rhythms, leading the SCN to be more sensitive to feeding cues than in wild‐type littermates.     

广东省2020年首次报道E基因型柯萨奇病毒B组3型的鉴定及基因特征分析

柯萨奇病毒B组3型(Coxsackievirus B3,CVB3)是肠道病毒中流行较为广泛的血清型之一,在全球多个国家和地区曾报道儿童急性心肌炎、无菌性脑膜炎、手足口病等的暴发流行,严重威胁儿童健康和公共卫生安全。本研究对广东省2020年手足口病患者标本中分离到的8株CVB3进行基因特征和进化分析,结果显示分离到的8株CVB3 VP1区核苷酸序列相似性为98.2%~99.5%,与原型株Nancy的核苷酸序列相似性在77.9%~78.5%之间,与其他CVB3中国大陆流行株的核苷酸序列相似性为79.6%~82.2%。8株CVB3均为E基因型,为广东省首次报道。8株CVB3分离株在进化树上聚集,提示病毒发生了局部传播。全基因组序列分析提示2株广东CVB3分离株在非结构蛋白区有重组现象的发生。本研究为E基因型CVB3在我国的流行传播和疾病防控提供基础资料。