Genetic analysis of sleep

Almost 20 years ago, the gene underlying fatal familial insomnia was discovered, and first suggested the concept that a single gene can regulate sleep. In the two decades since, there have been many advances in the field of behavioral genetics, but it is only in the past 10 years that the genetic analysis of sleep has emerged as an important discipline. Major findings include the discovery of a single gene underlying the sleep disorder narcolepsy, and identification of loci that make quantitative contributions to sleep characteristics. The sleep field has also expanded its focus from mammalian model organisms to Drosophila, zebrafish, and worms, which is allowing the application of novel genetic approaches. Researchers have undertaken large-scale screens to identify new genes that regulate sleep, and are also probing questions of sleep circuitry and sleep function on a molecular level. As genetic tools continue to be refined in each model organism, the genes that support a specific function in sleep will become more apparent. Thus, while our understanding of sleep still remains rudimentary, rapid progress is expected from these recently initiated studies.     

Barriers to engagement in sleep restriction and stimulus control in chronic insomnia

Sleep restriction (SRT) and stimulus control (SC) have been found to be effective interventions for chronic insomnia (Morgenthaler et al., 2006), and yet adherence to SRT and SC varies widely. The objective of this study was to investigate correlates to adherence to SC/SRT among 40 outpatients with primary or comorbid insomnia using a correlational design. Participants completed a self-report measure of sleepiness prior to completion of a 6-week cognitive behavioral treatment group for insomnia. At the posttreatment period, they rated their ability to engage in SC/SRT using a survey. Results from standard multiple regression analyses showed that perceiving fewer barriers (i.e., less boredom, annoyance) to engaging in SC/SRT and experiencing less pretreatment sleepiness were each associated with better adherence to SC/SRT. Adherence to SC/SRT was associated with outcome. Implications of these findings are that more work is needed to make SC/SRT less uncomfortable, possibly by augmenting energy levels prior to introducing these approaches.     

Translation of sensory signals into commands for control of saccadic eye movements: role of primate superior colliculus

Afferent signals that guide orienting movements converge in the deeper layers of the SC in a wide variety of animals. The sensory cells are arranged topographically according to their receptive-field locations and, thereby, form maps of sensory space. Maps of visual, somatosensory, and/or auditory space have been obtained in the iguana, mouse, hamster, barn owl, chinchilla, cat, and monkey. The deeper layers of the SC also contain neurons involved in the generation of movements of the eyes, head, vibrissae, and pinnae. Thus the SC, a site containing multiple sensory maps and perhaps multiple motor maps, has been selected by many investigators as a structure for investigating the problem of sensorimotor integration. In the mammalian nervous system, emphasized in this review, much remains to be learned about the structure, organization, and function of the SC. While anatomical studies continue to add to the knowledge of the sources of afferent projections, their pattern of laminar termination, and the source and destination of efferent projections, relatively little is known about the intrinsic organization of the colliculus, especially the deeper layers. Recently, electrophysiological studies have moved from an emphasis on the sensory and motor properties of collicular neurons to an examination of the maps of auditory and somatosensory space and the correspondence of these maps. In the future, major efforts aimed at identifying the functional properties of cells that project to the SC from diverse brain regions as well as the functional properties that project to the various structures receiving input from the colliculus are needed. A combination of anatomical and electrophysiological methods is required to describe the signal transforms that occur between the SC and motor areas (such as the paramedian pontine reticular formation) closer to the final common pathway. Conceptual and empirical work is needed to develop and test models of how the dynamic visual and auditory maps found in the primate SC are generated. In general, new and/or improved models of the role of the SC in sensorimotor integration are needed as guides for future research. A point of view emphasized here is that it may be fruitful to examine the function of the SC from a motor perspective. The nature of the motor command imposes constraints on the configuration of signals that can initiate movements and thereby determines the required transformation of sensory signals.     

Quantitative evidence for conserved longevity pathways between divergent eukaryotic species

Studies in invertebrate model organisms have been a driving force in aging research, leading to the identification of many genes that influence life span. Few of these genes have been examined in the context of mammalian aging, however, and it remains an open question as to whether and to what extent the pathways that modulate longevity are conserved across different eukaryotic species. Using a comparative functional genomics approach, we have performed the first quantitative analysis of the degree to which longevity genes are conserved between two highly divergent eukaryotic species, the yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans. Here, we report the replicative life span phenotypes for single-gene deletions of the yeast orthologs of worm aging genes. We find that 15% of these yeast deletions are long-lived. In contrast, only 3.4% of a random set of deletion mutants are long-lived-a statistically significant difference. These data suggest that genes that modulate aging have been conserved not only in sequence, but also in function, over a billion years of evolution. Among the longevity determining ortholog pairs, we note a substantial enrichment for genes involved in an evolutionarily conserved pathway linking nutrient sensing and protein translation. In addition, we have identified several conserved aging genes that may represent novel longevity pathways. Together, these findings indicate that the genetic component of life span determination is significantly conserved between divergent eukaryotic species, and suggest pathways that are likely to play a similar role in mammalian aging.     

Mammalian fertilization as seen with the scanning electron microscope

For several years we have been looking at mammalian gametes and their interactions with the scanning electron microscope (SEM). Examining the images produced by the SEM has given us a three-dimensional view of sperm, eggs, and egg investments. We are particularly impressed with the structural variation among gametes of different mammalian species. In this short report we examine the structure of mammalian spermatozoa, eggs, zonae pellucidae, and cumuli. Our observations and those of others have led us to believe that variation in gamete structure and function may have evolved as a mechanism for reproductive isolation of mammalian species.     

Pleomorphic mammalian tumor-derived bacteria self-organize as multicellular mammalian eukaryotic-like organisms: morphogenetic properties in vitro, possible origins, and possible roles in mammalian 'tumor ecologies'

Highly pleomorphic bacteria have regularly been isolated from mammalian tumors and leukemic bloods. Here, it is shown that highly pleomorphic, cell-wall deficient bacteria derived from a mammalian tumor self-organize in vitro into mammalian tissue-like morphogenetic patterns consisting of multicellular tissue-like sheets and capillary-like networks. It is proposed that these pleomorphic mammalian tumor-derived (MTD) bacteria, during morphogenesis, express mammalian tissue morphogenesis-related genes that were acquired through eukaryote-to-prokaryote DNA transfer. Similar pleomorphic MTD bacteria might play important roles as symbiotic multicellular mammalian eukaryotic-like organisms in mammalian 'tumor ecologies' that include malignant and nonmalignant mammalian eukaryotic cells. From a mammalian tumor ecology perspective, eradication of tumors in some mammalian hosts may depend upon the elimination of pleomorphic MTD bacteria self-organized as symbiotic multicellular mammalian eukaryotic-like organisms. Further investigations of the extraordinary mammalian eukaryotic-like multicellularity of these bacteria may yield fundamental insights into the evolution of multicellularity and multicellular development and may challenge basic assumptions regarding cellular evolution.     

The mammalian testis-specific thioredoxin system

Redox control of cell physiology is one of the most important regulatory mechanisms in all living organisms. The thioredoxin system, composed of thioredoxin and thioredoxin reductase, has emerged as a key player in cellular redox-mediated reactions. For many years, only one thioredoxin system had been described in higher organisms, ubiquitously expressed in the cytoplasm of eukaryotic cells. However, during the last decade, we and others have identified and characterized novel thioredoxin systems with unique properties, such as organelle-specific localization in mitochondria or endoplasmic reticulum, tissue-specific distribution mostly in the testis, and features novel for thioredoxins, such as microtubule-binding properties. In this review, we will focus on the mammalian testis-specific thioredoxin system that comprises three thioredoxins exclusively expressed in spermatids (named Sptrx-1, Sptrx-2, and Sptrx-3) and an additional thioredoxin highly expressed in testis, but also present in lung and other ciliated tissues (Txl-2). The implications of these findings in the context of male fertility and testicular cancer, as well as evolutionary aspects, will be discussed.     

Nutraceuticals-Based Immunotherapeutic Concepts and Opportunities for the Mitigation of Cellular Senescence and Aging: A Narrative Review

The role of increased tissue senescent cell (SC) burden in driving the process of ageing and associated disorders is rapidly gaining attention. Amongst various plausible factors, impairment in immune functions is emerging as a critical regulator of known age-associated accumulation of SC. Immune cells dysfunctions with age are multi-faceted and are uniquely attributed to the independent processes of immunosenescence and cellular senescence which may collectively impair immune system mediated clearance of SC. Moreover, being functionally and phenotypically heterogenic, immune cells are also liable to be affected by senescence microenvironment in other tissues. Therefore, strategies aimed at improving immunosenescence and cellular senescence in immune cells can have pleiotropic effects on ageing physiology including the accumulation of SC. In this regard, nutraceutical’s immunomodulatory attributes are well documented which may have implications in developing nutrition-oriented immunotherapeutic approaches against SC. In particular, the three diverse sources of bioactive ingredients, viz., phytochemicals, probiotic bacteria and omega-3-fatty acids have shown promising anti-immunosenescence and anti-cellular senescence potential in immune cells influencing aging and immunity in ways beyond modest stimulation of immune responses. The present narrative review describes the preventive and therapeutic attributes of phytochemicals such as polyphenols, probiotic microbes and omega-3-fatty acids in influencing the emerging nexus of immunosenescence, cellular senescence and SC during aging. Outstanding questions and nutraceuticals-based pro-longevity and niche research areas have been deliberated. Further research using integrative approaches is recommended for developing nutrition-based holistic immunotherapeutic strategies for ‘healthy ageing’.     

Concise review: trends in stem cell proteomics

Gene expression analyses of stem cells (SCs) will help to uncover or further define signaling pathways and molecular mechanisms involved in the maintenance of self-renewal, pluripotency, and/or multipotency. In recent years, proteomic approaches have produced a wealth of data identifying proteins and mechanisms involved in SC proliferation and differentiation. Although many proteomics techniques have been developed and improved in peptide and protein separation, as well as mass spectrometry, several important issues, including sample heterogeneity, post-translational modifications, protein-protein interaction, and high-throughput quantification of hydrophobic and low-abundance proteins, still remain to be addressed and require further technical optimization. This review summarizes the methodologies used and the information gathered with proteome analyses of SCs, and it discusses biological and technical challenges for proteomic study of SCs. Disclosure of potential conflicts of interest is found at the end of this article.     

Sterols of Pneumocystis carinii hominis organisms isolated from human lungs.

The opportunistic pathogen Pneumocystis carinii causes pneumonia (P. carinii pneumonia, or PCP) in immunocompromised individuals such as AIDS patients. Rat-derived P. carinii carinii organisms have distinct sterols which are not synthesized by mammals and not found in other microbes infecting mammalian lungs. The dominant sterol present in the organism is cholesterol (which is believed to be scavenged from the host), but other sterols in P. carinii carinii have an alkyl group at C-24 of the sterol side chain (C(28) and C(29) 24-alkylsterols) and a double bond at C-7 of the nucleus. Recently, pneumocysterol (C(32)), which is essentially lanosterol with a C-24 ethylidene group, was detected in lipids extracted from a formalin-fixed human P. carinii-infected lung, and its structures were elucidated by gas-liquid chromatography, mass spectrometry, and nuclear magnetic resonance spectrometry in conjunction with analyses of chemically synthesized authentic standards. The sterol composition of isolated P. carinii hominis organisms has yet to be reported. If P. carinii from animal models is to be used for identifying potential drug targets and for developing chemotherapeutic approaches to clear human infections, it is important to determine whether the 24-alkylsterols of organisms found in rats are also present in organisms in humans. In the present study, sterol analyses of P. carinii hominis organisms isolated from cryopreserved human P. carinii-infected lungs and from bronchoalveolar lavage fluid were performed. Several of the same distinct sterols (e.g., fungisterol and methylcholest-7-ene-3beta-ol) previously identified in P. carinii carinii were also present in organisms isolated from human specimens. Pneumocysterol was detected in only some of the samples.     

Streptococcal M protein: molecular design and biological behavior.

M protein is a major virulence determinant for the group A streptococcus by virtue of its ability to allow the organism to resist phagocytosis. Common in eucaryotes, the fibrillar coiled-coil design for the M molecule may prove to be a common motif for surface proteins in gram-positive organisms. This type of structure offers the organism several distinct advantages, ranging from antigenic variation to multiple functional domains. The close resemblance of this molecular design to that of certain mammalian proteins could help explain on a molecular level the formation of epitopes responsible for serological cross-reactions between microbial and mammalian proteins. Many of the approaches described in the elucidation of the M-protein structure may be applied for characterizing similar molecules in other microbial systems.     

Review of the mutagenicity of ethylene oxide

Ethylene oxide has been shown to be an effective mutagen in a variety of organisms ranging from bacteria to mammalian cells. There is also an association between ethylene oxide exposure and human somatic cell cytogenetic damage. Furthermore, ethylene oxide has been shown to alkylate protein and DNA at exposure levels that have been encountered occupationally. Ethylene oxide is not only effective at producing somatic cell mutations but also at inducing genetic damage in germ cells. While it is clear that ethylene oxide is a germ cell mutagen in whole mammals, the mechanism(s) by which it produces genetic lesions in germ cells is uncertain.     

Counting cross-overs: characterizing meiotic recombination in mammals

Until recently, most of our understanding of meiotic recombination has come from studies of lower eukaryotes. However, over the past few years several components of the mammalian meiotic recombination pathway have been identified, and new molecular and cytological approaches to the analysis of mammalian meiosis have been developed. In this review, we discuss recent advances in three areas: the application of new techniques to study genome-wide levels of recombination in individual meioses; studies analyzing temporal aspects of the mammalian recombination pathway; and studies linking the genesis of human trisomies to alterations in meiotic exchange patterns.     

Production and characterization of recombinant IgA.

Existence of secretory immunity at the mucosal surfaces was first postulated in 1919. Since then experimental and clinical studies have indicated that it is immunoglobulin A (IgA) that provides the first line of immune defense at the mucosal surfaces. While a number of expression systems--including viral, plant and mammalian cells--have been used to produce recombinant IgA, we used the mammalian expression system to produce IgA1 and the three allotypes of IgA2. By introducing the gene coding for human secretory component (SC) into transfectants producing IgA1, we have generated a single mammalian cell system that produces covalently assembled secretory IgA (sIgA). Using pulse-chase analysis, we determined the covalent assembly pathways of IgA1, IgA2 and sIgA and identified some of the structural differences leading to the different assembly patterns. Using affinity purified proteins, we have shown that neither IgA1 nor any of the allotypes of IgA2 activate either the classical or the alternative complement pathways, but modulate the complement activity of IgG or IgM. The two N-linked glycosylation sites in IgA1 are not required for its binding to the polymeric Ig receptor (pIgR). Finally, we have shown that sIgA1 was more stable than dIgA1 in the gastrointestinal tract of mice, suggesting that SC provides resistance to IgA in the gastrointestinal tract.     

Fast forward to new genes in mammalian reproduction

The study of reproductive genetics in mammals has lagged behind that of simpler and more tractable model organisms, such as D. melanogaster , C. elegans and various yeast models. Although much valuable information has been generated using these organisms, they do not model the genetic and biological complexity of mammalian reproduction. Thus, the majority of genes required for gametogenesis in mammals remain unidentified. To expand on the existing knowledge of mammalian reproductive genetics, we have carried out forward genetic screens in mice to identify infertility mutants and the underlying mutant genes. Two different approaches were used: mutagenesis of the germline in whole mice, and mutagenesis of embryonic stem cells. This was followed by two- or three-generation breeding schemes to identify pedigrees segregating infertility mutations, which were then phenotypically characterized, genetically mapped, and in some cases, positionally cloned. This whole-genome approach has generated a wide collection of mutants with defects ranging from problems with germ cell development to abnormal sperm morphology. These models have allowed us to study the genetics, as well as the physiology, of reproduction in mammals. This review focuses on describing some of the genes identified in these screens and the ongoing effort to characterize additional mutants.     

NADPH-diaphorase distribution in the rabbit superior colliculus and co-localization with calcium-binding proteins

Nitric oxide (NO) and calcium‐binding proteins (CaBP) are important neuromodulators implicated in brain plasticity and brain disease. In addition, the mammalian superior colliculus (SC) has one of the highest concentrations of NO within the brain. The present study was designed to determine the distribution of nitric oxide‐synthesizing neurons in the SC of the rabbit by enzyme histochemistry for reduced nicotinamide adenine dinucleotide phosphate‐diaphorase (NADPH‐d), and its degree of co‐localization with CaBP, parvalbumin (PV) and calbindin (CB). NADPH‐d‐labelled fibres formed dense patches of terminal buttons within the intermediate grey layer and streams of fibres within the deepest layers of SC. Cells expressing NOS constitute a subpopulation of neurons in which practically all cell types are represented. Combined PV/NADPH‐d experiments showed a complete lack of co‐localization within individual neurons and fibres. On the contrary, double‐labelled neurons appeared in CB/NADPH‐d‐stained sections, only in the superficial layers, and mostly in the SGS and SO. These cells, which were intermingled with other neurons containing either NADPH‐d or CB, appear to be a subtype of narrow‐field and wide‐field vertical cells, and display an anterior–posterior gradient of density. Owing to the involvement of the superficial layers of the SC in the organization and integration of the visual information, it is suggested that these neurons may play a concrete role within the visual circuits. Our data indicate a clear selectivity in the expression of NADPH‐d, PV and CB in the SC, and that NO and CB probably serve as co‐modulators and/or co‐transmitters in the connectivity of the superficial layers of this midbrain structure.     

Construction of a biological tissue model based on a single-cell model: a computer simulation of metabolic heterogeneity in the liver lobule

An enormous body of information has been obtained by molecular and cellular biology in the last half century. However, even these powerful approaches are not adequate when it comes to higher-level biological structures, such as tissues, organs, and individual organisms, because of the complexities involved. Thus, accumulation of data at the higher levels supports and broadens the context for that obtained on the molecular and cellular levels. Under such auspices, an attempt to elucidate mesoscopic and macroscopic subjects based on plentiful nanoscopic and microscopic data is of great potential value. On the other hand, fully realistic simulation is impracticable because of the extensive cost entailed and enormous amount of data required. Abstraction and modeling that balance the dual requirements of prediction accuracy and manageable calculation cost are of great importance for systems biology. We have constructed an ammonia metabolism model of the hepatic lobule, a histological component of the liver, based on a single-hepatocyte model that consists of the biochemical kinetics of enzymes and transporters. To bring the calculation cost within reason, the porto-central axis, which is an elemental structure of the lobule, is defined as the systems biological unit of the liver, and is accordingly modeled. A model including both histological structure and position-specific gene expression of major enzymes largely represents the physiological dynamics of the hepatic lobule in nature. In addition, heterogeneous gene expression is suggested to have evolved to optimize the energy efficiency of ammonia detoxification at the macroscopic level, implying that approaches like this may elucidate how properties at the molecular and cellular levels, such as regulated gene expression, modify higher-level phenomena of multicellular tissue, organs, and organisms.     

Visual responses of the human superior colliculus: a high-resolution functional magnetic resonance imaging study

The superior colliculus (SC) is a multimodal laminar structure located on the roof of the brain stem. The SC is a key structure in a distributed network of areas that mediate saccadic eye movements and shifts of attention across the visual field and has been extensively studied in nonhuman primates. In humans, it has proven difficult to study the SC with functional MRI (fMRI) because of its small size, deep location, and proximity to pulsating vascular structures. Here, we performed a series of high-resolution fMRI studies at 3 T to investigate basic visual response properties of the SC. The retinotopic organization of the SC was determined using the traveling wave method with flickering checkerboard stimuli presented at different polar angles and eccentricities. SC activations were confined to stimulation of the contralateral hemifield. Although a detailed retinotopic map was not observed, across subjects, the upper and lower visual fields were represented medially and laterally, respectively. Responses were dominantly evoked by stimuli presented along the horizontal meridian of the visual field. We also measured the sensitivity of the SC to luminance contrast, which has not been previously reported in primates. SC responses were nearly saturated by low contrast stimuli and showed only small response modulation with higher contrast stimuli, indicating high sensitivity to stimulus contrast. Responsiveness to stimulus motion in the SC was shown by robust activations evoked by moving versus static dot stimuli that could not be attributed to eye movements. The responses to contrast and motion stimuli were compared with those in the human lateral geniculate nucleus. Our results provide first insights into basic visual responses of the human SC and show the feasibility of studying subcortical structures using high-resolution fMRI.