Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes

Background  

A theoretical model of genetic redundancy has proposed that the fates of redundant genes depend on the degree of functional redundancy, and that functionally redundant genes will not be inherited together. However, no example of actual gene evolution has been reported that can be used to test this model. Here, we analyzed the molecular evolution of the ribonuclease H (RNase H) family in prokaryotes and used the results to examine the implications of functional redundancy for gene evolution.     

脑铁代谢及调控

随着研究的深入,脑铁代谢相关分子突变引起的疾病越来越多的被人们所认识。脑铁代谢紊乱可能是神经退行性疾病的发病原因之一。对脑铁代谢机理的认识将为预防和治疗脑铁代谢紊乱相关疾病提供重要的理论根据。对脑铁代谢的过程,脑铁代谢的相关分子以及这些分子对脑内铁稳态的调控作用作一介绍。     

The genetic variation of RELN expression in schizophrenia and bipolar disorder

Reelin plays an important role in the development and function of the brain and has been linked to different neuropsychiatric diseases. To further clarify the connection between reelin and psychiatric disorders, we studied the factors that influence the expression of reelin gene (RELN) and its different isoforms. We examined the total expression of RELN, allelic expression, and two alternative RELN isoforms in postmortem brain samples from patients with schizophrenia and bipolar disorder, as well as unaffected controls. We did not find a significant reduction in the total expression of RELN in schizophrenia or bipolar disorder. However, we did find a significant reduction of the proportion of the short RELN isoform, missing the C-terminal region in bipolar disorder, and imbalance in the allelic expression of RELN in schizophrenia. In addition, we tested the association between variation in RELN expression and rs7341475, an intronic SNP that was found to be associated with schizophrenia in women. We did not find an association between rs7341474 and the total expression of RELN either in women or in the entire sample. However, we observed a nominally significant effect of genotype-by-sex interaction on the variation in microexon skipping. Women with the risk genotype of rs7341475 (GG) had a higher proportion of microexon skipping, which is the isoform predominant in tissues outside the brain, while men had the opposite trend. Finally, we tested 83 SNPs in the gene region for association with expression variation of RELN, but none were significant. Our study further supports the connection between RELN dysfunction and psychiatric disorders, and provides a possible functional role for a schizophrenia associated SNP. Nevertheless, the positive associations observed in this study needs further replication as it may have implications for understanding the biological causes of schizophrenia and bipolar disorder.     

Redundant cell death mechanisms as relics and backups

Here we review recent observations indicating the existence of redundant cell death mechanisms. We speculate that this redundancy reflects a particular evolutionary history for cellular demise. Autophagic or apoptotic elements might have been added to a primordial death mechanism, initially improving cell dismantling and later acquiring the ability to act themselves as death effectors. The resulting redundancy of cell death mechanisms has pathophysiological implications.     

Assessing functional redundancy in chronically trawled benthic communities

Fishing disturbance on ecosystems leads to changes in community structure and composition, which may have drastic implications for ecosystem functional performance. Functional redundancy, defined as species sharing similar functional roles, is a community property that plays an important role in preventing functional changes in ecosystems under pressure. In this study, we suggest that functional redundancy may be achieved through trait abundance (i.e. large amounts of a trait, hereafter “common traits”), or through trait richness (i.e. large numbers of distinct taxa exhibiting the same trait, hereafter “widespread traits”). We assessed the variability of both measures obtained from epifaunal and infaunal communities in soft-bottom trawling grounds. Sampling sites were located in four Mediterranean areas that were subjected to different levels of trawling effort. Common and widespread traits measures were based on the analysis of biological traits linked to key soft-bottoms functions such as nutrient cycling, bentho-pelagic coupling and habitat provision. The role of rare species in both measures was also assessed and we observed that, in our study sites, rare species generally exhibited the same traits as the most abundant species. Common and widespread traits measures provided complementary information on benthic functional redundancy. Thus, we suggest that a combination of the two measures should be used to appropriately assess benthic functional redundancy in trawling grounds. As redundancy is a component of ecosystem resilience, functional redundancy evaluation is important to assess the overall integrity of ecosystems.     

Genetic architectures of psychiatric disorders: the emerging picture and its implications

Psychiatric disorders are among the most intractable enigmas in medicine. In the past 5 years, there has been unprecedented progress on the genetics of many of these conditions. In this Review, we discuss the genetics of nine cardinal psychiatric disorders (namely, Alzheimer's disease, attention-deficit hyperactivity disorder, alcohol dependence, anorexia nervosa, autism spectrum disorder, bipolar disorder, major depressive disorder, nicotine dependence and schizophrenia). Empirical approaches have yielded new hypotheses about aetiology and now provide data on the often debated genetic architectures of these conditions, which have implications for future research strategies. Further study using a balanced portfolio of methods to assess multiple forms of genetic variation is likely to yield many additional new findings.     

Schizophrenia and the neurodevelopmental continuum:evidence from genomics

The idea that disturbances occurring early in brain development contribute to the pathogenesis of schizophrenia, often referred to as the neurodevelopmental hypothesis, has become widely accepted. Despite this, the disorder is viewed as being distinct nosologically, and by implication pathophysiologically and clinically, from syndromes such as autism spectrum disorders, attention‐deficit/hyperactivity disorder (ADHD) and intellectual disability, which typically present in childhood and are grouped together as “neurodevelopmental disorders”. An alternative view is that neurodevelopmental disorders, including schizophrenia, rather than being etiologically discrete entities, are better conceptualized as lying on an etiological and neurodevelopmental continuum, with the major clinical syndromes reflecting the severity, timing and predominant pattern of abnormal brain development and resulting functional abnormalities. It has also been suggested that, within the neurodevelopmental continuum, severe mental illnesses occupy a gradient of decreasing neurodevelopmental impairment as follows: intellectual disability, autism spectrum disorders, ADHD, schizophrenia and bipolar disorder. Recent genomic studies have identified large numbers of specific risk DNA changes and offer a direct and robust test of the predictions of the neurodevelopmental continuum model and gradient hypothesis. These findings are reviewed in detail. They not only support the view that schizophrenia is a disorder whose origins lie in disturbances of brain development, but also that it shares genetic risk and pathogenic mechanisms with the early onset neurodevelopmental disorders (intellectual disability, autism spectrum disorders and ADHD). They also support the idea that these disorders lie on a gradient of severity, implying that they differ to some extent quantitatively as well as qualitatively. These findings have important implications for nosology, clinical practice and research.     

Network Redundancy Analysis of Effective Brain Networks; a Comparison of Healthy Controls and Patients with Major Depression

This study investigated electroencephalographic correlates in chronically depressed patients compared to healthy controls using intracutaneously applied electrical pain stimulus, to better understand the interaction between pain processing and depression. A close interaction between pain and depression is generally recognized although the precise mechanisms are not yet fully understood. The present study focuses on the hypothesis that effective brain connectivity in major depression patients is altered. Multifunctional interactions between brain regions represent a robust index of effective interactions within the brain, and can be quantified by network redundancy. Thus, structural network differences between 18 normal controls and 18 major depression patients before as well as during the processing of moderately painful intracutaneous electrical stimuli were investigated on the basis of network redundancy differences. In our sample, both patients and control subjects exhibit comparable network redundancies before stimulus application. Caused by the stimulus, there is a global increase of network redundancy in both groups. This increase is diminished in the group of major depression patients. We found clear differences between patients and controls during the stimulus processing, where the network redundancy in normal controls is larger in comparison to patients. The differences might be explained by the fact that major depression patients are more restricted to the affective component of the processing. The well-established biasing to affective processing might suppress the somatosensory processing resulting in a lower number of connections within the considered network. This might then lead to a reduction in network redundancy during stimulus processing.     

Community impacts of two invasive crabs: the interactive roles of density, prey recruitment, and indirect effects

Assessing the implications of species invasion for native communities requires determining whether effects of invaders are novel, or are redundant with effects of species that are already present. Using a pair of field experiments conducted over two successive years, we examined factors that influence community impacts of a recent predatory crab invader (Hemigrapsus sanguineus) and a previously established invasive crab (Carcinus maenas) on New England coasts. We demonstrate that effects of these species differ temporally with changes in the ambient prey community, and are influenced by density differences between the two species and by different strengths and types of indirect effects that each elicits. Our study highlights the importance of including bottom-up processes (i.e., prey recruitment) when examining the redundancy of consumers.     

Focus: The Science of Stress: Potential Societal and Cultural Implications of Transgenerational Epigenetic Methylation of Trauma and PTSD: Pathology or Resilience?

Psychological trauma is unique in that it is an environmental event that could induce biological changes and post-traumatic stress disorder (PTSD), depression, or other mood disorders in some patients. On the other hand, there may be no psychopathology (in most cases), or even sometimes post-traumatic growth and resilience. According to the DSM-5, trauma is a prerequisite for PTSD and traumatic stress disorder, but not for depressive episodes or mood disorders, or other psychiatric conditions. This paper brings attention to the preliminary literature on transgenerational inheritance due to trauma exposure and its societal and cultural implications. There is accumulating evidence that exposure to trauma can be passed transgenerationally through epigenetic inheritance leading to changes in gene expression and possible disorders or resilience. The effects of resilience from transgenerational inheritance have not been studied, but should be, for a full understanding not only of the disease risk across generations, but also of its social and cultural implications. The epigenetic pathologic effects across generations also need further studies, as the current research is preliminary; larger replications are needed for definitive and more complete understanding. I present here a glimpse of where we are, a vision of where we should go in terms of future research direction for disease risk transmission, and recommend studies of resilience and post-traumatic growth across generations, as well as other studies related to the societal implications at the population level.     

Microbiota-gut-brain axis in autism spectrum disorder

Extensive studies, largely during the past decade, identify the dynamic and bidirectional interaction between the bacteria resident in the intestines and their host brain along the "microbiota-gut-brain axis". This interaction modulates the development and function of the central nervous system and is implicated in neurological disorders. As a neurodevelopmental disorder, autism spectrum disorder (ASD) is considered a historically defect in the brain. With accumulating evidence showing how the microorganisms modulate neural activities, more and more research is focusing on the role of the gut microbiota in mitigating ASD symptoms and the underlying mechanisms. In this review, we describe the intricate and crucial pathways via which the gut microbiota communicates with the brain, the microbiota-gut-brain axis, and summarize the specific pathways that mediate the crosstalk of the gut microbiota to the brain in ASD.     

Why minimal is not optimal: Driving the mammalian cell cycle—and drug discovery—with a physiologic CDK control network

Progression through the eukaryotic cell division cycle is governed by the activity of cyclin-dependent kinases (CDKs). For a CDK to become active it must (1) bind a positive regulatory subunit (cyclin) and (2) be phosphorylated on its activation (T) loop. In metazoans, multiple CDK catalytic subunits, each with a distinct set of preferred cyclin partners, regulate the cell cycle, but it has been difficult to assign functions to individual CDKs in vivo. Biochemical analyses and experiments with dominant-negative alleles suggested that specific CDK/cyclin complexes regulate different events, but genetic loss of interphase CDKs (Cdk2, -4 and -6), alone or in combination, did not block proliferation of cells in culture. These knockout and knockdown studies suggested redundancy or plasticity built into the CDK network but did not address whether there was true redundancy in normal cells with a full complement of CDKs. Here, we discuss recent work that took a chemical-genetic approach to reveal that the activity of a genetically non-essential CDK, Cdk2, is required for cell proliferation when normal cyclin pairing is maintained. These results have implications for the systems-level organization of the cell cycle, for regulation of the restriction point and G?/S transition and for efforts to target Cdk2 therapeutically in human cancers.     

Why minimal is not optimal: Driving the mammalian cell cycle—and drug discovery—with a physiologic CDK control network

Progression through the eukaryotic cell division cycle is governed by the activity of cyclin-dependent kinases (CDKs). For a CDK to become active it must (1) bind a positive regulatory subunit (cyclin) and (2) be phosphorylated on its activation (T) loop. In metazoans, multiple CDK catalytic subunits, each with a distinct set of preferred cyclin partners, regulate the cell cycle, but it has been difficult to assign functions to individual CDKs in vivo. Biochemical analyses and experiments with dominant-negative alleles suggested that specific CDK/cyclin complexes regulate different events, but genetic loss of interphase CDKs (Cdk2, -4 and -6), alone or in combination, did not block proliferation of cells in culture. These knockout and knockdown studies suggested redundancy or plasticity built into the CDK network but did not address whether there was true redundancy in normal cells with a full complement of CDKs. Here, we discuss recent work that took a chemical-genetic approach to reveal that the activity of a genetically non-essential CDK, Cdk2, is required for cell proliferation when normal cyclin pairing is maintained. These results have implications for the systems-level organization of the cell cycle, for regulation of the restriction point and G₁/S transition and for efforts to target Cdk2 therapeutically in human cancers.     

Neurodevelopmental involvement in schizophrenia: the olfactory epithelium as an alternative model for research

It has been suggested that disturbances during neurodevelopment may play a crucial role in the etiology of schizophrenia (SZ). This premise is supported by brain imaging, epidemiological, and pathological studies as well as the discovery of susceptibility genes for SZ that appear to be implicated in development of the central nervous system. Here, we discuss the limitations of the current methods and models for studying the neurodevelopmental implications in SZ. We agree with the proposal that the olfactory epithelium, in which neurodevelopment continues throughout life, might represent an alternative model for understanding the pathophysiology of the disorder.     

Differentiation of Neuronal Cells in Fragile X Syndrome

Neural stem cells are multipotent cells which give rise to neurons and glia of the mammalian central nervous system. Recently, we found that differentiation of neural stem cells is altered in fragile X syndrome, a developmental brain disorder with disturbances in the molecular mechanisms that mediate learning and memory. The absence of fragile X mental retardation protein caused an increased number of new-born cells in the subventricular region of the embryonic mouse brain and substantial aberrances in the differentiation of both human and mouse neural stem cells in vitro. Here, alterations of neuronal cell differentiation in fragile X syndrome, the implications of our recent findings, and some open questions that need to be addressed, are discussed.     

Incremental generation of an EST set for the analysis of scrapie pathogenesis

As part of a functional genomic study of scrapie pathogenesis we have generated a complex non-redundant microarray from several tissues by the selection of unique clones and the incremental augmentation of the expressed sequence tag sets. The base set of about 15,000 expressed sequence tags had minimum redundancy and originated from bovine brain. The aim was to augment this set with clones from scrapie-infected brain and spleen and uninfected spleen with minimum redundancy. This was achieved by macroarray hybridization to identify unique sequences in the ovine library. Quality sequence of 4052 unique sheep clones were obtained from the sequencing of only 5000 which have been submitted to the dbEST database at GenBank.     

The maternal brain and its plasticity in humans

This article is part of a Special Issue “Parental Care”.Early mother–infant relationships play important roles in infants' optimal development. New mothers undergo neurobiological changes that support developing mother–infant relationships regardless of great individual differences in those relationships. In this article, we review the neural plasticity in human mothers' brains based on functional magnetic resonance imaging (fMRI) studies. First, we review the neural circuits that are involved in establishing and maintaining mother–infant relationships. Second, we discuss early postpartum factors (e.g., birth and feeding methods, hormones, and parental sensitivity) that are associated with individual differences in maternal brain neuroplasticity. Third, we discuss abnormal changes in the maternal brain related to psychopathology (i.e., postpartum depression, posttraumatic stress disorder, substance abuse) and potential brain remodeling associated with interventions. Last, we highlight potentially important future research directions to better understand normative changes in the maternal brain and risks for abnormal changes that may disrupt early mother–infant relationships.     

Behavioural and ecological consequences of limited attention

Ecological research in the past few decades has shown that most animals acquire and respond adaptively to information that affects survival and reproduction. At the same time, neurobiological studies have established that the rate of information processing by the brain is much lower than the rate at which information is encountered in the environment, and that attentional mechanisms enable the brain to focus only on the most essential information at any given time. Recent integration of the ecological and neurobiological approaches helps us to understand key behaviours with broad ecological and evolutionary implications. Specifically, current data indicate that limited attention affects diet choice and constrains animals' ability simultaneously to feed and attend to predators. Recent experiments also suggest that limited attention influences social interactions, courtship and mating behaviour.     

Mapping brains without coordinates

Brain mapping has evolved considerably over the last century. While most emphasis has been placed on coordinate-based spatial atlases, coordinate-independent parcellation-based mapping is an important technique for accessing the multitude of structural and functional data that have been reported from invasive experiments, and provides for flexible and efficient representations of information. Here. we provide an introduction to motivations, concepts, techniques and implications of coordinate-independent mapping of microstructurally or functionally defined brain structures. In particular, we explain the problems of constructing mapping paths and finding adequate heuristics for their evaluation. We then introduce the three auxiliary concepts of acronym-based mapping (AM), of a generalized hierarchy (GM ontology), and of a topographically oriented regional map (RM) with adequate granularity for mapping between individual brains with different cortical folding and between humans and non-human primates. Examples from the CoCoMac database of primate brain connectivity demonstrate how these concepts enhance coordinate-independent mapping based on published relational statements. Finally, we discuss the strengths and weaknesses of spatial coordinate-based versus coordinate-independent microstructural brain mapping and show perspectives for a wider application of parcellation-based approaches in the integration of multi-model structural, functional, and clinical data.