WorldWideScience

Sample records for ancestral mammalian regulatorysequences

  1. Detection of Weakly Conserved Ancestral Mammalian RegulatorySequences by Primate Comparisons

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Qian-fei; Prabhakar, Shyam; Chanan, Sumita; Cheng,Jan-Fang; Rubin, Edward M.; Boffelli, Dario

    2006-06-01

    Genomic comparisons between human and distant, non-primatemammals are commonly used to identify cis-regulatory elements based onconstrained sequence evolution. However, these methods fail to detectcryptic functional elements, which are too weakly conserved among mammalsto distinguish from nonfunctional DNA. To address this problem, weexplored the potential of deep intra-primate sequence comparisons. Wesequenced the orthologs of 558 kb of human genomic sequence, coveringmultiple loci involved in cholesterol homeostasis, in 6 nonhumanprimates. Our analysis identified 6 noncoding DNA elements displayingsignificant conservation among primates, but undetectable in more distantcomparisons. In vitro and in vivo tests revealed that at least three ofthese 6 elements have regulatory function. Notably, the mouse orthologsof these three functional human sequences had regulatory activity despitetheir lack of significant sequence conservation, indicating that they arecryptic ancestral cis-regulatory elements. These regulatory elementscould still be detected in a smaller set of three primate speciesincluding human, rhesus and marmoset. Since the human and rhesus genomesequences are already available, and the marmoset genome is activelybeing sequenced, the primate-specific conservation analysis describedhere can be applied in the near future on a whole-genome scale, tocomplement the annotation provided by more distant speciescomparisons.

  2. Phylogenetic analysis of a newfound bat-borne hantavirus supports a laurasiatherian host association for ancestral mammalian hantaviruses.

    Science.gov (United States)

    Witkowski, Peter T; Drexler, Jan F; Kallies, René; Ličková, Martina; Bokorová, Silvia; Mananga, Gael D; Szemes, Tomáš; Leroy, Eric M; Krüger, Detlev H; Drosten, Christian; Klempa, Boris

    2016-07-01

    Until recently, hantaviruses (family Bunyaviridae) were believed to originate from rodent reservoirs. However, genetically distinct hantaviruses were lately found in shrews and moles, as well as in bats from Africa and Asia. Bats (order Chiroptera) are considered important reservoir hosts for emerging human pathogens. Here, we report on the identification of a novel hantavirus, provisionally named Makokou virus (MAKV), in Noack's Roundleaf Bat (Hipposideros ruber) in Gabon, Central Africa. Phylogenetic analysis of the genomic l-segment showed that MAKV was the most closely related to other bat-borne hantaviruses and shared a most recent common ancestor with the Asian hantaviruses Xuan Son and Laibin. Breakdown of the virus load in a bat animal showed that MAKV resembles rodent-borne hantaviruses in its organ distribution in that it predominantly occurred in the spleen and kidney; this provides a first insight into the infection pattern of bat-borne hantaviruses. Ancestral state reconstruction based on a tree of l gene sequences of all relevant hantavirus lineages was combined with phylogenetic fossil host hypothesis testing, leading to a statistically significant rejection of the mammalian superorder Euarchontoglires (including rodents) but not the superorder Laurasiatheria (including shrews, moles, and bats) as potential hosts of ancestral hantaviruses at most basal tree nodes. Our data supports the emerging concept of bats as previously overlooked hantavirus reservoir hosts. PMID:27051047

  3. Estimating Ancestral Population Parameters

    OpenAIRE

    Wakeley, J.; Hey, J.

    1997-01-01

    The expected numbers of different categories of polymorphic sites are derived for two related models of population history: the isolation model, in which an ancestral population splits into two descendents, and the size-change model, in which a single population undergoes an instantaneous change in size. For the isolation model, the observed numbers of shared, fixed, and exclusive polymorphic sites are used to estimate the relative sizes of the three populations, ancestral plus two descendent...

  4. Ancestral Relationships Using Metafounders

    DEFF Research Database (Denmark)

    Legarra, Andres; Christensen, Ole Fredslund; Vitezica, Zulma G;

    2015-01-01

    Recent use of genomic (marker-based) relationships shows that relationships exist within and across base population (breeds or lines). However, current treatment of pedigree relationships is unable to consider relationships within or across base populations, although such relationships must exist...... due to finite size of the ancestral population and connections between populations. This complicates the conciliation of both approaches and, in particular, combining pedigree with genomic relationships. We present a coherent theoretical framework to consider base population in pedigree relationships....... We suggest a conceptual framework that considers each ancestral population as a finite-sized pool of gametes. This generates across-individual relationships and contrasts with the classical view where each population is considered as an infinite, unrelated pool. Several ancestral populations may be...

  5. Ancestral gene and "complementary" antibody dominate early ontogeny.

    Science.gov (United States)

    Arend, Peter

    2013-05-01

    According to N.K. Jerne the somatic generation of immune recognition occurs in conjunction with germ cell evolution and precedes the formation of the zygote, i.e. operates before clonal selection. We propose that it is based on interspecies inherent, ancestral forces maintaining the lineage. Murine oogenesis may be offered as a model. So in C57BL/10BL sera an anti-A reactive, mercapto-ethanol sensitive glycoprotein of up to now unknown cellular origin, but exhibiting immunoglobulin M character, presents itself "complementary" to a syngeneic epitope, which encoded by histocompatibility gene A or meanwhile accepted ancestor of the ABO gene family, arises predominantly in ovarian tissue and was detected statistically significant exclusively in polar glycolipids. Reports either on loss, pronounced expressions or de novo appearances of A-type structures in various conditions of accelerated growth like germ cell evolution, wound healing, inflammation and tumor proliferation in man and ABO related animals might show the dynamics of ancestral functions guarantying stem cell fidelity in maturation and tissue renewal processes. Procedures vice versa generating pluripotent stem cells for therapeutical reasons may indicate, that any artificially started growth should somehow pass through the germ line from the beginning, where according to growing knowledge exclusively the oocyte's genome provides a completely channeling ancestral information. In predatory animals such as the modern-day sea anemone, ancestral proteins, particularly those of the p53 gene family govern the reproduction processes, and are active up to the current mammalian female germ line. Lectins, providing the dual function of growth promotion and defense in higher plants, are suggested to represent the evolutionary precursors of the mammalian immunoglobulin M molecules, or protein moiety implying the greatest functional diversity in nature. And apart from any established mammalian genetic tree, a common vetch

  6. Ancestral reconstruction of tick lineages.

    Science.gov (United States)

    Mans, Ben J; de Castro, Minique H; Pienaar, Ronel; de Klerk, Daniel; Gaven, Philasande; Genu, Siyamcela; Latif, Abdalla A

    2016-06-01

    Ancestral reconstruction in its fullest sense aims to describe the complete evolutionary history of a lineage. This depends on accurate phylogenies and an understanding of the key characters of each parental lineage. An attempt is made to delineate our current knowledge with regard to the ancestral reconstruction of the tick (Ixodida) lineage. Tick characters may be assigned to Core of Life, Lineages of Life or Edges of Life phenomena depending on how far back these characters may be assigned in the evolutionary Tree of Life. These include housekeeping genes, sub-cellular systems, heme processing (Core of Life), development, moulting, appendages, nervous and organ systems, homeostasis, respiration (Lineages of Life), specific adaptations to a blood-feeding lifestyle, including the complexities of salivary gland secretions and tick-host interactions (Edges of Life). The phylogenetic relationships of lineages, their origins and importance in ancestral reconstruction are discussed. Uncertainties with respect to systematic relationships, ancestral reconstruction and the challenges faced in comparative transcriptomics (next-generation sequencing approaches) are highlighted. While almost 150 years of information regarding tick biology have been assembled, progress in recent years indicates that we are in the infancy of understanding tick evolution. Even so, broad reconstructions can be made with relation to biological features associated with various lineages. Conservation of characters shared with sister and parent lineages are evident, but appreciable differences are present in the tick lineage indicating modification with descent, as expected for Darwinian evolutionary theory. Many of these differences can be related to the hematophagous lifestyle of ticks. PMID:26868413

  7. Enhancer evolution across 20 mammalian species

    DEFF Research Database (Denmark)

    Villar, Diego; Berthelot, Camille; Aldridge, Sarah;

    2015-01-01

    The mammalian radiation has corresponded with rapid changes in noncoding regions of the genome, but we lack a comprehensive understanding of regulatory evolution in mammals. Here, we track the evolution of promoters and enhancers active in liver across 20 mammalian species from six diverse orders...... by profiling genomic enrichment of H3K27 acetylation and H3K4 trimethylation. We report that rapid evolution of enhancers is a universal feature of mammalian genomes. Most of the recently evolved enhancers arise from ancestral DNA exaptation, rather than lineage-specific expansions of repeat elements...... sequences. These results provide important insight into the functional genetics underpinning mammalian regulatory evolution....

  8. Evolution of the mammalian placenta revealed by phylogenetic analysis

    OpenAIRE

    Wildman, Derek E.; Chen, Caoyi; Erez, Offer; Grossman, Lawrence I.; Goodman, Morris; Romero, Roberto

    2006-01-01

    The placenta is essential for the success of therian mammalian reproduction. Intense selective pressure has shaped changes in placental anatomy and function during mammalian cladogenesis. Here we challenge the view that the hemochorial placenta is a derived feature in haplorhine primates. Using phylogenetic and statistical analyses of molecular and morphological data, we demonstrate that the ancestral eutherian mammalian placenta had the distinctive features of (i) hemochorial placental inter...

  9. Shrinkage Effect in Ancestral Maximum Likelihood

    CERN Document Server

    Mossel, Elchanan; Steel, Mike

    2008-01-01

    Ancestral maximum likelihood (AML) is a method that simultaneously reconstructs a phylogenetic tree and ancestral sequences from extant data (sequences at the leaves). The tree and ancestral sequences maximize the probability of observing the given data under a Markov model of sequence evolution, in which branch lengths are also optimized but constrained to take the same value on any edge across all sequence sites. AML differs from the more usual form of maximum likelihood (ML) in phylogenetics because ML averages over all possible ancestral sequences. ML has long been known to be statistically consistent -- that is, it converges on the correct tree with probability approaching 1 as the sequence length grows. However, the statistical consistency of AML has not been formally determined, despite informal remarks in a literature that dates back 20 years. In this short note we prove a general result that implies that AML is statistically inconsistent. In particular we show that AML can `shrink' short edges in a t...

  10. The Africa Madagascar connection and mammalian migrations

    Science.gov (United States)

    Rabinowitz, Philip D.; Woods, Stephen

    2006-03-01

    Madagascar separated from Africa in the Middle-Late Jurassic and has been in its present position relative to Africa since the Early Cretaceous (˜120-130 my). Several Early Eocene to Late Oligocene (˜50-26 my) terrestrial mammalian groups are observed on Madagascar that have a similar ancestral lineage to those found in Africa. These mammalian groups means of transport across the Mozambique Channel from Africa to Madagascar was either by traversing on exposed land masses across a land bridge or by swimming/rafting, since (1) Madagascar has been separated from mainland Africa for at least 70 my before their arrival, and (2) it is unlikely that similar ancestral lineage's evolved simultaneously in separated regions. No evidence has been found for a land bridge across the Mozambique Channel. The mammals thus either swam or have been swept away on vegetation mats from rivers flowing out of Mozambique or Tanzania.

  11. Algorithms of Ancestral Gene Length Reconstruction

    Directory of Open Access Journals (Sweden)

    Alexander Bolshoy

    2013-01-01

    Full Text Available Ancestral sequence reconstruction is a well-known problem in molecular evolution. The problem presented in this study is inspired by sequence reconstruction, but instead of leaf-associated sequences we consider only their lengths. We call this problem ancestral gene length reconstruction. It is a problem of finding an optimal labeling which minimizes the total length’s sum of the edges, where both a tree and nonnegative integers associated with corresponding leaves of the tree are the input. In this paper we give a linear algorithm to solve the problem on binary trees for the Manhattan cost function .

  12. Mammalian pheromones.

    Science.gov (United States)

    Liberles, Stephen D

    2014-01-01

    Mammalian pheromones control a myriad of innate social behaviors and acutely regulate hormone levels. Responses to pheromones are highly robust, reproducible, and stereotyped and likely involve developmentally predetermined neural circuits. Here, I review several facets of pheromone transduction in mammals, including (a) chemosensory receptors and signaling components of the main olfactory epithelium and vomeronasal organ involved in pheromone detection; (b) pheromone-activated neural circuits subject to sex-specific and state-dependent modulation; and (c) the striking chemical diversity of mammalian pheromones, which range from small, volatile molecules and sulfated steroids to large families of proteins. Finally, I review (d) molecular mechanisms underlying various behavioral and endocrine responses, including modulation of puberty and estrous; control of reproduction, aggression, suckling, and parental behaviors; individual recognition; and distinguishing of own species from predators, competitors, and prey. Deconstruction of pheromone transduction mechanisms provides a critical foundation for understanding how odor response pathways generate instinctive behaviors. PMID:23988175

  13. Reconstructing the ancestral germ line methylation state of young repeats.

    Science.gov (United States)

    Feuerbach, Lars; Lyngsø, Rune B; Lengauer, Thomas; Hein, Jotun

    2011-06-01

    One of the key objectives of comparative genomics is the characterization of the forces that shape genomes over the course of evolution. In the last decades, evidence has been accumulated that for vertebrate genomes also epigenetic modifications have to be considered in this context. Especially, the elevated mutation frequency of 5-methylcytosine (5mC) is assumed to facilitate the depletion of CpG dinucleotides in species that exhibit global DNA methylation. For instance, the underrepresentation of CpG dinucleotides in many mammalian genomes is attributed to this effect, which is only neutralized in so-called CpG islands (CGIs) that are preferentially unmethylated and thus partially protected from rapid CpG decay. For primate-specific CpG-rich transposable elements from the ALU family, it is unclear whether their elevated CpG frequency is caused by their small age or by the absence of DNA methylation. In consequence, these elements are often misclassified in CGI annotations. We present a method for the estimation of germ line methylation from pairwise ancestral-descendant alignments. The approach is validated in a simulation study and tested on DNA repeats from the AluSx family. We conclude that a predicted unmethylated state in the germ line is highly correlated with epigenetic activity of the respective genomic region. Thus, CpG-rich repeats can be facilitated as in silico probes for the epigenetic potential of their genomic neighborhood. PMID:21212152

  14. Hypothesis on the dual origin of the mammalian subplate

    Directory of Open Access Journals (Sweden)

    Juan F Montiel

    2011-04-01

    Full Text Available The development of the mammalian neocortex relies heavily on subplate. The proportion of this cell population varies considerably in different mammalian species. Subplate is almost undetectable in marsupials, forms a thin, but distinct layer in mouse and rat, a larger layer in carnivores and big-brained mammals as pig and a highly developed embryonic structure in human and non-human primates. The evolutionary origin of subplate neurons is the subject of current debate. Some hypothesize that subplate represents the ancestral cortex of sauropsids, while others consider it to be an increasingly complex phylogenetic novelty of the mammalian neocortex. Here we review recent work on expression of several genes that were originally identified in rodent as highly and differentially expressed in subplate. We relate these observations to cellular morphology, birthdating and hodology in the dorsal cortex/dorsal pallium of several amniote species. Based on this reviewed evidence we argue for a third hypothesis according to which subplate contains both ancestral and newly derived cell populations. We propose that the mammalian subplate originally derived from a phylogenetically ancient structure in the dorsal pallium of stem amniotes, but subsequently expanded with additional cell populations in the synapsid lineage to support an increasingly complex cortical plate development. Further understanding of the detailed molecular taxonomy, somatodendritic morphology and connectivity of subplate in a comparative context should contribute to the identification of the ancestral and newly evolved populations of subplate neurons.

  15. Ancestral state reconstruction of body size in the Caniformia (Carnivora, Mammalia): the effects of incorporating data from the fossil record.

    Science.gov (United States)

    Finarelli, John A; Flynn, John J

    2006-04-01

    A recent molecular phylogeny of the mammalian order Carnivora implied large body size as the ancestral condition for the caniform subclade Arctoidea using the distribution of species mean body sizes among living taxa. "Extant taxa-only" approaches such as these discount character state observations for fossil members of living clades and completely ignore data from extinct lineages. To more rigorously reconstruct body sizes of ancestral forms within the Caniformia, body size and first appearance data were collected for 149 extant and 367 extinct taxa. Body sizes were reconstructed for four ancestral nodes using weighted squared-change parsimony on log-transformed body mass data. Reconstructions based on extant taxa alone favored large body sizes (on the order of 10 to 50 kg) for the last common ancestors of both the Caniformia and Arctoidea. In contrast, reconstructions incorporating fossil data support small body sizes (fossil data was discarded, body size reconstructions became ambiguous, demonstrating that incorporating both character state and temporal information from fossil taxa unambiguously supports a small ancestral body size, thereby falsifying hypotheses derived from extant taxa alone. Body size reconstructions for Caniformia, Arctoidea, and Musteloidea were not sensitive to potential errors introduced by uncertainty in the position of extinct lineages relative to the molecular topology, or to missing body size data for extinct members of an entire major clade (the aquatic Pinnipedia). Incorporating character state observations and temporal information from the fossil record into hypothesis testing has a significant impact on the ability to reconstruct ancestral characters and constrains the range of potential hypotheses of character evolution. Fossil data here provide the evidence to reliably document trends of both increasing and decreasing body size in several caniform clades. More generally, including fossils in such analyses incorporates evidence of

  16. Genome-wide inference of ancestral recombination graphs.

    Science.gov (United States)

    Rasmussen, Matthew D; Hubisz, Melissa J; Gronau, Ilan; Siepel, Adam

    2014-01-01

    The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG), a complete record of coalescence and recombination events in the history of the sample. However, existing methods for ARG inference are computationally intensive, highly approximate, or limited to small numbers of sequences, and, as a consequence, explicit ARG inference is rarely used in applied population genomics. Here, we introduce a new algorithm for ARG inference that is efficient enough to apply to dozens of complete mammalian genomes. The key idea of our approach is to sample an ARG of [Formula: see text] chromosomes conditional on an ARG of [Formula: see text] chromosomes, an operation we call "threading." Using techniques based on hidden Markov models, we can perform this threading operation exactly, up to the assumptions of the sequentially Markov coalescent and a discretization of time. An extension allows for threading of subtrees instead of individual sequences. Repeated application of these threading operations results in highly efficient Markov chain Monte Carlo samplers for ARGs. We have implemented these methods in a computer program called ARGweaver. Experiments with simulated data indicate that ARGweaver converges rapidly to the posterior distribution over ARGs and is effective in recovering various features of the ARG for dozens of sequences generated under realistic parameters for human populations. In applications of ARGweaver to 54 human genome sequences from Complete Genomics, we find clear signatures of natural selection, including regions of unusually ancient ancestry associated with balancing selection and reductions in allele age in sites under directional selection. The patterns we observe near protein-coding genes are consistent with a primary influence from background selection rather than hitchhiking, although we cannot rule out a contribution from recurrent selective sweeps. PMID:24831947

  17. Genome-wide inference of ancestral recombination graphs.

    Directory of Open Access Journals (Sweden)

    Matthew D Rasmussen

    Full Text Available The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG, a complete record of coalescence and recombination events in the history of the sample. However, existing methods for ARG inference are computationally intensive, highly approximate, or limited to small numbers of sequences, and, as a consequence, explicit ARG inference is rarely used in applied population genomics. Here, we introduce a new algorithm for ARG inference that is efficient enough to apply to dozens of complete mammalian genomes. The key idea of our approach is to sample an ARG of [Formula: see text] chromosomes conditional on an ARG of [Formula: see text] chromosomes, an operation we call "threading." Using techniques based on hidden Markov models, we can perform this threading operation exactly, up to the assumptions of the sequentially Markov coalescent and a discretization of time. An extension allows for threading of subtrees instead of individual sequences. Repeated application of these threading operations results in highly efficient Markov chain Monte Carlo samplers for ARGs. We have implemented these methods in a computer program called ARGweaver. Experiments with simulated data indicate that ARGweaver converges rapidly to the posterior distribution over ARGs and is effective in recovering various features of the ARG for dozens of sequences generated under realistic parameters for human populations. In applications of ARGweaver to 54 human genome sequences from Complete Genomics, we find clear signatures of natural selection, including regions of unusually ancient ancestry associated with balancing selection and reductions in allele age in sites under directional selection. The patterns we observe near protein-coding genes are consistent with a primary influence from background selection rather than hitchhiking, although we cannot rule out a contribution from recurrent selective

  18. Mammalian hairs in Early Cretaceous amber

    Science.gov (United States)

    Vullo, Romain; Girard, Vincent; Azar, Dany; Néraudeau, Didier

    2010-07-01

    Two mammalian hairs have been found in association with an empty puparium in a ˜100-million-year-old amber (Early Cretaceous) from France. Although hair is known to be an ancestral, ubiquitous feature in the crown Mammalia, the structure of Mesozoic hair has never been described. In contrast to fur and hair of some Jurassic and Cretaceous mammals preserved as carbonized filaments, the exceptional preservation of the fossils described here allows for the study of the cuticular structure. Results show the oldest direct evidence of hair with a modern scale pattern. This discovery implies that the morphology of hair cuticula may have remained unchanged throughout most of mammalian evolution. The association of these hairs with a possible fly puparium provides paleoecological information and indicates peculiar taphonomic conditions.

  19. Reconstruction of ancestral protein sequences and its applications

    Directory of Open Access Journals (Sweden)

    Grishin Nick V

    2004-09-01

    Full Text Available Abstract Background Modern-day proteins were selected during long evolutionary history as descendants of ancient life forms. In silico reconstruction of such ancestral protein sequences facilitates our understanding of evolutionary processes, protein classification and biological function. Additionally, reconstructed ancestral protein sequences could serve to fill in sequence space thus aiding remote homology inference. Results We developed ANCESCON, a package for distance-based phylogenetic inference and reconstruction of ancestral protein sequences that takes into account the observed variation of evolutionary rates between positions that more precisely describes the evolution of protein families. To improve the accuracy of evolutionary distance estimation and ancestral sequence reconstruction, two approaches are proposed to estimate position-specific evolutionary rates. Comparisons show that at large evolutionary distances our method gives more accurate ancestral sequence reconstruction than PAML, PHYLIP and PAUP*. We apply the reconstructed ancestral sequences to homology inference and functional site prediction. We show that the usage of hypothetical ancestors together with the present day sequences improves profile-based sequence similarity searches; and that ancestral sequence reconstruction methods can be used to predict positions with functional specificity. Conclusions As a computational tool to reconstruct ancestral protein sequences from a given multiple sequence alignment, ANCESCON shows high accuracy in tests and helps detection of remote homologs and prediction of functional sites. ANCESCON is freely available for non-commercial use. Pre-compiled versions for several platforms can be downloaded from ftp://iole.swmed.edu/pub/ANCESCON/.

  20. Characterisation of monotreme caseins reveals lineage-specific expansion of an ancestral casein locus in mammals.

    Science.gov (United States)

    Lefèvre, Christophe M; Sharp, Julie A; Nicholas, Kevin R

    2009-01-01

    Using a milk-cell cDNA sequencing approach we characterised milk-protein sequences from two monotreme species, platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus) and found a full set of caseins and casein variants. The genomic organisation of the platypus casein locus is compared with other mammalian genomes, including the marsupial opossum and several eutherians. Physical linkage of casein genes has been seen in the casein loci of all mammalian genomes examined and we confirm that this is also observed in platypus. However, we show that a recent duplication of beta-casein occurred in the monotreme lineage, as opposed to more ancient duplications of alpha-casein in the eutherian lineage, while marsupials possess only single copies of alpha- and beta-caseins. Despite this variability, the close proximity of the main alpha- and beta-casein genes in an inverted tail-tail orientation and the relative orientation of the more distant kappa-casein genes are similar in all mammalian genome sequences so far available. Overall, the conservation of the genomic organisation of the caseins indicates the early, pre-monotreme development of the fundamental role of caseins during lactation. In contrast, the lineage-specific gene duplications that have occurred within the casein locus of monotremes and eutherians but not marsupials, which may have lost part of the ancestral casein locus, emphasises the independent selection on milk provision strategies to the young, most likely linked to different developmental strategies. The monotremes therefore provide insight into the ancestral drivers for lactation and how these have adapted in different lineages. PMID:19874726

  1. Reconstruction of ancestral protein sequences and its applications

    OpenAIRE

    Grishin Nick V; Pei Jimin; Cai Wei

    2004-01-01

    Abstract Background Modern-day proteins were selected during long evolutionary history as descendants of ancient life forms. In silico reconstruction of such ancestral protein sequences facilitates our understanding of evolutionary processes, protein classification and biological function. Additionally, reconstructed ancestral protein sequences could serve to fill in sequence space thus aiding remote homology inference. Results We developed ANCESCON, a package for distance-based phylogenetic ...

  2. Molecular paleontology: a biochemical model of the ancestral ribosome

    OpenAIRE

    Hsiao, Chiaolong; Lenz, Timothy K.; Peters, Jessica K; Fang, Po-Yu; Schneider, Dana M.; Anderson, Eric J.; Preeprem, Thanawadee; Bowman, Jessica C.; O'Neill, Eric B.; Lie, Lively; Athavale, Shreyas S.; Gossett, J. Jared; Trippe, Catherine; Murray, Jason; Anton S. Petrov

    2013-01-01

    Ancient components of the ribosome, inferred from a consensus of previous work, were constructed in silico, in vitro and in vivo. The resulting model of the ancestral ribosome presented here incorporates ∼20% of the extant 23S rRNA and fragments of five ribosomal proteins. We test hypotheses that ancestral rRNA can: (i) assume canonical 23S rRNA-like secondary structure, (ii) assume canonical tertiary structure and (iii) form native complexes with ribosomal protein fragments. Footprinting exp...

  3. Isolation of ancestral sylvatic dengue virus type 1, Malaysia.

    Science.gov (United States)

    Teoh, Boon-Teong; Sam, Sing-Sin; Abd-Jamil, Juraina; AbuBakar, Sazaly

    2010-11-01

    Ancestral sylvatic dengue virus type 1, which was isolated from a monkey in 1972, was isolated from a patient with dengue fever in Malaysia. The virus is neutralized by serum of patients with endemic DENV-1 infection. Rare isolation of this virus suggests a limited spillover infection from an otherwise restricted sylvatic cycle. PMID:21029545

  4. Isolation of Ancestral Sylvatic Dengue Virus Type 1, Malaysia

    OpenAIRE

    Teoh, Boon-Teong; Sam, Sing-Sin; Abd-Jamil, Juraina; AbuBakar, Sazaly

    2010-01-01

    Ancestral sylvatic dengue virus type 1, which was isolated from a monkey in 1972, was isolated from a patient with dengue fever in Malaysia. The virus is neutralized by serum of patients with endemic DENV-1 infection. Rare isolation of this virus suggests a limited spillover infection from an otherwise restricted sylvatic cycle.

  5. Are survival processing memory advantages based on ancestral priorities?

    Science.gov (United States)

    Soderstrom, Nicholas C; McCabe, David P

    2011-06-01

    Recent research has suggested that our memory systems are especially tuned to process information according to its survival relevance, and that inducing problems of "ancestral priorities" faced by our ancestors should lead to optimal recall performance (Nairne & Pandeirada, Cognitive Psychology, 2010). The present study investigated the specificity of this idea by comparing an ancestor-consistent scenario and a modern survival scenario that involved threats that were encountered by human ancestors (e.g., predators) or threats from fictitious creatures (i.e., zombies). Participants read one of four survival scenarios in which the environment and the explicit threat were either consistent or inconsistent with ancestrally based problems (i.e., grasslands-predators, grasslands-zombies, city-attackers, city-zombies), or they rated words for pleasantness. After rating words based on their survival relevance (or pleasantness), the participants performed a free recall task. All survival scenarios led to better recall than did pleasantness ratings, but recall was greater when zombies were the threat, as compared to predators or attackers. Recall did not differ for the modern (i.e., city) and ancestral (i.e., grasslands) scenarios. These recall differences persisted when valence and arousal ratings for the scenarios were statistically controlled as well. These data challenge the specificity of ancestral priorities in survival-processing advantages in memory. PMID:21327372

  6. Mammalian cell biology

    International Nuclear Information System (INIS)

    This section contains summaries of research on mechanisms of lethality and radioinduced changes in mammalian cell properties, new cell systems for the study of the biology of mutation and neoplastic transformation, and comparative properties of ionizing radiations

  7. Multiway admixture deconvolution using phased or unphased ancestral panels.

    Science.gov (United States)

    Churchhouse, Claire; Marchini, Jonathan

    2013-01-01

    We describe a novel method for inferring the local ancestry of admixed individuals from dense genome-wide single nucleotide polymorphism data. The method, called MULTIMIX, allows multiple source populations, models population linkage disequilibrium between markers and is applicable to datasets in which the sample and source populations are either phased or unphased. The model is based upon a hidden Markov model of switches in ancestry between consecutive windows of loci. We model the observed haplotypes within each window using a multivariate normal distribution with parameters estimated from the ancestral panels. We present three methods to fit the model-Markov chain Monte Carlo sampling, the Expectation Maximization algorithm, and a Classification Expectation Maximization algorithm. The performance of our method on individuals simulated to be admixed with European and West African ancestry shows it to be comparable to HAPMIX, the ancestry calls of the two methods agreeing at 99.26% of loci across the three parameter groups. In addition to it being faster than HAPMIX, it is also found to perform well over a range of extent of admixture in a simulation involving three ancestral populations. In an analysis of real data, we estimate the contribution of European, West African and Native American ancestry to each locus in the Mexican samples of HapMap, giving estimates of ancestral proportions that are consistent with those previously reported. PMID:23136122

  8. An orphaned mammalian β-globin gene of ancient evolutionary origin

    OpenAIRE

    Wheeler, David; Hope, Rory; Cooper, Steven J. B.; Dolman, Gaynor; Webb, Graham C.; Bottema, Cynthia D. K.; Gooley, Andrew A; Goodman, Morris; Holland, Robert A. B.

    2001-01-01

    Mammals possess multiple, closely linked β-globin genes that differ in the timing of their expression during development. These genes have been thought to be derived from a single ancestral gene, by duplication events that occurred after the separation of the mammals and birds. We report the isolation and characterization of an atypical β-like globin gene (ω-globin) in marsupials that appears to be more closely related to avian β-globin genes than to other mammalian ...

  9. Lung development of monotremes: evidence for the mammalian morphotype.

    Science.gov (United States)

    Ferner, Kirsten; Zeller, Ulrich; Renfree, Marilyn B

    2009-02-01

    The reproductive strategies and the extent of development of neonates differ markedly between the three extant mammalian groups: the Monotremata, Marsupialia, and Eutheria. Monotremes and marsupials produce highly altricial offspring whereas the neonates of eutherian mammals range from altricial to precocial. The ability of the newborn mammal to leave the environment in which it developed depends highly on the degree of maturation of the cardio-respiratory system at the time of birth. The lung structure is thus a reflection of the metabolic capacity of neonates. The lung development in monotremes (Ornithorhynchus anatinus, Tachyglossus aculeatus), in one marsupial (Monodelphis domestica), and one altricial eutherian (Suncus murinus) species was examined. The results and additional data from the literature were integrated into a morphotype reconstruction of the lung structure of the mammalian neonate. The lung parenchyma of monotremes and marsupials was at the early terminal air sac stage at birth, with large terminal air sacs. The lung developed slowly. In contrast, altricial eutherian neonates had more advanced lungs at the late terminal air sac stage and postnatally, lung maturation proceeded rapidly. The mammalian lung is highly conserved in many respects between monotreme, marsupial, and eutherian species and the structural differences in the neonatal lungs can be explained mainly by different developmental rates. The lung structure of newborn marsupials and monotremes thus resembles the ancestral condition of the mammalian lung at birth, whereas the eutherian newborns have a more mature lung structure. PMID:19051249

  10. Ancestral Origins and Genetic History of Tibetan Highlanders.

    Science.gov (United States)

    Lu, Dongsheng; Lou, Haiyi; Yuan, Kai; Wang, Xiaoji; Wang, Yuchen; Zhang, Chao; Lu, Yan; Yang, Xiong; Deng, Lian; Zhou, Ying; Feng, Qidi; Hu, Ya; Ding, Qiliang; Yang, Yajun; Li, Shilin; Jin, Li; Guan, Yaqun; Su, Bing; Kang, Longli; Xu, Shuhua

    2016-09-01

    The origin of Tibetans remains one of the most contentious puzzles in history, anthropology, and genetics. Analyses of deeply sequenced (30×-60×) genomes of 38 Tibetan highlanders and 39 Han Chinese lowlanders, together with available data on archaic and modern humans, allow us to comprehensively characterize the ancestral makeup of Tibetans and uncover their origins. Non-modern human sequences compose ∼6% of the Tibetan gene pool and form unique haplotypes in some genomic regions, where Denisovan-like, Neanderthal-like, ancient-Siberian-like, and unknown ancestries are entangled and elevated. The shared ancestry of Tibetan-enriched sequences dates back to ∼62,000-38,000 years ago, predating the Last Glacial Maximum (LGM) and representing early colonization of the plateau. Nonetheless, most of the Tibetan gene pool is of modern human origin and diverged from that of Han Chinese ∼15,000 to ∼9,000 years ago, which can be largely attributed to post-LGM arrivals. Analysis of ∼200 contemporary populations showed that Tibetans share ancestry with populations from East Asia (∼82%), Central Asia and Siberia (∼11%), South Asia (∼6%), and western Eurasia and Oceania (∼1%). Our results support that Tibetans arose from a mixture of multiple ancestral gene pools but that their origins are much more complicated and ancient than previously suspected. We provide compelling evidence of the co-existence of Paleolithic and Neolithic ancestries in the Tibetan gene pool, indicating a genetic continuity between pre-historical highland-foragers and present-day Tibetans. In particular, highly differentiated sequences harbored in highlanders' genomes were most likely inherited from pre-LGM settlers of multiple ancestral origins (SUNDer) and maintained in high frequency by natural selection. PMID:27569548

  11. Mammalian cardiolipin biosynthesis.

    Science.gov (United States)

    Mejia, Edgard M; Nguyen, Hieu; Hatch, Grant M

    2014-04-01

    Cardiolipin is a major phospholipid in mitochondria and is involved in the generation of cellular energy in the form of ATP. In mammalian and eukaryotic cells it is synthesized via the cytidine-5'-diphosphate-1,2-diacyl-sn-glycerol phosphate pathway. This brief review will describe some of the more recent studies on mammalian cardiolipin biosynthesis and provide an overview of regulation of cardiolipin biosynthesis. In addition, the important role that this key phospholipid plays in disease processes including heart failure, diabetes, thyroid hormone disease and the genetic disease Barth Syndrome will be discussed. PMID:24144810

  12. Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals

    Directory of Open Access Journals (Sweden)

    Danchin Etienne GJ

    2006-01-01

    Full Text Available Abstract Background Gene losses played a role which may have been as important as gene and genome duplications and rearrangements, in modelling today species' genomes from a common ancestral set of genes. The set and diversity of protein-coding genes in a species has direct output at the functional level. While gene losses have been reported in all the major lineages of the metazoan tree of life, none have proposed a focus on specific losses in the vertebrates and mammals lineages. In contrast, genes lost in protostomes (i.e. arthropods and nematodes but still present in vertebrates have been reported and extensively detailed. This probable over-anthropocentric way of comparing genomes does not consider as an important phenomena, gene losses in species that are usually described as "higher". However reporting universally conserved genes throughout evolution that have recently been lost in vertebrates and mammals could reveal interesting features about the evolution of our genome, particularly if these losses can be related to losses of capability. Results We report 11 gene families conserved throughout eukaryotes from yeasts (such as Saccharomyces cerevisiae to bilaterian animals (such as Drosophila melanogaster or Caenorhabditis elegans. This evolutionarily wide conservation suggests they were present in the last common ancestors of fungi and metazoan animals. None of these 11 gene families are found in human nor mouse genomes, and their absence generally extends to all vertebrates. A total of 8 out of these 11 gene families have orthologs in plants, suggesting they were present in the Last Eukaryotic Common Ancestor (LECA. We investigated known functional information for these 11 gene families. This allowed us to correlate some of the lost gene families to loss of capabilities. Conclusion Mammalian and vertebrate genomes lost evolutionary conserved ancestral genes that are probably otherwise not dispensable in eukaryotes. Hence, the human

  13. Fast phylogeny reconstruction through learning of ancestral sequences

    CERN Document Server

    Mihaescu, Radu; Rao, Satish

    2008-01-01

    Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial but reliable information about the tree (\\cite{Mo07, DMR08,DHJ06,GMS08}), and reaching "deeper" in the tree through reconstruction of ancestral sequences. In the latter category, \\cite{DMR06} settled an important conjecture of M.Steel, showing that, under the CFN model of evolution, all trees on $n$ leaves with edge lengths bounded by the Ising model phase transition can be recovered with high probability from genomes of length $O(\\log n)$ with a polynomial time algorithm. Their methods had a running time of $O(n^{10})$. Here we enhance our methods from \\cite{DHJ06} with the learning of ancestral sequences and provide an algorithm for reconstructing a sub-forest of the tree which is reliable given available data, without requiring a-priori known bounds on the edge lengths o...

  14. The ancestral process of long term seed bank models

    CERN Document Server

    Blath, Jochen; Kurt, Noemi; Spanò, Dario

    2012-01-01

    We present a new model for the evolution of genetic types in the presence of so-called seed banks, i.e., where individuals may obtain their genetic type from ancestors which have lived in the near as well as the very far past. The classical Wright-Fisher model, as well as a seed bank model with bounded age distribution considered by Kaj, Krone and Lascoux (2001) are special cases of our model. We discern three parameter regimes of the seed bank age distribution, which lead to substantially different behaviour in terms of genetic variability, in particular with respect to fixation of types and time to the most recent common ancestor. We prove that for age distributions with finite mean, the rescaled ancestral process converges to a time-changed Kingman coalescent, while in the case of infinite mean, ancestral lineages might not merge at all with positive probability. Further, we present a construction of the forward in time process in equilibrium. The mathematical methods are based on renewal theory, the urn p...

  15. Building the mammalian testis

    DEFF Research Database (Denmark)

    Svingen, Terje; Koopman, Peter

    2013-01-01

    Development of testes in the mammalian embryo requires the formation and assembly of several cell types that allow these organs to achieve their roles in male reproduction and endocrine regulation. Testis development is unusual in that several cell types such as Sertoli, Leydig, and spermatogonial...... the architecture of the testis unfolds and highlights the questions that remain to be explored, thus providing a roadmap for future studies that may help illuminate the causes of XY disorders of sex development, infertility, and testicular cancers....

  16. Mammalian gut immunity

    OpenAIRE

    Benoit Chassaing; Manish Kumar; Mark T Baker; Vishal Singh; Matam Vijay-Kumar

    2014-01-01

    The mammalian intestinal tract is the largest immune organ in the body and comprises cells from non-hemopoietic (epithelia, Paneth cells, goblet cells) and hemopoietic (macrophages, dendritic cells, T-cells) origin, and is also a dwelling for trillions of microbes collectively known as the microbiota. The homeostasis of this large microbial biomass is prerequisite to maintain host health by maximizing beneficial symbiotic relationships and minimizing the risks of living in such close proximit...

  17. Mitochondria and mammalian reproduction

    OpenAIRE

    Ramalho-Santos, J; Amaral, Sandra

    2013-01-01

    Mitochondria are cellular organelles with crucial roles in ATP synthesis, metabolic integration, reactive oxygen species (ROS) synthesis and management, the regulation of apoptosis (namely via the intrinsic pathway), among many others. Additionally, mitochondria in different organs or cell types may have distinct properties that can decisively influence functional analysis. In terms of the importance of mitochondria in mammalian reproduction, and although there are species-specifi...

  18. Global Alignment of Molecular Sequences via Ancestral State Reconstruction

    CERN Document Server

    Andoni, Alexandr; Hassidim, Avinatan; Roch, Sebastien

    2009-01-01

    Molecular phylogenetic techniques do not generally account for such common evolutionary events as site insertions and deletions (known as indels). Instead tree building algorithms and ancestral state inference procedures typically rely on substitution-only models of sequence evolution. In practice these methods are extended beyond this simplified setting with the use of heuristics that produce global alignments of the input sequences--an important problem which has no rigorous model-based solution. In this paper we consider a new version of the multiple sequence alignment in the context of stochastic indel models. More precisely, we introduce the following {\\em trace reconstruction problem on a tree} (TRPT): a binary sequence is broadcast through a tree channel where we allow substitutions, deletions, and insertions; we seek to reconstruct the original sequence from the sequences received at the leaves of the tree. We give a recursive procedure for this problem with strong reconstruction guarantees at low mut...

  19. Haplotype ancestral AH8.1 dans la mucoviscidose

    OpenAIRE

    Beucher, Julie

    2012-01-01

    La mucoviscidose est une maladie à transmission autosomique récessive, due à des mutations du gène CFTR. Les patients, partageant de mêmes mutations de CFTR et un même environnement, ont une expression phénotypique variable, suggérant l'influence d'autres gènes modifiant la sévérité de la maladie, appelés gènes modificateurs. L'atteinte respiratoire, caractérisée par une inflammation exacerbée, est un facteur principal de morbimortalité. L'haplotype ancestral AH8.1, impliqué dans la réponse i...

  20. Ancestral genome inference using a genetic algorithm approach.

    Science.gov (United States)

    Gao, Nan; Yang, Ning; Tang, Jijun

    2013-01-01

    Recent advancement of technologies has now made it routine to obtain and compare gene orders within genomes. Rearrangements of gene orders by operations such as reversal and transposition are rare events that enable researchers to reconstruct deep evolutionary histories. An important application of genome rearrangement analysis is to infer gene orders of ancestral genomes, which is valuable for identifying patterns of evolution and for modeling the evolutionary processes. Among various available methods, parsimony-based methods (including GRAPPA and MGR) are the most widely used. Since the core algorithms of these methods are solvers for the so called median problem, providing efficient and accurate median solver has attracted lots of attention in this field. The "double-cut-and-join" (DCJ) model uses the single DCJ operation to account for all genome rearrangement events. Because mathematically it is much simpler than handling events directly, parsimony methods using DCJ median solvers has better speed and accuracy. However, the DCJ median problem is NP-hard and although several exact algorithms are available, they all have great difficulties when given genomes are distant. In this paper, we present a new algorithm that combines genetic algorithm (GA) with genomic sorting to produce a new method which can solve the DCJ median problem in limited time and space, especially in large and distant datasets. Our experimental results show that this new GA-based method can find optimal or near optimal results for problems ranging from easy to very difficult. Compared to existing parsimony methods which may severely underestimate the true number of evolutionary events, the sorting-based approach can infer ancestral genomes which are much closer to their true ancestors. The code is available at http://phylo.cse.sc.edu. PMID:23658708

  1. Placental expression of pituitary hormones is an ancestral feature of therian mammals

    Directory of Open Access Journals (Sweden)

    Menzies Brandon R

    2011-08-01

    Full Text Available Abstract Background The placenta is essential for supplying nutrients and gases to the developing mammalian young before birth. While all mammals have a functional placenta, only in therian mammals (marsupials and eutherians does the placenta closely appose or invade the uterine endometrium. The eutherian placenta secretes hormones that are structurally and functionally similar to pituitary growth hormone (GH, prolactin (PRL and luteinizing hormone (LH. Marsupial and eutherian mammals diverged from a common ancestor approximately 125 to 148 million years ago and developed distinct reproductive strategies. As in eutherians, marsupials rely on a short-lived but functional placenta for embryogenesis. Results We characterized pituitary GH, GH-R, IGF-2, PRL and LHβ in a macropodid marsupial, the tammar wallaby, Macropus eugenii. These genes were expressed in the tammar placenta during the last third of gestation when most fetal growth occurs and active organogenesis is initiated. The mRNA of key growth genes GH, GH-R, IGF-2 and PRL were expressed during late pregnancy. We found significant up-regulation of GH, GH-R and IGF-2 after the start of the rapid growth phase of organogenesis which suggests that the placental growth hormones regulate the rapid phase of fetal growth. Conclusions This is the first demonstration of the existence of pituitary hormones in the marsupial placenta. Placental expression of these pituitary hormones has clearly been conserved in marsupials as in eutherian mammals, suggesting an ancestral origin of the evolution of placental expression and a critical function of these hormones in growth and development of all therian mammals.

  2. Phylogenetic analysis of a newfound bat-borne hantavirus supports a laurasiatherian host association for ancestral mammalian hantaviruses

    OpenAIRE

    Witkowski, P. T.; Drexler, J. F.; Kallies, R.; Lickova, M; Bokorova, S.; Mananga, G. D.; Szemes, T.; Leroy, Eric; Kruger, D H; Drosten, C.; Klempa, B.

    2016-01-01

    Until recently, hantaviruses (family Bunyaviridae) were believed to originate from rodent reservoirs. However, genetically distinct hantaviruses were lately found in shrews and moles, as well as in bats from Africa and Asia. Bats (order Chiroptera) are considered important reservoir hosts for emerging human pathogens. Here, we report on the identification of a novel hantavirus, provisionally named Makokou virus (MAKV), in Noack's Roundleaf Bat (Hipposideros ruber) in Gabon, Central Africa. Ph...

  3. Contrasting GC-content dynamics across 33 mammalian genomes: Relationship with life-history traits and chromosome sizes

    OpenAIRE

    Romiguier, J.; Ranwez, V.; Douzery, E. J. P.; Galtier, N

    2010-01-01

    The origin, evolution, and functional relevance of genomic variations in GC content are a long-debated topic, especially in mammals. Most of the existing literature, however, has focused on a small number of model species and/or limited sequence data sets. We analyzed more than 1000 orthologous genes in 33 fully sequenced mammalian genomes, reconstructed their ancestral isochore organization in the maximum likelihood framework, and explored the evolution of third-codon position GC content in ...

  4. A syntenic region conserved from fish to Mammalian x chromosome.

    Science.gov (United States)

    Guan, Guijun; Yi, Meisheng; Kobayashi, Tohru; Hong, Yunhan; Nagahama, Yoshitaka

    2014-01-01

    Sex chromosomes bearing the sex-determining gene initiate development along the male or female pathway, no matter which sex is determined by XY male or ZW female heterogamety. Sex chromosomes originate from ancient autosomes but evolved rapidly after the acquisition of sex-determining factors which are highly divergent between species. In the heterogametic male system (XY system), the X chromosome is relatively evolutionary silent and maintains most of its ancestral genes, in contrast to its Y counterpart that has evolved rapidly and degenerated. Sex in a teleost fish, the Nile tilapia (Oreochromis niloticus), is determined genetically via an XY system, in which an unpaired region is present in the largest chromosome pair. We defined the differences in DNA contents present in this chromosome with a two-color comparative genomic hybridization (CGH) and the random amplified polymorphic DNA (RAPD) approach in XY males. We further identified a syntenic segment within this region that is well conserved in several teleosts. Through comparative genome analysis, this syntenic segment was also shown to be present in mammalian X chromosomes, suggesting a common ancestral origin of vertebrate sex chromosomes. PMID:25506037

  5. A Syntenic Region Conserved from Fish to Mammalian X Chromosome

    Directory of Open Access Journals (Sweden)

    Guijun Guan

    2014-01-01

    Full Text Available Sex chromosomes bearing the sex-determining gene initiate development along the male or female pathway, no matter which sex is determined by XY male or ZW female heterogamety. Sex chromosomes originate from ancient autosomes but evolved rapidly after the acquisition of sex-determining factors which are highly divergent between species. In the heterogametic male system (XY system, the X chromosome is relatively evolutionary silent and maintains most of its ancestral genes, in contrast to its Y counterpart that has evolved rapidly and degenerated. Sex in a teleost fish, the Nile tilapia (Oreochromis niloticus, is determined genetically via an XY system, in which an unpaired region is present in the largest chromosome pair. We defined the differences in DNA contents present in this chromosome with a two-color comparative genomic hybridization (CGH and the random amplified polymorphic DNA (RAPD approach in XY males. We further identified a syntenic segment within this region that is well conserved in several teleosts. Through comparative genome analysis, this syntenic segment was also shown to be present in mammalian X chromosomes, suggesting a common ancestral origin of vertebrate sex chromosomes.

  6. Composition and evolution of the vertebrate and mammalian selenoproteomes.

    Directory of Open Access Journals (Sweden)

    Marco Mariotti

    Full Text Available BACKGROUND: Selenium is an essential trace element in mammals due to its presence in proteins in the form of selenocysteine (Sec. Human genome codes for 25 Sec-containing protein genes, and mouse and rat genomes for 24. METHODOLOGY/PRINCIPAL FINDINGS: We characterized the selenoproteomes of 44 sequenced vertebrates by applying gene prediction and phylogenetic reconstruction methods, supplemented with the analyses of gene structures, alternative splicing isoforms, untranslated regions, SECIS elements, and pseudogenes. In total, we detected 45 selenoprotein subfamilies. 28 of them were found in mammals, and 41 in bony fishes. We define the ancestral vertebrate (28 proteins and mammalian (25 proteins selenoproteomes, and describe how they evolved along lineages through gene duplication (20 events, gene loss (10 events and replacement of Sec with cysteine (12 events. We show that an intronless selenophosphate synthetase 2 gene evolved in early mammals and replaced functionally the original multiexon gene in placental mammals, whereas both genes remain in marsupials. Mammalian thioredoxin reductase 1 and thioredoxin-glutathione reductase evolved from an ancestral glutaredoxin-domain containing enzyme, still present in fish. Selenoprotein V and GPx6 evolved specifically in placental mammals from duplications of SelW and GPx3, respectively, and GPx6 lost Sec several times independently. Bony fishes were characterized by duplications of several selenoprotein families (GPx1, GPx3, GPx4, Dio3, MsrB1, SelJ, SelO, SelT, SelU1, and SelW2. Finally, we report identification of new isoforms for several selenoproteins and describe unusually conserved selenoprotein pseudogenes. CONCLUSIONS/SIGNIFICANCE: This analysis represents the first comprehensive survey of the vertebrate and mammal selenoproteomes, and depicts their evolution along lineages. It also provides a wealth of information on these selenoproteins and their forms.

  7. An ancestral HIV-2/simian immunodeficiency virus peptide with potent HIV-1 and HIV-2 fusion inhibitor activity

    OpenAIRE

    Borrego, Pedro; Calado, Rita; Marcelino, José M.; Pereira, Patrícia MR; Quintas, Alexandre; Barroso, Helena; Taveira, Nuno

    2013-01-01

    "Objectives: To produce new fusion inhibitor peptides for HIV-1 and HIV-2 based on ancestral envelope sequences. Methods: HIV-2/simian immunodeficiency virus (SIV) ancestral transmembrane protein sequences were reconstructed and ancestral peptides were derived from the helical region 2 (HR2). The activity of one ancestral peptide (named P3) was examined against a panel of HIV-1 and HIV-2 primary isolates in TZM-bl cells and peripheral blood mononuclear cells and compared to ...

  8. Mammalian phospholipase C.

    Science.gov (United States)

    Kadamur, Ganesh; Ross, Elliott M

    2013-01-01

    Phospholipase C (PLC) converts phosphatidylinositol 4,5-bisphosphate (PIP(2)) to inositol 1,4,5-trisphosphate (IP(3)) and diacylglycerol (DAG). DAG and IP(3) each control diverse cellular processes and are also substrates for synthesis of other important signaling molecules. PLC is thus central to many important interlocking regulatory networks. Mammals express six families of PLCs, each with both unique and overlapping controls over expression and subcellular distribution. Each PLC also responds acutely to its own spectrum of activators that includes heterotrimeric G protein subunits, protein tyrosine kinases, small G proteins, Ca(2+), and phospholipids. Mammalian PLCs are autoinhibited by a region in the catalytic TIM barrel domain that is the target of much of their acute regulation. In combination, the PLCs act as a signaling nexus that integrates numerous signaling inputs, critically governs PIP(2) levels, and regulates production of important second messengers to determine cell behavior over the millisecond to hour timescale. PMID:23140367

  9. Mammalian cell biology

    International Nuclear Information System (INIS)

    Studies of the action of N-ethylmaleimide (NEM), as an inhibitor of repair of x radioinduced injuries were extended from synchronous Chinese hamster cells to synchronous human HeLa cells. These studies showed a similar mode of action in both cell types lending support to the notion that conclusions may be extracted from such observations that are of fairly general applicability to mammalian cells. Radiation studies with NEM are being extended to hypoxic cells to inquire if NEM is effective relative to oxygen-independent damage. Observations relative to survival, DNA synthesis, and DNA strand elongation resulting from the addition products to DNA when cells were exposed to near uv in the presence of psoralen were extended. (U.S.)

  10. The mammalian blastocyst.

    Science.gov (United States)

    Frankenberg, Stephen R; de Barros, Flavia R O; Rossant, Janet; Renfree, Marilyn B

    2016-01-01

    The blastocyst is a mammalian invention that carries the embryo from cleavage to gastrulation. For such a simple structure, it exhibits remarkable diversity in its mode of formation, morphology, longevity, and intimacy with the uterine endometrium. This review explores this diversity in the light of the evolution of viviparity, comparing the three main groups of mammals: monotremes, marsupials, and eutherians. The principal drivers in blastocyst evolution were loss of yolk coupled with evolution of the placenta. An important outcome of blastocyst development is differentiation of two extraembryonic lineages (trophoblast and hypoblast) that contribute to the placenta. While in many species trophoblast segregation is often coupled with blastocyst formation, in marsupials and at least some Afrotherians, these events do not coincide. Thus, many questions regarding the conservation of molecular mechanisms controlling these events are of great interest but currently unresolved. For further resources related to this article, please visit the WIREs website. PMID:26799266

  11. Ancestral Genomes, Sex, and the Population Structure of Trypanosoma cruzi.

    Directory of Open Access Journals (Sweden)

    2006-03-01

    Full Text Available Acquisition of detailed knowledge of the structure and evolution of Trypanosoma cruzi populations is essential for control of Chagas disease. We profiled 75 strains of the parasite with five nuclear microsatellite loci, 24Salpha RNA genes, and sequence polymorphisms in the mitochondrial cytochrome oxidase subunit II gene. We also used sequences available in GenBank for the mitochondrial genes cytochrome B and NADH dehydrogenase subunit 1. A multidimensional scaling plot (MDS based in microsatellite data divided the parasites into four clusters corresponding to T. cruzi I (MDS-cluster A, T. cruzi II (MDS-cluster C, a third group of T. cruzi strains (MDS-cluster B, and hybrid strains (MDS-cluster BH. The first two clusters matched respectively mitochondrial clades A and C, while the other two belonged to mitochondrial clade B. The 24Salpha rDNA and microsatellite profiling data were combined into multilocus genotypes that were analyzed by the haplotype reconstruction program PHASE. We identified 141 haplotypes that were clearly distributed into three haplogroups (X, Y, and Z. All strains belonging to T. cruzi I (MDS-cluster A were Z/Z, the T. cruzi II strains (MDS-cluster C were Y/Y, and those belonging to MDS-cluster B (unclassified T. cruzi had X/X haplogroup genotypes. The strains grouped in the MDS-cluster BH were X/Y, confirming their hybrid character. Based on these results we propose the following minimal scenario for T. cruzi evolution. In a distant past there were at a minimum three ancestral lineages that we may call, respectively, T. cruzi I, T. cruzi II, and T. cruzi III. At least two hybridization events involving T. cruzi II and T. cruzi III produced evolutionarily viable progeny. In both events, the mitochondrial recipient (as identified by the mitochondrial clade of the hybrid strains was T. cruzi II and the mitochondrial donor was T. cruzi III.

  12. The Korarchaeota: Archaeal orphans representing an ancestral lineage of life

    Energy Technology Data Exchange (ETDEWEB)

    Elkins, James G.; Kunin, Victor; Anderson, Iain; Barry, Kerrie; Goltsman, Eugene; Lapidus, Alla; Hedlund, Brian; Hugenholtz, Phil; Kyrpides, Nikos; Graham, David; Keller, Martin; Wanner, Gerhard; Richardson, Paul; Stetter, Karl O.

    2007-05-01

    Based on conserved cellular properties, all life on Earth can be grouped into different phyla which belong to the primary domains Bacteria, Archaea, and Eukarya. However, tracing back their evolutionary relationships has been impeded by horizontal gene transfer and gene loss. Within the Archaea, the kingdoms Crenarchaeota and Euryarchaeota exhibit a profound divergence. In order to elucidate the evolution of these two major kingdoms, representatives of more deeply diverged lineages would be required. Based on their environmental small subunit ribosomal (ss RNA) sequences, the Korarchaeota had been originally suggested to have an ancestral relationship to all known Archaea although this assessment has been refuted. Here we describe the cultivation and initial characterization of the first member of the Korarchaeota, highly unusual, ultrathin filamentous cells about 0.16 {micro}m in diameter. A complete genome sequence obtained from enrichment cultures revealed an unprecedented combination of signature genes which were thought to be characteristic of either the Crenarchaeota, Euryarchaeota, or Eukarya. Cell division appears to be mediated through a FtsZ-dependent mechanism which is highly conserved throughout the Bacteria and Euryarchaeota. An rpb8 subunit of the DNA-dependent RNA polymerase was identified which is absent from other Archaea and has been described as a eukaryotic signature gene. In addition, the representative organism possesses a ribosome structure typical for members of the Crenarchaeota. Based on its gene complement, this lineage likely diverged near the separation of the two major kingdoms of Archaea. Further investigations of these unique organisms may shed additional light onto the evolution of extant life.

  13. β-Propeller blades as ancestral peptides in protein evolution.

    Directory of Open Access Journals (Sweden)

    Klaus O Kopec

    Full Text Available Proteins of the β-propeller fold are ubiquitous in nature and widely used as structural scaffolds for ligand binding and enzymatic activity. This fold comprises between four and twelve four-stranded β-meanders, the so called blades that are arranged circularly around a central funnel-shaped pore. Despite the large size range of β-propellers, their blades frequently show sequence similarity indicative of a common ancestry and it has been proposed that the majority of β-propellers arose divergently by amplification and diversification of an ancestral blade. Given the structural versatility of β-propellers and the hypothesis that the first folded proteins evolved from a simpler set of peptides, we investigated whether this blade may have given rise to other folds as well. Using sequence comparisons, we identified proteins of four other folds as potential homologs of β-propellers: the luminal domain of inositol-requiring enzyme 1 (IRE1-LD, type II β-prisms, β-pinwheels, and WW domains. Because, with increasing evolutionary distance and decreasing sequence length, the statistical significance of sequence comparisons becomes progressively harder to distinguish from the background of convergent similarities, we complemented our analyses with a new method that evaluates possible homology based on the correlation between sequence and structure similarity. Our results indicate a homologous relationship of IRE1-LD and type II β-prisms with β-propellers, and an analogous one for β-pinwheels and WW domains. Whereas IRE1-LD most likely originated by fold-changing mutations from a fully formed PQQ motif β-propeller, type II β-prisms originated by amplification and differentiation of a single blade, possibly also of the PQQ type. We conclude that both β-propellers and type II β-prisms arose by independent amplification of a blade-sized fragment, which represents a remnant of an ancient peptide world.

  14. β-Propeller Blades as Ancestral Peptides in Protein Evolution

    Science.gov (United States)

    Kopec, Klaus O.; Lupas, Andrei N.

    2013-01-01

    Proteins of the β-propeller fold are ubiquitous in nature and widely used as structural scaffolds for ligand binding and enzymatic activity. This fold comprises between four and twelve four-stranded β-meanders, the so called blades that are arranged circularly around a central funnel-shaped pore. Despite the large size range of β-propellers, their blades frequently show sequence similarity indicative of a common ancestry and it has been proposed that the majority of β-propellers arose divergently by amplification and diversification of an ancestral blade. Given the structural versatility of β-propellers and the hypothesis that the first folded proteins evolved from a simpler set of peptides, we investigated whether this blade may have given rise to other folds as well. Using sequence comparisons, we identified proteins of four other folds as potential homologs of β-propellers: the luminal domain of inositol-requiring enzyme 1 (IRE1-LD), type II β-prisms, β-pinwheels, and WW domains. Because, with increasing evolutionary distance and decreasing sequence length, the statistical significance of sequence comparisons becomes progressively harder to distinguish from the background of convergent similarities, we complemented our analyses with a new method that evaluates possible homology based on the correlation between sequence and structure similarity. Our results indicate a homologous relationship of IRE1-LD and type II β-prisms with β-propellers, and an analogous one for β-pinwheels and WW domains. Whereas IRE1-LD most likely originated by fold-changing mutations from a fully formed PQQ motif β-propeller, type II β-prisms originated by amplification and differentiation of a single blade, possibly also of the PQQ type. We conclude that both β-propellers and type II β-prisms arose by independent amplification of a blade-sized fragment, which represents a remnant of an ancient peptide world. PMID:24143202

  15. Analysis of the stone ancestral hall of Guo’s tomb on Xiaotang mountainin Han dynasty architectural features

    Institute of Scientific and Technical Information of China (English)

    刘国庆

    2014-01-01

    The stone ancestral hall of Guo’s tomb in Xiaotang mountain is the earliest existing buildings on the ground in China. It has a very high historical, cultural and artistic value, and it was described by the ancient and modern scholars and experts in their books and articles. But the study of architectural of ancestral hall was emphasized from 1930s, and became a brilliant star in the Chinese historic buildings. In this article, the architectural characteristics of the stone ancestral hall are discussed through fieldworks, in order to clarify the real architecture appearance of the ancestral hall and refer more informations for comprehensive study of Xiaotang stone ancestral hall.

  16. An ancestral role for the mitochondrial pyruvate carrier in glucose-stimulated insulin secretion

    Directory of Open Access Journals (Sweden)

    Kyle S. McCommis

    2016-08-01

    Conclusions: Altogether, these studies suggest that the MPC plays an important and ancestral role in insulin-secreting cells in mediating glucose sensing, regulating insulin secretion, and controlling systemic glycemia.

  17. Mapping ancestral genomes with massive gene loss: a matrix sandwich problem.

    OpenAIRE

    Gavranović, Haris; Chauve, Cedric; Salse, Jérôme; Tannier, Eric

    2011-01-01

    MOTIVATION: Ancestral genomes provide a better way to understand the structural evolution of genomes than the simple comparison of extant genomes. Most ancestral genome reconstruction methods rely on universal markers, that is, homologous families of DNA segments present in exactly one exemplar in every considered species. Complex histories of genes or other markers, undergoing duplications and losses, are rarely taken into account. It follows that some ancestors are inaccessible by these met...

  18. Mammalian cell biology

    International Nuclear Information System (INIS)

    Progress is reported on studies of the molecular biology and functional changes in cultured mammalian cells following exposure to x radiation, uv radiation, fission neutrons, or various chemical environmental pollutants alone or in combinations. Emphasis was placed on the separate and combined effects of polycyclic aromatic hydrocarbons released during combustion of fossil fuels and ionizing and nonionizing radiations. Sun lamps, which emit a continuous spectrum of near ultraviolet light of 290 nm to 315 nm were used for studies of predictive cell killing due to sunlight. Results showed that exposure to uv light (254 nm) may not be adequate to predict effects produced by sunlight. Data are included from studies on single-strand breaks and repair in DNA of cultured hamster cells exposed to uv or nearultraviolet light. The possible interactions of the polycyclic aromatic hydrocarbon 7,12-dimethylbenz(a)-anthracene (DmBA) alone or combined with exposure to x radiation, uv radiation (254 nm) or near ultraviolet simulating sunlight were compared for effects on cell survival

  19. Mammalian DNA Repair. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    None

    2003-01-24

    The Gordon Research Conference (GRC) on Mammalian DNA Repair was held at Harbortown Resort, Ventura Beach, CA. Emphasis was placed on current unpublished research and discussion of the future target areas in this field.

  20. Comparative mapping identifies the fusion point of an ancient mammalian X-autosomal rearrangement

    Energy Technology Data Exchange (ETDEWEB)

    Wilcox, S.A.; Watson, J.M.; Spencer, J.A. [La Trobe Univ., Victoria (Australia)] [and others

    1996-07-01

    Previous comparisons of gene location in the three major groups of mammals (eutherians, marsupials, and monotremes) have suggested that the long arm of the human X represents the ancestral mammalian X chromosome, whereas the short arm represents an autosomal region(s) recently added to the eutherian X chromosome. To identify the fusion point of this ancient X-autosome rearrangement, we have mapped four genes, three of which map near the centromere of the human Xp, in marsupials and in a monotreme. We found that ARAF1, and GATA1 are located on the X chromosome in marsupials, and ALA2 and GATA1 are also located on the X in the platypus. This implies that the proximal short arm of the human X chromosome, including the centromere, was part of the ancestral mammalian X chromosome. The fusion point between the conserved region and the recently added regions therefore maps to human Xp11.23, although gene order on the human X indicates that there has been some rearrangement of this region. 26 refs., 3 figs., 1 tab.

  1. Social capital and health: evidence that ancestral trust promotes health among children of immigrants.

    Science.gov (United States)

    Ljunge, Martin

    2014-12-01

    This paper presents evidence that generalized trust promotes health. Children of immigrants in a broad set of European countries with ancestry from across the world are studied. Individuals are examined within country of residence using variation in trust across countries of ancestry. The approach addresses reverse causality and concerns that the trust measure picks up institutional factors in the individual's contextual setting. There is a significant positive estimate of ancestral trust in explaining self-assessed health. The finding is robust to accounting for individual, parental, and extensive ancestral country characteristics. Individuals with higher ancestral trust are also less likely to be hampered by health problems in their daily life, providing evidence of trust influencing real life outcomes. Individuals with high trust feel and act healthier, enabling a more productive life. PMID:25464341

  2. Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties.

    Science.gov (United States)

    Hobbs, Joanne K; Prentice, Erica J; Groussin, Mathieu; Arcus, Vickery L

    2015-10-01

    Ancestral sequence reconstruction has been widely used to study historical enzyme evolution, both from biochemical and cellular perspectives. Two properties of reconstructed ancestral proteins/enzymes are commonly reported--high thermostability and high catalytic activity--compared with their contemporaries. Increased protein stability is associated with lower aggregation rates, higher soluble protein abundance and a greater capacity to evolve, and therefore, these proteins could be considered "superior" to their contemporary counterparts. In this study, we investigate the relationship between the favourable in vitro biochemical properties of reconstructed ancestral enzymes and the organismal fitness they confer in vivo. We have previously reconstructed several ancestors of the enzyme LeuB, which is essential for leucine biosynthesis. Our initial fitness experiments revealed that overexpression of ANC4, a reconstructed LeuB that exhibits high stability and activity, was only able to partially rescue the growth of a ΔleuB strain, and that a strain complemented with this enzyme was outcompeted by strains carrying one of its descendants. When we expanded our study to include five reconstructed LeuBs and one contemporary, we found that neither in vitro protein stability nor the catalytic rate was correlated with fitness. Instead, fitness showed a strong, negative correlation with estimated evolutionary age (based on phylogenetic relationships). Our findings suggest that, for reconstructed ancestral enzymes, superior in vitro properties do not translate into organismal fitness in vivo. The molecular basis of the relationship between fitness and the inferred age of ancestral LeuB enzymes is unknown, but may be related to the reconstruction process. We also hypothesise that the ancestral enzymes may be incompatible with the other, contemporary enzymes of the metabolic network. PMID:26349578

  3. The primary structure of fatty-acid-binding protein from nurse shark liver. Structural and evolutionary relationship to the mammalian fatty-acid-binding protein family.

    Science.gov (United States)

    Medzihradszky, K F; Gibson, B W; Kaur, S; Yu, Z H; Medzihradszky, D; Burlingame, A L; Bass, N M

    1992-02-01

    The primary structure of a fatty-acid-binding protein (FABP) isolated from the liver of the nurse shark (Ginglymostoma cirratum) was determined by high-performance tandem mass spectrometry (employing multichannel array detection) and Edman degradation. Shark liver FABP consists of 132 amino acids with an acetylated N-terminal valine. The chemical molecular mass of the intact protein determined by electrospray ionization mass spectrometry (Mr = 15124 +/- 2.5) was in good agreement with that calculated from the amino acid sequence (Mr = 15121.3). The amino acid sequence of shark liver FABP displays significantly greater similarity to the FABP expressed in mammalian heart, peripheral nerve myelin and adipose tissue (61-53% sequence similarity) than to the FABP expressed in mammalian liver (22% similarity). Phylogenetic trees derived from the comparison of the shark liver FABP amino acid sequence with the members of the mammalian fatty-acid/retinoid-binding protein gene family indicate the initial divergence of an ancestral gene into two major subfamilies: one comprising the genes for mammalian liver FABP and gastrotropin, the other comprising the genes for mammalian cellular retinol-binding proteins I and II, cellular retinoic-acid-binding protein myelin P2 protein, adipocyte FABP, heart FABP and shark liver FABP, the latter having diverged from the ancestral gene that ultimately gave rise to the present day mammalian heart-FABP, adipocyte FABP and myelin P2 protein sequences. The sequence for intestinal FABP from the rat could be assigned to either subfamily, depending on the approach used for phylogenetic tree construction, but clearly diverged at a relatively early evolutionary time point. Indeed, sequences proximately ancestral or closely related to mammalian intestinal FABP, liver FABP, gastrotropin and the retinoid-binding group of proteins appear to have arisen prior to the divergence of shark liver FABP and should therefore also be present in elasmobranchs

  4. Evolutionary dynamics of mammalian karyotypes

    Directory of Open Access Journals (Sweden)

    Carlo Alberto Redi

    2012-12-01

    Full Text Available This special volume of Cytogenetic and Genome Research (edited by Roscoe Stanyon, University of Florence and Alexander Graphodatsky, Siberian division of the Russian Academy of Sciences is dedicated to the fascinating long search of the forces behind the evolutionary dynamics of mammalian karyotypes, revealed after the hypotonic miracle of the 1950s....

  5. DNA repair in mammalian embryos.

    Science.gov (United States)

    Jaroudi, Souraya; SenGupta, Sioban

    2007-01-01

    Mammalian cells have developed complex mechanisms to identify DNA damage and activate the required response to maintain genome integrity. Those mechanisms include DNA damage detection, DNA repair, cell cycle arrest and apoptosis which operate together to protect the conceptus from DNA damage originating either in parental gametes or in the embryo's somatic cells. DNA repair in the newly fertilized preimplantation embryo is believed to rely entirely on the oocyte's machinery (mRNAs and proteins deposited and stored prior to ovulation). DNA repair genes have been shown to be expressed in the early stages of mammalian development. The survival of the embryo necessitates that the oocyte be sufficiently equipped with maternal stored products and that embryonic gene expression commences at the correct time. A Medline based literature search was performed using the keywords 'DNA repair' and 'embryo development' or 'gametogenesis' (publication dates between 1995 and 2006). Mammalian studies which investigated gene expression were selected. Further articles were acquired from the citations in the articles obtained from the preliminary Medline search. This paper reviews mammalian DNA repair from gametogenesis to preimplantation embryos to late gestational stages. PMID:17141556

  6. Anaho Island: Mammalian species richness report

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This study assessed the mammalian species richness on Anaho Island using live trapping between July 18th and July 23rd 2005. The last mammalian species richness...

  7. A skull might lie: modelling ancestral ranges and diet from genes and shape of tree squirrels

    Czech Academy of Sciences Publication Activity Database

    Pečnerová, Patrícia; Moravec, Jiří C.; Martínková, Natália

    2015-01-01

    Roč. 64, č. 6 (2015), s. 1074-1088. ISSN 1063-5157 EU Projects: European Commission(XE) CZ.1.07/2.4.00/17.0138 Institutional support: RVO:68081766 Keywords : Sciurini * multilocus phylogeny * geometric morphometry * speciation * ancestral range reconstruction * diet modelling Subject RIV: EG - Zoology Impact factor: 14.387, year: 2014

  8. Investigating the potential of ancestral state reconstruction algorithms in historical linguistics

    OpenAIRE

    Jäger, Gerhard; List, Johann-Mattis

    2016-01-01

    Current efforts in computational historical linguistics are predominantly concerned with phylogenetic inference. However, methods for ancestral state reconstruction have been only sporadically applied. This is surprising since reconstruction is considered essential both in evolutionary biology and in classical historical linguistics. In contradistinction to phylogenetic algorithms, automatic reconstruction methods presuppose phylogenetic information in order to explain what has evolved whe...

  9. Inheritance of the 8.1 ancestral haplotype in recurrent pregnancy loss

    OpenAIRE

    Kolte, Astrid M.; Nielsen, Henriette S.; Steffensen, Rudi; Crespi, Bernard; Christiansen, Ole B

    2015-01-01

    A segment of DNA called the 8.1 ancestral haplotype is hypothesized to cause fetal loss due to a ‘selfish gene’ effect. The hypothesis was not supported, although the haplotype tended to be inherited more often than expected among girls (p=0.11) in a study of 110 mother-child pairs. Further studies are warranted.

  10. Mechanisms and evolutionary patterns of mammalian and avian dosage compensation.

    Directory of Open Access Journals (Sweden)

    Philippe Julien

    Full Text Available As a result of sex chromosome differentiation from ancestral autosomes, male mammalian cells only contain one X chromosome. It has long been hypothesized that X-linked gene expression levels have become doubled in males to restore the original transcriptional output, and that the resulting X overexpression in females then drove the evolution of X inactivation (XCI. However, this model has never been directly tested and patterns and mechanisms of dosage compensation across different mammals and birds generally remain little understood. Here we trace the evolution of dosage compensation using extensive transcriptome data from males and females representing all major mammalian lineages and birds. Our analyses suggest that the X has become globally upregulated in marsupials, whereas we do not detect a global upregulation of this chromosome in placental mammals. However, we find that a subset of autosomal genes interacting with X-linked genes have become downregulated in placentals upon the emergence of sex chromosomes. Thus, different driving forces may underlie the evolution of XCI and the highly efficient equilibration of X expression levels between the sexes observed for both of these lineages. In the egg-laying monotremes and birds, which have partially homologous sex chromosome systems, partial upregulation of the X (Z in birds evolved but is largely restricted to the heterogametic sex, which provides an explanation for the partially sex-biased X (Z expression and lack of global inactivation mechanisms in these lineages. Our findings suggest that dosage reductions imposed by sex chromosome differentiation events in amniotes were resolved in strikingly different ways.

  11. Frequency of carriers of 8.1 ancestral haplotype and its fragments in two Caucasian populations.

    Science.gov (United States)

    Kiszel, Petra; Kovács, Margit; Szalai, Csaba; Yang, Yan; Pozsonyi, Eva; Blaskó, Bernadett; Laki, Judit; Prohászka, Zoltán; Fazakas, Adám; Pánczél, Pál; Hosszúfalusi, Nóra; Rajczy, Katalin; Wu, Yee-Ling; Chung, Erwin K; Zhou, Bi; Blanchong, Carol A; Vatay, Agnes; Yu, C Yung; Füst, G

    2007-01-01

    Within the human MHC region larger stretches of conserved DNA, called conserved ancestral haplotypes exist. However, many MHC haplotypes contain only fragments of an ancestral haplotype. Little is known, however, on relative distribution of the ancestral haplotypes to their fragments. Therefore we determined the frequency of carriers of the whole ancestral haplotype 8.1 (AH8.1) and its fragments in 127 healthy Hungarian people, 101 healthy Ohioian females, and in nine Hungarian families. The HLA-DQ2, HLA-DR3(17), RAGE -429C allele, the mono-S-C4B genotype, the HSP70-2 1267G allele and the TNF -308A (TNF2) allele were used as markers of the AH8.1. Frequency of carriers of the whole AH8.1 and its fragments was similar in the both populations. 18% of the subjects carried the whole AH8.1 in at least one chromosome, while 17-20%, 36-39%, and 24-29%, respectively carried two or three constituents of the haplotype, only one constituent or none of them. Similar results were obtained in the family study. In addition, marked differences were found in the relationship of the constituents' alleles to the whole AH8.1. In both populations, 29%, 50-59%, 52-56% and 76-96%, respectively of the carriers of HSP70-2 1267G, RAGE-429C, TNF2, and mono-S carriers carried the whole 8.1 haplotype. These findings may have important implications for studies of the disease associations with different MHC ancestral haplotypes. PMID:17558713

  12. Mammalian sex hormones in plants

    OpenAIRE

    Andrzej Skoczowski; Anna Janeczko

    2011-01-01

    The occurrence of mammalian sex hormones and their physiological role in plants is reviewed. These hormones, such as 17β-estradiol, androsterone, testosterone or progesterone, were present in 60-80% of the plant species investigated. Enzymes responsible for their biosynthesis and conversion were also found in plants. Treatment of the plants with sex hormones or their precursors influenced plant development: cell divisions, root and shoot growth, embryo growth, flowering, pollen tube ...

  13. Molecular aspects of mammalian fertilization

    Institute of Scientific and Technical Information of China (English)

    Hector Serrano; Dolores Garcia-Suarez

    2001-01-01

    Mammalian fertilization is a highly regulated process, much of which are not clearly understood. Here we present some information in order to elaborate a working hypothesis for this process, beginning with the sperm modifications in the epidydimis up to sperm and egg plasmalemma interaction and fusion. We also discuss the still poorly understood capacitation process, the phenomenon of sperm chemo-attraction that brings the capacitated sperm to interact with the oocyte vestments and certain aspects of the acrosome reaction.

  14. Patterning of the mammalian cochlea

    OpenAIRE

    Cantos, Raquel; Cole, Laura K.; Acampora, Dario; Simeone, Antonio; Wu, Doris K.

    2000-01-01

    The mammalian cochlea is sophisticated in its function and highly organized in its structure. Although the anatomy of this sense organ has been well documented, the molecular mechanisms underlying its development have remained elusive. Information generated from mutant and knockout mice in recent years has increased our understanding of cochlear development and physiology. This article discusses factors important for the development of the inner ear and summarizes coch...

  15. Olfactory sensitivity in mammalian species.

    Science.gov (United States)

    Wackermannová, M; Pinc, L; Jebavý, L

    2016-07-18

    Olfaction enables most mammalian species to detect and discriminate vast numbers of chemical structures called odorants and pheromones. The perception of such chemical compounds is mediated via two major olfactory systems, the main olfactory system and the vomeronasal system, as well as minor systems, such as the septal organ and the Grueneberg ganglion. Distinct differences exist not only among species but also among individuals in terms of their olfactory sensitivity; however, little is known about the mechanisms that determine these differences. In research on the olfactory sensitivity of mammals, scientists thus depend in most cases on behavioral testing. In this article, we reviewed scientific studies performed on various mammalian species using different methodologies and target chemical substances. Human and non-human primates as well as rodents and dogs are the most frequently studied species. Olfactory threshold studies on other species do not exist with the exception of domestic pigs. Olfactory testing performed on seals, elephants, and bats focused more on discriminative abilities than on sensitivity. An overview of olfactory sensitivity studies as well as olfactory detection ability in most studied mammalian species is presented here, focusing on comparable olfactory detection thresholds. The basics of olfactory perception and olfactory sensitivity factors are also described. PMID:27070753

  16. Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi

    Science.gov (United States)

    Medina, Edgar M; Turner, Jonathan J; Gordân, Raluca; Skotheim, Jan M; Buchler, Nicolas E

    2016-01-01

    Although cell cycle control is an ancient, conserved, and essential process, some core animal and fungal cell cycle regulators share no more sequence identity than non-homologous proteins. Here, we show that evolution along the fungal lineage was punctuated by the early acquisition and entrainment of the SBF transcription factor through horizontal gene transfer. Cell cycle evolution in the fungal ancestor then proceeded through a hybrid network containing both SBF and its ancestral animal counterpart E2F, which is still maintained in many basal fungi. We hypothesize that a virally-derived SBF may have initially hijacked cell cycle control by activating transcription via the cis-regulatory elements targeted by the ancestral cell cycle regulator E2F, much like extant viral oncogenes. Consistent with this hypothesis, we show that SBF can regulate promoters with E2F binding sites in budding yeast. DOI: http://dx.doi.org/10.7554/eLife.09492.001 PMID:27162172

  17. Diaspora of diaspora: Adyge-Abkhaz returnees in the ancestral homeland

    OpenAIRE

    Erciyes, Cemre

    2008-01-01

    Focusing on the diasporic characteristics shown by ancestral return migrants, this case study looks at the Abkhaz-Adyge (Circassian) returnees from Turkey to the Caucasus and how they become the “diaspora of the diaspora.” The next generations of diasporans continue to dream of return, and, with recent developments in communication technologies and cheaper transportation, many find ways to realize this dream. There are many different forms of return, but some “return-migrate” and settle in an...

  18. COMPONENTES NUTRICIONALES Y ANTIOXIDANTES DE DOS ESPECIES DE GUAJE (Leucaena spp.): UN RECURSO ANCESTRAL SUBUTILIZADO

    OpenAIRE

    Nallely Román-Cortés; María del Rosario García-Mateos; Ana María Castillo-González; Jaime Sahagún-Castellanos; Adelina Jiménez-Arellanes

    2014-01-01

    El guaje ( Leucaena spp.) es una planta de vaina y semillas comestibles, un recurso ancestral subutilizado por los pueblos mesoamericanos. El valor nutricional y nutracéutico del guaje se desconoce pese a su consumo vigente en las poblaciones rurales. El objetivo de este trabajo fue evaluar el contenido de minerales, compo - nentes nutricionales y antioxidantes para contribuir a la revalorización alimentaria del guaje rojo ( L. esculenta Benth.) y verde ( L. leucocephala Lam.). Los contenidos...

  19. Ancestral informative marker selection and population structure visualization using sparse Laplacian eigenfunctions.

    Directory of Open Access Journals (Sweden)

    Jun Zhang

    Full Text Available Identification of a small panel of population structure informative markers can reduce genotyping cost and is useful in various applications, such as ancestry inference in association mapping, forensics and evolutionary theory in population genetics. Traditional methods to ascertain ancestral informative markers usually require the prior knowledge of individual ancestry and have difficulty for admixed populations. Recently Principal Components Analysis (PCA has been employed with success to select SNPs which are highly correlated with top significant principal components (PCs without use of individual ancestral information. The approach is also applicable to admixed populations. Here we propose a novel approach based on our recent result on summarizing population structure by graph laplacian eigenfunctions, which differs from PCA in that it is geometric and robust to outliers. Our approach also takes advantage of the priori sparseness of informative markers in the genome. Through simulation of a ring population and the real global population sample HGDP of 650K SNPs genotyped in 940 unrelated individuals, we validate the proposed algorithm at selecting most informative markers, a small fraction of which can recover the similar underlying population structure efficiently. Employing a standard Support Vector Machine (SVM to predict individuals' continental memberships on HGDP dataset of seven continents, we demonstrate that the selected SNPs by our method are more informative but less redundant than those selected by PCA. Our algorithm is a promising tool in genome-wide association studies and population genetics, facilitating the selection of structure informative markers, efficient detection of population substructure and ancestral inference.

  20. Distinct actions of ancestral vinclozolin and juvenile stress on neural gene expression in the male rat

    Directory of Open Access Journals (Sweden)

    Ross eGillette

    2015-03-01

    Full Text Available Exposure to the endocrine disrupting chemical vinclozolin during gestation of an F0 generation and/or chronic restraint stress during adolescence of the F3 descendants affects behavior, physiology, and gene expression in the brain. Genes related to the networks of growth factors, signaling peptides and receptors, steroid hormone receptors and enzymes, and epigenetic related factors were measured using quantitative polymerase chain reaction via Taqman low density arrays targeting 48 genes in the central amygdaloid nucleus, medial amygdaloid nucleus, medial preoptic area, lateral hypothalamus, and the ventromedial nucleus of the hypothalamus. We found that growth factors are particularly vulnerable to ancestral exposure in the central and medial amygdala; restraint stress during adolescence affected neural growth factors in the medial amygdala. Signaling peptides were affected by both ancestral exposure and stress during adolescence primarily in hypothalamic nuclei. Steroid hormone receptors and enzymes were strongly affected by restraint stress in the medial preoptic area. Epigenetic related genes were affected by stress in the ventromedial hypothalamus and by both ancestral exposure and stress during adolescence independently in the central amygdala. It is noteworthy that the lateral hypothalamus showed no effects of either manipulation. Gene expression is discussed in the context of behavioral and physiological measures previously published.

  1. AAV ancestral reconstruction library enables selection of broadly infectious viral variants.

    Science.gov (United States)

    Santiago-Ortiz, J; Ojala, D S; Westesson, O; Weinstein, J R; Wong, S Y; Steinsapir, A; Kumar, S; Holmes, I; Schaffer, D V

    2015-12-01

    Adeno-associated virus (AAV) vectors have achieved clinical efficacy in treating several diseases. However, enhanced vectors are required to extend these landmark successes to other indications and protein engineering approaches may provide the necessary vector improvements to address such unmet medical needs. To generate new capsid variants with potentially enhanced infectious properties and to gain insights into AAV's evolutionary history, we computationally designed and experimentally constructed a putative ancestral AAV library. Combinatorial variations at 32 amino acid sites were introduced to account for uncertainty in their identities. We then analyzed the evolutionary flexibility of these residues, the majority of which have not been previously studied, by subjecting the library to iterative selection on a representative cell line panel. The resulting variants exhibited transduction efficiencies comparable to the most efficient extant serotypes and, in general, ancestral libraries were broadly infectious across the cell line panel, indicating that they favored promiscuity over specificity. Interestingly, putative ancestral AAVs were more thermostable than modern serotypes and did not use sialic acids, galactose or heparan sulfate proteoglycans for cellular entry. Finally, variants mediated 19- to 31-fold higher gene expression in the muscle compared with AAV1, a clinically used serotype for muscle delivery, highlighting their promise for gene therapy. PMID:26186661

  2. Evolutionary paths to mammalian cochleae.

    Science.gov (United States)

    Manley, Geoffrey A

    2012-12-01

    Evolution of the cochlea and high-frequency hearing (>20 kHz; ultrasonic to humans) in mammals has been a subject of research for many years. Recent advances in paleontological techniques, especially the use of micro-CT scans, now provide important new insights that are here reviewed. True mammals arose more than 200 million years (Ma) ago. Of these, three lineages survived into recent geological times. These animals uniquely developed three middle ear ossicles, but these ossicles were not initially freely suspended as in modern mammals. The earliest mammalian cochleae were only about 2 mm long and contained a lagena macula. In the multituberculate and monotreme mammalian lineages, the cochlea remained relatively short and did not coil, even in modern representatives. In the lineage leading to modern therians (placental and marsupial mammals), cochlear coiling did develop, but only after a period of at least 60 Ma. Even Late Jurassic mammals show only a 270 ° cochlear coil and a cochlear canal length of merely 3 mm. Comparisons of modern organisms, mammalian ancestors, and the state of the middle ear strongly suggest that high-frequency hearing (>20 kHz) was not realized until the early Cretaceous (~125 Ma). At that time, therian mammals arose and possessed a fully coiled cochlea. The evolution of modern features of the middle ear and cochlea in the many later lineages of therians was, however, a mosaic and different features arose at different times. In parallel with cochlear structural evolution, prestins in therian mammals evolved into effective components of a new motor system. Ultrasonic hearing developed quite late-the earliest bat cochleae (~60 Ma) did not show features characteristic of those of modern bats that are sensitive to high ultrasonic frequencies. PMID:22983571

  3. The shape of mammalian phylogeny

    DEFF Research Database (Denmark)

    Purvis, Andy; Fritz, Susanne A; Rodríguez, Jesús;

    2011-01-01

    six simple macroevolutionary models, showing that those where speciation slows down as geographical or niche space is filled, produce more realistic phylogenies than do models involving key innovations. Lastly, an analysis of the spatial scaling of imbalance shows that the phylogeny of species within...... an assemblage, ecoregion or larger area always tends to be more unbalanced than expected from the phylogeny of species at the next more inclusive spatial scale. We conclude with a verbal model of mammalian macroevolution, which emphasizes the importance to diversification of accessing new regions...... of geographical or niche space....

  4. Ancestral sleep.

    Science.gov (United States)

    de la Iglesia, Horacio O; Moreno, Claudia; Lowden, Arne; Louzada, Fernando; Marqueze, Elaine; Levandovski, Rosa; Pilz, Luisa K; Valeggia, Claudia; Fernandez-Duque, Eduardo; Golombek, Diego A; Czeisler, Charles A; Skene, Debra J; Duffy, Jeanne F; Roenneberg, Till

    2016-04-01

    While we do not yet understand all the functions of sleep, its critical role for normal physiology and behaviour is evident. Its amount and temporal pattern depend on species and condition. Humans sleep about a third of the day with the longest, consolidated episode during the night. The change in lifestyle from hunter-gatherers via agricultural communities to densely populated industrialized centres has certainly affected sleep, and a major concern in the medical community is the impact of insufficient sleep on health [1,2]. One of the causal mechanisms leading to insufficient sleep is altered exposure to the natural light-dark cycle. This includes the wide availability of electric light, attenuated exposure to daylight within buildings, and evening use of light-emitting devices, all of which decrease the strength of natural light-dark signals that entrain circadian systems [3]. PMID:27046809

  5. Mammalian synthetic biology: emerging medical applications

    OpenAIRE

    Kis, Zoltán; Pereira, Hugo Sant'Ana; Homma, Takayuki; Pedrigi, Ryan M.; Krams, Rob

    2015-01-01

    In this review, we discuss new emerging medical applications of the rapidly evolving field of mammalian synthetic biology. We start with simple mammalian synthetic biological components and move towards more complex and therapy-oriented gene circuits. A comprehensive list of ON–OFF switches, categorized into transcriptional, post-transcriptional, translational and post-translational, is presented in the first sections. Subsequently, Boolean logic gates, synthetic mammalian oscillators and tog...

  6. Recent advances in mammalian protein production

    OpenAIRE

    Bandaranayake, Ashok D.; Almo, Steven C.

    2013-01-01

    Mammalian protein production platforms have had a profound impact in many areas of basic and applied research, and an increasing number of blockbuster drugs are recombinant mammalian proteins. With global sales of these drugs exceeding US$120 billion per year, both industry and academic research groups continue to develop cost effective methods for producing mammalian proteins to support preclinical and clinical evaluations of potential therapeutics. While a wide range of platforms have been ...

  7. Mammalian phylogeny reveals recent diversification rate shifts

    OpenAIRE

    Stadler, Tanja

    2011-01-01

    Phylogenetic trees of present-day species allow investigation of the rate of evolution that led to the present-day diversity. A recent analysis of the mammalian phylogeny challenged the view of explosive mammalian evolution after the Cretaceous–Tertiary (K/T) boundary (65 Mya). However, due to lack of appropriate methods, the diversification (speciation minus extinction) rates in the more recent past of mammalian evolution could not be determined. In this paper, I provide a method that reveal...

  8. Mast cells in mammalian brain.

    Science.gov (United States)

    Dropp, J J

    1976-01-01

    Mast cells, which had until recently been believed to be not present in the mammalian brain, were studied in the brains of 29 mammalian species. Although there was considerable intraspecific and interspecific variation, mast cells were most numerous within the leptomeninges (especially in those overlying the cerebrum and the dorsal thalamus - most rodents, most carnivores, chimpanzees, squirrel monkeys and elephant), the cerebral cortex (most rodents, tiger, fox, chimpanzee, tarsier, and elephant) and in many nuclei of the dorsal thalamus (most rodents, tiger, lion, and fox). In some mammals, mast cells were also numerous in the stroma of the telencephalic choroid plexuses (chimpanzee, squirrel monkey), the putamen and the claustrum (chimpanzee), the subfornical organ (pack rat, tiger, chimpanzee), the olfactory peduncles (hooded rat, albino rat), the stroma of the diencephalic choroid plexus (lion, chimpanzee, squirrel monkey), the pineal organ (chimpanzee, squirrel monkey), some nuclei of the hypothalamus (tiger), the infundibulum (hooded rat, tiger, fox) the area postrema (pack rat, chinchilla, lion, spider monkey, chimpanzee, fox) and some nuclei and tracts of the metencephalon and the myelencephalon (tiger). Neither the sex of the animal nor electrolytic lesions made in the brains of some of the animals at various times prior to sacrifice appeared to effect the number and the distribution of mast cells. Age-related changes in mast cell number and distribution were detected in the albino rat. PMID:961335

  9. ABO (histo) blood group phenotype development and human reproduction as they relate to ancestral IgM formation: A hypothesis.

    Science.gov (United States)

    Arend, Peter

    2016-01-01

    The formation of a histo (blood) group) ABO phenotype and the exclusion of an autoreactive IgM or isoagglutinin activity arise apparently in identical glycosylation of complementary domains on cell surfaces and plasma proteins. The fundamental O-glycan emptiness of the circulating IgM, which during the neonatal amino acid sequencing of the variable regions is exerting germline-specific O-GalNAc glycan-reactive serine/threonine residues that in the plasma of the adult human blood group O individuals apparently remain associated with the open glycosidic sites on the ABOH convertible red cell surface, must raise suggestions on a transient expression of developmental glycans, which have been "lost" over the course of maturation. In fact, while the mammalian non-somatic, embryogenic stem cell (ESC)- germ cell (GC) transformation is characterized by a transient and genetically as-yet-undefined trans-species-functional O-GalNAc glycan expression, in the C57BL/10 mouse such expression was potentially identified in growth-dependent, blood group A-like GalNAc glycan-bearing, ovarian glycolipids complementary with the syngeneic anti-A reactive IgM, which does not appear in early ovariectomized animals. This non-somatically encoded, polyreactive, ancestral IgM molecule has not undergone clonal selection and does primarily not differentiate between self and non-self and might, due to amino acid hydroxyl groups, highly suggest substrate competition with subsequent O-glycosylations in ongoing ESC-GC transformations and affecting GC maturation. However, the membrane-bound somatic N/O-glycotransferases, which initiate, after formation of the zygote, the complex construction of the human ABO phenotypes in the trans cisternae of the Golgi apparatus, are associated and/or completed with soluble enzyme versions exerting identical specificities in plasma and likely competing vice versa by glycosylation of neonatal IgM amino acids, where they suggest to accomplish the clearance of anti

  10. Mammalian Mitochondrial ncRNA Database

    OpenAIRE

    Anandakumar, Shanmugam; Vijayakumar, Saravanan; Arumugam, Nagarajan; Gromiha, M. Michael

    2015-01-01

    Mammalian Mitochondrial ncRNA is a web-based database, which provides specific information on non-coding RNA in mammals. This database includes easy searching, comparing with BLAST and retrieving information on predicted structure and its function about mammalian ncRNAs. Availability The database is available for free at http://www.iitm.ac.in/bioinfo/mmndb/

  11. Neanderthal and Denisova genetic affinities with contemporary humans: introgression versus common ancestral polymorphisms.

    Science.gov (United States)

    Lowery, Robert K; Uribe, Gabriel; Jimenez, Eric B; Weiss, Mark A; Herrera, Kristian J; Regueiro, Maria; Herrera, Rene J

    2013-11-01

    Analyses of the genetic relationships among modern humans, Neanderthals and Denisovans have suggested that 1-4% of the non-Sub-Saharan African gene pool may be Neanderthal derived, while 6-8% of the Melanesian gene pool may be the product of admixture between the Denisovans and the direct ancestors of Melanesians. In the present study, we analyzed single nucleotide polymorphism (SNP) diversity among a worldwide collection of contemporary human populations with respect to the genetic constitution of these two archaic hominins and Pan troglodytes (chimpanzee). We partitioned SNPs into subsets, including those that are derived in both archaic lineages, those that are ancestral in both archaic lineages and those that are only derived in one archaic lineage. By doing this, we have conducted separate examinations of subsets of mutations with higher probabilities of divergent phylogenetic origins. While previous investigations have excluded SNPs from common ancestors in principal component analyses, we included common ancestral SNPs in our analyses to visualize the relative placement of the Neanderthal and Denisova among human populations. To assess the genetic similarities among the various hominin lineages, we performed genetic structure analyses to provide a comparison of genetic patterns found within contemporary human genomes that may have archaic or common ancestral roots. Our results indicate that 3.6% of the Neanderthal genome is shared with roughly 65.4% of the average European gene pool, which clinally diminishes with distance from Europe. Our results suggest that Neanderthal genetic associations with contemporary non-Sub-Saharan African populations, as well as the genetic affinities observed between Denisovans and Melanesians most likely result from the retention of ancient mutations in these populations. PMID:23872234

  12. Chromosome painting in three-toed sloths: a cytogenetic signature and ancestral karyotype for Xenarthra

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    Azevedo Nathália F

    2012-03-01

    Full Text Available Abstract Background Xenarthra (sloths, armadillos and anteaters represent one of four currently recognized Eutherian mammal supraorders. Some phylogenomic studies point to the possibility of Xenarthra being at the base of the Eutherian tree, together or not with the supraorder Afrotheria. We performed painting with human autosomes and X-chromosome specific probes on metaphases of two three-toed sloths: Bradypus torquatus and B. variegatus. These species represent the fourth of the five extant Xenarthra families to be studied with this approach. Results Eleven human chromosomes were conserved as one block in both B. torquatus and B. variegatus: (HSA 5, 6, 9, 11, 13, 14, 15, 17, 18, 20, 21 and the X chromosome. B. torquatus, three additional human chromosomes were conserved intact (HSA 1, 3 and 4. The remaining human chromosomes were represented by two or three segments on each sloth. Seven associations between human chromosomes were detected in the karyotypes of both B. torquatus and B. variegatus: HSA 3/21, 4/8, 7/10, 7/16, 12/22, 14/15 and 17/19. The ancestral Eutherian association 16/19 was not detected in the Bradypus species. Conclusions Our results together with previous reports enabled us to propose a hypothetical ancestral Xenarthran karyotype with 48 chromosomes that would differ from the proposed ancestral Eutherian karyotype by the presence of the association HSA 7/10 and by the split of HSA 8 into three blocks, instead of the two found in the Eutherian ancestor. These same chromosome features point to the monophyly of Xenarthra, making this the second supraorder of placental mammals to have a chromosome signature supporting its monophyly.

  13. Chromosome painting in three-toed sloths: a cytogenetic signature and ancestral karyotype for Xenarthra

    Science.gov (United States)

    2012-01-01

    Background Xenarthra (sloths, armadillos and anteaters) represent one of four currently recognized Eutherian mammal supraorders. Some phylogenomic studies point to the possibility of Xenarthra being at the base of the Eutherian tree, together or not with the supraorder Afrotheria. We performed painting with human autosomes and X-chromosome specific probes on metaphases of two three-toed sloths: Bradypus torquatus and B. variegatus. These species represent the fourth of the five extant Xenarthra families to be studied with this approach. Results Eleven human chromosomes were conserved as one block in both B. torquatus and B. variegatus: (HSA 5, 6, 9, 11, 13, 14, 15, 17, 18, 20, 21 and the X chromosome). B. torquatus, three additional human chromosomes were conserved intact (HSA 1, 3 and 4). The remaining human chromosomes were represented by two or three segments on each sloth. Seven associations between human chromosomes were detected in the karyotypes of both B. torquatus and B. variegatus: HSA 3/21, 4/8, 7/10, 7/16, 12/22, 14/15 and 17/19. The ancestral Eutherian association 16/19 was not detected in the Bradypus species. Conclusions Our results together with previous reports enabled us to propose a hypothetical ancestral Xenarthran karyotype with 48 chromosomes that would differ from the proposed ancestral Eutherian karyotype by the presence of the association HSA 7/10 and by the split of HSA 8 into three blocks, instead of the two found in the Eutherian ancestor. These same chromosome features point to the monophyly of Xenarthra, making this the second supraorder of placental mammals to have a chromosome signature supporting its monophyly. PMID:22429690

  14. Ancestral polymorphism and recent invasion of transposable elements in Drosophila species

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    Dias Elaine

    2012-07-01

    Full Text Available Abstract Background During the evolution of transposable elements, some processes, such as ancestral polymorphisms and horizontal transfer of sequences between species, can produce incongruences in phylogenies. We investigated the evolutionary history of the transposable elements Bari and 412 in the sequenced genomes of the Drosophila melanogaster group and in the sibling species D. melanogaster and D. simulans using traditional phylogenetic and network approaches. Results Maximum likelihood (ML phylogenetic analyses revealed incongruences and unresolved relationships for both the Bari and 412 elements. The DNA transposon Bari within the D. ananassae genome is more closely related to the element of the melanogaster complex than to the sequence in D. erecta, which is inconsistent with the species phylogeny. Divergence analysis and the comparison of the rate of synonymous substitutions per synonymous site of the Bari and host gene sequences explain the incongruence as an ancestral polymorphism that was inherited stochastically by the derived species. Unresolved relationships were observed in the ML phylogeny of both elements involving D. melanogaster, D. simulans and D. sechellia. A network approach was used to attempt to resolve these relationships. The resulting tree suggests recent transfers of both elements between D. melanogaster and D. simulans. The divergence values of the elements between these species support this conclusion. Conclusions We showed that ancestral polymorphism and recent invasion of genomes due to introgression or horizontal transfer between species occurred during the evolutionary history of the Bari and 412 elements in the melanogaster group. These invasions likely occurred in Africa during the Pleistocene, before the worldwide expansion of D. melanogaster and D. simulans.

  15. The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida is ancestral within the deuterostomes

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    Lanfear Robert

    2009-05-01

    Full Text Available Abstract Background Mitochondrial genome comparisons contribute in multiple ways when inferring animal relationships. As well as primary sequence data, rare genomic changes such as gene order, shared gene boundaries and genetic code changes, which are unlikely to have arisen through convergent evolution, are useful tools in resolving deep phylogenies. Xenoturbella bocki is a morphologically simple benthic marine worm recently found to belong among the deuterostomes. Here we present analyses comparing the Xenoturbella bocki mitochondrial gene order, genetic code and control region to those of other metazoan groups. Results The complete mitochondrial genome sequence of Xenoturbella bocki was determined. The gene order is most similar to that of the chordates and the hemichordates, indicating that this conserved mitochondrial gene order might be ancestral to the deuterostome clade. Using data from all phyla of deuterostomes, we infer the ancestral mitochondrial gene order for this clade. Using inversion and breakpoint analyses of metazoan mitochondrial genomes, we test conflicting hypotheses for the phylogenetic placement of Xenoturbella and find a closer affinity to the hemichordates than to other metazoan groups. Comparative analyses of the control region reveal similarities in the transcription initiation and termination sites and origin of replication of Xenoturbella with those of the vertebrates. Phylogenetic analyses of the mitochondrial sequence indicate a weakly supported placement as a basal deuterostome, a result that may be the effect of compositional bias. Conclusion The mitochondrial genome of Xenoturbella bocki has a very conserved gene arrangement in the deuterostome group, strikingly similar to that of the hemichordates and the chordates, and thus to the ancestral deuterostome gene order. Similarity to the hemichordates in particular is suggested by inversion and breakpoint analysis. Finally, while phylogenetic analyses of the

  16. Contrasting determinants of abundance in ancestral and colonized ranges of an invasive brood parasite

    Science.gov (United States)

    Hahn, D.C.; O'Connor, R.J.

    2002-01-01

    Avian species distributions are typically regarded as constrained by spatially extensive variables such as climate, habitat, spatial patchiness, and microhabitat attributes. We hypothesized that the distribution of a brood parasite depends as strongly on host distribution patterns as on biophysical factors and examined this hypothesis with respect to the national distribution of the Brown-headed Cowbird (Molothrus ater). We applied a classification and regression (CART) analysis to data from the Breeding Bird Survey (BBS) and the Christmas Bird Count (CBC) and derived hierarchically organized statistical models of the influence of climate and weather, cropping and land use, and host abundance and distribution on the distribution of the Brown-headed Cowbird within the conterminous United States. The model accounted for 47.2% of the variation in cowbird incidence, and host abundance was the top predictor with an R2 of 18.9%. The other predictors identified by the model (crops 15.7%, weather and climate 14.3%, and region 9.6%) fit the ecological profile of this cowbird. We showed that host abundance was independent of these environmental predictors of cowbird distribution. At the regional scale host abundance played a very strong role in determining cowbird abundance in the cowbird?s colonized range east and west of their ancestral range in the Great Plains (26.6%). Crops were not a major predictor for cowbirds in their ancestral range, although they are the most important predictive factor (33%) for the grassland passerines that are the cowbird?s ancestral hosts. Consequently our findings suggest that the distribution of hosts does indeed take precedence over habitat attributes in shaping the cowbird?s distribution at a national scale, within an envelope of constraint set by biophysical factors.

  17. Photodynamic Inactivation of Mammalian Viruses and Bacteriophages

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    Liliana Costa

    2012-06-01

    Full Text Available Photodynamic inactivation (PDI has been used to inactivate microorganisms through the use of photosensitizers. The inactivation of mammalian viruses and bacteriophages by photosensitization has been applied with success since the first decades of the last century. Due to the fact that mammalian viruses are known to pose a threat to public health and that bacteriophages are frequently used as models of mammalian viruses, it is important to know and understand the mechanisms and photodynamic procedures involved in their photoinactivation. The aim of this review is to (i summarize the main approaches developed until now for the photodynamic inactivation of bacteriophages and mammalian viruses and, (ii discuss and compare the present state of the art of mammalian viruses PDI with phage photoinactivation, with special focus on the most relevant mechanisms, molecular targets and factors affecting the viral inactivation process.

  18. Analysis of Ancestral and Functionally Relevant CD5 Variants in Systemic Lupus Erythematosus Patients

    OpenAIRE

    Maria Carmen Cenit; Mario Martínez-Florensa; Marta Consuegra; Lizette Bonet; Elena Carnero-Montoro; Noelia Armiger; Miguel Caballero-Baños; Maria Teresa Arias; Daniel Benitez; Norberto Ortego-Centeno; Enrique de Ramón; José Mario Sabio; García-Hernández, Francisco J; Carles Tolosa; Ana Suárez

    2014-01-01

    Objective: CD5 plays a crucial role in autoimmunity and is a well-established genetic risk factor of developing RA. Recently, evidence of positive selection has been provided for the CD5 Pro224-Val471 haplotype in East Asian populations. The aim of the present work was to further analyze the functional relevance of non-synonymous CD5 polymorphisms conforming the ancestral and the newly derived haplotypes (Pro224-Ala471 and Pro224-Val471, respectively) as well as to investigate the potential r...

  19. Ancestral heritage saves tribes during 1 April 2007 Solomon Islands tsunami

    Science.gov (United States)

    Fritz, Hermann M.; Kalligeris, Nikos

    2008-01-01

    The 1 April 2007 magnitude Ms 8.1 earthquake off the New Georgia Group in the Solomon Islands generated a tsunami that killed 52 with locally focused run-up heights of 12 m, local flow depths of 5 m as well as tectonic uplift up to 3.6 m and subsidence down to -1.5 m. A reconnaissance team deployed within one week investigated 65 coastal settlements on 13 remote Islands. The ancestral heritage ``run to high ground after an earthquake'' passed on to younger generations by survivors of smaller historic tsunamis triggered an immediate spontaneous self evacuation containing the death toll.

  20. Consistency and inconsistency of consensus methods for inferring species trees from gene trees in the presence of ancestral population structure.

    Science.gov (United States)

    DeGiorgio, Michael; Rosenberg, Noah A

    2016-08-01

    In the last few years, several statistically consistent consensus methods for species tree inference have been devised that are robust to the gene tree discordance caused by incomplete lineage sorting in unstructured ancestral populations. One source of gene tree discordance that has only recently been identified as a potential obstacle for phylogenetic inference is ancestral population structure. In this article, we describe a general model of ancestral population structure, and by relying on a single carefully constructed example scenario, we show that the consensus methods Democratic Vote, STEAC, STAR, R(∗) Consensus, Rooted Triple Consensus, Minimize Deep Coalescences, and Majority-Rule Consensus are statistically inconsistent under the model. We find that among the consensus methods evaluated, the only method that is statistically consistent in the presence of ancestral population structure is GLASS/Maximum Tree. We use simulations to evaluate the behavior of the various consensus methods in a model with ancestral population structure, showing that as the number of gene trees increases, estimates on the basis of GLASS/Maximum Tree approach the true species tree topology irrespective of the level of population structure, whereas estimates based on the remaining methods only approach the true species tree topology if the level of structure is low. However, through simulations using species trees both with and without ancestral population structure, we show that GLASS/Maximum Tree performs unusually poorly on gene trees inferred from alignments with little information. This practical limitation of GLASS/Maximum Tree together with the inconsistency of other methods prompts the need for both further testing of additional existing methods and development of novel methods under conditions that incorporate ancestral population structure. PMID:27086043

  1. Sporadic inclusion body myositis in Japanese is associated with the MHC ancestral haplotype 52.1.

    Science.gov (United States)

    Scott, Adrian Phillip; Allcock, Richard James Nigel; Mastaglia, Frank; Nishino, Ichizo; Nonaka, Ikuya; Laing, Nigel

    2006-05-01

    In Caucasians, sporadic inclusion body myositis has been associated with the MHC ancestral haplotypes; HLA-A1, B8, DR3 (8.1AH) and HLA-B35, DR1 (35.2AH). It is not known whether these haplotypes carry susceptibility for the disease in other ethnic groups. We report here the results of HLA-B and -DRB1 typing using a high-resolution sequence-based technique in a cohort of 31 Japanese patients with definite sIBM. Patient allele frequencies were 40.3% for HLA-B*5201 (10.7% in controls: pHLA-DRB1*1502 (10% in controls: p<0.001). Both alleles were found together as part of a conserved haplotype (52.1AH) at a frequency of 37.1% in patients (8.4% in controls: p<0.001). This is the first description of a haplotypic MHC association with sporadic inclusion body myositis in Japanese patients. These findings indicate that different MHC ancestral haplotypes are associated with sIBM in different ethnic groups and further emphasize the importance of genetic factors in this condition. PMID:16564169

  2. Contributions of ancestral inter-species recombination to the genetic diversity of extant Streptomyces lineages.

    Science.gov (United States)

    Andam, Cheryl P; Choudoir, Mallory J; Vinh Nguyen, Anh; Sol Park, Han; Buckley, Daniel H

    2016-07-01

    Streptomyces species produce many important antibiotics and have a crucial role in soil nutrient cycling. However, their evolutionary history remains poorly characterized. We have evaluated the impact of homologous recombination on the evolution of Streptomyces using multi-locus sequence analysis of 234 strains that represent at least 11 species clusters. Evidence of inter-species recombination is widespread but not uniform within the genus and levels of mosaicism vary between species clusters. Most phylogenetically incongruent loci are monophyletic at the scale of species clusters and their subclades, suggesting that these recombination events occurred in shared ancestral lineages. Further investigation of two mosaic species clusters suggests that genes acquired by inter-species recombination may have become fixed in these lineages during periods of demographic expansion; implicating a role for phylogeography in determining contemporary patterns of genetic diversity. Only by examining the phylogeny at the scale of the genus is apparent that widespread phylogenetically incongruent loci in Streptomyces are derived from a far smaller number of ancestral inter-species recombination events. PMID:26849310

  3. Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family

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    Velasco Riccardo

    2011-01-01

    Full Text Available Abstract Background Comparative genome mapping studies in Rosaceae have been conducted until now by aligning genetic maps within the same genus, or closely related genera and using a limited number of common markers. The growing body of genomics resources and sequence data for both Prunus and Fragaria permits detailed comparisons between these genera and the recently released Malus × domestica genome sequence. Results We generated a comparative analysis using 806 molecular markers that are anchored genetically to the Prunus and/or Fragaria reference maps, and physically to the Malus genome sequence. Markers in common for Malus and Prunus, and Malus and Fragaria, respectively were 784 and 148. The correspondence between marker positions was high and conserved syntenic blocks were identified among the three genera in the Rosaceae. We reconstructed a proposed ancestral genome for the Rosaceae. Conclusions A genome containing nine chromosomes is the most likely candidate for the ancestral Rosaceae progenitor. The number of chromosomal translocations observed between the three genera investigated was low. However, the number of inversions identified among Malus and Prunus was much higher than any reported genome comparisons in plants, suggesting that small inversions have played an important role in the evolution of these two genera or of the Rosaceae.

  4. Bearing the unbearable: ancestral transmission through dreams and moving metaphors in the analtyic field.

    Science.gov (United States)

    Pickering, Judith

    2012-11-01

    This paper explores how untold and unresolved intergenerational trauma may be transmitted through unconscious channels of communication, manifesting in the dreams of descendants. Unwitting carriers for that which was too horrific for their ancestors to bear, descendants may enter analysis through an unconscious need to uncover past secrets, piece together ancestral histories before the keys to comprehending their terrible inheritance die with their forebears. They seek the relational containment of the analytic relationship to provide psychological conditions to bear the unbearable, know the unknowable, speak the unspeakable and redeem the unredeemable. In the case of 'Rachael', initial dreams gave rise to what Hobson (1984) called 'moving metaphors of self' in the analytic field. Dream imagery, projective and introjective processes in the transference-countertransference dynamics gradually revealed an unknown ancestral history. I clarify the back and forth process from dream to waking dream thoughts to moving metaphors and differentiate the moving metaphor from a living symbol. I argue that the containment of the analytic relationship nested within the security of the analytic space is a necessary precondition for such healing processes to occur. PMID:23130614

  5. RNA-DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA.

    Science.gov (United States)

    Bar-Yaacov, Dan; Avital, Gal; Levin, Liron; Richards, Allison L; Hachen, Naomi; Rebolledo Jaramillo, Boris; Nekrutenko, Anton; Zarivach, Raz; Mishmar, Dan

    2013-11-01

    RNA transcripts are generally identical to the underlying DNA sequences. Nevertheless, RNA-DNA differences (RDDs) were found in the nuclear human genome and in plants and animals but not in human mitochondria. Here, by deep sequencing of human mitochondrial DNA (mtDNA) and RNA, we identified three RDD sites at mtDNA positions 295 (C-to-U), 13710 (A-to-U, A-to-G), and 2617 (A-to-U, A-to-G). Position 2617, within the 16S rRNA, harbored the most prevalent RDDs (>30% A-to-U and ∼15% A-to-G of the reads in all tested samples). The 2617 RDDs appeared already at the precursor polycistrone mitochondrial transcript. By using traditional Sanger sequencing, we identified the A-to-U RDD in six different cell lines and representative primates (Gorilla gorilla, Pongo pigmaeus, and Macaca mulatta), suggesting conservation of the mechanism generating such RDD. Phylogenetic analysis of more than 1700 vertebrate mtDNA sequences supported a thymine as the primate ancestral allele at position 2617, suggesting that the 2617 RDD recapitulates the ancestral 16S rRNA. Modeling U or G (the RDDs) at position 2617 stabilized the large ribosomal subunit structure in contrast to destabilization by an A (the pre-RDDs). Hence, these mitochondrial RDDs are likely functional. PMID:23913925

  6. Ancestral origin of the ATTCT repeat expansion in spinocerebellar ataxia type 10 (SCA10.

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    Teresa Almeida

    Full Text Available Spinocerebellar ataxia type 10 (SCA10 is an autosomal dominant neurodegenerative disease characterized by cerebellar ataxia and seizures. The disease is caused by a large ATTCT repeat expansion in the ATXN10 gene. The first families reported with SCA10 were of Mexican origin, but the disease was soon after described in Brazilian families of mixed Portuguese and Amerindian ancestry. The origin of the SCA10 expansion and a possible founder effect that would account for its geographical distribution have been the source of speculation over the last years. To unravel the mutational origin and spread of the SCA10 expansion, we performed an extensive haplotype study, using closely linked STR markers and intragenic SNPs, in families from Brazil and Mexico. Our results showed (1 a shared disease haplotype for all Brazilian and one of the Mexican families, and (2 closely-related haplotypes for the additional SCA10 Mexican families; (3 little or null genetic distance in small normal alleles of different repeat sizes, from the same SNP lineage, indicating that they are being originated by a single step mechanism; and (4 a shared haplotype for pure and interrupted expanded alleles, pointing to a gene conversion model for its generation. In conclusion, we show evidence for an ancestral common origin for SCA10 in Latin America, which might have arisen in an ancestral Amerindian population and later have been spread into the mixed populations of Mexico and Brazil.

  7. In silico resurrection of the major vault protein suggests it is ancestral in modern eukaryotes.

    Science.gov (United States)

    Daly, Toni K; Sutherland-Smith, Andrew J; Penny, David

    2013-01-01

    Vaults are very large oligomeric ribonucleoproteins conserved among a variety of species. The rat vault 3D structure shows an ovoid oligomeric particle, consisting of 78 major vault protein monomers, each of approximately 861 amino acids. Vaults are probably the largest ribonucleoprotein structures in eukaryote cells, being approximately 70 nm in length with a diameter of 40 nm--the size of three ribosomes and with a lumen capacity of 50 million Å(3). We use both protein sequences and inferred ancestral sequences for in silico virtual resurrection of tertiary and quaternary structures to search for vaults in a wide variety of eukaryotes. We find that the vault's phylogenetic distribution is widespread in eukaryotes, but is apparently absent in some notable model organisms. Our conclusion from the distribution of vaults is that they were present in the last eukaryote common ancestor but they have apparently been lost from a number of groups including fungi, insects, and probably plants. Our approach of inferring ancestral 3D and quaternary structures is expected to be useful generally. PMID:23887922

  8. Phylogenetic memory of developing mammalian dentition.

    Science.gov (United States)

    Peterkova, Renata; Lesot, Hervé; Peterka, Miroslav

    2006-05-15

    Structures suppressed during evolution can be retraced due to atavisms and vestiges. Atavism is an exceptional emergence of an ancestral form in a living individual. In contrast, ancestral vestige regularly occurs in all members of an actual species. We surveyed data about the vestigial and atavistic teeth in mammals, updated them by recent findings in mouse and human embryos, and discussed their ontogenetic and evolutionary implications. In the mouse incisor and diastema regions, dental placodes are transiently distinct being morphologically similar to the early tooth primordia in reptiles. Two large vestigial buds emerge in front of the prospective first molar and presumably correspond to the premolars eliminated during mouse evolution. The incorporation of the posterior premolar vestige into the lower first molar illustrates the putative mechanism of evolutionary disappearance of the last premolar in the mice. In mutant mice, devious development of the ancestral tooth primordia might lead to their revivification and origin of atavistic supernumerary teeth. Similarity in the developmental schedule between three molars in mice and the respective third and fourth deciduous premolar and the first molar in humans raises a question about putative homology of these teeth. The complex patterning of the vestibular and dental epithelium in human embryos is reminiscent of the pattern of "Zahnreihen" in lower vertebrates. A hypothesis was presented about the developmental relationship between the structures at the external aspect of the dentition in mammals (oral vestibule, pre-lacteal teeth, paramolar cusps/teeth), the tooth glands in reptiles, and the earliest teeth in lower vertebrates. PMID:16463376

  9. Fate Mapping Mammalian Corneal Epithelia.

    Science.gov (United States)

    Richardson, Alexander; Wakefield, Denis; Di Girolamo, Nick

    2016-04-01

    The anterior aspect of the cornea consists of a stratified squamous epithelium, thought to be maintained by a rare population of stem cells (SCs) that reside in the limbal transition zone. Although migration of cells that replenish the corneal epithelium has been studied for over a century, the process is still poorly understood and not well characterized. Numerous techniques have been employed to examine corneal epithelial dynamics, including visualization by light microscopy, the incorporation of vital dyes and DNA labels, and transplantation of genetically marked cells that have acted as cell and lineage beacons. Modern-day lineage tracing utilizes molecular methods to determine the fate of a specific cell and its progeny over time. Classically employed in developmental biology, lineage tracing has been used more recently to track the progeny of adult SCs in a number of organs to pin-point their location and understand their movement and influence on tissue regeneration. This review highlights key discoveries that have led researchers to develop cutting-edge genetic tools to effectively and more accurately monitor turnover and displacement of cells within the mammalian corneal epithelium. Collating information on the basic biology of SCs will have clinical ramifications in furthering our knowledge of the processes that govern their role in homeostasis, wound-healing, transplantation, and how we can improve current unsatisfactory SC-based therapies for patients suffering blinding corneal disease. PMID:26774909

  10. Possible mechanisms of mammalian immunocontraception.

    Science.gov (United States)

    Barber, M R; Fayrer-Hosken, R A

    2000-03-01

    Ecological and conservation programs in ecosystems around the world have experienced varied success in population management. One of the greatest problems is that human expansion has led to the shrinking of wildlife habitat and, as a result, the overpopulation of many different species has occurred. The pressures exerted by the increased number of animals has caused environmental damage. The humane and practical control of these populations has solicited the scientific community to arrive at a safe, effective, and cost-efficient means of population control. Immunocontraception using zona pellucida antigens, specifically porcine zona pellucida (pZP), has become one of the most promising population control tools in the world today, with notable successes in horses and elephants. A conundrum has risen where pZP, a single vaccine, successfully induces an immunocontraceptive effect in multiple species of mammals. This review describes the most current data pertaining to the mammalian zona pellucida and immunocontraception, and from these studies, we suggest several potential mechanisms of immunocontraception. PMID:10706942

  11. Identification of the ancestral haplotype for apolipoprotein B suggests an African origin of Homo sapiens sapiens and traces their subsequent migration to Europe and the Pacific.

    OpenAIRE

    Rapacz, J; Chen, L.; Butler-Brunner, E; Wu, M J; Hasler-Rapacz, J O; Butler, R.; Schumaker, V N

    1991-01-01

    The probable ancestral haplotype for human apolipoprotein B (apoB) has been identified through immunological analysis of chimpanzee and gorilla serum and sequence analysis of their DNA. Moreover, the frequency of this ancestral apoB haplotype among different human populations provides strong support for the African origin of Homo sapiens sapiens and their subsequent migration from Africa to Europe and to the Pacific. The approach used here for the identification of the ancestral human apoB ha...

  12. Evolution of mammalian sensorimotor cortex: Thalamic projections to parietal cortical areas in Monodelphis domestica

    Directory of Open Access Journals (Sweden)

    James Clinton Dooley

    2015-01-01

    Full Text Available The current experiments build upon previous studies designed to reveal the network of parietal cortical areas present in the common mammalian ancestor. Understanding this ancestral network is essential for highlighting the basic somatosensory circuitry present in all mammals, and how this basic plan was modified to generate species specific behaviors. Our animal model, the short-tailed opossum (Monodelphis domestica, is a South American marsupial that has been proposed to have a similar ecological niche and morphology to the earliest common mammalian ancestor. In this investigation, we injected retrograde neuroanatomical tracers into the face and body representations of primary somatosensory cortex (S1, the rostral and caudal somatosensory fields (SR and SC, as well as a multimodal region (MM. Projections from different architectonically defined thalamic nuclei were then quantified. Our results provide further evidence to support the hypothesized basic mammalian plan of thalamic projections to S1, with the lateral and medial ventral posterior thalamic nuclei (VPl and VPm projecting to S1 body and S1 face, respectively. Additional strong projections are from the medial division of posterior nucleus (Pom. SR receives projections from several midline nuclei, including the medial dorsal, ventral medial nucleus, and Pom. SC and MM show similar patterns of connectivity, with projections from the ventral anterior and ventral lateral nuclei, VPm and VPl, and the entire posterior nucleus (medial and lateral. Notably, MM is distinguished from SC by relatively dense projections from the dorsal division of the lateral geniculate nucleus and pulvinar. We discuss the finding that S1 of the short-tailed opossum has a similar pattern of projections as other marsupials and mammals, but also some distinct projections not present in other mammals. Further we provide additional support for a primitive posterior parietal cortex which receives input from multiple

  13. A comparative study and a phylogenetic exploration of the compositional architectures of mammalian nuclear genomes.

    Directory of Open Access Journals (Sweden)

    Eran Elhaik

    2014-11-01

    Full Text Available For the past four decades the compositional organization of the mammalian genome posed a formidable challenge to molecular evolutionists attempting to explain it from an evolutionary perspective. Unfortunately, most of the explanations adhered to the "isochore theory," which has long been rebutted. Recently, an alternative compositional domain model was proposed depicting the human and cow genomes as composed mostly of short compositionally homogeneous and nonhomogeneous domains and a few long ones. We test the validity of this model through a rigorous sequence-based analysis of eleven completely sequenced mammalian and avian genomes. Seven attributes of compositional domains are used in the analyses: (1 the number of compositional domains, (2 compositional domain-length distribution, (3 density of compositional domains, (4 genome coverage by the different domain types, (5 degree of fit to a power-law distribution, (6 compositional domain GC content, and (7 the joint distribution of GC content and length of the different domain types. We discuss the evolution of these attributes in light of two competing phylogenetic hypotheses that differ from each other in the validity of clade Euarchontoglires. If valid, the murid genome compositional organization would be a derived state and exhibit a high similarity to that of other mammals. If invalid, the murid genome compositional organization would be closer to an ancestral state. We demonstrate that the compositional organization of the murid genome differs from those of primates and laurasiatherians, a phenomenon previously termed the "murid shift," and in many ways resembles the genome of opossum. We find no support to the "isochore theory." Instead, our findings depict the mammalian genome as a tapestry of mostly short homogeneous and nonhomogeneous domains and few long ones thus providing strong evidence in favor of the compositional domain model and seem to invalidate clade Euarchontoglires.

  14. Simplified Bioreactor For Growing Mammalian Cells

    Science.gov (United States)

    Spaulding, Glenn F.

    1995-01-01

    Improved bioreactor for growing mammalian cell cultures developed. Designed to support growth of dense volumes of mammalian cells by providing ample, well-distributed flows of nutrient solution with minimal turbulence. Cells relatively delicate and, unlike bacteria, cannot withstand shear forces present in turbulent flows. Bioreactor vessel readily made in larger sizes to accommodate greater cell production quantities. Molding equipment presently used makes cylinders up to 30 centimeters long. Alternative sintered plastic techniques used to vary pore size and quantity, as necessary.

  15. A novel bifunctional N-acetylglutamate synthase-kinase from Xanthomonas campestris that is closely related to mammalian N-acetylglutamate synthase

    Directory of Open Access Journals (Sweden)

    Tuchman Mendel

    2007-04-01

    Full Text Available Abstract Background In microorganisms and plants, the first two reactions of arginine biosynthesis are catalyzed by N-acetylglutamate synthase (NAGS and N-acetylglutamate kinase (NAGK. In mammals, NAGS produces an essential activator of carbamylphosphate synthetase I, the first enzyme of the urea cycle, and no functional NAGK homolog has been found. Unlike the other urea cycle enzymes, whose bacterial counterparts could be readily identified by their sequence conservation with arginine biosynthetic enzymes, mammalian NAGS gene was very divergent, making it the last urea cycle gene to be discovered. Limited sequence similarity between E. coli NAGS and fungal NAGK suggests that bacterial and eukaryotic NAGS, and fungal NAGK arose from the fusion of genes encoding an ancestral NAGK (argB and an acetyltransferase. However, mammalian NAGS no longer retains any NAGK catalytic activity. Results We identified a novel bifunctional N-acetylglutamate synthase and kinase (NAGS-K in the Xanthomonadales order of gamma-proteobacteria that appears to resemble this postulated primordial fusion protein. Phylogenetic analysis indicated that xanthomonad NAGS-K is more closely related to mammalian NAGS than to other bacterial NAGS. We cloned the NAGS-K gene from Xanthomonas campestis, and characterized the recombinant NAGS-K protein. Mammalian NAGS and its bacterial homolog have similar affinities for substrates acetyl coenzyme A and glutamate as well as for their allosteric regulator arginine. Conclusion The close phylogenetic relationship and similar biochemical properties of xanthomonad NAGS-K and mammalian NAGS suggest that we have identified a close relative to the bacterial antecedent of mammalian NAGS and that the enzyme from X. campestris could become a good model for mammalian NAGS in structural, biochemical and biophysical studies.

  16. ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun.

    Directory of Open Access Journals (Sweden)

    Ruiqiang Li

    2005-09-01

    Full Text Available We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist at high copy numbers across the genome and must not be so old that they are no longer recognizable in comparison to their ancestral sequences. Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repository of known TEs, and increase the effectiveness of RepeatMasker in identifying TEs from genome sequences.

  17. Brain scaling in mammalian evolution as a consequence of concerted and mosaic changes in numbers of neurons and average neuronal cell size

    Directory of Open Access Journals (Sweden)

    Suzana eHerculano-Houzel

    2014-08-01

    Full Text Available Enough species have now been subject to systematic quantitative analysis of the relationship between the morphology and cellular composition of their brain that patterns begin to emerge and shed light on the evolutionary path that led to mammalian brain diversity. Based on an analysis of the shared and clade-specific characteristics of 41 modern mammalian species in 6 clades, and in light of the phylogenetic relationships among them, here we propose that ancestral mammal brains were composed and scaled in their cellular composition like modern afrotherian and glire brains: with an addition of neurons that is accompanied by a decrease in neuronal density and very little modification in glial cell density, implying a significant increase in average neuronal cell size in larger brains, and the allocation of approximately 2 neurons in the cerebral cortex and 8 neurons in the cerebellum for every neuron allocated to the rest of brain. We also propose that in some clades the scaling of different brain structures has diverged away from the common ancestral layout through clade-specific (or clade-defining changes in how average neuronal cell mass relates to numbers of neurons in each structure, and how numbers of neurons are differentially allocated to each structure relative to the number of neurons in the rest of brain. Thus, the evolutionary expansion of mammalian brains has involved both concerted and mosaic patterns of scaling across structures. This is, to our knowledge, the first mechanistic model that explains the generation of brains large and small in mammalian evolution, and it opens up new horizons for seeking the cellular pathways and genes involved in brain evolution.

  18. The imperfect ancestral recombination graph reconstruction problem: upper bounds for recombination and homoplasy.

    Science.gov (United States)

    Lam, Fumei; Tarpine, Ryan; Istrail, Sorin

    2010-06-01

    One of the central problems in computational biology is the reconstruction of evolutionary histories. While models incorporating recombination and homoplasy have been studied separately, a missing component in the theory is a robust and flexible unifying model which incorporates both of these major biological events shaping genetic diversity. In this article, we introduce the first such unifying model and develop algorithms to find the optimal ancestral recombination graph incorporating recombinations and homoplasy events. The power of our framework is the connection between our formulation and the Directed Steiner Arborescence Problem in combinatorial optimization. We implement linear programming techniques as well as heuristics for the Directed Steiner Arborescence Problem, and use our methods to construct evolutionary histories for both simulated and real data sets. PMID:20583925

  19. Where did the chili get its spice? Biogeography of capsaicinoid production in ancestral wild chili species.

    Science.gov (United States)

    Tewksbury, Joshua J; Manchego, Carlos; Haak, David C; Levey, Douglas J

    2006-03-01

    The biogeography of pungency in three species of wild chili in the chaco and surrounding highland habitats of southeastern Bolivia is described. We report that Capsicum chacoense, C. baccatum, and C. eximium are polymorphic for production of capsaicin and its analogs, such that completely pungent and completely nonpungent individuals co-occur in some populations. In C. chacoense, the density of plants and the proportion of pungent plants increased with elevation. Above 900 m, all individuals in all populations except two were pungent; nonpungent individuals in at least one of the two polymorphic populations were likely a result of spreading by humans. The occurrence of pungent and nonpungent individuals in three species of ancestral Capsicum and the geographic variation of pungency within species suggest that production of capsaicin and its analogs entails both costs and benefits, which shift from one locality to another. Determining the selection pressures behind such shifts is necessary to understand the evolution of pungency in chilies. PMID:16572297

  20. Magmatism and Epithermal Gold-Silver Deposits of the Southern Ancestral Cascade Arc, Western Nevada and Eastern California

    Science.gov (United States)

    John, David A.; du Bray, Edward A.; Henry, Christopher D., (compiler); Vikre, Peter

    2015-01-01

    Many epithermal gold-silver deposits are temporally and spatially associated with late Oligocene to Pliocene magmatism of the southern ancestral Cascade arc in western Nevada and eastern California. These deposits, which include both quartz-adularia (low- and intermediate-sulfidation; Comstock Lode, Tonopah, Bodie) and quartz-alunite (high-sulfidation; Goldfield, Paradise Peak) types, were major producers of gold and silver. Ancestral Cascade arc magmatism preceded that of the modern High Cascades arc and reflects subduction of the Farallon plate beneath North America. Ancestral arc magmatism began about 45 Ma, continued until about 3 Ma, and extended from near the Canada-United States border in Washington southward to about 250 km southeast of Reno, Nevada. The ancestral arc was split into northern and southern segments across an inferred tear in the subducting slab between Mount Shasta and Lassen Peak in northern California. The southern segment extends between 42°N in northern California and 37°N in western Nevada and was active from about 30 to 3 Ma. It is bounded on the east by the northeast edge of the Walker Lane. Ancestral arc volcanism represents an abrupt change in composition and style of magmatism relative to that in central Nevada. Large volume, caldera-forming, silicic ignimbrites associated with the 37 to 19 Ma ignimbrite flareup are dominant in central Nevada, whereas volcanic centers of the ancestral arc in western Nevada consist of andesitic stratovolcanoes and dacitic to rhyolitic lava domes that mostly formed between 25 and 4 Ma. Both ancestral arc and ignimbrite flareup magmatism resulted from rollback of the shallowly dipping slab that began about 45 Ma in northeast Nevada and migrated south-southwest with time. Most southern segment ancestral arc rocks have oxidized, high potassium, calc-alkaline compositions with silica contents ranging continuously from about 55 to 77 wt%. Most lavas are porphyritic and contain coarse plagioclase

  1. Evolutionary history of assassin bugs (insecta: hemiptera: Reduviidae: insights from divergence dating and ancestral state reconstruction.

    Directory of Open Access Journals (Sweden)

    Wei Song Hwang

    Full Text Available Assassin bugs are one of the most successful clades of predatory animals based on their species numbers (∼6,800 spp. and wide distribution in terrestrial ecosystems. Various novel prey capture strategies and remarkable prey specializations contribute to their appeal as a model to study evolutionary pathways involved in predation. Here, we reconstruct the most comprehensive reduviid phylogeny (178 taxa, 18 subfamilies to date based on molecular data (5 markers. This phylogeny tests current hypotheses on reduviid relationships emphasizing the polyphyletic Reduviinae and the blood-feeding, disease-vectoring Triatominae, and allows us, for the first time in assassin bugs, to reconstruct ancestral states of prey associations and microhabitats. Using a fossil-calibrated molecular tree, we estimated divergence times for key events in the evolutionary history of Reduviidae. Our results indicate that the polyphyletic Reduviinae fall into 11-14 separate clades. Triatominae are paraphyletic with respect to the reduviine genus Opisthacidius in the maximum likelihood analyses; this result is in contrast to prior hypotheses that found Triatominae to be monophyletic or polyphyletic and may be due to the more comprehensive taxon and character sampling in this study. The evolution of blood-feeding may thus have occurred once or twice independently among predatory assassin bugs. All prey specialists evolved from generalist ancestors, with multiple evolutionary origins of termite and ant specializations. A bark-associated life style on tree trunks is ancestral for most of the lineages of Higher Reduviidae; living on foliage has evolved at least six times independently. Reduviidae originated in the Middle Jurassic (178 Ma, but significant lineage diversification only began in the Late Cretaceous (97 Ma. The integration of molecular phylogenetics with fossil and life history data as presented in this paper provides insights into the evolutionary history of

  2. Genes Suggest Ancestral Colour Polymorphisms Are Shared across Morphologically Cryptic Species in Arctic Bumblebees.

    Directory of Open Access Journals (Sweden)

    Paul H Williams

    Full Text Available Our grasp of biodiversity is fine-tuned through the process of revisionary taxonomy. If species do exist in nature and can be discovered with available techniques, then we expect these revisions to converge on broadly shared interpretations of species. But for the primarily arctic bumblebees of the subgenus Alpinobombus of the genus Bombus, revisions by some of the most experienced specialists are unusual for bumblebees in that they have all reached different conclusions on the number of species present. Recent revisions based on skeletal morphology have concluded that there are from four to six species, while variation in colour pattern of the hair raised questions as to whether at least seven species might be present. Even more species are supported if we accept the recent move away from viewing species as morphotypes to viewing them instead as evolutionarily independent lineages (EILs using data from genes. EILs are recognised here in practice from the gene coalescents that provide direct evidence for their evolutionary independence. We show from fitting both general mixed Yule/coalescent (GMYC models and Poisson-tree-process (PTP models to data for the mitochondrial COI gene that there is support for nine species in the subgenus Alpinobombus. Examination of the more slowly evolving nuclear PEPCK gene shows further support for a previously unrecognised taxon as a new species in northwestern North America. The three pairs of the most morphologically similar sister species are separated allopatrically and prevented from interbreeding by oceans. We also find that most of the species show multiple shared colour patterns, giving the appearance of mimicry among parts of the different species. However, reconstructing ancestral colour-pattern states shows that speciation is likely to have cut across widespread ancestral polymorphisms, without or largely without convergence. In the particular case of Alpinobombus, morphological, colour-pattern, and

  3. Wnt signalling pathway parameters for mammalian cells.

    Science.gov (United States)

    Tan, Chin Wee; Gardiner, Bruce S; Hirokawa, Yumiko; Layton, Meredith J; Smith, David W; Burgess, Antony W

    2012-01-01

    Wnt/β-catenin signalling regulates cell fate, survival, proliferation and differentiation at many stages of mammalian development and pathology. Mutations of two key proteins in the pathway, APC and β-catenin, have been implicated in a range of cancers, including colorectal cancer. Activation of Wnt signalling has been associated with the stabilization and nuclear accumulation of β-catenin and consequential up-regulation of β-catenin/TCF gene transcription. In 2003, Lee et al. constructed a computational model of Wnt signalling supported by experimental data from analysis of time-dependent concentration of Wnt signalling proteins in Xenopus egg extracts. Subsequent studies have used the Xenopus quantitative data to infer Wnt pathway dynamics in other systems. As a basis for understanding Wnt signalling in mammalian cells, a confocal live cell imaging measurement technique is developed to measure the cell and nuclear volumes of MDCK, HEK293T cells and 3 human colorectal cancer cell lines and the concentrations of Wnt signalling proteins β-catenin, Axin, APC, GSK3β and E-cadherin. These parameters provide the basis for formulating Wnt signalling models for kidney/intestinal epithelial mammalian cells. There are significant differences in concentrations of key proteins between Xenopus extracts and mammalian whole cell lysates. Higher concentrations of Axin and lower concentrations of APC are present in mammalian cells. Axin concentrations are greater than APC in kidney epithelial cells, whereas in intestinal epithelial cells the APC concentration is higher than Axin. Computational simulations based on Lee's model, with this new data, suggest a need for a recalibration of the model.A quantitative understanding of Wnt signalling in mammalian cells, in particular human colorectal cancers requires a detailed understanding of the concentrations of key protein complexes over time. Simulations of Wnt signalling in mammalian cells can be initiated with the parameters

  4. Wnt signalling pathway parameters for mammalian cells.

    Directory of Open Access Journals (Sweden)

    Chin Wee Tan

    Full Text Available Wnt/β-catenin signalling regulates cell fate, survival, proliferation and differentiation at many stages of mammalian development and pathology. Mutations of two key proteins in the pathway, APC and β-catenin, have been implicated in a range of cancers, including colorectal cancer. Activation of Wnt signalling has been associated with the stabilization and nuclear accumulation of β-catenin and consequential up-regulation of β-catenin/TCF gene transcription. In 2003, Lee et al. constructed a computational model of Wnt signalling supported by experimental data from analysis of time-dependent concentration of Wnt signalling proteins in Xenopus egg extracts. Subsequent studies have used the Xenopus quantitative data to infer Wnt pathway dynamics in other systems. As a basis for understanding Wnt signalling in mammalian cells, a confocal live cell imaging measurement technique is developed to measure the cell and nuclear volumes of MDCK, HEK293T cells and 3 human colorectal cancer cell lines and the concentrations of Wnt signalling proteins β-catenin, Axin, APC, GSK3β and E-cadherin. These parameters provide the basis for formulating Wnt signalling models for kidney/intestinal epithelial mammalian cells. There are significant differences in concentrations of key proteins between Xenopus extracts and mammalian whole cell lysates. Higher concentrations of Axin and lower concentrations of APC are present in mammalian cells. Axin concentrations are greater than APC in kidney epithelial cells, whereas in intestinal epithelial cells the APC concentration is higher than Axin. Computational simulations based on Lee's model, with this new data, suggest a need for a recalibration of the model.A quantitative understanding of Wnt signalling in mammalian cells, in particular human colorectal cancers requires a detailed understanding of the concentrations of key protein complexes over time. Simulations of Wnt signalling in mammalian cells can be initiated

  5. Antiquity of Ediacaran Fossils, Early Shelled Organisms, Recent Radiometric Age-Dates from India and Ancestral Biota

    Science.gov (United States)

    Basu, A.

    2008-03-01

    U-Pb zircon ages and Pb-Pb limestone ages assign Ediacaran and shelly fossils reported from India between 1750 and 950 Ma indicating ancestral diversification of metazoans. Simple bacterial life must have began earlier and may be found in meteorites.

  6. ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Ye, Jia; Li, Songgang;

    2005-01-01

    in comparison to their ancestral sequences. Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repository of known TEs, and increase the effectiveness of RepeatMasker in identifying TEs from genome sequences. Udgivelsesdato: 2005-Sep...

  7. Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders

    OpenAIRE

    Gómez-Marín, Carlos; Tena, Juan J.; Acemel, Rafael D.; López-Mayorga, Macarena; Naranjo, Silvia; de la Calle-Mustienes, Elisa; Maeso, Ignacio; Beccari, Leonardo; Aneas, Ivy; Vielmas, Erika; Bovolenta, Paola; Nobrega, Marcelo A.; Carvajal, Jaime; Gómez-Skarmeta, José Luis

    2015-01-01

    Increasing evidence in the last years indicates that the vast amount of regulatory information contained in mammalian genomes is organized in precise 3D chromatin structures. However, the impact of this spatial chromatin organization on gene expression and its degree of evolutionary conservation is still poorly understood. The Six homeobox genes are essential developmental regulators organized in gene clusters conserved during evolution. Here, we reveal that the Six clusters share a deeply ev...

  8. A Comparative Study of Mammalian Diversification Pattern

    Directory of Open Access Journals (Sweden)

    Wenhua Yu, Junxiao Xu, Yi Wu, Guang Yang

    2012-01-01

    Full Text Available Although mammals have long been regarded as a successful radiation, the diversification pattern among the clades is still poorly known. Higher-level phylogenies are conflicting and comprehensive comparative analyses are still lacking. Using a recently published supermatrix encompassing nearly all extant mammalian families and a novel comparative likelihood approach (MEDUSA, the diversification pattern of mammalian groups was examined. Both order- and family-level phylogenetic analyses revealed the rapid radiation of Boreoeutheria and Euaustralidelphia in the early mammalian history. The observation of a diversification burst within Boreoeutheria at approximately 100 My supports the Long Fuse model in elucidating placental diversification progress, and the rapid radiation of Euaustralidelphia suggests an important role of biogeographic dispersal events in triggering early Australian marsupial rapid radiation. Diversification analyses based on family-level diversity tree revealed seven additional clades with exceptional diversification rate shifts, six of which represent accelerations in net diversification rate as compared to the background pattern. The shifts gave origin to the clades Muridae+Cricetidae, Bovidae+Moschidae+Cervidae, Simiiformes, Echimyidae, Odontoceti (excluding Physeteridae+Kogiidae+Platanistidae, Macropodidae, and Vespertilionidae. Moderate to high extinction rates from background and boreoeutherian diversification patterns indicate the important role of turnovers in shaping the heterogeneous taxonomic richness observed among extant mammalian groups. Furthermore, the present results emphasize the key role of extinction on erasing unusual diversification signals, and suggest that further studies are needed to clarify the historical radiation of some mammalian groups for which MEDUSA did not detect exceptional diversification rates.

  9. Mammalian Cell-Based Sensor System

    Science.gov (United States)

    Banerjee, Pratik; Franz, Briana; Bhunia, Arun K.

    Use of living cells or cellular components in biosensors is receiving increased attention and opens a whole new area of functional diagnostics. The term "mammalian cell-based biosensor" is designated to biosensors utilizing mammalian cells as the biorecognition element. Cell-based assays, such as high-throughput screening (HTS) or cytotoxicity testing, have already emerged as dependable and promising approaches to measure the functionality or toxicity of a compound (in case of HTS); or to probe the presence of pathogenic or toxigenic entities in clinical, environmental, or food samples. External stimuli or changes in cellular microenvironment sometimes perturb the "normal" physiological activities of mammalian cells, thus allowing CBBs to screen, monitor, and measure the analyte-induced changes. The advantage of CBBs is that they can report the presence or absence of active components, such as live pathogens or active toxins. In some cases, mammalian cells or plasma membranes are used as electrical capacitors and cell-cell and cell-substrate contact is measured via conductivity or electrical impedance. In addition, cytopathogenicity or cytotoxicity induced by pathogens or toxins resulting in apoptosis or necrosis could be measured via optical devices using fluorescence or luminescence. This chapter focuses mainly on the type and applications of different mammalian cell-based sensor systems.

  10. 周代宗庙礼制考%The Research on the Etiquettes of Zhou Dynasty’s Ancestral Temple

    Institute of Scientific and Technical Information of China (English)

    王启敏

    2015-01-01

    周代社会中与宗庙相关的礼制多种多样。宗庙始成要举行落成典礼,作歌诗以纪之。祭庙的形式可谓五花八门,而且祭者的态度要十分的恭敬、严谨。诸侯有丧事了,要在宗庙吊唁,规矩也很多。此外,如天子即位,天子(或诸侯)娶妻、嫁女、出国、归国、出征、凯旋等都要在宗庙举行郑重的祭告仪式。在宗庙的守护、装饰、迁移等方面,在当时也有着严格的、不同的礼节制度要遵守。%In Zhou dynasty the related ancestral temple customs are various. After the completion of ancestral temple, it should be inaugurated and poems should be made to memorize. The forms of memorial temples are varied. The attitude of the emperor and monarch muse be very respectful. The same was the monarch’s condolences at the ancestral temple. In addition, the ascending to the throne as emperor, or monarch, getting married or married abroad, returning to the homeland and triumphing must be held in the ancestral temple solemnly and be reported to ancestral temple. The temple’s guardian, decoration, migration and the others also have restricted rules to obey.

  11. Mechanisms of DNA Repair in Mammalian Cells

    International Nuclear Information System (INIS)

    The authors examined DNA synthesis in cultured mammalian cells after irradiation with X-rays or ultraviolet light, using equilibrium density gradient and autoradiographic techniques. Unscheduled DNA synthesis (the synthesis of DNA by cells not in S phase of the cell cycle) occurs at doses of u.v. where survival is greater than 90% and at doses of X-rays where survival is of the order of 50%. At higher doses it was established that repair replication (insertion of precursors into parental strands of DNA ) occurs in these cells, and it is presumed that these two phenomena (unscheduled DNA synthesis and repair replication) are manifestations of the same repair process. During the time that these phenomena occur, very little degradation of DNA takes place, as measured by appearance of prelabelled components of DNA in the medium or in the acid soluble portion of the cell. This is in direct contrast to the situation in bacteria, in which extensive degradation of DNA occurs after irradiation, presumably as a result of enzymatic processes that remove many undamaged bases in addition to the ones injured by the irradiation. A small amount of radioactivity does appear in the acid soluble portion and in the media from prelabelled cells from both irradiated and control mammalian cell cultures. The amount in the medium from irradiated cultures is slightly, but significantly, greater than that from controls; thus there does appear to be a very low level of degradation of DNA in irradiated mammalian cells. These data indicate that the repair of DNA in mammalian cells does not involve the same steps as those that occur in bacteria. The results suggest instead that mammalian cells have a much more specific system for repair, which involves excision of only the damaged portion of the DNA. Possible mechanisms of repair of mammalian DNA are considered. (author)

  12. Analysis on the reconstruction accuracy of the Fitch method for inferring ancestral states

    Directory of Open Access Journals (Sweden)

    Grünewald Stefan

    2011-01-01

    Full Text Available Abstract Background As one of the most widely used parsimony methods for ancestral reconstruction, the Fitch method minimizes the total number of hypothetical substitutions along all branches of a tree to explain the evolution of a character. Due to the extensive usage of this method, it has become a scientific endeavor in recent years to study the reconstruction accuracies of the Fitch method. However, most studies are restricted to 2-state evolutionary models and a study for higher-state models is needed since DNA sequences take the format of 4-state series and protein sequences even have 20 states. Results In this paper, the ambiguous and unambiguous reconstruction accuracy of the Fitch method are studied for N-state evolutionary models. Given an arbitrary phylogenetic tree, a recurrence system is first presented to calculate iteratively the two accuracies. As complete binary tree and comb-shaped tree are the two extremal evolutionary tree topologies according to balance, we focus on the reconstruction accuracies on these two topologies and analyze their asymptotic properties. Then, 1000 Yule trees with 1024 leaves are generated and analyzed to simulate real evolutionary scenarios. It is known that more taxa not necessarily increase the reconstruction accuracies under 2-state models. The result under N-state models is also tested. Conclusions In a large tree with many leaves, the reconstruction accuracies of using all taxa are sometimes less than those of using a leaf subset under N-state models. For complete binary trees, there always exists an equilibrium interval [a, b] of conservation probability, in which the limiting ambiguous reconstruction accuracy equals to the probability of randomly picking a state. The value b decreases with the increase of the number of states, and it seems to converge. When the conservation probability is greater than b, the reconstruction accuracies of the Fitch method increase rapidly. The reconstruction

  13. Elongation Factor-Tu (EF-Tu) proteins structural stability and bioinformatics in ancestral gene reconstruction

    Science.gov (United States)

    Dehipawala, Sunil; Nguyen, A.; Tremberger, G.; Cheung, E.; Schneider, P.; Lieberman, D.; Holden, T.; Cheung, T.

    2013-09-01

    A paleo-experimental evolution report on elongation factor EF-Tu structural stability results has provided an opportunity to rewind the tape of life using the ancestral protein sequence reconstruction modeling approach; consistent with the book of life dogma in current biology and being an important component in the astrobiology community. Fractal dimension via the Higuchi fractal method and Shannon entropy of the DNA sequence classification could be used in a diagram that serves as a simple summary. Results from biomedical gene research provide examples on the diagram methodology. Comparisons between biomedical genes such as EEF2 (elongation factor 2 human, mouse, etc), WDR85 in epigenetics, HAR1 in human specificity, DLG1 in cognitive skill, and HLA-C in mosquito bite immunology with EF Tu DNA sequences have accounted for the reported circular dichroism thermo-stability data systematically; the results also infer a relatively less volatility geologic time period from 2 to 3 Gyr from adaptation viewpoint. Comparison to Thermotoga maritima MSB8 and Psychrobacter shows that Thermus thermophilus HB8 EF-Tu calibration sequence could be an outlier, consistent with free energy calculation by NUPACK. Diagram methodology allows computer simulation studies and HAR1 shows about 0.5% probability from chimp to human in terms of diagram location, and SNP simulation results such as amoebic meningoencephalitis NAF1 suggest correlation. Extensions to the studies of the translation and transcription elongation factor sequences in Megavirus Chiliensis, Megavirus Lba and Pandoravirus show that the studied Pandoravirus sequence could be an outlier with the highest fractal dimension and lowest entropy, as compared to chicken as a deviant in the DNMT3A DNA methylation gene sequences from zebrafish to human and to the less than one percent probability in computer simulation using the HAR1 0.5% probability as reference. The diagram methodology would be useful in ancestral gene

  14. Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European.

    Science.gov (United States)

    Olalde, Iñigo; Allentoft, Morten E; Sánchez-Quinto, Federico; Santpere, Gabriel; Chiang, Charleston W K; DeGiorgio, Michael; Prado-Martinez, Javier; Rodríguez, Juan Antonio; Rasmussen, Simon; Quilez, Javier; Ramírez, Oscar; Marigorta, Urko M; Fernández-Callejo, Marcos; Prada, María Encina; Encinas, Julio Manuel Vidal; Nielsen, Rasmus; Netea, Mihai G; Novembre, John; Sturm, Richard A; Sabeti, Pardis; Marquès-Bonet, Tomàs; Navarro, Arcadi; Willerslev, Eske; Lalueza-Fox, Carles

    2014-03-13

    Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe. The adoption of farming, stock breeding and sedentary societies during the Neolithic may have resulted in adaptive changes in genes associated with immunity and diet. However, the limited data available from earlier hunter-gatherers preclude an understanding of the selective processes associated with this crucial transition to agriculture in recent human evolution. Here we sequence an approximately 7,000-year-old Mesolithic skeleton discovered at the La Braña-Arintero site in León, Spain, to retrieve a complete pre-agricultural European human genome. Analysis of this genome in the context of other ancient samples suggests the existence of a common ancient genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic. The La Braña individual carries ancestral alleles in several skin pigmentation genes, suggesting that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times. Moreover, we provide evidence that a significant number of derived, putatively adaptive variants associated with pathogen resistance in modern Europeans were already present in this hunter-gatherer. PMID:24463515

  15. Major Chromosomal Rearrangements Distinguish Willow and Poplar After the Ancestral "Salicoid" Genome Duplication.

    Science.gov (United States)

    Hou, Jing; Ye, Ning; Dong, Zhongyuan; Lu, Mengzhu; Li, Laigeng; Yin, Tongming

    2016-01-01

    Populus (poplar) and Salix (willow) are sister genera in the Salicaceae family. In both lineages extant species are predominantly diploid. Genome analysis previously revealed that the two lineages originated from a common tetraploid ancestor. In this study, we conducted a syntenic comparison of the corresponding 19 chromosome members of the poplar and willow genomes. Our observations revealed that almost every chromosomal segment had a parallel paralogous segment elsewhere in the genomes, and the two lineages shared a similar syntenic pinwheel pattern for most of the chromosomes, which indicated that the two lineages diverged after the genome reorganization in the common progenitor. The pinwheel patterns showed distinct differences for two chromosome pairs in each lineage. Further analysis detected two major interchromosomal rearrangements that distinguished the karyotypes of willow and poplar. Chromosome I of willow was a conjunction of poplar chromosome XVI and the lower portion of poplar chromosome I, whereas willow chromosome XVI corresponded to the upper portion of poplar chromosome I. Scientists have suggested that Populus is evolutionarily more primitive than Salix. Therefore, we propose that, after the "salicoid" duplication event, fission and fusion of the ancestral chromosomes first give rise to the diploid progenitor of extant Populus species. During the evolutionary process, fission and fusion of poplar chromosomes I and XVI subsequently give rise to the progenitor of extant Salix species. This study contributes to an improved understanding of genome divergence after ancient genome duplication in closely related lineages of higher plants. PMID:27352946

  16. Transgenerational actions of environmental compounds on reproductive disease and identification of epigenetic biomarkers of ancestral exposures.

    Directory of Open Access Journals (Sweden)

    Mohan Manikkam

    Full Text Available Environmental factors during fetal development can induce a permanent epigenetic change in the germ line (sperm that then transmits epigenetic transgenerational inheritance of adult-onset disease in the absence of any subsequent exposure. The epigenetic transgenerational actions of various environmental compounds and relevant mixtures were investigated with the use of a pesticide mixture (permethrin and insect repellant DEET, a plastic mixture (bisphenol A and phthalates, dioxin (TCDD and a hydrocarbon mixture (jet fuel, JP8. After transient exposure of F0 gestating female rats during the period of embryonic gonadal sex determination, the subsequent F1-F3 generations were obtained in the absence of any environmental exposure. The effects on the F1, F2 and F3 generations pubertal onset and gonadal function were assessed. The plastics, dioxin and jet fuel were found to promote early-onset female puberty transgenerationally (F3 generation. Spermatogenic cell apoptosis was affected transgenerationally. Ovarian primordial follicle pool size was significantly decreased with all treatments transgenerationally. Differential DNA methylation of the F3 generation sperm promoter epigenome was examined. Differential DNA methylation regions (DMR were identified in the sperm of all exposure lineage males and found to be consistent within a specific exposure lineage, but different between the exposures. Several genomic features of the DMR, such as low density CpG content, were identified. Exposure-specific epigenetic biomarkers were identified that may allow for the assessment of ancestral environmental exposures associated with adult onset disease.

  17. Evidence from cyclostomes for complex regionalization of the ancestral vertebrate brain.

    Science.gov (United States)

    Sugahara, Fumiaki; Pascual-Anaya, Juan; Oisi, Yasuhiro; Kuraku, Shigehiro; Aota, Shin-ichi; Adachi, Noritaka; Takagi, Wataru; Hirai, Tamami; Sato, Noboru; Murakami, Yasunori; Kuratani, Shigeru

    2016-03-01

    The vertebrate brain is highly complex, but its evolutionary origin remains elusive. Because of the absence of certain developmental domains generally marked by the expression of regulatory genes, the embryonic brain of the lamprey, a jawless vertebrate, had been regarded as representing a less complex, ancestral state of the vertebrate brain. Specifically, the absence of a Hedgehog- and Nkx2.1-positive domain in the lamprey subpallium was thought to be similar to mouse mutants in which the suppression of Nkx2-1 leads to a loss of the medial ganglionic eminence. Here we show that the brain of the inshore hagfish (Eptatretus burgeri), another cyclostome group, develops domains equivalent to the medial ganglionic eminence and rhombic lip, resembling the gnathostome brain. Moreover, further investigation of lamprey larvae revealed that these domains are also present, ruling out the possibility of convergent evolution between hagfish and gnathostomes. Thus, brain regionalization as seen in crown gnathostomes is not an evolutionary innovation of this group, but dates back to the latest vertebrate ancestor before the divergence of cyclostomes and gnathostomes more than 500 million years ago. PMID:26878236

  18. WEB LOG PREPROCESSING BASED ON PARTIAL ANCESTRAL GRAPH TECHNIQUE FOR SESSION CONSTRUCTION

    Directory of Open Access Journals (Sweden)

    S.Chitra

    2012-10-01

    Full Text Available Web access log analysis is to analyze the patterns of web site usage and the features of users behavior. It is the fact that the normal Log data is very noisy and unclear and it is vital to preprocess the log data for efficient web usage mining process. Preprocessing comprises of three phases which includes data cleaning, user identification and session construction. Session construction is very vital and numerous real world problems can be modeled as traversals on graph and mining from these traversals would provide the requirement for preprocessing phase. On the other hand, the traversals on unweighted graph have been taken into consideration in existing works. This paper oversimplifies this to the case where vertices of graph are given weights to reflect their significance. The proposed method constructs sessions as a Partial Ancestral Graph which contains pages with calculated weights. This will help site administrators to find the interesting pages for users and to redesign their web pages. After weighting each page according to browsing time a PAG structure is constructed for each user session. Existing system in which there is a problem of learning with the latent variables of the data and the problem can be overcome by the proposed method.

  19. The ancestral circadian clock of monarch butterflies: role in time-compensated sun compass orientation.

    Science.gov (United States)

    Reppert, S M

    2007-01-01

    The circadian clock has a vital role in monarch butterfly (Danaus plexippus) migration by providing the timing component of time-compensated sun compass orientation, which contributes to navigation to the overwintering grounds. The location of circadian clock cells in monarch brain has been identified in the dorsolateral protocerebrum (pars lateralis); these cells express PERIOD, TIMELESS, and a Drosophila-like cryptochrome designated CRY1. Monarch butterflies, like all other nondrosophilid insects examined so far, express a second cry gene (designated insect CRY2) that encodes a vertebrate-like CRY that is also expressed in pars lateralis. An ancestral circadian clock mechanism has been defined in monarchs, in which CRY1 functions as a blue light photoreceptor for photic entrainment, whereas CRY2 functionswithin the clockwork as themajor transcriptional repressor of an intracellular negative transcriptional feedback loop. A CRY1-staining neural pathway has been identified that may connect the circadian (navigational) clock to polarized light input important for sun compass navigation, and a CRY2-positive neural pathway has been discovered that may communicate circadian information directly from the circadian clock to the central complex, the likely site of the sun compass. The monarch butterfly may thus use the CRY proteins as components of the circadian mechanism and also as output molecules that connect the clock to various aspects of the sun compass apparatus. PMID:18419268

  20. The vomeronasal complex of nocturnal strepsirhines and implications for the ancestral condition in primates.

    Science.gov (United States)

    Garrett, Eva C; Dennis, John C; Bhatnagar, Kunwar P; Durham, Emily L; Burrows, Anne M; Bonar, Christopher J; Steckler, Natalie K; Morrison, Edward E; Smith, Timothy D

    2013-12-01

    This study investigates the vomeronasal organ in extant nocturnal strepsirhines as a model for ancestral primates. Cadaveric samples from 10 strepsirhine species, ranging from fetal to adult ages, were studied histologically. Dimensions of structures in the vomeronasal complex, such as the vomeronasal neuroepithelium (VNNE) and vomeronasal cartilage (VNC) were measured in serial sections and selected specimens were studied immunohistochemically to determine physiological aspects of the vomeronasal sensory neurons (VSNs). Osteological features corresponding to vomeronasal structures were studied histologically and related to 3-D CT reconstructions. The VNC consistently rests in a depression on the palatal portion of the maxilla, which we refer to as the vomeronasal groove (VNG). Most age comparisons indicate that in adults VNNE is about twice the length compared with perinatal animals. In VNNE volume, adults are 2- to 3-fold larger compared with perinatal specimens. Across ages, a strong linear relationship exists between VNNE dimensions and body length, mass, and midfacial length. Results indicate that the VNNE of nocturnal strepsirhines is neurogenic postnatally based on GAP43 expression. In addition, based on Olfactory Marker Protein expression, terminally differentiated VSNs are present in the VNNE. Therefore, nocturnal strepsirhines have basic similarities to rodents in growth and maturational characteristics of VSNs. These results indicate that a functional vomeronasal system is likely present in all nocturnal strepsirhines. Finally, given that osteological features such as the VNG are visible on midfacial bones, primate fossils can be assessed to determine whether primate ancestors possessed a vomeronasal complex morphologically similar to that of modern nocturnal strepsirhines. PMID:24249398

  1. Major Chromosomal Rearrangements Distinguish Willow and Poplar After the Ancestral “Salicoid” Genome Duplication

    Science.gov (United States)

    Hou, Jing; Ye, Ning; Dong, Zhongyuan; Lu, Mengzhu; Li, Laigeng; Yin, Tongming

    2016-01-01

    Populus (poplar) and Salix (willow) are sister genera in the Salicaceae family. In both lineages extant species are predominantly diploid. Genome analysis previously revealed that the two lineages originated from a common tetraploid ancestor. In this study, we conducted a syntenic comparison of the corresponding 19 chromosome members of the poplar and willow genomes. Our observations revealed that almost every chromosomal segment had a parallel paralogous segment elsewhere in the genomes, and the two lineages shared a similar syntenic pinwheel pattern for most of the chromosomes, which indicated that the two lineages diverged after the genome reorganization in the common progenitor. The pinwheel patterns showed distinct differences for two chromosome pairs in each lineage. Further analysis detected two major interchromosomal rearrangements that distinguished the karyotypes of willow and poplar. Chromosome I of willow was a conjunction of poplar chromosome XVI and the lower portion of poplar chromosome I, whereas willow chromosome XVI corresponded to the upper portion of poplar chromosome I. Scientists have suggested that Populus is evolutionarily more primitive than Salix. Therefore, we propose that, after the “salicoid” duplication event, fission and fusion of the ancestral chromosomes first give rise to the diploid progenitor of extant Populus species. During the evolutionary process, fission and fusion of poplar chromosomes I and XVI subsequently give rise to the progenitor of extant Salix species. This study contributes to an improved understanding of genome divergence after ancient genome duplication in closely related lineages of higher plants. PMID:27352946

  2. A PCA-based method for ancestral informative markers selection in structured populations

    Institute of Scientific and Technical Information of China (English)

    ZHANG Feng; ZHANG Lei; DENG Hong-Wen

    2009-01-01

    Identification of population structure can help trace population histories and identify disease genes.Structured association (SA) is a commonly used approach for population structure identification and association mapping. A major issue with SA is that its performance greatly depends on the informativeness and the numbers of ancestral informative markers (AIMs). Present major AIM selection methods mostly require prior individual ancestry information, which is usually not available or uncertain in practice. To address this potential weakness, we herein develop a novel approach for AIM selection based on principle component analysis (PCA), which does not require prior ancestry information of study subjects. Our simulation and real genetic data analysis results suggest that, with equivalent AIMs,PCA-based selected AIMs can significantly increase the accuracy of inferred individual ancestries compared with traditionally randomly selected AIMs. Our method can easily be applied to whole genome data to select a set of highly informative AIMs in population structure, which can then be used to identify potential population structure and correct possible statistical biases caused by population stratification.

  3. The hypothetical ancestral animal. the Urmetazoa: telomerase activity in sponges (Porifera

    Directory of Open Access Journals (Sweden)

    ISABEL M. MÜLLER

    2003-05-01

    Full Text Available Sponges (Porifera represent the lowest metazoan phylum, characterized by a pronounced plasticity in the determination of cell lineages, and they are the closest related taxon to the hypothetical ancestral animal, the Urmetazoa, from which the metazoan lineages diverged. In a first approach to elucidate the molecular mechanisms controlling the switch from the cell lineage with a putative indefinite growth capacity to senescent, somatic cells, the activity of the telomerase as an indicator for immortality has been determined. The studies were performed with the marine demosponges Suberites domuncula and Geodia cydonium, in vivo with tissue but also in vitro using the primmorph system. Primmorphs are formed from dissociated cells which have retained their proliferation potency. It was found that the activity of telomerase in tissue of both sponges is high. Based on this and additional findings it is assumed that the separation of the senescent sponge cell lineage from the immortal germ-/somatic cell lineage is triggered by the loss of contact to cell adhesion factors. First evidence is included which suggests that the final progress of the senescent, telomerase-negative cells to cell death is caused by apoptosis.

  4. Evolutionary Psychology: How Psychological Mechanisms Shaped by Natural Selection for Ancestral Environments Produce Current Behaviours

    Institute of Scientific and Technical Information of China (English)

    Charles Crawford

    2009-01-01

    The central purpose of this paper is to explain how Darwin's theory of evolution by natural selection can be used in understanding current human behaviour. First, Darwin's logic is briefly described. Development is an important issue when applying evolutionary theory to human behaviour. The notion of innate developmental orga-nization of psychological mechanisms is introduced. The possible social and political outcomes produced when differ-ent levels of innate developmental organization are paired with different beliefs about it are considered. The notion of psychological mechanisms as evolved adaptations is considered in some detail. Then I discuss different ways evo-htionists think about how genes are involved in the development of adaptations. The paper concludes with a frame-work for considering how ancestral adaptations function in current environments and outlines some ways of studying them. In China and many other parts of the world people desire a more harmonious society. Ⅰ hope that this paper will be of some small help in achieving this great task.

  5. A PCA-based method for ancestral informative markers selection in structured populations

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Identification of population structure can help trace population histories and identify disease genes. Structured association (SA) is a commonly used approach for population structure identification and association mapping. A major issue with SA is that its performance greatly depends on the informa-tiveness and the numbers of ancestral informative markers (AIMs). Present major AIM selection meth-ods mostly require prior individual ancestry information, which is usually not available or uncertain in practice. To address this potential weakness, we herein develop a novel approach for AIM selection based on principle component analysis (PCA), which does not require prior ancestry information of study subjects. Our simulation and real genetic data analysis results suggest that, with equivalent AIMs, PCA-based selected AIMs can significantly increase the accuracy of inferred individual ancestries compared with traditionally randomly selected AIMs. Our method can easily be applied to whole genome data to select a set of highly informative AIMs in population structure, which can then be used to identify potential population structure and correct possible statistical biases caused by population stratification.

  6. Inheritance of the 8.1 ancestral haplotype in recurrent pregnancy loss

    DEFF Research Database (Denmark)

    Kolte, Astrid M; Nielsen, Henriette S; Steffensen, Rudi;

    2015-01-01

    BACKGROUND AND OBJECTIVES: The 8.1 ancestral haplotype (AH) (HLA-A1, C7, B8, C4AQ0, C4B1, DR3, DQ2) is a remarkably long and conserved haplotype in the human major histocompatibility complex. It has been associated with both beneficial and detrimental effects, consistent with antagonistic....... The objective was to test the gestational drive theory for the 8.1AH in women with RPL and their live born children. METHODOLOGY: We investigated the inheritance of the 8.1AH from 82 heterozygous RPL women to 110 live born children. All participants were genotyped for HLA-A, -B and -DRB1 in DNA from...... EDTA-treated blood or buccal swaps. Inheritance was compared with a Mendelian inheritance of 50% using a two-sided exact binomial test. RESULTS: We found that 55% of the live born children had inherited the 8.1AH, which was not significantly higher than the expected 50% (P = 0.29). Interestingly, we...

  7. Structure and function of mammalian cilia

    DEFF Research Database (Denmark)

    Satir, Peter; Christensen, Søren T

    2008-01-01

    In the past half century, beginning with electron microscopic studies of 9 + 2 motile and 9 + 0 primary cilia, novel insights have been obtained regarding the structure and function of mammalian cilia. All cilia can now be viewed as sensory cellular antennae that coordinate a large number of...

  8. Erythropoietin binding protein from mammalian serum

    Energy Technology Data Exchange (ETDEWEB)

    Clemons, G.K.

    1997-04-29

    Purified mammalian erythropoietin binding-protein is disclosed, and its isolation, identification, characterization, purification, and immunoassay are described. The erythropoietin binding protein can be used for regulation of erythropoiesis by regulating levels and half-life of erythropoietin. A diagnostic kit for determination of level of erythropoietin binding protein is also described. 11 figs.

  9. Erythropoietin binding protein from mammalian serum

    Energy Technology Data Exchange (ETDEWEB)

    Clemons, Gisela K. (Berkeley, CA)

    1997-01-01

    Purified mammalian erythropoietin binding-protein is disclosed, and its isolation, identification, characterization, purification, and immunoassay are described. The erythropoietin binding protein can be used for regulation of erythropoiesis by regulating levels and half-life of erythropoietin. A diagnostic kit for determination of level of erythropoietin binding protein is also described.

  10. A promoter-level mammalian expression atlas

    KAUST Repository

    Forest, Alistair R R

    2014-03-26

    Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly ‘housekeeping’, whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research.

  11. Mutagenesis and DNA repair in mammalian cells

    International Nuclear Information System (INIS)

    Two aspects of DNA damage and repair in mammalian cells were investigated. Using a lambda phage shuttle vector, a system was developed to study mutations arising in the DNA of mammalian cells. This system was used to determine the spectrum of mutations induced in cellular DNA by ultraviolet light. Also, the repair of base pair mismatches in DNA was studied by the development of a method to detect a DNA mismatch repair activity in extracts made from cultured human cells. In order to study mutations arising in mammalian cells, stable mouse L cell lines were established with multiple copies of lambda phage vector which contains the supF gene of E. coli as a target for mutagenesis. Rescue of viable phage from high molecular weight mouse cell DNA using lambda in vitro packaging extracts was efficient and yielded a negligible background of phage with mutations in the supF gene. From mouse cells exposed to 12 J/m2 of 254 nm ultraviolet (UV) light, 78,510 phage were rescued of which eight were found to have mutant supF genes. DNA sequence analysis of the mutants suggests that the primary site of UV mutagenesis in mammalian cells is at pyrimidine-cytosine (Py-C) sequences, and that the most frequent mutation at this site is a C to T transition

  12. Crossroads between Bacterial and Mammalian Glycosyltransferases

    Science.gov (United States)

    Brockhausen, Inka

    2014-01-01

    Bacterial glycosyltransferases (GT) often synthesize the same glycan linkages as mammalian GT; yet, they usually have very little sequence identity. Nevertheless, enzymatic properties, folding, substrate specificities, and catalytic mechanisms of these enzyme proteins may have significant similarity. Thus, bacterial GT can be utilized for the enzymatic synthesis of both bacterial and mammalian types of complex glycan structures. A comparison is made here between mammalian and bacterial enzymes that synthesize epitopes found in mammalian glycoproteins, and those found in the O antigens of Gram-negative bacteria. These epitopes include Thomsen–Friedenreich (TF or T) antigen, blood group O, A, and B, type 1 and 2 chains, Lewis antigens, sialylated and fucosylated structures, and polysialic acids. Many different approaches can be taken to investigate the substrate binding and catalytic mechanisms of GT, including crystal structure analyses, mutations, comparison of amino acid sequences, NMR, and mass spectrometry. Knowledge of the protein structures and functions helps to design GT for specific glycan synthesis and to develop inhibitors. The goals are to develop new strategies to reduce bacterial virulence and to synthesize vaccines and other biologically active glycan structures. PMID:25368613

  13. Metabolic-flux analysis of mammalian-cell culture.

    NARCIS (Netherlands)

    Bonarius, H.P.J.

    1998-01-01

    In the biopharmaceutical industry mammalian cells are cultivated for the production of recombinant glycoproteins, vaccines, and monoclonal antibodies. In contrast to other expression systems, such as prokaryotes or yeasts, mammalian cells are able to glycosylate and fold therapeutic proteins correct

  14. Divergent evolution of vitamin B9 binding underlies Juno-mediated adhesion of mammalian gametes.

    Science.gov (United States)

    Han, Ling; Nishimura, Kaoru; Sadat Al Hosseini, Hamed; Bianchi, Enrica; Wright, Gavin J; Jovine, Luca

    2016-02-01

    The interaction between egg and sperm is the first necessary step of fertilization in all sexually reproducing organisms. A decade-long search for a protein pair mediating this event in mammals culminated in the identification of the glycosylphosphatidylinositol (GPI)-anchored glycoprotein Juno as the egg plasma membrane receptor of sperm Izumo1 [1,2]. The Juno-Izumo1 interaction was shown to be essential for fertilization since mice lacking either gene exhibit sex-specific sterility, making these proteins promising non-hormonal contraceptive targets [1,3]. No structural information is available on how gamete membranes interact at fertilization, and it is unclear how Juno - which was previously named folate receptor (FR) 4, based on sequence similarity considerations - triggers membrane adhesion by binding Izumo1. Here, we report the crystal structure of Juno and find that the overall fold is similar to that of FRα and FRβ but with significant flexibility within the area that corresponds to the rigid ligand-binding site of these bona fide folate receptors. This explains both the inability of Juno to bind vitamin B9/folic acid [1], and why mutations within the flexible region can either abolish or change the species specificity of this interaction. Furthermore, structural similarity between Juno and the cholesterol-binding Niemann-Pick disease type C1 protein (NPC1) suggests how the modified binding surface of Juno may recognize the helical structure of the amino-terminal domain of Izumo1. As Juno appears to be a mammalian innovation, our study indicates that a key evolutionary event in mammalian reproduction originated from the neofunctionalization of the vitamin B9-binding pocket of an ancestral folate receptor molecule. PMID:26859261

  15. Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders.

    Science.gov (United States)

    Gómez-Marín, Carlos; Tena, Juan J; Acemel, Rafael D; López-Mayorga, Macarena; Naranjo, Silvia; de la Calle-Mustienes, Elisa; Maeso, Ignacio; Beccari, Leonardo; Aneas, Ivy; Vielmas, Erika; Bovolenta, Paola; Nobrega, Marcelo A; Carvajal, Jaime; Gómez-Skarmeta, José Luis

    2015-06-16

    Increasing evidence in the last years indicates that the vast amount of regulatory information contained in mammalian genomes is organized in precise 3D chromatin structures. However, the impact of this spatial chromatin organization on gene expression and its degree of evolutionary conservation is still poorly understood. The Six homeobox genes are essential developmental regulators organized in gene clusters conserved during evolution. Here, we reveal that the Six clusters share a deeply evolutionarily conserved 3D chromatin organization that predates the Cambrian explosion. This chromatin architecture generates two largely independent regulatory landscapes (RLs) contained in two adjacent topological associating domains (TADs). By disrupting the conserved TAD border in one of the zebrafish Six clusters, we demonstrate that this border is critical for preventing competition between promoters and enhancers located in separated RLs, thereby generating different expression patterns in genes located in close genomic proximity. Moreover, evolutionary comparison of Six-associated TAD borders reveals the presence of CCCTC-binding factor (CTCF) sites with diverging orientations in all studied deuterostomes. Genome-wide examination of mammalian HiC data reveals that this conserved CTCF configuration is a general signature of TAD borders, underscoring that common organizational principles underlie TAD compartmentalization in deuterostome evolution. PMID:26034287

  16. Identification of the ancestral haplotype for apolipoprotein B suggests an African origin of Homo sapiens sapiens and traces their subsequent migration to Europe and the Pacific

    International Nuclear Information System (INIS)

    The probable ancestral haplotype for human apolipoprotein B (apoB) has been identified through immunological analysis of chimpanzee and gorilla serum and sequence analysis of their DNA. Moreover, the frequency of this ancestral apoB haplotype among different human populations provides strong support for the African origin of Homo sapiens sapiens and their subsequent migration from Africa to Europe and to the Pacific. The approach used here for the identification of the ancestral human apoB haplotype is likely to be applicable to many other genes

  17. Identification of the ancestral haplotype for apolipoprotein B suggests an African origin of Homo sapiens sapiens and traces their subsequent migration to Europe and the Pacific

    Energy Technology Data Exchange (ETDEWEB)

    Rapacz, J.; Hasler-Rapacz, J.O. (Univ. of Wisconsin, Madison (United States)); Chen, L.; Wu, Mingjiuan; Schumaker, V.N. (Univ. of California, Los Angeles (United States)); Butler-Brunner, E.; Butler, R. (Swiss Red Cross Blood Transfusion Service, Bern (Switzerland))

    1991-02-15

    The probable ancestral haplotype for human apolipoprotein B (apoB) has been identified through immunological analysis of chimpanzee and gorilla serum and sequence analysis of their DNA. Moreover, the frequency of this ancestral apoB haplotype among different human populations provides strong support for the African origin of Homo sapiens sapiens and their subsequent migration from Africa to Europe and to the Pacific. The approach used here for the identification of the ancestral human apoB haplotype is likely to be applicable to many other genes.

  18. Metabolic-flux analysis of mammalian-cell culture.

    OpenAIRE

    Bonarius, H.P.J.

    1998-01-01

    In the biopharmaceutical industry mammalian cells are cultivated for the production of recombinant glycoproteins, vaccines, and monoclonal antibodies. In contrast to other expression systems, such as prokaryotes or yeasts, mammalian cells are able to glycosylate and fold therapeutic proteins correctly, and therefore the only possible production system for many (recombinant) therapeutics.Cultivated mammalian cells are similar to tumor cells: in contrast to normal cells in mammalian tissue they...

  19. The Crystal Structure of Aq_328 from the Hyperthermophilic Bacteria Aquifex aeolicus Shows an Ancestral Histone Fold

    OpenAIRE

    Qiu, Yang; Tereshko, Valentina; Kim, Youngchang; Zhang, Rongguang; Collart, Frank; Yousef, Mohammed; Kossiakoff, Anthony; Joachimiak, Andrzej

    2006-01-01

    The structure of Aq_328, an uncharacterized protein from hyperthermophilic bacteria Aquifex aeolicus, has been determined to 1.9 Å by using multi-wavelength anomalous diffraction (MAD) phasing. Although the amino acid sequence analysis shows that Aq_328 has no significant similarity to proteins with a known structure and function, the structure comparison by using the Dali server reveals that it: (1) assumes a histone-like fold, and (2) is similar to an ancestral nuclear histone protein (PDB ...

  20. Genotype-based ancestral background consistently predicts efficacy and side effects across treatments in CATIE and STAR*D.

    Directory of Open Access Journals (Sweden)

    Daniel E Adkins

    Full Text Available Only a subset of patients will typically respond to any given prescribed drug. The time it takes clinicians to declare a treatment ineffective leaves the patient in an impaired state and at unnecessary risk for adverse drug effects. Thus, diagnostic tests robustly predicting the most effective and safe medication for each patient prior to starting pharmacotherapy would have tremendous clinical value. In this article, we evaluated the use of genetic markers to estimate ancestry as a predictive component of such diagnostic tests. We first estimated each patient's unique mosaic of ancestral backgrounds using genome-wide SNP data collected in the Clinical Antipsychotic Trials of Intervention Effectiveness (CATIE (n = 765 and the Sequenced Treatment Alternatives to Relieve Depression (STAR*D (n = 1892. Next, we performed multiple regression analyses to estimate the predictive power of these ancestral dimensions. For 136/89 treatment-outcome combinations tested in CATIE/STAR*D, results indicated 1.67/1.84 times higher median test statistics than expected under the null hypothesis assuming no predictive power (p<0.01, both samples. Thus, ancestry showed robust and pervasive correlations with drug efficacy and side effects in both CATIE and STAR*D. Comparison of the marginal predictive power of MDS ancestral dimensions and self-reported race indicated significant improvements to model fit with the inclusion of MDS dimensions, but mixed evidence for self-reported race. Knowledge of each patient's unique mosaic of ancestral backgrounds provides a potent immediate starting point for developing algorithms identifying the most effective and safe medication for a wide variety of drug-treatment response combinations. As relatively few new psychiatric drugs are currently under development, such personalized medicine offers a promising approach toward optimizing pharmacotherapy for psychiatric conditions.

  1. Genetic evidence for the ancestral loss of short-wavelength-sensitive cone pigments in mysticete and odontocete cetaceans.

    OpenAIRE

    Levenson, D H; Dizon, A

    2003-01-01

    All mammals ancestrally possessed two types of cone pigments, an arrangement that persists in nearly all contemporary species. However, the absence of one of these cone types, the short-wavelength-sensitive (SWS) cone, has recently been established in several delphinoid cetacean species, indicating that the loss of this pigment type may be widespread among cetaceans. To evaluate the functional condition of SWS cones in cetaceans, partial SWS cone-opsin gene sequences were obtained from nuclea...

  2. Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals

    Directory of Open Access Journals (Sweden)

    Keightley Peter D

    2008-09-01

    Full Text Available Abstract Background Molecular evolutionary studies in mammals often estimate nucleotide substitution rates within and outside CpG dinucleotides separately. Frequently, in alignments of two sequences, the division of sites into CpG and non-CpG classes is based simply on the presence or absence of a CpG dinucleotide in either sequence, a procedure that we refer to as CpG/non-CpG assignment. Although it likely that this procedure is biased, it is generally assumed that the bias is negligible if species are very closely related. Results Using simulations of DNA sequence evolution we show that assignment of the ancestral CpG state based on the simple presence/absence of the CpG dinucleotide can seriously bias estimates of the substitution rate, because many true non-CpG changes are misassigned as CpG. Paradoxically, this bias is most severe between closely related species, because a minimum of two substitutions are required to misassign a true ancestral CpG site as non-CpG whereas only a single substitution is required to misassign a true ancestral non-CpG site as CpG in a two branch tree. We also show that CpG misassignment bias differentially affects fourfold degenerate and noncoding sites due to differences in base composition such that fourfold degenerate sites can appear to be evolving more slowly than noncoding sites. We demonstrate that the effects predicted by our simulations occur in a real evolutionary setting by comparing substitution rates estimated from human-chimp coding and intronic sequence using CpG/non-CpG assignment with estimates derived from a method that is largely free from bias. Conclusion Our study demonstrates that a common method of assigning sites into CpG and non CpG classes in pairwise alignments is seriously biased and recommends against the adoption of ad hoc methods of ancestral state assignment.

  3. Impacts of Plant-Based Foods in Ancestral Hominin Diets on the Metabolism and Function of Gut Microbiota In Vitro

    OpenAIRE

    Gary S Frost; Walton, Gemma E; Jonathan R Swann; Psichas, Arianna; Costabile, Adele; Johnson, Laura P.; Sponheimer, Matt; Glenn R Gibson; Barraclough, Timothy G.

    2014-01-01

    ABSTRACT Ancestral human populations had diets containing more indigestible plant material than present-day diets in industrialized countries. One hypothesis for the rise in prevalence of obesity is that physiological mechanisms for controlling appetite evolved to match a diet with plant fiber content higher than that of present-day diets. We investigated how diet affects gut microbiota and colon cells by comparing human microbial communities with those from a primate that has an extreme plan...

  4. Impacts of plant-based foods in ancestral hominin diets on the metabolism and function of gut microbiota in vitro

    OpenAIRE

    Gary S Frost; Gemma E Walton; Swann, Jonathan R.; Psichas, Arianna; Costabile, Adele; Laura P. Johnson; Sponheimer, Matt; Glenn R Gibson; Barraclough, Timothy G.

    2014-01-01

    Ancestral human populations had diets containing more indigestible plant material than present-day diets in industrialized countries. One hypothesis for the rise in prevalence of obesity is that physiological mechanisms for controlling appetite evolved to match a diet with plant fiber content higher than that of present-day diets. We investigated how diet affects gut microbiota and colon cells by comparing human microbial communities with those from a primate that has an extreme plant-based d...

  5. Are Hox genes ancestrally involved in axial patterning? Evidence from the hydrozoan Clytia hemisphaerica (Cnidaria.

    Directory of Open Access Journals (Sweden)

    Roxane Chiori

    Full Text Available BACKGROUND: The early evolution and diversification of Hox-related genes in eumetazoans has been the subject of conflicting hypotheses concerning the evolutionary conservation of their role in axial patterning and the pre-bilaterian origin of the Hox and ParaHox clusters. The diversification of Hox/ParaHox genes clearly predates the origin of bilaterians. However, the existence of a "Hox code" predating the cnidarian-bilaterian ancestor and supporting the deep homology of axes is more controversial. This assumption was mainly based on the interpretation of Hox expression data from the sea anemone, but growing evidence from other cnidarian taxa puts into question this hypothesis. METHODOLOGY/PRINCIPAL FINDINGS: Hox, ParaHox and Hox-related genes have been investigated here by phylogenetic analysis and in situ hybridisation in Clytia hemisphaerica, an hydrozoan species with medusa and polyp stages alternating in the life cycle. Our phylogenetic analyses do not support an origin of ParaHox and Hox genes by duplication of an ancestral ProtoHox cluster, and reveal a diversification of the cnidarian HOX9-14 genes into three groups called A, B, C. Among the 7 examined genes, only those belonging to the HOX9-14 and the CDX groups exhibit a restricted expression along the oral-aboral axis during development and in the planula larva, while the others are expressed in very specialised areas at the medusa stage. CONCLUSIONS/SIGNIFICANCE: Cross species comparison reveals a strong variability of gene expression along the oral-aboral axis and during the life cycle among cnidarian lineages. The most parsimonious interpretation is that the Hox code, collinearity and conservative role along the antero-posterior axis are bilaterian innovations.

  6. Allelic lineages of the ficolin genes (FCNs are passed from ancestral to descendant primates.

    Directory of Open Access Journals (Sweden)

    Tina Hummelshøj

    Full Text Available The ficolins recognize carbohydrates and acetylated compounds on microorganisms and dying host cells and are able to activate the lectin pathway of the complement system. In humans, three ficolin genes have been identified: FCN1, FCN2 and FCN3, which encode ficolin-1, ficolin-2 and ficolin-3, respectively. Rodents have only two ficolins designated ficolin-A and ficolin-B that are closely related to human ficolin-1, while the rodent FCN3 orthologue is a pseudogene. Ficolin-2 and ficolin-3 have so far only been observed in humans. Thus, we performed a systematic investigation of the FCN genes in non-human primates. The exons and intron-exon boundaries of the FCN1-3 genes were sequenced in the following primate species: chimpanzee, gorilla, orangutan, rhesus macaque, cynomolgus macaque, baboon and common marmoset. We found that the exon organisation of the FCN genes was very similar between all the non-human primates and the human FCN genes. Several variations in the FCN genes were found in more than one primate specie suggesting that they were carried from one species to another including humans. The amino acid diversity of the ficolins among human and non-human primate species was estimated by calculating the Shannon entropy revealing that all three proteins are generally highly conserved. Ficolin-1 and ficolin-2 showed the highest diversity, whereas ficolin-3 was more conserved. Ficolin-2 and ficolin-3 were present in non-human primate sera with the same characteristic oligomeric structures as seen in human serum. Taken together all the FCN genes show the same characteristics in lower and higher primates. The existence of trans-species polymorphisms suggests that different FCN allelic lineages may be passed from ancestral to descendant species.

  7. An Ancestral Role for CONSTITUTIVE TRIPLE RESPONSE1 Proteins in Both Ethylene and Abscisic Acid Signaling.

    Science.gov (United States)

    Yasumura, Yuki; Pierik, Ronald; Kelly, Steven; Sakuta, Masaaki; Voesenek, Laurentius A C J; Harberd, Nicholas P

    2015-09-01

    Land plants have evolved adaptive regulatory mechanisms enabling the survival of environmental stresses associated with terrestrial life. Here, we focus on the evolution of the regulatory CONSTITUTIVE TRIPLE RESPONSE1 (CTR1) component of the ethylene signaling pathway that modulates stress-related changes in plant growth and development. First, we compare CTR1-like proteins from a bryophyte, Physcomitrella patens (representative of early divergent land plants), with those of more recently diverged lycophyte and angiosperm species (including Arabidopsis [Arabidopsis thaliana]) and identify a monophyletic CTR1 family. The fully sequenced P. patens genome encodes only a single member of this family (PpCTR1L). Next, we compare the functions of PpCTR1L with that of related angiosperm proteins. We show that, like angiosperm CTR1 proteins (e.g. AtCTR1 of Arabidopsis), PpCTR1L modulates downstream ethylene signaling via direct interaction with ethylene receptors. These functions, therefore, likely predate the divergence of the bryophytes from the land-plant lineage. However, we also show that PpCTR1L unexpectedly has dual functions and additionally modulates abscisic acid (ABA) signaling. In contrast, while AtCTR1 lacks detectable ABA signaling functions, Arabidopsis has during evolution acquired another homolog that is functionally distinct from AtCTR1. In conclusion, the roles of CTR1-related proteins appear to have functionally diversified during land-plant evolution, and angiosperm CTR1-related proteins appear to have lost an ancestral ABA signaling function. Our study provides new insights into how molecular events such as gene duplication and functional differentiation may have contributed to the adaptive evolution of regulatory mechanisms in plants. PMID:26243614

  8. Identification of the ancestral killer immunoglobulin-like receptor gene in primates

    Directory of Open Access Journals (Sweden)

    Coggill Penny

    2006-08-01

    Full Text Available Abstract Background Killer Immunoglobulin-like Receptors (KIR are essential immuno-surveillance molecules. They are expressed on natural killer and T cells, and interact with human leukocyte antigens. KIR genes are highly polymorphic and contribute vital variability to our immune system. Numerous KIR genes, belonging to five distinct lineages, have been identified in all primates examined thus far and shown to be rapidly evolving. Since few KIR remain orthologous between species, with only one of them, KIR2DL4, shown to be common to human, apes and monkeys, the evolution of the KIR gene family in primates remains unclear. Results Using comparative analyses, we have identified the ancestral KIR lineage (provisionally named KIR3DL0 in primates. We show KIR3DL0 to be highly conserved with the identification of orthologues in human (Homo sapiens, common chimpanzee (Pan troglodytes, gorilla (Gorilla gorilla, rhesus monkey (Macaca mulatta and common marmoset (Callithrix jacchus. We predict KIR3DL0 to encode a functional molecule in all primates by demonstrating expression in human, chimpanzee and rhesus monkey. Using the rhesus monkey as a model, we further show the expression profile to be typical of KIR by quantitative measurement of KIR3DL0 from an enriched population of natural killer cells. Conclusion One reason why KIR3DL0 may have escaped discovery for so long is that, in human, it maps in between two related leukocyte immunoglobulin-like receptor clusters outside the known KIR gene cluster on Chromosome 19. Based on genomic, cDNA, expression and phylogenetic data, we report a novel lineage of immunoglobulin receptors belonging to the KIR family, which is highly conserved throughout 50 million years of primate evolution.

  9. The ancestral activation promiscuity of ADP-glucose pyrophosphorylases from oxygenic photosynthetic organisms

    Directory of Open Access Journals (Sweden)

    Kuhn Misty L

    2013-02-01

    Full Text Available Abstract Background ADP-glucose pyrophosphorylase (ADP-Glc PPase catalyzes the first committed step in the synthesis of glycogen in bacteria and starch in algae and plants. In oxygenic photosynthetic organisms, ADP-Glc PPase is mainly activated by 3-phosphoglycerate (3-PGA and to a lesser extent by other metabolites. In this work, we analyzed the activation promiscuity of ADP-Glc PPase subunits from the cyanobacterium Anabaena PCC 7120, the green alga Ostreococcus tauri, and potato (Solanum tuberosum tuber by comparing a specificity constant for 3-PGA, fructose-1,6-bisphosphate (FBP, fructose-6-phosphate, and glucose-6-phosphate. Results The 3-PGA specificity constant for the enzymes from Anabaena (homotetramer, O. tauri, and potato tuber was considerably higher than for other activators. O. tauri and potato tuber enzymes were heterotetramers comprising homologous small and large subunits. Conversely, the O. tauri small subunit (OtaS homotetramer was more promiscuous because its FBP specificity constant was similar to that for 3-PGA. To explore the role of both OtaS and OtaL (O. tauri large subunit in determining the specificity of the heterotetramer, we knocked out the catalytic activity of each subunit individually by site-directed mutagenesis. Interestingly, the mutants OtaSD148A/OtaL and OtaS/OtaLD171A had higher specificity constants for 3-PGA than for FBP. Conclusions After gene duplication, OtaS seemed to have lost specificity for 3-PGA compared to FBP. This was physiologically and evolutionarily feasible because co-expression of both subunits restored the specificity for 3-PGA of the resulting heterotetrameric wild type enzyme. This widespread promiscuity seems to be ancestral and intrinsic to the enzyme family. Its presence could constitute an efficient evolutionary mechanism to accommodate the ADP-Glc PPase regulation to different metabolic needs.

  10. Toxic and nontoxic components of botulinum neurotoxin complex are evolved from a common ancestral zinc protein

    Energy Technology Data Exchange (ETDEWEB)

    Inui, Ken [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan); Japan Society for the Promotion of Science, 1-8 Chiyoda-ku, Tokyo 102-8472 (Japan); Sagane, Yoshimasa [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan); Miyata, Keita [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan); Japan Society for the Promotion of Science, 1-8 Chiyoda-ku, Tokyo 102-8472 (Japan); Miyashita, Shin-Ichiro [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan); Suzuki, Tomonori [Department of Bacteriology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558 (Japan); Shikamori, Yasuyuki [Agilent Technologies International Japan, Ltd. Takaura-cho 9-1, Hachioji-shi, Tokyo 192-0033 (Japan); Ohyama, Tohru; Niwa, Koichi [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan); Watanabe, Toshihiro, E-mail: t-watana@bioindustry.nodai.ac.jp [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan)

    2012-03-16

    Highlights: Black-Right-Pointing-Pointer BoNT and NTNHA proteins share a similar protein architecture. Black-Right-Pointing-Pointer NTNHA and BoNT were both identified as zinc-binding proteins. Black-Right-Pointing-Pointer NTNHA does not have a classical HEXXH zinc-coordinating motif similar to that found in all serotypes of BoNT. Black-Right-Pointing-Pointer Homology modeling implied probable key residues involved in zinc coordination. -- Abstract: Zinc atoms play an essential role in a number of enzymes. Botulinum neurotoxin (BoNT), the most potent toxin known in nature, is a zinc-dependent endopeptidase. Here we identify the nontoxic nonhemagglutinin (NTNHA), one of the BoNT-complex constituents, as a zinc-binding protein, along with BoNT. A protein structure classification database search indicated that BoNT and NTNHA share a similar domain architecture, comprising a zinc-dependent metalloproteinase-like, BoNT coiled-coil motif and concanavalin A-like domains. Inductively coupled plasma-mass spectrometry analysis demonstrated that every single NTNHA molecule contains a single zinc atom. This is the first demonstration of a zinc atom in this protein, as far as we know. However, the NTNHA molecule does not possess any known zinc-coordinating motif, whereas all BoNT serotypes possess the classical HEXXH motif. Homology modeling of the NTNHA structure implied that a consensus K-C-L-I-K-X{sub 35}-D sequence common among all NTNHA serotype molecules appears to coordinate a single zinc atom. These findings lead us to propose that NTNHA and BoNT may have evolved distinct functional specializations following their branching out from a common ancestral zinc protein.

  11. Toxic and nontoxic components of botulinum neurotoxin complex are evolved from a common ancestral zinc protein

    International Nuclear Information System (INIS)

    Highlights: ► BoNT and NTNHA proteins share a similar protein architecture. ► NTNHA and BoNT were both identified as zinc-binding proteins. ► NTNHA does not have a classical HEXXH zinc-coordinating motif similar to that found in all serotypes of BoNT. ► Homology modeling implied probable key residues involved in zinc coordination. -- Abstract: Zinc atoms play an essential role in a number of enzymes. Botulinum neurotoxin (BoNT), the most potent toxin known in nature, is a zinc-dependent endopeptidase. Here we identify the nontoxic nonhemagglutinin (NTNHA), one of the BoNT-complex constituents, as a zinc-binding protein, along with BoNT. A protein structure classification database search indicated that BoNT and NTNHA share a similar domain architecture, comprising a zinc-dependent metalloproteinase-like, BoNT coiled-coil motif and concanavalin A-like domains. Inductively coupled plasma-mass spectrometry analysis demonstrated that every single NTNHA molecule contains a single zinc atom. This is the first demonstration of a zinc atom in this protein, as far as we know. However, the NTNHA molecule does not possess any known zinc-coordinating motif, whereas all BoNT serotypes possess the classical HEXXH motif. Homology modeling of the NTNHA structure implied that a consensus K-C-L-I-K-X35-D sequence common among all NTNHA serotype molecules appears to coordinate a single zinc atom. These findings lead us to propose that NTNHA and BoNT may have evolved distinct functional specializations following their branching out from a common ancestral zinc protein.

  12. Paraphyly of organelle DNAs in Cycas Sect. Asiorientales due to ancient ancestral polymorphisms

    Directory of Open Access Journals (Sweden)

    Hsu Tsai-Wen

    2009-07-01

    Full Text Available Abstract Background This study addresses the apportionment of genetic diversity between Cycas revoluta and C. taitungensis, species that constitute the section Asiorientales and represent a unique, basal lineage of the Laurasian genus Cycas. Fossil evidence indicates divergence of the section from the rest of Cycas at least 30 million years ago. Geographically, C. taitungensis is limited to Taiwan whereas C. revoluta is found in the Ryukyu Archipelago and on mainland China. Results The phylogenies of ribosomal ITS region of mtDNA and the intergenic spacer between atpB and rbcL genes of cpDNA were reconstructed. Phylogenetic analyses revealed paraphyly of both loci in the two species and also in the section Asiorientales. The lack of reciprocal monophyly between these long isolated sections is likely due to persistent shared ancestral polymorphisms. Molecular dating estimated that mt- and cp DNA lineages coalesced to the most recent common ancestors (TMRCA about 327 (mt and 204 MYA (cp, corresponding with the divergence of cycad sections in the Mesozoic. Conclusion Fates of newly derived mutations of cycads follow Klopfstein et al.'s surfing model where the majority of new mutations do not spread geographically and remain at low frequencies or are eventually lost by genetic drift. Only successful 'surfing mutations' reach very high frequencies and occupy a large portion of a species range. These mutations exist as dominant cytotypes across populations and species. Geographical subdivision is lacking in both species, even though recurrent gene flow by both pollen and seed is severely limited. In total, the contrasting levels between historical and ongoing gene flow, large population sizes, a long lifespan, and slow mutation rates in both organelle DNAs have all likely contributed to the unusually long duration of paraphyly in cycads.

  13. Evidence for intron length conservation in a set of mammalian genes associated with embryonic development

    LENUS (Irish Health Repository)

    2011-10-05

    Abstract Background We carried out an analysis of intron length conservation across a diverse group of nineteen mammalian species. Motivated by recent research suggesting a role for time delays associated with intron transcription in gene expression oscillations required for early embryonic patterning, we searched for examples of genes that showed the most extreme conservation of total intron content in mammals. Results Gene sets annotated as being involved in pattern specification in the early embryo or containing the homeobox DNA-binding domain, were significantly enriched among genes with highly conserved intron content. We used ancestral sequences reconstructed with probabilistic models that account for insertion and deletion mutations to distinguish insertion and deletion events on lineages leading to human and mouse from their last common ancestor. Using a randomization procedure, we show that genes containing the homeobox domain show less change in intron content than expected, given the number of insertion and deletion events within their introns. Conclusions Our results suggest selection for gene expression precision or the existence of additional development-associated genes for which transcriptional delay is functionally significant.

  14. Mammalian Sperm Motility: Observation and Theory

    Science.gov (United States)

    Gaffney, E. A.; Gadêlha, H.; Smith, D. J.; Blake, J. R.; Kirkman-Brown, J. C.

    2011-01-01

    Mammalian spermatozoa motility is a subject of growing importance because of rising human infertility and the possibility of improving animal breeding. We highlight opportunities for fluid and continuum dynamics to provide novel insights concerning the mechanics of these specialized cells, especially during their remarkable journey to the egg. The biological structure of the motile sperm appendage, the flagellum, is described and placed in the context of the mechanics underlying the migration of mammalian sperm through the numerous environments of the female reproductive tract. This process demands certain specific changes to flagellar movement and motility for which further mechanical insight would be valuable, although this requires improved modeling capabilities, particularly to increase our understanding of sperm progression in vivo. We summarize current theoretical studies, highlighting the synergistic combination of imaging and theory in exploring sperm motility, and discuss the challenges for future observational and theoretical studies in understanding the underlying mechanics.

  15. Freezing mammalian cells for production of biopharmaceuticals.

    Science.gov (United States)

    Seth, Gargi

    2012-03-01

    Cryopreservation techniques utilize very low temperatures to preserve the structure and function of living cells. Various strategies have been developed for freezing mammalian cells of biological and medical significance. This paper highlights the importance and application of cryopreservation for recombinant mammalian cells used in the biopharmaceutical industry to produce high-value protein therapeutics. It is a primer that aims to give insight into the basic principles of cell freezing for the benefit of biopharmaceutical researchers with limited or no prior experience in cryobiology. For the more familiar researchers, key cell banking parameters such as the cell density and hold conditions have been reviewed to possibly help optimize their specific cell freezing protocols. It is important to understand the mechanisms underlying the freezing of complex and sensitive cellular entities as we implement best practices around the techniques and strategies used for cryopreservation. PMID:22226818

  16. Mammalian Sperm Motility: Observation and Theory

    KAUST Repository

    Gaffney, E.A.

    2011-01-21

    Mammalian spermatozoa motility is a subject of growing importance because of rising human infertility and the possibility of improving animal breeding. We highlight opportunities for fluid and continuum dynamics to provide novel insights concerning the mechanics of these specialized cells, especially during their remarkable journey to the egg. The biological structure of the motile sperm appendage, the flagellum, is described and placed in the context of the mechanics underlying the migration of mammalian sperm through the numerous environments of the female reproductive tract. This process demands certain specific changes to flagellar movement and motility for which further mechanical insight would be valuable, although this requires improved modeling capabilities, particularly to increase our understanding of sperm progression in vivo. We summarize current theoretical studies, highlighting the synergistic combination of imaging and theory in exploring sperm motility, and discuss the challenges for future observational and theoretical studies in understanding the underlying mechanics. © 2011 by Annual Reviews. All rights reserved.

  17. Wnt Signalling Pathway Parameters for Mammalian Cells

    OpenAIRE

    Tan, Chin Wee; Gardiner, Bruce S.; Hirokawa, Yumiko; Layton, Meredith J.; Smith, David W.; Burgess, Antony W.

    2012-01-01

    Wnt/β-catenin signalling regulates cell fate, survival, proliferation and differentiation at many stages of mammalian development and pathology. Mutations of two key proteins in the pathway, APC and β-catenin, have been implicated in a range of cancers, including colorectal cancer. Activation of Wnt signalling has been associated with the stabilization and nuclear accumulation of β-catenin and consequential up-regulation of β-catenin/TCF gene transcription. In 2003, Lee et al. constructed a c...

  18. Radiation effects in mammalian cells in vitro

    International Nuclear Information System (INIS)

    The purpose of this research effort is to elucidate the mechanisms for the radiation-induced changes in mammalian cells that lead to cell death, mutation, neoplastic transformation, DNA damage, and chromosomal alterations. Of particular interest are the effects of low-dose-rate and fractionated irradiation on these end points with respect to the mechanisms whereby these effects are influenced by cellular repair processes, inhibitors, and promoters that act at the genetic or biochemical level. 17 refs

  19. Neuropeptidomics applied to studies of mammalian reproduction

    OpenAIRE

    Le Thao T.; Lehnert Sigrid; Colgrave Michelle L

    2014-01-01

    Neuropeptidomics, a mass spectrometry-based technique which aims to uncover the complete suite of neuropeptides present in a tissue, organ or cell from the brain or nervous system, has found application in studies examining physiological responses (e.g. food intake, appetite and reproduction). Neuropeptides (and peptide hormones) have long been known as regulators of mammalian physiological processes, particularly reproduction. These peptides are derived from precursor proteins and become act...

  20. Sensory Feedback Control of Mammalian Vocalizations

    OpenAIRE

    Smotherman, Michael S.

    2007-01-01

    Somatosensory and auditory feedback mechanisms are dynamic components of the vocal motor pattern generator in mammals. This review explores how sensory cues arising from central auditory and somatosensory pathways actively guide the production of both simple sounds and complex phrases in mammals. While human speech is a uniquely sophisticated example of mammalian vocal behavior, other mammals can serve as examples of how sensory feedback guides complex vocal patterns. Echolocating bats in par...

  1. Hysteresis in a synthetic mammalian gene network

    OpenAIRE

    Kramer, Beat P.; Fussenegger, Martin

    2005-01-01

    Bistable and hysteretic switches, enabling cells to adopt multiple internal expression states in response to a single external input signal, have a pivotal impact on biological systems, ranging from cell-fate decisions to cell-cycle control. We have designed a synthetic hysteretic mammalian transcription network. A positive feedback loop, consisting of a transgene and transactivator (TA) cotranscribed by TA's cognate promoter, is repressed by constitutive expression of a macrolide-dependent t...

  2. Mammalian Developmental Genetics in the Twentieth Century

    OpenAIRE

    Artzt, Karen

    2012-01-01

    This Perspectives is a review of the breathtaking history of mammalian genetics in the past century and, in particular, of the ways in which genetic thinking has illuminated aspects of mouse development. To illustrate the power of that thinking, selected hypothesis-driven experiments and technical advances are discussed. Also included in this account are the beginnings of mouse genetics at the Bussey Institute, Columbia University, and The Jackson Laboratory and a retrospective discussion of ...

  3. The cellular code for mammalian thermosensation

    OpenAIRE

    Pogorzala, Leah A.; Mishra, Santosh K.; Hoon, Mark A

    2013-01-01

    Mammalian somatosenory neurons respond to thermal stimuli allowing animals to reliably discriminate hot from cold and select their preferred environments. We previously generated mice that are completely insensitive to temperatures from noxious cold to painful heat (−5 to 55 °C) by ablating several different classes of nociceptor early in development. Here we have adopted a selective ablation strategy in adult mice to dissect this phenotype and thereby demonstrated that separate populations o...

  4. [Telomere Recombination in Normal Mammalian Cells].

    Science.gov (United States)

    Zhdanova, N S; Rubtsov, N B

    2016-01-01

    Two mechanisms of telomere length maintenance are known to date. The first includes the use of a special enzymatic telomerase complex to solve the problems that arise during the replication of linear DNA in a normal diploid and part of tumor cells. Alternative lengthening of telomeres (ALT), which is based on the homologous recombination of telomere DNA, represents the second mechanism. Until recently, ALT was assumed to be expressed only in 15-20% of tumors lacking active telomerase and, together with telomerase reactivation represented one of two possibilities to overcome the replicative senescence observed in somatic mammalian cells due to aging or during cell culturing in vitro. Previously described sporadic cases of combinations of the two mechanisms of telomere length maintenance in several cell lines in vitro were attributed to the experimental design rather than to a real biological phenomenon, since active cellular division without active telomerase was considered to be the "gold standard" of ALT. The present review describes the morphological and functional reorganizations of mammalian telomeres observed with ALT activation, as well as recently observed,and well-documented cases of combinations between ALT-like and telomerase-dependent mechanisms in mammalian cells. The possible role of telomere recombination in telomerase-dependent cells is discussed. PMID:27183789

  5. Aneuploidy in mammalian somatic cells in vivo.

    Science.gov (United States)

    Cimino, M C; Tice, R R; Liang, J C

    1986-01-01

    Aneuploidy is an important potential source of human disease and of reproductive failure. Nevertheless, the ability of chemical agents to induce aneuploidy has been investigated only sporadically in intact (whole-animal) mammalian systems. A search of the available literature from the EMCT Aneuploidy File (for years 1970-1983) provided 112 papers that dealt with aneuploidy in mammalian somatic cells in vivo. 59 of these papers did not meet minimal criteria for analysis and were rejected from subsequent review. Of the remaining 53 papers that dealt with aneuploidy induction by chemical agents in mammalian somatic cells in vivo, only 3 (6%) contained data that were considered to be supported conclusively by adequate study designs, execution, and reporting. These 3 papers dealt with 2 chemicals, one of which, mercury, was negative for aneuploidy induction in humans, and the other, pyrimethamine, was positive in an experimental rodent study. The majority of papers (94%) were considered inconclusive for a variety of reasons. The most common reasons for calling a study inconclusive were (a) combining data on hyperploidy with those on hypoploidy and/or polyploidy, (b) an inadequate or unspecified number of animals and/or cells per animal scored per treatment group, and (c) poor data presentation such that animal-to-animal variability could not be assessed. Suggestions for protocol development are made, and the future directions of research into aneuploidy induction are discussed. PMID:3941670

  6. A Common Ancestral Mutation in CRYBB3 Identified in Multiple Consanguineous Families with Congenital Cataracts

    Science.gov (United States)

    Irum, Bushra; Khan, Arif O.; Wang, Qiwei; Li, David; Khan, Asma A.; Husnain, Tayyab; Akram, Javed; Riazuddin, Sheikh

    2016-01-01

    development. Conclusion Here, we report a common ancestral mutation in CRYBB3 associated with autosomal recessive congenital cataracts identified in four familial cases of Pakistani origin. PMID:27326458

  7. Effects of interleukin-10 on cutaneous wounds and scars in humans of African continental ancestral origin.

    Science.gov (United States)

    Kieran, Ingrid; Taylor, Catherine; Bush, Jim; Rance, Mark; So, Karen; Boanas, Adam; Metcalfe, Anthony; Hobson, Rosalind; Goldspink, Nick; Hutchison, John; Ferguson, Mark

    2014-01-01

    Scars in humans of African continental ancestry heal with an exaggerated inflammatory response and a generally wider scar. Interleukin-10 is an anti-inflammatory and antifibrotic cytokine. A randomized controlled trial in Caucasians found that exogenous interleukin-10 resulted in improved macroscopic scar appearance and reduced scar redness. We investigated the effects of interleukin-10 on cutaneous scarring in volunteers of African ancestral origin in an exploratory, single-center, within-subject, double-blind randomized controlled trial. Fifty-six subjects received two of four potential prerandomized concentrations of interleukin-10 (5, 25, 100, and 250 ng/100 µL) in two full-thickness incisions on the upper inner arms. Anatomically matching incisions on the contralateral arm were treated with placebo. Scars were excised at 1 month for histological analysis and were redosed with the same regimen. Resultant excision scars were followed up for 12 months for scar width measurement and scoring. Scoring was performed by trial doctors, subjects, and a panel. Incisions treated with 100 ng/100 µL interleukin-10 had significantly reduced microscopic scar widths. Incisions treated with 5 and 25 ng/100 µL interleukin-10 were also narrower, but not significantly. There were no differences observed in pro-inflammatory or pro-fibrotic markers between interleukin-10 and placebo treatment. There was no long-term evidence that 100 ng/100 µL interleukin-10 had a therapeutic effect on macroscopic scar width or appearance, as excisions treated with this concentration were significantly wider than placebo between 8 and 12 months of maturation. Doctors showed a trend toward favoring the macroscopic appearance of placebo-treated excisions compared with those treated with 250 ng/100 µL interleukin-10. Panelists scored placebo-treated excisions as significantly better-appearing than those treated with 250 ng/100 µL interleukin-10. Doctors' scores showed a

  8. La modernidad, el cuidado de la salud y la cultura ancestral.

    Directory of Open Access Journals (Sweden)

    Ana Cecilia Becerra

    2009-11-01

    Full Text Available La modernidad es tanto un período histórico como un concepto filosófico y sociológico que impuso la razón y el método formal sobre todos los actos políticos, sociales y epistemológicos de las distintas culturas del mundo. La modernidad se construyó en su momento sobre el imaginario de la superioridad europea1 y durante el período colonial fue la causante del proceso avasallador de exterminio y de desconocimiento de las sociedades y culturas indígenas de América. Ella, con sus valores patriarcales y formales, desplazó la ética del cuidado y del abrigo de los pueblos autóctonos imponiendo una lógica racional, calculadora e impersonal. Al desconocer y casi negar en su totalidad la cosmovisión ancestral de curar y cuidar, relegó los ejercicios profesionalizantes de la salud bajo el amparo de la mercantilización del capitalismo mundial integrado. La modernidad, desde el inicio y en la actualidad, ha impregnado la cultura de todos los pueblos y ha condicionado todos los actos académicos en las instituciones escolares y universitarias. La perpetuación de un modelo positivista y occidentalizado ha sido una constante en las aulas universitarias y en las disciplinas, sobre todo en las ciencias de la salud. Históricamente el conocimiento en salud ha sido construido con base en el enfoque positivista y la concepción biologista del proceso salud-enfermedad, lo cual lleva a una fragmentación del saber, disyunción del sujeto y el objeto en la producción del conocimiento, y a una incapacidad de asumir al ser humano en todas sus dimensiones, razón de ser de la acción en salud, como totalidad y unidad integral2. Este panorama aquí planteado deja un gran reto epistemológico a los profesionales y a los docentes de las ciencias de la salud en general y de enfermería en particular. Vista la enfermería desde la fundamentación del cuidado de la salud, no se puede descontextualizar ni escindir de nuestra propia cultura, pretendiendo

  9. La modernidad, el cuidado de la salud y la cultura ancestral

    Directory of Open Access Journals (Sweden)

    Ana Cecilia Becerra

    2008-09-01

    Full Text Available La modernidad es tanto un período histórico como un concepto filosófico y sociológico que impuso la razón y el método formal sobre todos los actos políticos, sociales y epistemológicos de las distintas culturas del mundo. La modernidad se construyó en su momento sobre el imaginario de la superioridad europea1 y durante el período colonial fue la causante del proceso avasallador de exterminio y de desconocimiento de las sociedades y culturas indígenas de América.Ella, con sus valores patriarcales y formales, desplazó la ética del cuidado y del abrigo de los pueblos autóctonos imponiendo una lógica racional, calculadora e impersonal. Al desconocer y casi negar en su totalidad la cosmovisión ancestral de curar y cuidar, relegó los ejercicios profesionalizantes de la salud bajo el amparo de la mercantilización del capitalismo mundial integrado.La modernidad, desde el inicio y en la actualidad, ha impregnado la cultura de todos los pueblos y ha condicionado todos los actos académicos en las instituciones escolares y universitarias. La perpetuación de un modelo positivista y occidentalizado ha sido una constante en las aulas universitarias y en las disciplinas, sobre todo en las ciencias de la salud. Históricamente el conocimiento en salud ha sido construido con base en el enfoque positivista y la concepción biologista del proceso salud-enfermedad, lo cual lleva a una fragmentación del saber, disyunción del sujeto y el objeto en la producción del conocimiento, y a una incapacidad de asumir al ser humano en todas sus dimensiones, razón de ser de la acción en salud, como totalidad y unidad integral2.Este panorama aquí planteado deja un gran reto epistemológico a los profesionales y a los docentes de las ciencias de la salud en general y de enfermería en particular. Vista la enfermería desde la fundamentación del cuidado de la salud, no se puede descontextualizar ni escindir de nuestra propia cultura, pretendiendo

  10. Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors.

    Science.gov (United States)

    Burgess, Ralph; Yang, Ziheng

    2008-09-01

    Estimation of population parameters for the common ancestors of humans and the great apes is important in understanding our evolutionary history. In particular, inference of population size for the human-chimpanzee common ancestor may shed light on the process by which the 2 species separated and on whether the human population experienced a severe size reduction in its early evolutionary history. In this study, the Bayesian method of ancestral inference of Rannala and Yang (2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics. 164:1645-1656) was extended to accommodate variable mutation rates among loci and random species-specific sequencing errors. The model was applied to analyze a genome-wide data set of approximately 15,000 neutral loci (7.4 Mb) aligned for human, chimpanzee, gorilla, orangutan, and macaque. We obtained robust and precise estimates for effective population sizes along the hominoid lineage extending back approximately 30 Myr to the cercopithecoid divergence. The results showed that ancestral populations were 5-10 times larger than modern humans along the entire hominoid lineage. The estimates were robust to the priors used and to model assumptions about recombination. The unusually low X chromosome divergence between human and chimpanzee could not be explained by variation in the male mutation bias or by current models of hybridization and introgression. Instead, our parameter estimates were consistent with a simple instantaneous process for human-chimpanzee speciation but showed a major reduction in X chromosome effective population size peculiar to the human-chimpanzee common ancestor, possibly due to selective sweeps on the X prior to separation of the 2 species. PMID:18603620

  11. Saccharomyces cerevisiae Bat1 and Bat2 aminotransferases have functionally diverged from the ancestral-like Kluyveromyces lactis orthologous enzyme.

    Directory of Open Access Journals (Sweden)

    Maritrini Colón

    Full Text Available BACKGROUND: Gene duplication is a key evolutionary mechanism providing material for the generation of genes with new or modified functions. The fate of duplicated gene copies has been amply discussed and several models have been put forward to account for duplicate conservation. The specialization model considers that duplication of a bifunctional ancestral gene could result in the preservation of both copies through subfunctionalization, resulting in the distribution of the two ancestral functions between the gene duplicates. Here we investigate whether the presumed bifunctional character displayed by the single branched chain amino acid aminotransferase present in K. lactis has been distributed in the two paralogous genes present in S. cerevisiae, and whether this conservation has impacted S. cerevisiae metabolism. PRINCIPAL FINDINGS: Our results show that the KlBat1 orthologous BCAT is a bifunctional enzyme, which participates in the biosynthesis and catabolism of branched chain aminoacids (BCAAs. This dual role has been distributed in S. cerevisiae Bat1 and Bat2 paralogous proteins, supporting the specialization model posed to explain the evolution of gene duplications. BAT1 is highly expressed under biosynthetic conditions, while BAT2 expression is highest under catabolic conditions. Bat1 and Bat2 differential relocalization has favored their physiological function, since biosynthetic precursors are generated in the mitochondria (Bat1, while catabolic substrates are accumulated in the cytosol (Bat2. Under respiratory conditions, in the presence of ammonium and BCAAs the bat1Δ bat2Δ double mutant shows impaired growth, indicating that Bat1 and Bat2 could play redundant roles. In K. lactis wild type growth is independent of BCAA degradation, since a Klbat1Δ mutant grows under this condition. CONCLUSIONS: Our study shows that BAT1 and BAT2 differential expression and subcellular relocalization has resulted in the distribution of the

  12. Extensive Chromosomal Reorganization in the Evolution of New World Muroid Rodents (Cricetidae, Sigmodontinae): Searching for Ancestral Phylogenetic Traits.

    Science.gov (United States)

    Pereira, Adenilson Leão; Malcher, Stella Miranda; Nagamachi, Cleusa Yoshiko; O'Brien, Patricia Caroline Mary; Ferguson-Smith, Malcolm Andrew; Mendes-Oliveira, Ana Cristina; Pieczarka, Julio Cesar

    2016-01-01

    Sigmodontinae rodents show great diversity and complexity in morphology and ecology. This diversity is accompanied by extensive chromosome variation challenging attempts to reconstruct their ancestral genome. The species Hylaeamys megacephalus--HME (Oryzomyini, 2n = 54), Necromys lasiurus--NLA (Akodontini, 2n = 34) and Akodon sp.--ASP (Akodontini, 2n = 10) have extreme diploid numbers that make it difficult to understand the rearrangements that are responsible for such differences. In this study we analyzed these changes using whole chromosome probes of HME in cross-species painting of NLA and ASP to construct chromosome homology maps that reveal the rearrangements between species. We include data from the literature for other Sigmodontinae previously studied with probes from HME and Mus musculus (MMU) probes. We also use the HME probes on MMU chromosomes for the comparative analysis of NLA with other species already mapped by MMU probes. Our results show that NLA and ASP have highly rearranged karyotypes when compared to HME. Eleven HME syntenic blocks are shared among the species studied here. Four syntenies may be ancestral to Akodontini (HME2/18, 3/25, 18/25 and 4/11/16) and eight to Sigmodontinae (HME26, 1/12, 6/21, 7/9, 5/17, 11/16, 20/13 and 19/14/19). Using MMU data we identified six associations shared among rodents from seven subfamilies, where MMU3/18 and MMU8/13 are phylogenetic signatures of Sigmodontinae. We suggest that the associations MMU2entire, MMU6proximal/12entire, MMU3/18, MMU8/13, MMU1/17, MMU10/17, MMU12/17, MMU5/16, MMU5/6 and MMU7/19 are part of the ancestral Sigmodontinae genome. PMID:26800516

  13. Consequences of ongoing retrotransposition in mammalian genomes

    Directory of Open Access Journals (Sweden)

    Maxwell PH

    2014-09-01

    Full Text Available Patrick H Maxwell Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA Abstract: Retrotransposons can have significant influences on gene expression and genome stability through their ability to integrate reverse-transcript copies of their sequences at new genomic locations by retrotransposition. These elements have been long known to retrotranspose in mammalian germ cells to give rise to inherited insertion alleles, but more recent work has also shown that retrotransposition can occur in mammalian somatic cells, particularly in brain tissue and tumors. Retrotransposition makes appreciable contributions to spontaneous disease-causing alleles in humans and a more significant contribution to spontaneous mutations in mice. Genome-wide studies have found high levels of polymorphic retrotransposon insertions in human populations that are consistent with ongoing retrotransposition. Many insertions do not disrupt exons, but insertions into introns or flanking genes can alter gene expression patterns, generate truncated or antisense gene transcripts, alter splicing patterns, or result in premature polyadenylation of gene transcripts. Furthermore, the very high genomic copy numbers of these elements can lead to nonallelic homologous recombination events that produce gene deletions/duplications and genome rearrangements, and can also lead to evolution of particular insertions or types of elements to have cellular functions through exaptation. Mobility of these elements occurs despite multiple epigenetic mechanisms to restrict their expression. While the potential for retrotransposons to significantly influence mammalian health and cellular functions is clear, substantial research efforts will be needed to fully elucidate the actual contributions of natural levels of mobility of endogenous elements to the health and development of humans and other mammals. Keywords: retrotransposon, human, mouse, mutations, epigenetics

  14. Mammalian niche conservation through deep time.

    Directory of Open Access Journals (Sweden)

    Larisa R G DeSantis

    Full Text Available Climate change alters species distributions, causing plants and animals to move north or to higher elevations with current warming. Bioclimatic models predict species distributions based on extant realized niches and assume niche conservation. Here, we evaluate if proxies for niches (i.e., range areas are conserved at the family level through deep time, from the Eocene to the Pleistocene. We analyze the occurrence of all mammalian families in the continental USA, calculating range area, percent range area occupied, range area rank, and range polygon centroids during each epoch. Percent range area occupied significantly increases from the Oligocene to the Miocene and again from the Pliocene to the Pleistocene; however, mammalian families maintain statistical concordance between rank orders across time. Families with greater taxonomic diversity occupy a greater percent of available range area during each epoch and net changes in taxonomic diversity are significantly positively related to changes in percent range area occupied from the Eocene to the Pleistocene. Furthermore, gains and losses in generic and species diversity are remarkably consistent with ~2.3 species gained per generic increase. Centroids demonstrate southeastern shifts from the Eocene through the Pleistocene that may correspond to major environmental events and/or climate changes during the Cenozoic. These results demonstrate range conservation at the family level and support the idea that niche conservation at higher taxonomic levels operates over deep time and may be controlled by life history traits. Furthermore, families containing megafauna and/or terminal Pleistocene extinction victims do not incur significantly greater declines in range area rank than families containing only smaller taxa and/or only survivors, from the Pliocene to Pleistocene. Collectively, these data evince the resilience of families to climate and/or environmental change in deep time, the absence of

  15. Ancestral polymorphism at the major histocompatibility complex (MHCIIß in the Nesospiza bunting species complex and its sister species (Rowettia goughensis

    Directory of Open Access Journals (Sweden)

    van Rensburg Alexandra

    2012-08-01

    Full Text Available Abstract Background The major histocompatibility complex (MHC is an important component of the vertebrate immune system and is frequently used to characterise adaptive variation in wild populations due to its co-evolution with pathogens. Passerine birds have an exceptionally diverse MHC with multiple gene copies and large numbers of alleles compared to other avian taxa. The Nesospiza bunting species complex (two species on Nightingale Island; one species with three sub-species on Inaccessible Island represents a rapid adaptive radiation at a small, isolated archipelago, and is thus an excellent model for the study of adaptation and speciation. In this first study of MHC in Nesospiza buntings, we aim to characterize MHCIIß variation, determine the strength of selection acting at this gene region and assess the level of shared polymorphism between the Nesospiza species complex and its putative sister taxon, Rowettia goughensis, from Gough Island. Results In total, 23 unique alleles were found in 14 Nesospiza and 2 R. goughensis individuals encoding at least four presumably functional loci and two pseudogenes. There was no evidence of ongoing selection on the peptide binding region (PBR. Of the 23 alleles, 15 were found on both the islands inhabited by Nesospiza species, and seven in both Nesospiza and Rowettia; indications of shared, ancestral polymorphism. A gene tree of Nesospiza MHCIIß alleles with several other passerine birds shows three highly supported Nesospiza-specific groups. All R. goughensis alleles were shared with Nesospiza, and these alleles were found in all three Nesospiza sequence groups in the gene tree, suggesting that most of the observed variation predates their phylogenetic split. Conclusions Lack of evidence of selection on the PBR, together with shared polymorphism across the gene tree, suggests that population variation of MHCIIß among Nesospiza and Rowettia is due to ancestral polymorphism rather than local selective

  16. Thermotolerant Yeast Strains Adapted by Laboratory Evolution Show Trade-Off at Ancestral Temperatures and Preadaptation to Other Stresses

    DEFF Research Database (Denmark)

    Caspeta, Luis; Nielsen, Jens

    2015-01-01

    adaptive laboratory evolution, we previously isolated seven Saccharomyces cerevisiae strains with improved growth at 40°C. Here, we show that genetic adaptations to high temperature caused a growth trade-off at ancestral temperatures, reduced cellular functions, and improved tolerance of other stresses...... proteins showed that the lethal temperature for yeast is around 49°C, as a large fraction of the yeast proteins denature above this temperature. Our analysis also indicated that the number of functions involved in controlling the growth rate decreased in the thermotolerant strains compared with the number...

  17. Genome Editing Using Mammalian Haploid Cells

    Directory of Open Access Journals (Sweden)

    Takuro Horii

    2015-10-01

    Full Text Available Haploid cells are useful for studying gene functions because disruption of a single allele can cause loss-of-function phenotypes. Recent success in generating haploid embryonic stem cells (ESCs in mice, rats, and monkeys provides a new platform for simple genetic manipulation of the mammalian genome. Use of haploid ESCs enhances the genome-editing potential of the CRISPR/Cas system. For example, CRISPR/Cas was used in haploid ESCs to generate multiple knockouts and large deletions at high efficiency. In addition, genome-wide screening is facilitated by haploid cell lines containing gene knockout libraries.

  18. Molecular mechanisms for transcription in mammalian mitochondria

    OpenAIRE

    Gaspari, Martina

    2006-01-01

    The circular double stranded mitochondrial genome (mtDNA), which is about 16,600 bp in humans and 16,300 bp in mice, encodes 13 of the -90 different proteins present in the respiratory chain of mammalian mitochondria. The remaining components of the respiratory chain are encoded by nuclear genes and imported into the mitochondrial network. The genes present in mtDNA, 13 mRNAs, 22 tRNAs, and 2 rRNAs, are all essential for oxidative phosphorylation. Therefore, mtDNA replicatio...

  19. Better Smelling Through Genetics: Mammalian Odor Perception

    OpenAIRE

    Keller, Andreas; Vosshall, Leslie B

    2008-01-01

    The increasing availability of genomic and genetic tools to study olfaction—the sense of smell—has brought important new insights into how this chemosensory modality functions in different species. Newly sequenced mammalian genomes—from platypus to dog—have made it possible to infer how smell has evolved to suit the needs of a given species and how variation within a species may affect individual olfactory perception. This review will focus on recent advances in the genetics and genomics of m...

  20. Stochastic resonance in mammalian neuronal networks.

    Science.gov (United States)

    Gluckman, Bruce J.; So, Paul; Netoff, Theoden I.; Spano, Mark L.; Schiff, Steven J.

    1998-09-01

    We present stochastic resonance observed in the dynamics of neuronal networks from mammalian brain. Both sinusoidal signals and random noise were superimposed into an applied electric field. As the amplitude of the noise component was increased, an optimization (increase then decrease) in the signal-to-noise ratio of the network response to the sinusoidal signal was observed. The relationship between the measures used to characterize the dynamics is discussed. Finally, a computational model of these neuronal networks that includes the neuronal interactions with the electric field is presented to illustrate the physics behind the essential features of the experiment. (c) 1998 American Institute of Physics. PMID:12779762

  1. Spiral Waves in Disinhibited Mammalian Neocortex

    OpenAIRE

    Huang, Xiaoying; Troy, William C.; Yang, Qian; Ma, Hongtao; Laing, Carlo R.; Steven J Schiff; Wu, Jian-young

    2004-01-01

    Spiral waves are a basic feature of excitable systems. Although such waves have been observed in a variety of biological systems, they have not been observed in mammalian cortex during neuronal activity. We here report stable rotating spiral waves in rat neocortical slices visualized by voltage-sensitive dye imaging. Tissue from the occipital cortex (visual) was sectioned parallel to cortical lamina to preserve horizontal connections in layers III to V (500 μm thick, about 4 × 6 mm2). In such...

  2. Effect of endocrine disruptors on mammalian fertlity

    Czech Academy of Sciences Publication Activity Database

    Pěknicová, Jana; Nováková, Vendula; Buckiová, Daniela; Boubelík, Michael

    Moskva : Medi Expo, 2008, s. 60-61. ISBN 978-5-94943-043-9. [European Congress of Reproductive Immunology /6./. Moskva (RU), 30.06.2008-03.07.2008] R&D Projects: GA MŠk(CZ) 1M06011; GA MŠk(CZ) 2B06151; GA MŠk(CZ) OE 211 Institutional research plan: CEZ:AV0Z50520701; CEZ:AV0Z5039906; CEZ:AV0Z5052915 Keywords : endocrine disruptor * mammalian fertility * spermatozoa Subject RIV: DN - Health Impact of the Environment Quality

  3. Stochastic resonance in mammalian neuronal networks

    International Nuclear Information System (INIS)

    We present stochastic resonance observed in the dynamics of neuronal networks from mammalian brain. Both sinusoidal signals and random noise were superimposed into an applied electric field. As the amplitude of the noise component was increased, an optimization (increase then decrease) in the signal-to-noise ratio of the network response to the sinusoidal signal was observed. The relationship between the measures used to characterize the dynamics is discussed. Finally, a computational model of these neuronal networks that includes the neuronal interactions with the electric field is presented to illustrate the physics behind the essential features of the experiment. copyright 1998 American Institute of Physics

  4. Mitochondrial toxicity of triclosan on mammalian cells

    OpenAIRE

    Ajao, Charmaine; Andersson, Maria; Teplova, Vera V; Nagy, Szabolcs; Gahmberg, Carl G; Andersson, Leif C.; Hautaniemi, Maria; Kakasi, Balazs; Roivainen, Merja; Salkinoja-Salonen, Mirja Sinikka

    2015-01-01

    Effects of triclosan (5-chloro-2’-(2,4-dichlorophenoxy)phenol) on mammalian cells were investigated using human peripheral blood mono nuclear cells (PBMC), keratinocytes (HaCaT), porcine spermatozoa and kidney tubular epithelial cells (PK-15), murine pancreatic islets (MIN-6) and neuroblastoma cells (MNA) as targets. We show that triclosan (1 – 10 ÎŒg ml-1) depolarised the mitochondria, upshifted the rate of glucose consumption in PMBC, HaCaT, PK-15 and MNA, and subsequently induced metab...

  5. Preservation of mammalian germ plasm by freezing

    Energy Technology Data Exchange (ETDEWEB)

    Mazur, P.

    1978-01-01

    Embryos of several mammalian species can be frozen to -196/sup 0/C (or below) by procedures that result in the thawed embryos being indistinguishable from their unfrozen counterparts. The survival often exceeds 90%, and in liquid nitrogen it should remain at that high level for centuries. Sublethal biochemical changes are also precluded at -196/sup 0/C. No developmental abnormalities have been detected in mouse offspring derived from frozen-thawed embryos, and, since all the manipulations are carried out on the preimplantation stages, none would be expected.

  6. Application of a sensitive collection heuristic for very large protein families: Evolutionary relationship between adipose triglyceride lipase (ATGL and classic mammalian lipases

    Directory of Open Access Journals (Sweden)

    Berezovsky Igor

    2006-03-01

    Full Text Available Abstract Background Manually finding subtle yet statistically significant links to distantly related homologues becomes practically impossible for very populated protein families due to the sheer number of similarity searches to be invoked and analyzed. The unclear evolutionary relationship between classical mammalian lipases and the recently discovered human adipose triglyceride lipase (ATGL; a patatin family member is an exemplary case for such a problem. Results We describe an unsupervised, sensitive sequence segment collection heuristic suitable for assembling very large protein families. It is based on fan-like expanding, iterative database searches. To prevent inclusion of unrelated hits, additional criteria are introduced: minimal alignment length and overlap with starting sequence segments, finding starting sequences in reciprocal searches, automated filtering for compositional bias and repetitive patterns. This heuristic was implemented as FAMILYSEARCHER in the ANNIE sequence analysis environment and applied to search for protein links between the classical lipase family and the patatin-like group. Conclusion The FAMILYSEARCHER is an efficient tool for tracing distant evolutionary relationships involving large protein families. Although classical lipases and ATGL have no obvious sequence similarity and differ with regard to fold and catalytic mechanism, homology links detected with FAMILYSEARCHER show that they are evolutionarily related. The conserved sequence parts can be narrowed down to an ancestral core module consisting of three β-strands, one α-helix and a turn containing the typical nucleophilic serine. Moreover, this ancestral module also appears in numerous enzymes with various substrate specificities, but that critically rely on nucleophilic attack mechanisms.

  7. The mammalian fauna from the Central Himalaya, Nepal

    OpenAIRE

    Hem Bahadur Katuwal; Bhaiya Khanal; Khadga Basnet; Bhim Rai; Shiva Devkota

    2013-01-01

    Nepal harbors unique mammalian fauna, but it is poorly studied at higher elevation. Mammalian fauna were recorded in Manaslu Conservation Area, Dudhkunda and Dudhkoshi valley of Solukhumbu district and Kanchenjunga Conservation Area of Nepal during March 2011 to April 2013 along the trail and the study plots from 700m to 4400m a.s.l. Semi-structured interviews were made with local people to understand their behavior and habitats. Altogether, 29 mammalian fauna were recorded. Five species were...

  8. USE OF NON-MAMMALIAN ALTERNATIVE MODELS FOR NEUROTOXICOLOGICAL STUDY

    OpenAIRE

    Peterson, Randall T.; Nass, Richard; Boyd, Windy A; Jonathan H Freedman; Dong, Ke; Narahashi, Toshio

    2008-01-01

    The field of neurotoxicology needs to satisfy two opposing demands: the testing of a growing list of chemicals, and resource limitations and ethical concerns associated with testing using traditional mammalian species. National and international government agencies have defined a need to reduce, refine or replace mammalian species in toxicological testing with alternative testing methods and non-mammalian models. Toxicological assays using alternative animal models may relieve some of this pr...

  9. Focusing on RISC assembly in mammalian cells

    International Nuclear Information System (INIS)

    RISC (RNA-induced silencing complex) is a central protein complex in RNAi, into which a siRNA strand is assembled to become effective in gene silencing. By using an in vitro RNAi reaction based on Drosophila embryo extract, an asymmetric model was recently proposed for RISC assembly of siRNA strands, suggesting that the strand that is more loosely paired at its 5' end is selectively assembled into RISC and results in target gene silencing. However, in the present study, we were unable to establish such a correlation in cell-based RNAi assays, as well as in large-scale RNAi data analyses. This suggests that the thermodynamic stability of siRNA is not a major determinant of gene silencing in mammalian cells. Further studies on fork siRNAs showed that mismatch at the 5' end of the siRNA sense strand decreased RISC assembly of the antisense strand, but surprisingly did not increase RISC assembly of the sense strand. More interestingly, measurements of melting temperature showed that the terminal stability of fork siRNAs correlated with the positions of the mismatches, but not gene silencing efficacy. In summary, our data demonstrate that there is no definite correlation between siRNA stability and gene silencing in mammalian cells, which suggests that instead of thermodynamic stability, other features of the siRNA duplex contribute to RISC assembly in RNAi

  10. Conservation of shh cis-regulatory architecture of the coelacanth is consistent with its ancestral phylogenetic position

    Directory of Open Access Journals (Sweden)

    Lang Michael

    2010-11-01

    Full Text Available Abstract Background The modern coelacanth (Latimeria is the extant taxon of a basal sarcopterygian lineage and sister group to tetrapods. Apart from certain apomorphic traits, its morphology is characterized by a high degree of retention of ancestral vertebrate structures and little morphological change. An insight into the molecular evolution that may explain the unchanged character of Latimeria morphology requires the analysis of the expression patterns of developmental regulator genes and their cis-regulatory modules (CRMs. Results We describe the comparative and functional analysis of the sonic hedgehog (shh genomic region of Latimeria menadoensis. Several putative enhancers in the Latimeria shh locus have been identified by comparisons to sarcopterygian and actinopterygian extant species. Specific sequence conservation with all known actinopterygian enhancer elements has been detected. However, these elements are selectively missing in more recently diverged actinopterygian and sarcopterygian species. The functionality of the putative Latimeria enhancers was confirmed by reporter gene expression analysis in transient transgenic zebrafish and chick embryos. Conclusions Latimeria shh CRMs represent the ancestral set of enhancers that have emerged before the split of lobe-finned and ray-finned fishes. In contrast to lineage-specific losses and differentiations in more derived lineages, Latimeria shh enhancers reveal low levels of sequence diversification. High overall sequence conservation of shh conserved noncoding elements (CNE is consistent with the general trend of high levels of conservation of noncoding DNA in the slowly evolving Latimeria genome.

  11. The Grooved Rodent Incisor Recapitulates Rudimentary Teeth Characteristics of Ancestral Mammals.

    Science.gov (United States)

    Li, L; Tang, Q; Jung, H-S

    2016-07-01

    It is known from the paleontology studies of eutherian mammals that incisor numbers were reduced during evolution. The evolutionary lost incisors may remain as vestigial structures at embryonic stages. The recapitulation of the incisor patterns among mammalian species will potentially uncover the mechanisms underlying the phenotypic transition of incisors during evolution. Here, we showed that a minute tooth formed in the presumptive groove region of the gerbil upper incisor at the early developmental stages, during which multiple epithelial swellings and Shh transcription domains spatiotemporally appeared in the dental epithelium, suggests the existence of vestigial dental primordia. Interestingly, when we trimmed the surrounding mesenchyme from incisor tooth germs at or before the bud stage prior to ex vivo culture, the explants developed different incisor phenotypes ranging from triplicated incisors, duplicated incisors, to Lagomorpha-like incisors, corresponding to the incisor patterns in the eutherian mammals. These results imply that the phenotypic transition of incisors during evolution, as well as the achievement of ultimate incisors in adults, arose from differential integrations of primordia. However, when the incisor tooth germ was trimmed at the cap stage, a grooved incisor developed similar to the normal condition. Furthermore, the incisor tooth germ developed a small but smooth incisor after the additional removal of the minute tooth and a lateral rudiment. These results suggest that multiple dental primordia integrated before the cap stage, with the labial primordia contributing to the labial face of the functional incisor. The minute tooth that occupied the boundary of the 2 labial primordia might be implicated in the groove formation. This study sheds light on how rudiments incorporate into functional organs and aids the understanding of incisor evolution. PMID:26912224

  12. Conservation and diversification of an ancestral chordate gene regulatory network for dorsoventral patterning.

    Directory of Open Access Journals (Sweden)

    Iryna Kozmikova

    Full Text Available Formation of a dorsoventral axis is a key event in the early development of most animal embryos. It is well established that bone morphogenetic proteins (Bmps and Wnts are key mediators of dorsoventral patterning in vertebrates. In the cephalochordate amphioxus, genes encoding Bmps and transcription factors downstream of Bmp signaling such as Vent are expressed in patterns reminiscent of those of their vertebrate orthologues. However, the key question is whether the conservation of expression patterns of network constituents implies conservation of functional network interactions, and if so, how an increased functional complexity can evolve. Using heterologous systems, namely by reporter gene assays in mammalian cell lines and by transgenesis in medaka fish, we have compared the gene regulatory network implicated in dorsoventral patterning of the basal chordate amphioxus and vertebrates. We found that Bmp but not canonical Wnt signaling regulates promoters of genes encoding homeodomain proteins AmphiVent1 and AmphiVent2. Furthermore, AmphiVent1 and AmphiVent2 promoters appear to be correctly regulated in the context of a vertebrate embryo. Finally, we show that AmphiVent1 is able to directly repress promoters of AmphiGoosecoid and AmphiChordin genes. Repression of genes encoding dorsal-specific signaling molecule Chordin and transcription factor Goosecoid by Xenopus and zebrafish Vent genes represents a key regulatory interaction during vertebrate axis formation. Our data indicate high evolutionary conservation of a core Bmp-triggered gene regulatory network for dorsoventral patterning in chordates and suggest that co-option of the canonical Wnt signaling pathway for dorsoventral patterning in vertebrates represents one of the innovations through which an increased morphological complexity of vertebrate embryo is achieved.

  13. Crystal structure of mammalian acid sphingomyelinase.

    Science.gov (United States)

    Gorelik, Alexei; Illes, Katalin; Heinz, Leonhard X; Superti-Furga, Giulio; Nagar, Bhushan

    2016-01-01

    Acid sphingomyelinase (ASMase, ASM, SMPD1) converts sphingomyelin into ceramide, modulating membrane properties and signal transduction. Inactivating mutations in ASMase cause Niemann-Pick disease, and its inhibition is also beneficial in models of depression and cancer. To gain a better understanding of this critical therapeutic target, we determined crystal structures of mammalian ASMase in various conformations. The catalytic domain adopts a calcineurin-like fold with two zinc ions and a hydrophobic track leading to the active site. Strikingly, the membrane interacting saposin domain assumes either a closed globular conformation independent from the catalytic domain, or an open conformation, which establishes an interface with the catalytic domain essential for activity. Structural mapping of Niemann-Pick mutations reveals that most of them likely destabilize the protein's fold. This study sheds light on the molecular mechanism of ASMase function, and provides a platform for the rational development of ASMase inhibitors and therapeutic use of recombinant ASMase. PMID:27435900

  14. Peromyscus as a Mammalian Epigenetic Model

    Directory of Open Access Journals (Sweden)

    Kimberly R. Shorter

    2012-01-01

    Full Text Available Deer mice (Peromyscus offer an opportunity for studying the effects of natural genetic/epigenetic variation with several advantages over other mammalian models. These advantages include the ability to study natural genetic variation and behaviors not present in other models. Moreover, their life histories in diverse habitats are well studied. Peromyscus resources include genome sequencing in progress, a nascent genetic map, and >90,000 ESTs. Here we review epigenetic studies and relevant areas of research involving Peromyscus models. These include differences in epigenetic control between species and substance effects on behavior. We also present new data on the epigenetic effects of diet on coat-color using a Peromyscus model of agouti overexpression. We suggest that in terms of tying natural genetic variants with environmental effects in producing specific epigenetic effects, Peromyscus models have a great potential.

  15. Fundamentals of Expression in Mammalian Cells.

    Science.gov (United States)

    Dyson, Michael R

    2016-01-01

    Expression of proteins in mammalian cells is a key technology important for many functional studies on human and higher eukaryotic genes. Studies include the mapping of protein interactions, solving protein structure by crystallization and X-ray diffraction or solution phase NMR and the generation of antibodies to enable a range of studies to be performed including protein detection in vivo. In addition the production of therapeutic proteins and antibodies, now a multi billion dollar industry, has driven major advances in cell line engineering for the production of grams per liter of active proteins and antibodies. Here the key factors that need to be considered for successful expression in HEK293 and CHO cells are reviewed including host cells, expression vector design, transient transfection methods, stable cell line generation and cultivation conditions. PMID:27165328

  16. Nomenclature for mammalian soluble glutathione transferases.

    Science.gov (United States)

    Mannervik, Bengt; Board, Philip G; Hayes, John D; Listowsky, Irving; Pearson, William R

    2005-01-01

    The nomenclature for human soluble glutathione transferases (GSTs) is extended to include new members of the GST superfamily that have been discovered, sequenced, and shown to be expressed. The GST nomenclature is based on primary structure similarities and the division of GSTs into classes of more closely related sequences. The classes are designated by the names of the Greek letters: Alpha, Mu, Pi, etc., abbreviated in Roman capitals: A, M, P, and so on. (The Greek characters should not be used.) Class members are distinguished by Arabic numerals and the native dimeric protein structures are named according to their subunit composition (e.g., GST A1-2 is the enzyme composed of subunits 1 and 2 in the Alpha class). Soluble GSTs from other mammalian species can be classified in the same manner as the human enzymes, and this chapter presents the application of the nomenclature to the rat and mouse GSTs. PMID:16399376

  17. Mechanosensor Channels in Mammalian Somatosensory Neurons

    Directory of Open Access Journals (Sweden)

    Patrick Delmas

    2007-09-01

    Full Text Available Mechanoreceptive sensory neurons innervating the skin, skeletal muscles andviscera signal both innocuous and noxious information necessary for proprioception, touchand pain. These neurons are responsible for the transduction of mechanical stimuli intoaction potentials that propagate to the central nervous system. The ability of these cells todetect mechanical stimuli impinging on them relies on the presence of mechanosensitivechannels that transduce the external mechanical forces into electrical and chemical signals.Although a great deal of information regarding the molecular and biophysical properties ofmechanosensitive channels in prokaryotes has been accumulated over the past two decades,less is known about the mechanosensitive channels necessary for proprioception and thesenses of touch and pain. This review summarizes the most pertinent data onmechanosensitive channels of mammalian somatosensory neurons, focusing on theirproperties, pharmacology and putative identity.

  18. Sensory feedback control of mammalian vocalizations.

    Science.gov (United States)

    Smotherman, Michael S

    2007-09-01

    Somatosensory and auditory feedback mechanisms are dynamic components of the vocal motor pattern generator in mammals. This review explores how sensory cues arising from central auditory and somatosensory pathways actively guide the production of both simple sounds and complex phrases in mammals. While human speech is a uniquely sophisticated example of mammalian vocal behavior, other mammals can serve as examples of how sensory feedback guides complex vocal patterns. Echolocating bats in particular are unique in their absolute dependence on voice control for survival: these animals must constantly adjust the acoustic and temporal patterns of their orientation sounds to efficiently navigate and forage for insects at high speeds under the cover of darkness. Many species of bats also utter a broad repertoire of communication sounds. The functional neuroanatomy of the bat vocal motor pathway is basically identical to other mammals, but the acute significance of sensory feedback in echolocation has made this a profitable model system for studying general principles of sensorimotor integration with regard to vocalizing. Bats and humans are similar in that they both maintain precise control of many different voice parameters, both exhibit a similar suite of responses to altered auditory feedback, and for both the efficacy of sensory feedback depends upon behavioral context. By comparing similarities and differences in the ways sensory feedback influences voice in humans and bats, we may shed light on the basic architecture of the mammalian vocal motor system and perhaps be able to better distinguish those features of human vocal control that evolved uniquely in support of speech and language. PMID:17449116

  19. Recent integrations of mammalian Hmg retropseudogenes

    Indian Academy of Sciences (India)

    Eillen Tecle; Leann Zielinski; David H. Kass

    2006-12-01

    We propose that select retropseudogenes of the high mobility group nonhistone chromosomal protein genes have recently integrated into mammalian genomes on the basis of the high sequence identity of the copies to the cDNA sequences derived from the original genes. These include the Hmg1 gene family in mice and the Hmgn2 family in humans. We investigated orthologous loci of several strains and species of Mus for presence or absence of apparently young Hmg1 retropseudogenes. Three of four analysed elements were specific to Mus musculus, two of which were not fixed, indicative of recent evolutionary origins. Additionally, we datamined a presumptive subfamily (Hmgz) of mouse Hmg1, but only identified one true element in the GenBank database, which is not consistent with a separate subfamily status. Two of four analysed Hmgn2 retropseudogenes were specific for the human genome, whereas a third was identified in human, chimpanzee and gorilla genomes, and a fourth additionally found in orangutan but absent in African green monkey. Flanking target-site duplications were consistent with LINE integration sites supporting LINE machinery for their mechanism of amplification. The human Hmgn2 retropseudogenes were full length, whereas the mouse Hmg1 elements were either full length or 3′-truncated at specific positions, most plausibly the result of use of alternative polyadenylation sites. The nature of their recent amplification success in relation to other retropseudogenes is unclear, although availability of a large number of transcripts during gametogenesis may be a reason. It is apparent that retropseudogenes continue to shape mammalian genomes, and may provide insight into the process of retrotransposition, as well as offer potential use as phylogenetic markers.

  20. The architecture of mammalian ribosomal protein promoters

    Directory of Open Access Journals (Sweden)

    Perry Robert P

    2005-02-01

    Full Text Available Abstract Background Mammalian ribosomes contain 79 different proteins encoded by widely scattered single copy genes. Coordinate expression of these genes at transcriptional and post-transcriptional levels is required to ensure a roughly equimolar accumulation of ribosomal proteins. To date, detailed studies of only a very few ribosomal protein (rp promoters have been made. To elucidate the general features of rp promoter architecture, I made a detailed sequence comparison of the promoter regions of the entire set of orthologous human and mouse rp genes. Results A striking evolutionarily conserved feature of most rp genes is the separation by an intron of the sequences involved in transcriptional and translational regulation from the sequences with protein encoding function. Another conserved feature is the polypyrimidine initiator, which conforms to the consensus (Y2C+1TY(T2(Y3. At least 60 % of the rp promoters contain a largely conserved TATA box or A/T-rich motif, which should theoretically have TBP-binding capability. A remarkably high proportion of the promoters contain conserved binding sites for transcription factors that were previously implicated in rp gene expression, namely upstream GABP and Sp1 sites and downstream YY1 sites. Over 80 % of human and mouse rp genes contain a transposable element residue within 900 bp of 5' flanking sequence; very little sequence identity between human and mouse orthologues was evident more than 200 bp upstream of the transcriptional start point. Conclusions This analysis has provided some valuable insights into the general architecture of mammalian rp promoters and has identified parameters that might coordinately regulate the transcriptional activity of certain subsets of rp genes.

  1. Adult Neurogenesis in the Mammalian Hippocampus: Why the Dentate Gyrus?

    Science.gov (United States)

    Drew, Liam J.; Fusi, Stefano; Hen, René

    2013-01-01

    In the adult mammalian brain, newly generated neurons are continuously incorporated into two networks: interneurons born in the subventricular zone migrate to the olfactory bulb, whereas the dentate gyrus (DG) of the hippocampus integrates locally born principal neurons. That the rest of the mammalian brain loses significant neurogenic capacity…

  2. A versatile expression vector system for mammalian cell factories

    DEFF Research Database (Denmark)

    Lund, Anne Mathilde; Kildegaard, Helene Faustrup; Hansen, Bjarne Gram; Andersen, Mikael Rørdam; Mortensen, Uffe Hasbro

    The development of the field of mammalian cell factories requests fast and high-throughput methods which means high need for simpler and more efficient cloning techniques. This project applies the ligation-free USERTM (uracil-specific excision reagent) cloning technique to construct mammalian...... expression vectors with maximum flexibility....

  3. 40 CFR 799.9539 - TSCA mammalian erythrocyte micronucleus test.

    Science.gov (United States)

    2010-07-01

    ... endpoint of the assay when animals are treated continuously for 4 weeks or more. This mammalian in vivo... TESTING REQUIREMENTS Health Effects Test Guidelines § 799.9539 TSCA mammalian erythrocyte micronucleus test. (a) Scope. This section is intended to meet the testing requirements under section 4 of TSCA....

  4. The scalable mammalian brain: Emergent distributions of glia and neurons

    NARCIS (Netherlands)

    J.F.M. Jehee; J.M.J. Murre

    2008-01-01

    In this paper, we demonstrate that two characteristic properties of mammalian brains emerge when scaling-up modular, cortical structures. Firstly, the glia-to-neuron ratio is not constant across brains of different sizes: large mammalian brains have more glia per neuron than smaller brains. Our anal

  5. Human microRNAs originated from two periods at accelerated rates in mammalian evolution.

    Science.gov (United States)

    Iwama, Hisakazu; Kato, Kiyohito; Imachi, Hitomi; Murao, Koji; Masaki, Tsutomu

    2013-03-01

    MicroRNAs (miRNAs) are short, noncoding RNAs that modulate genes posttranscriptionally. Frequent gains and losses of miRNA genes have been reported to occur during evolution. However, little is known systematically about the periods of evolutionary origin of the present miRNA gene repertoire of an extant mammalian species. Thus, in this study, we estimated the evolutionary periods during which each of 1,433 present human miRNA genes originated within 15 periods, from human to platypus-human common ancestral branch and a class "conserved beyond theria," primarily using multiple genome alignments of 38 species, plus the pairwise genome alignments of five species. The results showed two peak periods in which the human miRNA genes originated at significantly accelerated rates. The most accelerated rate appeared in the period of the initial phase of hominoid lineage, and the second appeared shortly before Laurasiatherian divergence. Approximately 53% of the present human miRNA genes have originated within the simian lineage to human. In particular, approximately 28% originated within the hominoid lineage. The early phase of placental mammal radiation comprises approximately 28%, while no more than 15% of human miRNAs have been conserved beyond placental mammals. We also clearly showed a general trend, in which the miRNA expression level decreases as the miRNA becomes younger. Intriguingly, amid this decreasing trend of expression, we found one significant rise in the expression level that corresponded to the initial phase of the hominoid lineage, suggesting that increased functional acquisitions of miRNAs originated at this particular period. PMID:23171859

  6. Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies Using a Coalescent Hidden Markov Model

    DEFF Research Database (Denmark)

    Mailund, Thomas; Dutheil, Julien; Hobolth, Asger;

    2011-01-01

    ue to genetic variation in the ancestor of two populations or two species, the divergence time for DNA sequences from two populations is variable along the genome. Within genomic segments all bases will share the same divergence—because they share a most recent common ancestor—when no recombination...... event has occurred to split them apart. The size of these segments of constant divergence depends on the recombination rate, but also on the speciation time, the effective population size of the ancestral population, as well as demographic effects and selection. Thus, inference of these parameters may...... be possible if we can decode the divergence times along a genomic alignment. Here, we present a new hidden Markov model that infers the changing divergence (coalescence) times along the genome alignment using a coalescent framework, in order to estimate the speciation time, the recombination rate...

  7. An Interpretation of the Ancestral Codon from Miller’s Amino Acids and Nucleotide Correlations in Modern Coding Sequences

    Science.gov (United States)

    Carels, Nicolas; de Leon, Miguel Ponce

    2015-01-01

    Purine bias, which is usually referred to as an “ancestral codon”, is known to result in short-range correlations between nucleotides in coding sequences, and it is common in all species. We demonstrate that RWY is a more appropriate pattern than the classical RNY, and purine bias (Rrr) is the product of a network of nucleotide compensations induced by functional constraints on the physicochemical properties of proteins. Through deductions from universal correlation properties, we also demonstrate that amino acids from Miller’s spark discharge experiment are compatible with functional primeval proteins at the dawn of living cell radiation on earth. These amino acids match the hydropathy and secondary structures of modern proteins. PMID:25922573

  8. Early evolution of ionotropic GABA receptors and selective regimes acting on the mammalian-specific theta and epsilon subunits.

    Directory of Open Access Journals (Sweden)

    Christopher J Martyniuk

    Full Text Available BACKGROUND: The amino acid neurotransmitter GABA is abundant in the central nervous system (CNS of both invertebrates and vertebrates. Receptors of this neurotransmitter play a key role in important processes such as learning and memory. Yet, little is known about the mode and tempo of evolution of the receptors of this neurotransmitter. Here, we investigate the phylogenetic relationships of GABA receptor subunits across the chordates and detail their mode of evolution among mammals. PRINCIPAL FINDINGS: Our analyses support two major monophyletic clades: one clade containing GABA(A receptor alpha, gamma, and epsilon subunits, and another one containing GABA(A receptor rho, beta, delta, theta, and pi subunits. The presence of GABA receptor subunits from each of the major clades in the Ciona intestinalis genome suggests that these ancestral duplication events occurred before the divergence of urochordates. However, while gene divergence proceeded at similar rates on most receptor subunits, we show that the mammalian-specific subunits theta and epsilon experienced an episode of positive selection and of relaxed constraints, respectively, after the duplication event. Sites putatively under positive selection are placed on a three-dimensional model obtained by homology-modeling. CONCLUSIONS: Our results suggest an early divergence of the GABA receptor subunits, before the split from urochordates. We show that functional changes occurred in the lineages leading to the mammalian-specific subunit theta, and we identify the amino acid sites putatively responsible for the functional divergence. We discuss potential consequences for the evolution of mammals and of their CNS.

  9. Low pathogenic avian influenza (H9N2) in chicken: Evaluation of an ancestral H9-MVA vaccine.

    Science.gov (United States)

    Ducatez, Mariette F; Becker, Jens; Freudenstein, Astrid; Delverdier, Maxence; Delpont, Mattias; Sutter, Gerd; Guérin, Jean-Luc; Volz, Asisa

    2016-06-30

    Modified Vaccinia Ankara (MVA) has proven its efficacy as a recombinant vector vaccine for numerous pathogens including influenza virus. The present study aimed at evaluating a recombinant MVA candidate vaccine against low pathogenic avian influenza virus subtype H9N2 in the chicken model. As the high genetic and antigenic diversity of H9N2 viruses increases vaccine design complexity, one strategy to widen the range of vaccine coverage is to use an ancestor sequence. We therefore generated a recombinant MVA encoding for the gene sequence of an ancestral hemagglutinin H9 protein (a computationally derived amino acid sequence of the node of the H9N2 G1 lineage strains was obtained using the ANCESCON program). We analyzed the genetics and the growth properties of the MVA vector virus confirming suitability for use under biosafety level 1 and tested its efficacy when applied either as an intra-muscular (IM) or an oral vaccine in specific pathogen free chickens challenged with A/chicken/Tunisia/12/2010(H9N2). Two control groups were studied in parallel (unvaccinated and inoculated birds; unvaccinated and non-inoculated birds). IM vaccinated birds seroconverted as early as four days post vaccination and neutralizing antibodies were detected against A/chicken/Tunisia/12/2010(H9N2) in all the birds before challenge. The role of local mucosal immunity is unclear here as no antibodies were detected in eye drop or aerosol vaccinated birds. Clinical signs were not detected in any of the infected birds even in absence of vaccination. Virus replication was observed in both vaccinated and unvaccinated chickens, suggesting the MVA-ancestral H9 vaccine may not stop virus spread in the field. However vaccinated birds showed less histological damage, fewer influenza-positive cells and shorter virus shedding than their unvaccinated counterparts. PMID:27259828

  10. The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times

    Institute of Scientific and Technical Information of China (English)

    Konstantinos ANGELIS; Mario DOS REIS

    2015-01-01

    Although the effects of the coalescent process on sequence divergence and genealogies are well understood, the vir-tual majority of studies that use molecular sequences to estimate times of divergence among species have failed to account for the coalescent process. Here we study the impact of ancestral population size and incomplete lineage sorting on Bayesian estimates of species divergence times under the molecular clock when the inference model ignores the coalescent process. Using a combi-nation of mathematical analysis, computer simulations and analysis of real data, we find that the errors on estimates of times and the molecular rate can be substantial when ancestral populations are large and when there is substantial incomplete lineage sort-ing. For example, in a simple three-species case, we find that if the most precise fossil calibration is placed on the root of the phylogeny, the age of the internal node is overestimated, while if the most precise calibration is placed on the internal node, then the age of the root is underestimated. In both cases, the molecular rate is overestimated. Using simulations on a phylogeny of nine species, we show that substantial errors in time and rate estimates can be obtained even when dating ancient divergence events. We analyse the hominoid phylogeny and show that estimates of the neutral mutation rate obtained while ignoring the coalescent are too high. Using a coalescent-based technique to obtain geological times of divergence, we obtain estimates of the mutation rate that are within experimental estimates and we also obtain substantially older divergence times within the phylogeny [Current Zoology 61 (5): 874–885, 2015].

  11. PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories

    Science.gov (United States)

    Hanson-Smith, Victor; Johnson, Alexander

    2016-01-01

    The method of phylogenetic ancestral sequence reconstruction is a powerful approach for studying evolutionary relationships among protein sequence, structure, and function. In particular, this approach allows investigators to (1) reconstruct and “resurrect” (that is, synthesize in vivo or in vitro) extinct proteins to study how they differ from modern proteins, (2) identify key amino acid changes that, over evolutionary timescales, have altered the function of the protein, and (3) order historical events in the evolution of protein function. Widespread use of this approach has been slow among molecular biologists, in part because the methods require significant computational expertise. Here we present PhyloBot, a web-based software tool that makes ancestral sequence reconstruction easy. Designed for non-experts, it integrates all the necessary software into a single user interface. Additionally, PhyloBot provides interactive tools to explore evolutionary trajectories between ancestors, enabling the rapid generation of hypotheses that can be tested using genetic or biochemical approaches. Early versions of this software were used in previous studies to discover genetic mechanisms underlying the functions of diverse protein families, including V-ATPase ion pumps, DNA-binding transcription regulators, and serine/threonine protein kinases. PhyloBot runs in a web browser, and is available at the following URL: http://www.phylobot.com. The software is implemented in Python using the Django web framework, and runs on elastic cloud computing resources from Amazon Web Services. Users can create and submit jobs on our free server (at the URL listed above), or use our open-source code to launch their own PhyloBot server. PMID:27472806

  12. Stem cell-specific activation of an ancestral myc protooncogene with conserved basic functions in the early metazoan Hydra

    Science.gov (United States)

    Hartl, Markus; Mitterstiller, Anna-Maria; Valovka, Taras; Breuker, Kathrin; Hobmayer, Bert; Bister, Klaus

    2010-01-01

    The c-myc protooncogene encodes a transcription factor (Myc) with oncogenic potential. Myc and its dimerization partner Max are bHLH-Zip DNA binding proteins controlling fundamental cellular processes. Deregulation of c-myc leads to tumorigenesis and is a hallmark of many human cancers. We have identified and extensively characterized ancestral forms of myc and max genes from the early diploblastic cnidarian Hydra, the most primitive metazoan organism employed so far for the structural, functional, and evolutionary analysis of these genes. Hydra myc is specifically activated in all stem cells and nematoblast nests which represent the rapidly proliferating cell types of the interstitial stem cell system and in proliferating gland cells. In terminally differentiated nerve cells, nematocytes, or epithelial cells, myc expression is not detectable by in situ hybridization. Hydra max exhibits a similar expression pattern in interstitial cell clusters. The ancestral Hydra Myc and Max proteins display the principal design of their vertebrate derivatives, with the highest degree of sequence identities confined to the bHLH-Zip domains. Furthermore, the 314-amino acid Hydra Myc protein contains basic forms of the essential Myc boxes I through III. A recombinant Hydra Myc/Max complex binds to the consensus DNA sequence CACGTG with high affinity. Hybrid proteins composed of segments from the retroviral v-Myc oncoprotein and the Hydra Myc protein display oncogenic potential in cell transformation assays. Our results suggest that the principal functions of the Myc master regulator arose very early in metazoan evolution, allowing their dissection in a simple model organism showing regenerative ability but no senescence. PMID:20142507

  13. ¿Con o sin ancestros? Vigencia de lo ancestral en la Amazonía peruana

    Directory of Open Access Journals (Sweden)

    Thomas Mouriès

    2014-07-01

    Full Text Available The existence —or not— of the concept of ancestors in the indigenous Amazon has been the subject of much debate. However, regional leaders do not hesitate to call upon ‘ancestral’ knowledge, customs, or territories in the sense that, from an academic point of view, could appear enigmatic. «Ancestral, but… with or without ancestors?» is the question a confused anthropologist might ask. In this article, I propose to offer elements of a response to this question,based on a case study in Peru. First I analyze how Amazonian indigenous leaders, following international law, have adopted the legal notion of ‘ancestral possession’ of their territory to adapt it to the political sphere. This approach accounts for the recent generalization and uniformization of the term ‘ancestral’, but poses the problem of how it articulates with the indigenous cosmologies that it supposes to reflect. For this reason, I explore in the second section the pertinence of the category of ‘ancestor’ in the indigenous Amazon, briefly drawing upon the academic debate in order to define inwhat way this category takes on meaning. Based on testimony from an experienced Awajún leader, we thus return in the third section more explicitly to the different meanings and planes of reference that unfold when one uses the term ‘ancestral’, showing how Amazonian indigenous people not only adopt external conceptual elements and arguments, but also transform them based on their own cosmological singularities and political perspectives.

  14. PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories.

    Science.gov (United States)

    Hanson-Smith, Victor; Johnson, Alexander

    2016-07-01

    The method of phylogenetic ancestral sequence reconstruction is a powerful approach for studying evolutionary relationships among protein sequence, structure, and function. In particular, this approach allows investigators to (1) reconstruct and "resurrect" (that is, synthesize in vivo or in vitro) extinct proteins to study how they differ from modern proteins, (2) identify key amino acid changes that, over evolutionary timescales, have altered the function of the protein, and (3) order historical events in the evolution of protein function. Widespread use of this approach has been slow among molecular biologists, in part because the methods require significant computational expertise. Here we present PhyloBot, a web-based software tool that makes ancestral sequence reconstruction easy. Designed for non-experts, it integrates all the necessary software into a single user interface. Additionally, PhyloBot provides interactive tools to explore evolutionary trajectories between ancestors, enabling the rapid generation of hypotheses that can be tested using genetic or biochemical approaches. Early versions of this software were used in previous studies to discover genetic mechanisms underlying the functions of diverse protein families, including V-ATPase ion pumps, DNA-binding transcription regulators, and serine/threonine protein kinases. PhyloBot runs in a web browser, and is available at the following URL: http://www.phylobot.com. The software is implemented in Python using the Django web framework, and runs on elastic cloud computing resources from Amazon Web Services. Users can create and submit jobs on our free server (at the URL listed above), or use our open-source code to launch their own PhyloBot server. PMID:27472806

  15. Orangutan fish eating, primate aquatic fauna eating, and their implications for the origins of ancestral hominin fish eating.

    Science.gov (United States)

    Russon, Anne E; Compost, Alain; Kuncoro, Purwo; Ferisa, Agnes

    2014-12-01

    This paper presents new evidence of fish eating in rehabilitant orangutans living on two Bornean islands and explores its contributions to understanding nonhuman primates' aquatic fauna eating and the origins of ancestral hominin fish eating. We assessed the prevalence of orangutans' fish eating, their techniques for obtaining fish, and possible contributors (ecology, individual differences, humans). We identified 61 events in which orangutans tried to obtain fish, including 19 in which they ate fish. All the orangutans were juvenile-adolescent; all the fish were disabled catfish; and most were obtained and eaten in drier seasons in or near shallow, slow-moving water. Orangutans used several techniques to obtain fish (inadvertent, opportunistic and deliberate hand-catch, scrounge, tool-assisted catch) and probably learned them in that order. Probable contributing factors were orangutan traits (age, pre-existing water or tool skills), island features (social density, water accessibility), and local human fishing. Our review of primates' aquatic fauna eating showed orangutans to be one of 20 species that eat aquatic fauna, one of nine confirmed to eat fish, and one of three that use tools to obtain fish. Primate fish eating is also site-specific within species, partly as a function of habitat (e.g., marine-freshwater, seasonality) and human influence (possibly fostered eating fish or other aquatic fauna at most sites, clearly induced it at some). At tropical freshwater sites, fish eating occurred most often in drier seasons around shallow water. Orangutan and primate findings are generally consistent with Stewart's (2010) reconstruction of the origins of ancestral hominin fish eating, but suggest that it, and tool-assisted fish catching, were possible much earlier. PMID:25038033

  16. Cis-by-Trans regulatory divergence causes the asymmetric lethal effects of an ancestral hybrid incompatibility gene.

    Directory of Open Access Journals (Sweden)

    Shamoni Maheshwari

    Full Text Available The Dobzhansky and Muller (D-M model explains the evolution of hybrid incompatibility (HI through the interaction between lineage-specific derived alleles at two or more loci. In agreement with the expectation that HI results from functional divergence, many protein-coding genes that contribute to incompatibilities between species show signatures of adaptive evolution, including Lhr, which encodes a heterochromatin protein whose amino acid sequence has diverged extensively between Drosophila melanogaster and D. simulans by natural selection. The lethality of D. melanogaster/D. simulans F1 hybrid sons is rescued by removing D. simulans Lhr, but not D. melanogaster Lhr, suggesting that the lethal effect results from adaptive evolution in the D. simulans lineage. It has been proposed that adaptive protein divergence in Lhr reflects antagonistic coevolution with species-specific heterochromatin sequences and that defects in LHR protein localization cause hybrid lethality. Here we present surprising results that are inconsistent with this coding-sequence-based model. Using Lhr transgenes expressed under native conditions, we find no evidence that LHR localization differs between D. melanogaster and D. simulans, nor do we find evidence that it mislocalizes in their interspecific hybrids. Rather, we demonstrate that Lhr orthologs are differentially expressed in the hybrid background, with the levels of D. simulans Lhr double that of D. melanogaster Lhr. We further show that this asymmetric expression is caused by cis-by-trans regulatory divergence of Lhr. Therefore, the non-equivalent hybrid lethal effects of Lhr orthologs can be explained by asymmetric expression of a molecular function that is shared by both orthologs and thus was presumably inherited from the ancestral allele of Lhr. We present a model whereby hybrid lethality occurs by the interaction between evolutionarily ancestral and derived alleles.

  17. Mammalian septins in health and disease

    Directory of Open Access Journals (Sweden)

    Montagna C

    2015-02-01

    Full Text Available Cristina Montagna,1,2 Michal Bejerano-Sagie,1 Jenna R Zechmeister3 1Department of Genetics, 2Department of Pathology, Albert Einstein College of Medicine, Yeshiva University, 3Department of Obstetrics and Gynecology and Women's Health, Montefiore Medical Center, New York, NY, USA Abstract: Septins embrace a large family of proteins highly conserved among eukaryotic species. They were originally identified in budding yeast in the early 1970s as proteins essential for completion of cytokinesis. In humans, septins comprise a group of 13 genes, most of which are present in several isoform variants, leading to a complex pattern of expression. The biological functions achieved by septins have been extensively investigated in yeast, and while several questions remain unanswered, details on the mechanisms of action and pathways relative to their major role in orchestrating the mitotic process, cell polarity, and diffusion barriers have been elucidated. In mammalian cells, the biological processes in which septins play important roles are emerging as increasingly complex. Septins are found with a broad range of expression in most tissues, and like in yeast, are essential for the successful completion of cytokinesis and for the establishment of cell polarity and diffusion barriers. However, they have also been shown to be important for phagocytosis and migration. Owing to their widespread expression in most mammalian cell subtypes and the plethora of functions to which they have been associated, it is not surprising that septins have been implicated in a large variety of human diseases. This review summarizes the current knowledge of septins' cellular functions and the mechanisms of regulation of their assembly. In addition, we present the broad range of human diseases where septins have been shown to be important for the etiology of the disease, including areas where septins have been recently implemented as biomarkers. Because of the growing evidence

  18. A Syntenic Region Conserved from Fish to Mammalian X Chromosome

    OpenAIRE

    Guijun Guan; Meisheng Yi; Tohru Kobayashi; Yunhan Hong; Yoshitaka Nagahama

    2014-01-01

    Sex chromosomes bearing the sex-determining gene initiate development along the male or female pathway, no matter which sex is determined by XY male or ZW female heterogamety. Sex chromosomes originate from ancient autosomes but evolved rapidly after the acquisition of sex-determining factors which are highly divergent between species. In the heterogametic male system (XY system), the X chromosome is relatively evolutionary silent and maintains most of its ancestral genes, in contrast to its ...

  19. Origins and Impacts of New Mammalian Exons

    Directory of Open Access Journals (Sweden)

    Jason J. Merkin

    2015-03-01

    Full Text Available Mammalian genes are composed of exons, but the evolutionary origins and functions of new internal exons are poorly understood. Here, we analyzed patterns of exon gain using deep cDNA sequencing data from five mammals and one bird, identifying thousands of species- and lineage-specific exons. Most new exons derived from unique rather than repetitive intronic sequence. Unlike exons conserved across mammals, species-specific internal exons were mostly located in 5′ UTRs and alternatively spliced. They were associated with upstream intronic deletions, increased nucleosome occupancy, and RNA polymerase II pausing. Genes containing new internal exons had increased gene expression, but only in tissues in which the exon was included. Increased expression correlated with the level of exon inclusion, promoter proximity, and signatures of cotranscriptional splicing. Altogether, these findings suggest that increased splicing at the 5′ ends of genes enhances expression and that changes in 5′ end splicing alter gene expression between tissues and between species.

  20. Sources of Error in Mammalian Genetic Screens.

    Science.gov (United States)

    Sack, Laura Magill; Davoli, Teresa; Xu, Qikai; Li, Mamie Z; Elledge, Stephen J

    2016-01-01

    Genetic screens are invaluable tools for dissection of biological phenomena. Optimization of such screens to enhance discovery of candidate genes and minimize false positives is thus a critical aim. Here, we report several sources of error common to pooled genetic screening techniques used in mammalian cell culture systems, and demonstrate methods to eliminate these errors. We find that reverse transcriptase-mediated recombination during retroviral replication can lead to uncoupling of molecular tags, such as DNA barcodes (BCs), from their associated library elements, leading to chimeric proviral genomes in which BCs are paired to incorrect ORFs, shRNAs, etc This effect depends on the length of homologous sequence between unique elements, and can be minimized with careful vector design. Furthermore, we report that residual plasmid DNA from viral packaging procedures can contaminate transduced cells. These plasmids serve as additional copies of the PCR template during library amplification, resulting in substantial inaccuracies in measurement of initial reference populations for screen normalization. The overabundance of template in some samples causes an imbalance between PCR cycles of contaminated and uncontaminated samples, which results in a systematic artifactual depletion of GC-rich library elements. Elimination of contaminating plasmid DNA using the bacterial endonuclease Benzonase can restore faithful measurements of template abundance and minimize GC bias. PMID:27402361

  1. Presence of thiamine pyrophosphate in mammalian peroxisomes

    Directory of Open Access Journals (Sweden)

    Van Veldhoven Paul P

    2007-06-01

    Full Text Available Abstract Background Thiamine pyrophosphate (TPP is a cofactor for 2-hydroxyacyl-CoA lyase 1 (HACL1, a peroxisomal enzyme essential for the α-oxidation of phytanic acid and 2-hydroxy straight chain fatty acids. So far, HACL1 is the only known peroxisomal TPP-dependent enzyme in mammals. Little is known about the transport of metabolites and cofactors across the peroxisomal membrane and no peroxisomal thiamine or TPP carrier has been identified in mammals yet. This study was undertaken to get a better insight into these issues and to shed light on the role of TPP in peroxisomal metabolism. Results Because of the crucial role of the cofactor TPP, we reanalyzed its subcellular localization in rat liver. In addition to the known mitochondrial and cytosolic pools, we demonstrated, for the first time, that peroxisomes contain TPP (177 ± 2 pmol/mg protein. Subsequently, we verified whether TPP could be synthesized from its precursor thiamine, in situ, by a peroxisomal thiamine pyrophosphokinase (TPK. However, TPK activity was exclusively recovered in the cytosol. Conclusion Our results clearly indicate that mammalian peroxisomes do contain TPP but that no pyrophosphorylation of thiamine occurs in these organelles, implying that thiamine must enter the peroxisome already pyrophosphorylated. Consequently, TPP entry may depend on a specific transport system or, in a bound form, on HACL1 translocation.

  2. Nitric oxide negatively regulates mammalian adult neurogenesis

    Science.gov (United States)

    Packer, Michael A.; Stasiv, Yuri; Benraiss, Abdellatif; Chmielnicki, Eva; Grinberg, Alexander; Westphal, Heiner; Goldman, Steven A.; Enikolopov, Grigori

    2003-08-01

    Neural progenitor cells are widespread throughout the adult central nervous system but only give rise to neurons in specific loci. Negative regulators of neurogenesis have therefore been postulated, but none have yet been identified as subserving a significant role in the adult brain. Here we report that nitric oxide (NO) acts as an important negative regulator of cell proliferation in the adult mammalian brain. We used two independent approaches to examine the function of NO in adult neurogenesis. In a pharmacological approach, we suppressed NO production in the rat brain by intraventricular infusion of an NO synthase inhibitor. In a genetic approach, we generated a null mutant neuronal NO synthase knockout mouse line by targeting the exon encoding active center of the enzyme. In both models, the number of new cells generated in neurogenic areas of the adult brain, the olfactory subependyma and the dentate gyrus, was strongly augmented, which indicates that division of neural stem cells in the adult brain is controlled by NO and suggests a strategy for enhancing neurogenesis in the adult central nervous system.

  3. Repair of radiation damage in mammalian cells

    International Nuclear Information System (INIS)

    The responses, such as survival, mutation, and carcinogenesis, of mammalian cells and tissues to radiation are dependent not only on the magnitude of the damage to macromolecular structures - DNA, RNA, protein, and membranes - but on the rates of macromolecular syntheses of cells relative to the half-lives of the damages. Cells possess a number of mechanisms for repairing damage to DNA. If the repair systems are rapid and error free, cells can tolerate much larger doses than if repair is slow or error prone. It is important to understand the effects of radiation and the repair of radiation damage because there exist reasonable amounts of epidemiological data that permits the construction of dose-response curves for humans. The shapes of such curves or the magnitude of the response will depend on repair. Radiation damage is emphasized because: (a) radiation dosimetry, with all its uncertainties for populations, is excellent compared to chemical dosimetry; (b) a number of cancer-prone diseases are known in which there are defects in DNA repair and radiation results in more chromosomal damage in cells from such individuals than in cells from normal individuals; (c) in some cases, specific radiation products in DNA have been correlated with biological effects, and (d) many chemical effects seem to mimic radiation effects. A further reason for emphasizing damage to DNA is the wealth of experimental evidence indicating that damages to DNA can be initiating events in carcinogenesis

  4. Neuropeptidomics applied to studies of mammalian reproduction

    Directory of Open Access Journals (Sweden)

    Le Thao T.

    2014-01-01

    Full Text Available Neuropeptidomics, a mass spectrometry-based technique which aims to uncover the complete suite of neuropeptides present in a tissue, organ or cell from the brain or nervous system, has found application in studies examining physiological responses (e.g. food intake, appetite and reproduction. Neuropeptides (and peptide hormones have long been known as regulators of mammalian physiological processes, particularly reproduction. These peptides are derived from precursor proteins and become active via proteolytic processes and post-translational modifications. A relatively large number of neuropeptides, mainly formed in the hypothalamus or the anterior pituitary of mammals, have been specifically associated with reproduction, including GnRH, NPY, PYY and kisspeptin. Here, we will present an overview of neuropeptides, their roles in reproduction and the application of neuropeptidomics in this field. We address the advantages of neuropeptidomics in reproductive studies including the high throughput identification, profiling and quantification of neuropeptides present in reproductive tissues and also discuss some of the challenges. The application of neuropeptidomics to the field of reproduction will provide the foundation for a greater understanding of how neuropeptides act to regulate reproductive function.

  5. Cell fate regulation in early mammalian development

    International Nuclear Information System (INIS)

    Preimplantation development in mammals encompasses a period from fertilization to implantation and results in formation of a blastocyst composed of three distinct cell lineages: epiblast, trophectoderm and primitive endoderm. The epiblast gives rise to the organism, while the trophectoderm and the primitive endoderm contribute to extraembryonic tissues that support embryo development after implantation. In many vertebrates, such as frog or fish, maternally supplied lineage determinants are partitioned within the egg. Cell cleavage that follows fertilization results in polarization of these factors between the individual blastomeres, which become restricted in their developmental fate. In contrast, the mouse oocyte and zygote lack clear polarity and, until the eight-cell stage, individual blastomeres retain the potential to form all lineages. How are cell lineages specified in the absence of a maternally supplied blueprint? This is a fundamental question in the field of developmental biology. The answer to this question lies in understanding the cell–cell interactions and gene networks involved in embryonic development prior to implantation and using this knowledge to create testable models of the developmental processes that govern cell fates. We provide an overview of classic and contemporary models of early lineage development in the mouse and discuss the emerging body of work that highlights similarities and differences between blastocyst development in the mouse and other mammalian species. (paper)

  6. Protection of cultured mammalian cells by rebamipide

    Energy Technology Data Exchange (ETDEWEB)

    Antoku, Shigetoshi; Aramaki, Ryoji [Kyushu Univ., Fukuoka (Japan). Faculty of Medicine; Tanaka, Hisashi; Kusumoto, Naotoshi

    1997-06-01

    Rebamipide which is used as a drug for gastritis and stomach ulcer has large capability for OH radical scavenging. It is expected that rebamipide has protective effect against ionizing radiations. The present paper deals with protective effect of rebamipide for cultured mammalian cells exposed to ionizing radiations. As rebamipide is insoluble in water, three solvents were used to dissolve. Rebamipide dissolved in dimethyl sulfoxide (DMSO), dimethyl formamide (DMFA) and 0.02 N NaOH was added to the cells in Eagle`s minimum essential medium (MEM) supplemented with 10% fetal calf serum and the cells were irradiated with X-rays. After irradiation, the cells were trypsinized, plated in MEM with 10% fetal calf serum and incubated for 7 days in a CO{sub 2} incubator to form colonies. Rebamipide dissolved in 0.02 N NaOH exhibited the protective effect expected its OH radical scavenging capability. However, the protective effect of rebamipide dissolved in DMSO was about half of that expected by its radical scavenging capability and that of rebamipide dissolved in DMFA was not observed. Uptake of rebamipide labeled with {sup 14}C increased with increasing contact time with rebamipide. These rebamipide mainly distributed in nucleus rather than cytoplasm. (author)

  7. Mammalian meiotic silencing exhibits sexually dimorphic features.

    Science.gov (United States)

    Cloutier, J M; Mahadevaiah, S K; ElInati, E; Tóth, A; Turner, James

    2016-06-01

    During mammalian meiotic prophase I, surveillance mechanisms exist to ensure that germ cells with defective synapsis or recombination are eliminated, thereby preventing the generation of aneuploid gametes and embryos. Meiosis in females is more error-prone than in males, and this is in part because the prophase I surveillance mechanisms are less efficient in females. A mechanistic understanding of this sexual dimorphism is currently lacking. In both sexes, asynapsed chromosomes are transcriptionally inactivated by ATR-dependent phosphorylation of histone H2AFX. This process, termed meiotic silencing, has been proposed to perform an important prophase I surveillance role. While the transcriptional effects of meiotic silencing at individual genes are well described in the male germ line, analogous studies in the female germ line have not been performed. Here we apply single- and multigene RNA fluorescence in situ hybridization (RNA FISH) to oocytes from chromosomally abnormal mouse models to uncover potential sex differences in the silencing response. Notably, we find that meiotic silencing in females is less efficient than in males. Within individual oocytes, genes located on the same asynapsed chromosome are silenced to differing extents, thereby generating mosaicism in gene expression profiles across oocyte populations. Analysis of sex-reversed XY female mice reveals that the sexual dimorphism in silencing is determined by gonadal sex rather than sex chromosome constitution. We propose that sex differences in meiotic silencing impact on the sexually dimorphic prophase I response to asynapsis. PMID:26712235

  8. Functional Amyloid Formation within Mammalian Tissue.

    Directory of Open Access Journals (Sweden)

    2005-11-01

    Full Text Available Amyloid is a generally insoluble, fibrous cross-beta sheet protein aggregate. The process of amyloidogenesis is associated with a variety of neurodegenerative diseases including Alzheimer, Parkinson, and Huntington disease. We report the discovery of an unprecedented functional mammalian amyloid structure generated by the protein Pmel17. This discovery demonstrates that amyloid is a fundamental nonpathological protein fold utilized by organisms from bacteria to humans. We have found that Pmel17 amyloid templates and accelerates the covalent polymerization of reactive small molecules into melanin-a critically important biopolymer that protects against a broad range of cytotoxic insults including UV and oxidative damage. Pmel17 amyloid also appears to play a role in mitigating the toxicity associated with melanin formation by sequestering and minimizing diffusion of highly reactive, toxic melanin precursors out of the melanosome. Intracellular Pmel17 amyloidogenesis is carefully orchestrated by the secretory pathway, utilizing membrane sequestration and proteolytic steps to protect the cell from amyloid and amyloidogenic intermediates that can be toxic. While functional and pathological amyloid share similar structural features, critical differences in packaging and kinetics of assembly enable the usage of Pmel17 amyloid for normal function. The discovery of native Pmel17 amyloid in mammals provides key insight into the molecular basis of both melanin formation and amyloid pathology, and demonstrates that native amyloid (amyloidin may be an ancient, evolutionarily conserved protein quaternary structure underpinning diverse pathways contributing to normal cell and tissue physiology.

  9. Radiation- induced aneuploidy in mammalian germ cells

    International Nuclear Information System (INIS)

    The ability of ionizing radiation to induce aneuploidy in mammalian germ cells has been investigated experimentally in the laboratory mouse using a variety of cytogenetic and genetic methods. These studies have provided unambiguous evidence of induced nondisjunction in both male and female germ cells when the effect of irradiation is screened in meiotic cells or preimplantation embryos. In contrast, however, cytogenetic analyses of post-implantation embryos and genetic assays for induced chromosome gains have not found a significant radiation effect. These apparently contradictory findings may be reconciled if (a) radiation induces tertiary rather than primary trisomy, or (b) induces embryo-lethal genetic damage, such as deletions, in addition to numerical anomalies. Either or both of these explanations may account for the apparent loss during gestation of radiation-induced trisomic embryos. Extrapolating from the information so far available, it seems unlikely that environmental exposure to low doses if low dose rate radiation will result in a detectable increase in the rate of aneuploidy in the human population. (author)

  10. Hibernation and daily torpor minimize mammalian extinctions

    Science.gov (United States)

    Geiser, Fritz; Turbill, Christopher

    2009-10-01

    Small mammals appear to be less vulnerable to extinction than large species, but the underlying reasons are poorly understood. Here, we provide evidence that almost all (93.5%) of 61 recently extinct mammal species were homeothermic, maintaining a constant high body temperature and thus energy expenditure, which demands a high intake of food, long foraging times, and thus exposure to predators. In contrast, only 6.5% of extinct mammals were likely heterothermic and employed multi-day torpor (hibernation) or daily torpor, even though torpor is widespread within more than half of all mammalian orders. Torpor is characterized by substantial reductions of body temperature and energy expenditure and enhances survival during adverse conditions by minimizing food and water requirements, and consequently reduces foraging requirements and exposure to predators. Moreover, because life span is generally longer in heterothermic mammals than in related homeotherms, heterotherms can employ a ‘sit-and-wait’ strategy to withstand adverse periods and then repopulate when circumstances improve. Thus, torpor is a crucial but hitherto unappreciated attribute of small mammals for avoiding extinction. Many opportunistic heterothermic species, because of their plastic energetic requirements, may also stand a better chance of future survival than homeothermic species in the face of greater climatic extremes and changes in environmental conditions caused by global warming.

  11. Mammalian oocyte growth and development in vitro.

    Science.gov (United States)

    Eppig, J J; O'Brien, M; Wigglesworth, K

    1996-06-01

    This paper is a review of the current status of technology for mammalian oocyte growth and development in vitro. It compares and contrasts the characteristics of the various culture systems that have been devised for the culture of either isolated preantral follicles or the oocyte-granulosa cell complexes form preantral follicles. The advantages and disadvantages of these various systems are discussed. Endpoints for the evaluation of oocyte development in vitro, including oocyte maturation and embryogenesis, are described. Considerations for the improvement of the culture systems are also presented. These include discussions of the possible effects of apoptosis and inappropriate differentiation of oocyte-associated granulosa cells on oocyte development. Finally, the potential applications of the technology for oocyte growth and development in vitro are discussed. For example, studies of oocyte development in vitro could help to identify specific molecules produced during oocyte development that are essential for normal early embryogenesis and perhaps recognize defects leading to infertility or abnormalities in embryonic development. Moreover, the culture systems may provide the methods necessary to enlarge the populations of valuable agricultural, pharmaceutical product-producing, and endangered animals, and to rescue the oocytes of women about to undergo clinical procedures that place oocytes at risk. PMID:9115726

  12. Cell fate regulation in early mammalian development

    Science.gov (United States)

    Oron, Efrat; Ivanova, Natalia

    2012-08-01

    Preimplantation development in mammals encompasses a period from fertilization to implantation and results in formation of a blastocyst composed of three distinct cell lineages: epiblast, trophectoderm and primitive endoderm. The epiblast gives rise to the organism, while the trophectoderm and the primitive endoderm contribute to extraembryonic tissues that support embryo development after implantation. In many vertebrates, such as frog or fish, maternally supplied lineage determinants are partitioned within the egg. Cell cleavage that follows fertilization results in polarization of these factors between the individual blastomeres, which become restricted in their developmental fate. In contrast, the mouse oocyte and zygote lack clear polarity and, until the eight-cell stage, individual blastomeres retain the potential to form all lineages. How are cell lineages specified in the absence of a maternally supplied blueprint? This is a fundamental question in the field of developmental biology. The answer to this question lies in understanding the cell-cell interactions and gene networks involved in embryonic development prior to implantation and using this knowledge to create testable models of the developmental processes that govern cell fates. We provide an overview of classic and contemporary models of early lineage development in the mouse and discuss the emerging body of work that highlights similarities and differences between blastocyst development in the mouse and other mammalian species.

  13. Analysis of mammalian ras effector functions

    International Nuclear Information System (INIS)

    Over the last 8 years or so, a great deal of effort has been put into understanding the biochemical function of the three mammalian p21ras proteins. Single-amino-acid alterations in these three proteins have been detected in 25-50% of some types of human cancers, and it is believed that the somatic mutational event that generated these amino acid substitutions is an important step in the development of these malignancies. The authors report here some of their efforts to look for a possible target for p21ras regulation. In a series of experiments, they have looked for ras-induced changes in another known second-messenger system, namely, the breakdown of phosphatidylinositol (PtdIns) lipids by a phospholipase C. The results lead to the conclusion that NIH-3T3 cells transformed by oncogenic p21ras have an increased basal phospholipase C activity. In a different approach to identify a target for ras, they have analyzed its interaction with the recently described cellular protein, GAP. They have shown that this protein appears to bind ras at a site previously identified as the effector site, strongly implicating GAP as the target protein for p21ras regulation

  14. Ion channels, phosphorylation and mammalian sperm capacitation

    Institute of Scientific and Technical Information of China (English)

    Pablo E Visconti; Dario Krapf; José Luis de la Vega-Beltrán; Juan José Acevedo; Alberto Darszon

    2011-01-01

    Sexually reproducing animals require an orchestrated communication between spermatozoa and the egg to generate a new individual. Capacitation, a maturational complex phenomenon that occurs in the female reproductive tract, renders spermatozoa capable of binding and fusing with the oocyte, and it is a requirement for mammalian fertilization. Capacitation encompasses plasma membrane reorganization, ion permeability regulation, cholesterol loss and changes in the phosphorylation state of many proteins. Novel tools to study sperm ion channels, image intracellular ionic changes and proteins with better spatial and temporal resolution, are unraveling how modifications in sperm ion transport and phosphorylation states lead to capacitation. Recent evidence indicates that two parallel pathways regulate phosphorylation events leading to capacitation, one of them requiring activation of protein kinase A and the second one involving inactivation of ser/thr phosphatases. This review examines the involvement of ion transporters and phosphorylation signaling processes needed for spermatozoa to achieve capacitation. Understanding the molecular mechanisms leading to fertilization is central for societies to deal with rising male infertility rates, to develop safe male gamete-based contraceptives and to preserve biodiversity through better assisted fertilization strategies.

  15. Modelling study of dimerization in mammalian defensins

    Directory of Open Access Journals (Sweden)

    Verma Chandra

    2006-12-01

    Full Text Available Abstract Background Defensins are antimicrobial peptides of innate immunity functioning by non-specific binding to anionic phospholipids in bacterial membranes. Their cationicity, amphipathicity and ability to oligomerize are considered key factors for their action. Based on structural information on human β-defensin 2, we examine homologous defensins from various mammalian species for conserved functional physico-chemical characteristics. Results Based on homology greater than 40%, structural models of 8 homologs of HBD-2 were constructed. A conserved pattern of electrostatics and dynamics was observed across 6 of the examined defensins; models backed by energetics suggest that the defensins in these 6 organisms are characterized by dimerization-linked enhanced functional potentials. In contrast, dimerization is not energetically favoured in the sheep, goat and mouse defensins, suggesting that they function efficiently as monomers. Conclusion β-defensin 2 from some mammals may work as monomers while those in others, including humans, work as oligomers. This could potentially be used to design human defensins that may be effective at lower concentrations and hence have therapeutic benefits.

  16. Tetracycline-Regulated Suppression of Amber Codons in Mammalian Cells

    OpenAIRE

    Park, Ho-Jin; RajBhandary, Uttam L.

    1998-01-01

    As an approach to inducible suppression of nonsense mutations in mammalian cells, we described recently an amber suppression system in mammalian cells dependent on coexpression of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) along with the E. coli glutamine-inserting amber suppressor tRNA. Here, we report on tetracycline-regulated expression of the E. coli GlnRS gene and, thereby, tetracycline-regulated suppression of amber codons in mammalian HeLa and COS-1 cells. The E. coli GlnRS co...

  17. GENE EXPRESSION IN PRE-IMPLANTATION MAMMALIAN EMBRYOS

    Science.gov (United States)

    The pre-implantation mammalian embryo is initially under the control of maternal informational macromolecules that are accumulated during oogenesis. ubsequently, the genetic program of development becomes dependent upon new transcription derived from activation of the embryonic g...

  18. Neuroanatomy: connectome connects fly and mammalian brain networks.

    Science.gov (United States)

    Kaiser, Marcus

    2015-05-18

    A recent study shows that brain connectivity in Drosophila melanogaster follows a small-world, modular and rich-club organisation that facilitates information processing. This organisation shows a striking similarity with the mammalian brain. PMID:25989081

  19. Evolution of the mammalian dentate gyrus.

    Science.gov (United States)

    Hevner, Robert F

    2016-02-15

    The dentate gyrus (DG), a part of the hippocampal formation, has important functions in learning, memory, and adult neurogenesis. Compared with homologous areas in sauropsids (birds and reptiles), the mammalian DG is larger and exhibits qualitatively different phenotypes: 1) folded (C- or V-shaped) granule neuron layer, concave toward the hilus and delimited by a hippocampal fissure; 2) nonperiventricular adult neurogenesis; and 3) prolonged ontogeny, involving extensive abventricular (basal) migration and proliferation of neural stem and progenitor cells (NSPCs). Although gaps remain, available data indicate that these DG traits are present in all orders of mammals, including monotremes and marsupials. The exception is Cetacea (whales, dolphins, and porpoises), in which DG size, convolution, and adult neurogenesis have undergone evolutionary regression. Parsimony suggests that increased growth and convolution of the DG arose in stem mammals concurrently with nonperiventricular adult hippocampal neurogenesis and basal migration of NSPCs during development. These traits could all result from an evolutionary change that enhanced radial migration of NSPCs out of the periventricular zones, possibly by epithelial-mesenchymal transition, to colonize and maintain nonperiventricular proliferative niches. In turn, increased NSPC migration and clonal expansion might be a consequence of growth in the cortical hem (medial patterning center), which produces morphogens such as Wnt3a, generates Cajal-Retzius neurons, and is regulated by Lhx2. Finally, correlations between DG convolution and neocortical gyrification (or capacity for gyrification) suggest that enhanced abventricular migration and proliferation of NSPCs played a transformative role in growth and folding of neocortex as well as archicortex. PMID:26179319

  20. Assays for mammalian tyrosinase: a comparative study

    International Nuclear Information System (INIS)

    This work describes a comparative study of the tyrosinase activity determined using three methods which are the most extensively employed; two radiometric assays using L-tyrosine as substrate (tyrosine hydroxylase and melanin formation activities) and one spectrophotometric assay using L-dopa (dopa oxidase activity). The three methods were simultaneously employed to measure the activities of the soluble, melanosomal, and microsomal tyrosinase isozymes from Harding-Passey mouse melanoma through their purification processes. The aim of this study was to find any correlation among the tyrosinase activities measured by the three different assays and to determine whether that correlation varied with the isozyme and its degree of purification. The results show that mammalian tyrosinase has a greater turnover number for L-dopa than for L-tyrosine. Thus, enzyme activity, expressed as mumol of substrate transformed per min, is higher in assays using L-dopa as substrate than those using L-tyrosine. Moreover, the percentage of hydroxylated L-tyrosine that is converted into melanin is low and is affected by several factors, apparently decreasing the tyrosinase activity measured by the melanin formation assay. Bearing these considerations in mind, average interassay factors are proposed. Their values are 10 to transform melanin formation into tyrosine hydroxylase activity, 100 to transform tyrosine hydroxylase into dopa oxidase activity, and 1,000 to transform melanin formation into dopa oxidase activity. Variations in these values due to the presence in the tyrosinase preparations of either inhibitors or regulatory factors in melanogenesis independent of tyrosinase are also discussed

  1. Insights into the evolution of mammalian telomerase: Platypus TERT shares similarities with genes of birds and other reptiles and localizes on sex chromosomes

    Directory of Open Access Journals (Sweden)

    Hrdličková Radmila

    2012-06-01

    Full Text Available Abstract Background The TERT gene encodes the catalytic subunit of the telomerase complex and is responsible for maintaining telomere length. Vertebrate telomerase has been studied in eutherian mammals, fish, and the chicken, but less attention has been paid to other vertebrates. The platypus occupies an important evolutionary position, providing unique insight into the evolution of mammalian genes. We report the cloning of a platypus TERT (OanTERT ortholog, and provide a comparison with genes of other vertebrates. Results The OanTERT encodes a protein with a high sequence similarity to marsupial TERT and avian TERT. Like the TERT of sauropsids and marsupials, as well as that of sharks and echinoderms, OanTERT contains extended variable linkers in the N-terminal region suggesting that they were present already in basal vertebrates and lost independently in ray-finned fish and eutherian mammals. Several alternatively spliced OanTERT variants structurally similar to avian TERT variants were identified. Telomerase activity is expressed in all platypus tissues like that of cold-blooded animals and murine rodents. OanTERT was localized on pseudoautosomal regions of sex chromosomes X3/Y2, expanding the homology between human chromosome 5 and platypus sex chromosomes. Synteny analysis suggests that TERT co-localized with sex-linked genes in the last common mammalian ancestor. Interestingly, female platypuses express higher levels of telomerase in heart and liver tissues than do males. Conclusions OanTERT shares many features with TERT of the reptilian outgroup, suggesting that OanTERT represents the ancestral mammalian TERT. Features specific to TERT of eutherian mammals have, therefore, evolved more recently after the divergence of monotremes.

  2. Supercomplexes in the respiratory chains of yeast and mammalian mitochondria

    OpenAIRE

    Schägger, Hermann; Pfeiffer, Kathy

    2000-01-01

    Around 30–40 years after the first isolation of the five complexes of oxidative phosphorylation from mammalian mitochondria, we present data that fundamentally change the paradigm of how the yeast and mammalian system of oxidative phosphorylation is organized. The complexes are not randomly distributed within the inner mitochondrial membrane, but assemble into supramolecular structures. We show that all cytochrome c oxidase (complex IV) of Saccharomyces cerevisiae is bound to cytochrome c red...

  3. Methylated DNA Immunoprecipitation Analysis of Mammalian Endogenous Retroviruses.

    Science.gov (United States)

    Rebollo, Rita; Mager, Dixie L

    2016-01-01

    Endogenous retroviruses are repetitive sequences found abundantly in mammalian genomes which are capable of modulating host gene expression. Nevertheless, most endogenous retrovirus copies are under tight epigenetic control via histone-repressive modifications and DNA methylation. Here we describe a common method used in our laboratory to detect, quantify, and compare mammalian endogenous retrovirus DNA methylation. More specifically we describe methylated DNA immunoprecipitation (MeDIP) followed by quantitative PCR. PMID:26895065

  4. Model of mammalian cell reproductive death. Pt. 2

    International Nuclear Information System (INIS)

    A general equation for mammalian cell survival has been derived in the previous paper. This paper presents the results of comparison of theoretical evaluations with survival data available from the literature, including different cell lines, variations. In linear energy transfer, dose rate and dose fractionation and the effects of ultrasoft X-rays and superheavy ions. Merits and demerits of the model are considered in comparison with other models of radiation-induced killing of mammalian cells published in the literature. (orig.)

  5. Secondary instabilities modulate cortical complexity in the mammalian brain

    OpenAIRE

    Budday, Silvia; Steinmann, Paul; Kuhl, Ellen

    2015-01-01

    Disclosing the origin of convolutions in the mammalian brain remains a scientific challenge. Primary folds form before we are born: they are static, well defined, and highly preserved across individuals. Secondary folds occur and disappear throughout our entire life time: they are dynamic, irregular, and highly variable among individuals. While extensive research has improved our understanding of primary folding in the mammalian brain, secondary folding remains understudied and poorly underst...

  6. Non-linear leak currents affect mammalian neuron physiology

    OpenAIRE

    Shiwei Huang; Sungho Hong

    2015-01-01

    In their seminal works on squid giant axons, Hodgkin, and Huxley approximated the membrane leak current as Ohmic, i.e., linear, since in their preparation, sub-threshold current rectification due to the influence of ionic concentration is negligible. Most studies on mammalian neurons have made the same, largely untested, assumption. Here we show that the membrane time constant and input resistance of mammalian neurons (when other major voltage-sensitive and ligand-gated ionic currents are dis...

  7. Functions of miRNAs during Mammalian Heart Development

    OpenAIRE

    Shun Yan; Kai Jiao

    2016-01-01

    MicroRNAs (miRNAs) play essential roles during mammalian heart development and have emerged as attractive therapeutic targets for cardiovascular diseases. The mammalian embryonic heart is mainly derived from four major cell types during development. These include cardiomyocytes, endocardial cells, epicardial cells, and neural crest cells. Recent data have identified various miRNAs as critical regulators of the proper differentiation, proliferation, and survival of these cell types. In this re...

  8. Incorporation of mammalian actin into microfilaments in plant cell nucleus

    Directory of Open Access Journals (Sweden)

    Paves Heiti

    2004-04-01

    Full Text Available Abstract Background Actin is an ancient molecule that shows more than 90% amino acid homology between mammalian and plant actins. The regions of the actin molecule that are involved in F-actin assembly are largely conserved, and it is likely that mammalian actin is able to incorporate into microfilaments in plant cells but there is no experimental evidence until now. Results Visualization of microfilaments in onion bulb scale epidermis cells by different techniques revealed that rhodamine-phalloidin stained F-actin besides cytoplasm also in the nuclei whereas GFP-mouse talin hybrid protein did not enter the nuclei. Microinjection of fluorescently labeled actin was applied to study the presence of nuclear microfilaments in plant cells. Ratio imaging of injected fluorescent rabbit skeletal muscle actin and phalloidin staining of the microinjected cells showed that mammalian actin was able to incorporate into plant F-actin. The incorporation occurred preferentially in the nucleus and in the perinuclear region of plant cells whereas part of plant microfilaments, mostly in the periphery of cytoplasm, did not incorporate mammalian actin. Conclusions Microinjected mammalian actin is able to enter plant cell's nucleus, whereas incorporation of mammalian actin into plant F-actin occurs preferentially in the nucleus and perinuclear area.

  9. Genesis of the vertebrate FoxP subfamily member genes occurred during two ancestral whole genome duplication events.

    Science.gov (United States)

    Song, Xiaowei; Tang, Yezhong; Wang, Yajun

    2016-08-22

    The vertebrate FoxP subfamily genes play important roles in the construction of essential functional modules involved in physiological and developmental processes. To explore the adaptive evolution of functional modules associated with the FoxP subfamily member genes, it is necessary to study the gene duplication process. We detected four member genes of the FoxP subfamily in sea lampreys (a representative species of jawless vertebrates) through genome screenings and phylogenetic analyses. Reliable paralogons (i.e. paralogous chromosome segments) have rarely been detected in scaffolds of FoxP subfamily member genes in sea lampreys due to the considerable existence of HTH_Tnp_Tc3_2 transposases. However, these transposases did not alter gene numbers of the FoxP subfamily in sea lampreys. The coincidence between the "1-4" gene duplication pattern of FoxP subfamily genes from invertebrates to vertebrates and two rounds of ancestral whole genome duplication (1R- and 2R-WGD) events reveal that the FoxP subfamily of vertebrates was quadruplicated in the 1R- and 2R-WGD events. Furthermore, we deduced that a synchronous gene duplication process occurred for the FoxP subfamily and for three linked gene families/subfamilies (i.e. MIT family, mGluR group III and PLXNA subfamily) in the 1R- and 2R-WGD events using phylogenetic analyses and mirror-dendrogram methods (i.e. algorithms to test protein-protein interactions). Specifically, the ancestor of FoxP1 and FoxP3 and the ancestor of FoxP2 and FoxP4 were generated in 1R-WGD event. In the subsequent 2R-WGD event, these two ancestral genes were changed into FoxP1, FoxP2, FoxP3 and FoxP4. The elucidation of these gene duplication processes shed light on the phylogenetic relationships between functional modules of the FoxP subfamily member genes. PMID:27188254

  10. Genetic control of immune response in carriers of ancestral haplotype 8.1: the study of chemotaxis.

    Science.gov (United States)

    Candore, Giuseppina; Balistreri, Carmela R; Campagna, Anna Maria; Colombo, Alfredo; Cuppari, Irene; Di-Carlo, Daniele; Grimaldi, Maria P; Orlando, Valentina; Piazza, Giuseppina; Vasto, Sonya; Lio, Domenico; Caruso, Calogero

    2006-11-01

    In all caucasian populations the association of an impressive number of autoimmune diseases with genes from the HLA-B8, DR3 haplotype that is part of the ancestral haplotype (AH) 8.1 HLA-A1, Cw7, B8, TNFAB*a2b3, TNFN*S, C2*C, Bf*s, C4A*Q0, C4B*1, DRB1*0301, DRB3*0101, DQA1*0501, DQB1*0201 has been reported by different research groups. This haplotype, which is more common in northern Europe, is also associated with a number of immune system dysfunctions in healthy subjects. Analyzing the data according to gender, some dysfunctions are observed in women but not in men, in agreement with the role of X-linked genes and/or estrogens in the development and progression of autoimmune diseases. It has been proposed that a small number of genes within the 8.1 AH modify immune responsiveness and hence affect multiple immunopathological diseases. In this article, we demonstrate that neutrophil chemotaxis is significantly decreased in carriers of this AH, suggesting that this impairment may also be related to the increased occurrence of autoimmune diseases in these individuals. PMID:17261794

  11. Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage.

    Science.gov (United States)

    Yeoh, Yun Kit; Sekiguchi, Yuji; Parks, Donovan H; Hugenholtz, Philip

    2016-04-01

    Candidate phylum TM6 is a major bacterial lineage recognized through culture-independent rRNA surveys to be low abundance members in a wide range of habitats; however, they are poorly characterized due to a lack of pure culture representatives. Two recent genomic studies of TM6 bacteria revealed small genomes and limited gene repertoire, consistent with known or inferred dependence on eukaryotic hosts for their metabolic needs. Here, we obtained additional near-complete genomes of TM6 populations from agricultural soil and upflow anaerobic sludge blanket reactor metagenomes which, together with the two publicly available TM6 genomes, represent seven distinct family level lineages in the TM6 phylum. Genome-based phylogenetic analysis confirms that TM6 is an independent phylum level lineage in the bacterial domain, possibly affiliated with the Patescibacteria superphylum. All seven genomes are small (1.0-1.5 Mb) and lack complete biosynthetic pathways for various essential cellular building blocks including amino acids, lipids, and nucleotides. These and other features identified in the TM6 genomes such as a degenerated cell envelope, ATP/ADP translocases for parasitizing host ATP pools, and protein motifs to facilitate eukaryotic host interactions indicate that parasitism is widespread in this phylum. Phylogenetic analysis of ATP/ADP translocase genes suggests that the ancestral TM6 lineage was also parasitic. We propose the name Dependentiae (phyl. nov.) to reflect dependence of TM6 bacteria on host organisms. PMID:26615204

  12. Food-Nonfood Discrimination in Ancestral Vertebrates: Gamete Cannibalism and the Origin of the Adaptive Immune System.

    Science.gov (United States)

    Corcos, D

    2015-11-01

    Adaptive immunity is a complex system that appeared twice in vertebrates (in gnathostomes and in jawless fish) although it is not required for invertebrate defence. The adaptive immune system is tightly associated with self-non-self discrimination, and it is now clear that this interplay is not limited to the prevention of autoreactivity. Micro-organisms are usually considered for their pathogenicity or symbiotic ability, but, for most small metazoans, they mainly constitute food. Vertebrates are characterized by feeding by predation on larger preys, when compared to their ancestors who were filter feeders and ate micro-organisms. Predation gives a strong selective advantage, not only due to the availability of new food resources but also by the ability to eliminate competitors for environmental resources (intraguild predation (IGP)). Unlike size-structured IGP, intraspecific predation of juveniles, zygotes or gametes can be detrimental for species fitness in some circumstances. The ability of individuals to recognize highly polymorphic molecules on the surface of gametes present in the plankton and so distinguish self versus non-self gametes might have constituted a strong selective advantage in intraspecific competition. Here, I propose the theory that the capacity to rearrange receptors has been selected in ancestral vertebrates as a consequence of this strong need for discriminating between hetero-cannibalism versus filial cannibalism. This evolutionary origin sheds light on presently unexplained features of the immune system, including the existence of regulatory T cells and of non-pathogenic natural autoimmunity. PMID:26286030

  13. What was the ancestral function of decidual stromal cells? A model for the evolution of eutherian pregnancy.

    Science.gov (United States)

    Chavan, Arun Rajendra; Bhullar, Bhart-Anjan S; Wagner, Günter P

    2016-04-01

    In human and mouse, decidual stromal cells (DSC) are necessary for the establishment (implantation) and the maintenance of pregnancy by preventing inflammation and the immune rejection of the semi-allograft conceptus. DSC originated along the stem lineage of eutherian mammals, coincidental with the origin of invasive placentation. Surprisingly, in many eutherian lineages decidual cells are lost after the implantation phase of pregnancy, making it unlikely that DSC are necessary for the maintenance of pregnancy in these animals. In order to understand this variation, we review the literature on the fetal-maternal interface in all major eutherian clades Euarchontoglires, Laurasiatheria, Xenarthra and Afrotheria, as well as the literature about the ancestral eutherian species. We conclude that maintaining pregnancy may not be a shared derived function of DSC among all eutherian mammals. Rather, we propose that DSC originated to manage the inflammatory reaction associated with invasive implantation. We envision that this happened in a stem eutherian that had invasive placenta but still a short gestation. We further propose that extended gestation evolved independently in the major eutherian clades explaining why the major lineages of eutherian mammals differ with respect to the mechanisms maintaining pregnancy. PMID:27016782

  14. Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure.

    Science.gov (United States)

    Basu, Analabha; Sarkar-Roy, Neeta; Majumder, Partha P

    2016-02-01

    India, occupying the center stage of Paleolithic and Neolithic migrations, has been underrepresented in genome-wide studies of variation. Systematic analysis of genome-wide data, using multiple robust statistical methods, on (i) 367 unrelated individuals drawn from 18 mainland and 2 island (Andaman and Nicobar Islands) populations selected to represent geographic, linguistic, and ethnic diversities, and (ii) individuals from populations represented in the Human Genome Diversity Panel (HGDP), reveal four major ancestries in mainland India. This contrasts with an earlier inference of two ancestries based on limited population sampling. A distinct ancestry of the populations of Andaman archipelago was identified and found to be coancestral to Oceanic populations. Analysis of ancestral haplotype blocks revealed that extant mainland populations (i) admixed widely irrespective of ancestry, although admixtures between populations was not always symmetric, and (ii) this practice was rapidly replaced by endogamy about 70 generations ago, among upper castes and Indo-European speakers predominantly. This estimated time coincides with the historical period of formulation and adoption of sociocultural norms restricting intermarriage in large social strata. A similar replacement observed among tribal populations was temporally less uniform. PMID:26811443

  15. Expression of segment polarity genes in brachiopods supports a non-segmental ancestral role of engrailed for bilaterians.

    Science.gov (United States)

    Vellutini, Bruno C; Hejnol, Andreas

    2016-01-01

    The diverse and complex developmental mechanisms of segmentation have been more thoroughly studied in arthropods, vertebrates and annelids-distantly related animals considered to be segmented. Far less is known about the role of "segmentation genes" in organisms that lack a segmented body. Here we investigate the expression of the arthropod segment polarity genes engrailed, wnt1 and hedgehog in the development of brachiopods-marine invertebrates without a subdivided trunk but closely related to the segmented annelids. We found that a stripe of engrailed expression demarcates the ectodermal boundary that delimits the anterior region of Terebratalia transversa and Novocrania anomala embryos. In T. transversa, this engrailed domain is abutted by a stripe of wnt1 expression in a pattern similar to the parasegment boundaries of insects-except for the expression of hedgehog, which is restricted to endodermal tissues of the brachiopod embryos. We found that pax6 and pax2/5/8, putative regulators of engrailed, also demarcate the anterior boundary in the two species, indicating these genes might be involved in the anterior patterning of brachiopod larvae. In a comparative phylogenetic context, these findings suggest that bilaterians might share an ancestral, non-segmental domain of engrailed expression during early embryogenesis. PMID:27561213

  16. Natural environments, ancestral diets, and microbial ecology: is there a modern "paleo-deficit disorder"? Part II.

    Science.gov (United States)

    Logan, Alan C; Katzman, Martin A; Balanzá-Martínez, Vicent

    2015-01-01

    Famed microbiologist René J. Dubos (1901-1982) was an early pioneer in the developmental origins of health and disease (DOHaD) construct. In the 1960s, he conducted groundbreaking research concerning the ways in which early-life experience with nutrition, microbiota, stress, and other environmental variables could influence later-life health outcomes. He recognized the co-evolutionary relationship between microbiota and the human host. Almost 2 decades before the hygiene hypothesis, he suggested that children in developed nations were becoming too sanitized (vs. our ancestral past) and that scientists should determine whether the childhood environment should be "dirtied up in a controlled manner." He also argued that oft-celebrated growth chart increases via changes in the global food supply and dietary patterns should not be equated to quality of life and mental health. Here in the second part of our review, we reflect the words of Dubos off contemporary research findings in the areas of diet, the gut-brain-axis (microbiota and anxiety and depression) and microbial ecology. Finally, we argue, as Dubos did 40 years ago, that researchers should more closely examine the relevancy of silo-sequestered, reductionist findings in the larger picture of human quality of life. In the context of global climate change and the epidemiological transition, an allergy epidemic and psychosocial stress, our review suggests that discussions of natural environments, urbanization, biodiversity, microbiota, nutrition, and mental health, are often one in the same. PMID:25889196

  17. Localization of Type 1 Diabetes susceptibility in the ancestral haplotype 18.2 by high density SNP mapping.

    Science.gov (United States)

    Santiago, Jose Luis; Li, Wentian; Lee, Annette; Martinez, Alfonso; Chandrasekaran, Alamelu; Fernandez-Arquero, Miguel; Khalili, Houman; de la Concha, Emilio G; Urcelay, Elena; Gregersen, Peter K

    2009-10-01

    Previous studies have suggested that the ancestral haplotype 18.2 (AH18.2) carries additional susceptibility gene to Type 1 Diabetes (T1D) on the Major Histocompatibility Complex (MHC). We analyzed 10 DR3/TNFa1b5 homozygous subjects in order to establish the conservation of the AH18.2 and then compared this conserved region with other DR3 haplotype, the AH8.1. The Illumina's HumanHap550 Bead chip was used to perform an extensive genotyping of the MHC region. The AH18.2 was highly conserved between DDR1 and HLA-DQA1 genes; therefore most probably the second susceptibility gene is located within this region. We can exclude the region centromeric to HLA-DRA gene and telomeric to DDR1 gene. A comparison between the AH18.2 and AH8.1 haplotypes showed that 233 SNPs were different in the aforementioned conserved region. These data suggest that the 1.65 Mb MHC region between DDR1 and HLA-DRA genes is likely to carry additional susceptibility alleles for T1D on the AH18.2 haplotype. PMID:19591919

  18. Ancestral polymorphisms and sex-biased migration shaped the demographic history of brown bears and polar bears.

    Directory of Open Access Journals (Sweden)

    Shigeki Nakagome

    Full Text Available Recent studies have reported discordant gene trees in the evolution of brown bears and polar bears. Genealogical histories are different among independent nuclear loci and between biparentally inherited autosomal DNA (aDNA and matrilineal mitochondrial DNA (mtDNA. Based on multi-locus genomic sequences from aDNA and mtDNA, we inferred the population demography of brown and polar bears and found that brown bears have 6 times (aDNA or more than 14 times (mtDNA larger population sizes than polar bears and that polar bear lineage is derived from within brown bear diversity. In brown bears, the effective population size ratio of mtDNA to aDNA was at least 0.62, which deviated from the expected value of 0.25, suggesting matriarchal population due to female philopatry and male-biased migration. These results emphasize that ancestral polymorphisms and sex-biased migration may have contributed to conflicting branching patterns in brown and polar bears across aDNA genes and mtDNA.

  19. Mammalian lipocalin allergens--insights into their enigmatic allergenicity.

    Science.gov (United States)

    Virtanen, T; Kinnunen, T; Rytkönen-Nissinen, M

    2012-04-01

    Most of the important mammal-derived respiratory allergens, as well as a milk allergen and a few insect allergens, belong to the lipocalin protein family. As mammalian lipocalin allergens are found in dander, saliva and urine, they disperse effectively and are widely present in the indoor environments. Initially, lipocalins were characterized as transport proteins for small, principally hydrophobic molecules, but now they are known to be involved in many other biological functions. Although the amino acid identity between lipocalins is generally at the level of 20-30%, it can be considerably higher. Lipocalin allergens do not exhibit any known physicochemical, functional or structural property that would account for their allergenicity, that is, the capacity to induce T-helper type 2 immunity against them. A distinctive feature of mammalian lipocalin allergens is their poor capacity to stimulate the cellular arm of the human or murine immune system. Nevertheless, they induce IgE production in a large proportion of atopic individuals exposed to the allergen source. The poor capacity of mammalian lipocalin allergens to stimulate the cellular immune system does not appear to result from the function of regulatory T cells. Instead, the T cell epitopes of mammalian lipocalin allergens are few and those examined have proved to be suboptimal. Moreover, the frequency of mammalian lipocalin allergen-specific CD4(+) T cells is very low in the peripheral blood. Importantly, recent research suggests that the lipocalin allergen-specific T cell repertoires differ considerably between allergic and healthy subjects. These observations are compatible with our hypothesis that the way CD4(+) T-helper cells recognize the epitopes of mammalian lipocalin allergens may be implicated in their allergenicity. Indeed, as several lipocalins exhibit homologies of 40-60% over species, mammalian lipocalin allergens may be immunologically at the borderline of self and non-self, which would not

  20. Creation of Functional Viruses from Non-Functional cDNA Clones Obtained from an RNA Virus Population by the Use of Ancestral Reconstruction

    DEFF Research Database (Denmark)

    Fahnøe, Ulrik; Pedersen, Anders Gorm; Dräger, Carolin;

    2015-01-01

    infectious RNA transcripts. Full length sequencing of cDNA clones and deep sequencing of the parental population identified substitutions important for the observed phenotypes. The investigated cDNA clones were furthermore used as the basis for inferring the sequence of functional viruses. Since each unique......-fitness, functional cDNAs and may also pose problems for sequence-based analysis of viral evolution. To address these challenges we have performed a study of the evolution of classical swine fever virus (CSFV) using deep sequencing and analysis of 84 full-length cDNA clones, each representing individual genomes from...... clone must necessarily be the descendant of a functional ancestor, we hypothesized that it should be possible to produce functional clones by reconstructing ancestral sequences. To test this we used phylogenetic methods to infer two ancestral sequences, which were then reconstructed as cDNA clones...

  1. Clan, ancestral hall, and sacrifice in the Song Dynasty%宋代的宗族祠堂、祭祀及其它

    Institute of Scientific and Technical Information of China (English)

    游彪

    2007-01-01

    The Song Dynasty is the most important period in Chinese history in terms of the establishment of a new type of clan system. During the Song, Chinese social organization, at the grass-roots level, experienced a fundamental change.In the wake of the late-Tang collapse of the local power system, it was necessary for the Song to replace the ancestral lineage structure and develop a new system to adapt itself to the new circumstances brought on by drastic changes in its economy. Song Confucians played a vital part in the changes. Not only did they gradually solve the theoretical problems of the new type of clan organization, but they also developed many feasible and standard models. Eventually this model would gain even wider acceptance after the Yuan Dynasty with the rise of Neo-Confucianism. Thus, ancestral halls, serving as the major centers for the new clan activities, became prevalent among common people.

  2. The mammalian fauna from the Central Himalaya, Nepal

    Directory of Open Access Journals (Sweden)

    Hem Bahadur Katuwal

    2013-07-01

    Full Text Available Nepal harbors unique mammalian fauna, but it is poorly studied at higher elevation. Mammalian fauna were recorded in Manaslu Conservation Area, Dudhkunda and Dudhkoshi valley of Solukhumbu district and Kanchenjunga Conservation Area of Nepal during March 2011 to April 2013 along the trail and the study plots from 700m to 4400m a.s.l. Semi-structured interviews were made with local people to understand their behavior and habitats. Altogether, 29 mammalian fauna were recorded. Five species were recorded new for the areas. Overall, Carnivore species (nine were encountered more, followed by species of the order Cetartiodactyla (seven. The highest number of mammalian fauna (18 was identified from Manaslu Conservation Area whereas the least (11 from Dudhkunda and Dudhkoshi valley. Human wildlife conflict was frequent with Himalayan Goral (Naemorhedus goral, Barking Deer (Muntiacus vaginalis, Himalayan Tahr (Hemitragus jemlahicus, Rhesus Macaque (Macaca mulatta, Nepal Grey Langur (Semnopithecus schistaceus and Himalayan Black Bear (Ursus thibetanus for crop depredation in these areas. Although mammalian research started a long time ago, scenario of comprehensive research is not satisfactory in the Central Himalaya, Nepal.

  3. Amino acids in the cultivation of mammalian cells.

    Science.gov (United States)

    Salazar, Andrew; Keusgen, Michael; von Hagen, Jörg

    2016-05-01

    Amino acids are crucial for the cultivation of mammalian cells. This importance of amino acids was realized soon after the development of the first cell lines, and a solution of a mixture of amino acids has been supplied to cultured cells ever since. The importance of amino acids is further pronounced in chemically defined mammalian cell culture media, making the consideration of their biological and chemical properties necessary. Amino acids concentrations have been traditionally adjusted to their cellular consumption rates. However, since changes in the metabolic equilibrium of amino acids can be caused by changes in extracellular concentrations, metabolomics in conjunction with flux balance analysis is being used in the development of culture media. The study of amino acid transporters is also gaining importance since they control the intracellular concentrations of these molecules and are influenced by conditions in cell culture media. A better understanding of the solubility, stability, dissolution kinetics, and interactions of these molecules is needed for an exploitation of these properties in the development of dry powdered chemically defined media for mammalian cells. Due to the complexity of these mixtures however, this has proven to be challenging. Studying amino acids in mammalian cell culture media will help provide a better understanding of how mammalian cells in culture interact with their environment. It would also provide insight into the chemical behavior of these molecules in solutions of complex mixtures, which is important in the understanding of the contribution of individual amino acids to protein structure. PMID:26832172

  4. Identifying variation in resistance to the take-all fungus, Gaeumannomyces graminis var. tritici, between different ancestral and modern wheat species

    OpenAIRE

    McMillan, Vanessa E; Gutteridge, Richard J; Hammond-Kosack, Kim E.

    2014-01-01

    Background Ancestral wheat relatives are important sources of genetic diversity for the introduction of novel traits for the improvement of modern bread wheat. In this study the aim was to assess the susceptibility of 34 accessions of the diploid wheat Triticum monococcum (A genome) to Gaeumannomyces graminis var. tritici (Ggt), the causal agent of take-all disease. The second aim was to explore the susceptibility of tetraploid wheat (T. durum) and the B genome progenitor species Aegilops spe...

  5. Personal and Social Transformation in the Health Area through Education: A Brief Journey from the Ancestral Indigenous Wisdom to the Modern Tyranny of Healthiness

    OpenAIRE

    Andrés de Muller

    2015-01-01

    This paper aims at claiming the ancestral wisdom of indigenous people in the health area. It analyzes how health has been commodified in the interest of large companies (particularly those related to the pharmaceutical industry) to the detriment of a holistic definition of wellness through education. Furthermore, the concept of health as a right disagrees with such commodification or sale to the highest bidder, which prompts dehumanization of health services and public misinformation. The abu...

  6. The Ancestral Carnivore Karyotype As Substantiated by Comparative Chromosome Painting of Three Pinnipeds, the Walrus, the Steller Sea Lion and the Baikal Seal (Pinnipedia, Carnivora)

    OpenAIRE

    Beklemisheva, Violetta R.; Perelman, Polina L.; Lemskaya, Natalya A.; Kulemzina, Anastasia I.; Proskuryakova, Anastasia A.; Burkanov, Vladimir N.; Alexander S Graphodatsky

    2016-01-01

    Karyotype evolution in Carnivora is thoroughly studied by classical and molecular cytogenetics and supplemented by reconstructions of Ancestral Carnivora Karyotype (ACK). However chromosome painting information from two pinniped families (Odobenidae and Otariidae) is noticeably missing. We report on the construction of the comparative chromosome map for species from each of the three pinniped families: the walrus (Odobenus rosmarus, Odobenidae-monotypic family), near threatened Steller sea li...

  7. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

    Science.gov (United States)

    Hurst, Laurence D; Ghanbarian, Avazeh T; Forrest, Alistair R R; Huminiecki, Lukasz

    2015-12-01

    X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression

  8. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

    Directory of Open Access Journals (Sweden)

    Laurence D Hurst

    2015-12-01

    Full Text Available X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE and data from the Functional Annotation of the Mammalian Genome (FANTOM5 project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds, as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased

  9. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

    KAUST Repository

    Hurst, Laurence D.

    2015-12-18

    X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression

  10. Phylogenomic analysis of vertebrate thrombospondins reveals fish-specific paralogues, ancestral gene relationships and a tetrapod innovation

    Directory of Open Access Journals (Sweden)

    Adams Josephine C

    2006-04-01

    Full Text Available Abstract Background Thrombospondins (TSPs are evolutionarily-conserved, extracellular, calcium-binding glycoproteins with important roles in cell-extracellular matrix interactions, angiogenesis, synaptogenesis and connective tissue organisation. Five TSPs, designated TSP-1 through TSP-5, are encoded in the human genome. All but one have known roles in acquired or inherited human diseases. To further understand the roles of TSPs in human physiology and pathology, it would be advantageous to extend the repertoire of relevant vertebrate models. In general the zebrafish is proving an excellent model organism for vertebrate biology, therefore we set out to evaluate the status of TSPs in zebrafish and two species of pufferfish. Results We identified by bioinformatics that three fish species encode larger numbers of TSPs than vertebrates, yet all these sequences group as homologues of TSP-1 to -4. By phylogenomic analysis of neighboring genes, we uncovered that, in fish, a TSP-4-like sequence is encoded from the gene corresponding to the tetrapod TSP-5 gene. Thus, all TSP genes show conservation of synteny between fish and tetrapods. In the human genome, the TSP-1, TSP-3, TSP-4 and TSP-5 genes lie within paralogous regions that provide insight into the ancestral genomic context of vertebrate TSPs. Conclusion A new model for TSP evolution in vertebrates is presented. The TSP-5 protein sequence has evolved rapidly from a TSP-4-like sequence as an innovation in the tetrapod lineage. TSP biology in fish is complicated by the presence of additional lineage- and species-specific TSP paralogues. These novel results give deeper insight into the evolution of TSPs in vertebrates and open new directions for understanding the physiological and pathological roles of TSP-4 and TSP-5 in humans.

  11. Somatostatin signaling system as an ancestral mechanism: Myoregulatory activity of an Allatostatin-C peptide in Hydra.

    Science.gov (United States)

    Alzugaray, María Eugenia; Hernández-Martínez, Salvador; Ronderos, Jorge Rafael

    2016-08-01

    The coordination of physiological processes requires precise communication between cells. Cellular interactions allow cells to be functionally related, facilitating the maintaining of homeostasis. Neuropeptides functioning as intercellular signals are widely distributed in Metazoa. It is assumed that neuropeptides were the first intercellular transmitters, appearing early during the evolution. In Cnidarians, neuropeptides are mainly involved in neurotransmission, acting directly or indirectly on epithelial muscle cells, and thereby controlling coordinated movements. Allatostatins are a group of chemically unrelated neuropeptides that were originally characterized based on their ability to inhibit juvenil hormone synthesis in insects. Allatostatin-C has pleiotropic functions, acting as myoregulator in several insects. In these studies, we analyzed the myoregulatory effect of Aedes aegypti Allatostatin-C in Hydra sp., a member of the phylum Cnidaria. Allatostatin-C peptide conjugated with Qdots revealed specifically distributed cell populations that respond to the peptide in different regions of hydroids. In vivo physiological assays using Allatostatin-C showed that the peptide induced changes in shape and length in tentacles, peduncle and gastrovascular cavity. The observed changes were dose and time dependent suggesting the physiological nature of the response. Furthermore, at highest doses, Allatostatin-C induced peristaltic movements of the gastrovascular cavity resembling those that occur during feeding. In silico search of putative Allatostatin-C receptors in Cnidaria showed that genomes predict the existence of proteins of the somatostatin/Allatostatin-C receptors family. Altogether, these results suggest that Allatostatin-C has myoregulatory activity in Hydra sp, playing a role in the control of coordinated movements during feeding, indicating that Allatostatin-C/Somatostatin based signaling might be an ancestral mechanism. PMID:27288244

  12. Systems Approaches for Synthetic Biology: A Pathway Toward Mammalian Design

    Directory of Open Access Journals (Sweden)

    RahulRekhi

    2013-10-01

    Full Text Available We review methods of understanding cellular interactions through computation in order to guide the synthetic design of mammalian cells for translational applications, such as regenerative medicine and cancer therapies. In doing so, we argue that the challenges of engineering mammalian cells provide a prime opportunity to leverage advances in computational systems biology. We support this claim systematically, by addressing each of the principal challenges to existing synthetic bioengineering approaches—stochasticity, complexity, and scale—with specific methods and paradigms in systems biology. Moreover, we characterize a key set of diverse computational techniques, including agent-based modeling, Bayesian network analysis, graph theory, and Gillespie simulations, with specific utility towards synthetic biology. Lastly, we examine the mammalian applications of synthetic biology for medicine and health, and how computational systems biology can aid in the continued development of these applications.

  13. Structure and Function of Mammalian Carbohydrate-Lectin Interactions

    Science.gov (United States)

    Anderson, Kevin; Evers, David; Rice, Kevin G.

    Over the past three decades the field of glycobiology has expanded beyond a basic understanding of the structure and biosynthesis of glycoprotein, proteoglycans, and glycolipids toward a more detailed picture of how these molecules afford communication through binding to mammalian lectins. Although the number of different mammalian lectin domains appears to be finite and even much smaller than early estimates predicated based on the diversity of glycan structures, nature appears capable of using these in numerous combinations to fine tune specificity. The following provides an overview of the major classes of mammalian lectins and discusses their glycan binding specificity. The review provides a snapshot of the field of glycobiology that continues to grow providing an increasing number of examples of biological processes that rely upon glycan-lectin binding.

  14. A mammalianized synthetic nitroreductase gene for high-level expression

    International Nuclear Information System (INIS)

    The nitroreductase/5-(azaridin-1-yl)-2,4-dinitrobenzamide (NTR/CB1954) enzyme/prodrug system is considered as a promising candidate for anti-cancer strategies by gene-directed enzyme prodrug therapy (GDEPT) and has recently entered clinical trials. It requires the genetic modification of tumor cells to express the E. coli enzyme nitroreductase that bioactivates the prodrug CB1954 to a powerful cytotoxin. This metabolite causes apoptotic cell death by DNA interstrand crosslinking. Enhancing the enzymatic NTR activity for CB1954 should improve the therapeutical potential of this enzyme-prodrug combination in cancer gene therapy. We performed de novo synthesis of the bacterial nitroreductase gene adapting codon usage to mammalian preferences. The synthetic gene was investigated for its expression efficacy and ability to sensitize mammalian cells to CB1954 using western blotting analysis and cytotoxicity assays. In our study, we detected cytoplasmic protein aggregates by expressing GFP-tagged NTR in COS-7 cells, suggesting an impaired translation by divergent codon usage between prokaryotes and eukaryotes. Therefore, we generated a synthetic variant of the nitroreductase gene, called ntro, adapted for high-level expression in mammalian cells. A total of 144 silent base substitutions were made within the bacterial ntr gene to change its codon usage to mammalian preferences. The codon-optimized ntro either tagged to gfp or c-myc showed higher expression levels in mammalian cell lines. Furthermore, the ntro rendered several cell lines ten times more sensitive to the prodrug CB1954 and also resulted in an improved bystander effect. Our results show that codon optimization overcomes expression limitations of the bacterial ntr gene in mammalian cells, thereby improving the NTR/CB1954 system at translational level for cancer gene therapy in humans

  15. A mammalianized synthetic nitroreductase gene for high-level expression

    Directory of Open Access Journals (Sweden)

    Grohmann Maik

    2009-08-01

    Full Text Available Abstract Background The nitroreductase/5-(azaridin-1-yl-2,4-dinitrobenzamide (NTR/CB1954 enzyme/prodrug system is considered as a promising candidate for anti-cancer strategies by gene-directed enzyme prodrug therapy (GDEPT and has recently entered clinical trials. It requires the genetic modification of tumor cells to express the E. coli enzyme nitroreductase that bioactivates the prodrug CB1954 to a powerful cytotoxin. This metabolite causes apoptotic cell death by DNA interstrand crosslinking. Enhancing the enzymatic NTR activity for CB1954 should improve the therapeutical potential of this enzyme-prodrug combination in cancer gene therapy. Methods We performed de novo synthesis of the bacterial nitroreductase gene adapting codon usage to mammalian preferences. The synthetic gene was investigated for its expression efficacy and ability to sensitize mammalian cells to CB1954 using western blotting analysis and cytotoxicity assays. Results In our study, we detected cytoplasmic protein aggregates by expressing GFP-tagged NTR in COS-7 cells, suggesting an impaired translation by divergent codon usage between prokaryotes and eukaryotes. Therefore, we generated a synthetic variant of the nitroreductase gene, called ntro, adapted for high-level expression in mammalian cells. A total of 144 silent base substitutions were made within the bacterial ntr gene to change its codon usage to mammalian preferences. The codon-optimized ntro either tagged to gfp or c-myc showed higher expression levels in mammalian cell lines. Furthermore, the ntro rendered several cell lines ten times more sensitive to the prodrug CB1954 and also resulted in an improved bystander effect. Conclusion Our results show that codon optimization overcomes expression limitations of the bacterial ntr gene in mammalian cells, thereby improving the NTR/CB1954 system at translational level for cancer gene therapy in humans.

  16. Role of Notch signaling in the mammalian heart

    International Nuclear Information System (INIS)

    Notch signaling is an evolutionarily ancient, highly conserved pathway important for deciding cell fate, cellular development, differentiation, proliferation, apoptosis, adhesion, and epithelial-to-mesenchymal transition. Notch signaling is also critical in mammalian cardiogenesis, as mutations in this signaling pathway are linked to human congenital heart disease. Furthermore, Notch signaling can repair myocardial injury by promoting myocardial regeneration, protecting ischemic myocardium, inducing angiogenesis, and negatively regulating cardiac fibroblast-myofibroblast transformation. This review provides an update on the known roles of Notch signaling in the mammalian heart. The goal is to assist in developing strategies to influence Notch signaling and optimize myocardial injury repair

  17. Role of Notch signaling in the mammalian heart

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, X.L.; Liu, J.C. [Department of Cardiac Surgery, The First Affiliated Hospital, Nanchang University, Donghu District, Nanchang, Jiangxi (China)

    2013-12-12

    Notch signaling is an evolutionarily ancient, highly conserved pathway important for deciding cell fate, cellular development, differentiation, proliferation, apoptosis, adhesion, and epithelial-to-mesenchymal transition. Notch signaling is also critical in mammalian cardiogenesis, as mutations in this signaling pathway are linked to human congenital heart disease. Furthermore, Notch signaling can repair myocardial injury by promoting myocardial regeneration, protecting ischemic myocardium, inducing angiogenesis, and negatively regulating cardiac fibroblast-myofibroblast transformation. This review provides an update on the known roles of Notch signaling in the mammalian heart. The goal is to assist in developing strategies to influence Notch signaling and optimize myocardial injury repair.

  18. Intrinsic control of electroresponsive properties of transplanted mammalian brain neurons

    DEFF Research Database (Denmark)

    Hounsgaard, J; Yarom, Y

    1985-01-01

    The present study presents the first analysis of neurons in mammalian brain transplants based on intracellular recording. The results, obtained in brain slices including both donor and host tissue, showed that neuronal precursor cells in embryonic transplants retained their ability to complete th...... their normal differentiation of cell-type-specific electroresponsive properties. Distortions in cell aggregation and synaptic connectivity did not affect this aspect of neuronal differentiation.......The present study presents the first analysis of neurons in mammalian brain transplants based on intracellular recording. The results, obtained in brain slices including both donor and host tissue, showed that neuronal precursor cells in embryonic transplants retained their ability to complete...

  19. Tetracycline regulator expression alters the transcriptional program of mammalian cells

    OpenAIRE

    Hackl, Hubert; Rommer, Anna; Konrad, Torsten A; Nassimbeni, Christine; Wieser, Rotraud

    2010-01-01

    Tetracycline regulated ectopic gene expression is a widely used tool to study gene function. However, the tetracycline regulator (tetR) itself has been reported to cause certain phenotypic changes in mammalian cells. We, therefore, asked whether human myeloid U937 cells expressing the tetR in an autoregulated manner would exhibit alterations in gene expression upon removal of tetracycline.

  20. A code for transcription initiation in mammalian genomes

    DEFF Research Database (Denmark)

    Frith, Martin C.; Valen, Eivind Dale; Krogh, Anders;

    2007-01-01

    Genome-wide detection of transcription start sites (TSSs) has revealed that RNA Polymerase II transcription initiates at millions of positions in mammalian genomes. Most core promoters do not have a single TSS, but an array of closely located TSSs with different rates of initiation. As a rule...

  1. The different shades of mammalian pluripotent stem cells

    NARCIS (Netherlands)

    Kuijk, E.W.; Lopes, S.M.; Geijsen, N.; Macklon, N.S.; Roelen, B.A.J.

    2011-01-01

    The different shades of mammalian pluripotent stem cells Abstract BACKGROUND Pluripotent stem cells have been derived from a variety of sources such as from the inner cell mass of preimplantation embryos, from primordial germ cells, from teratocarcinomas and from male germ cells. The recent developm

  2. Germ cells and the origins of mammalian pluripotent cells

    NARCIS (Netherlands)

    Kuijk, E.W.

    2009-01-01

    Mammalian embryonic stem (ES) cells originate from preimplantation embryos and can be propagated indefinitely without loss of pluripotency; i.e. the potential to develop into any embryonic cell type. ES cells have been described for mouse, rhesus monkey, and human. There is considerable interest in

  3. Diversity of Neural Precursors in the Adult Mammalian Brain.

    Science.gov (United States)

    Bonaguidi, Michael A; Stadel, Ryan P; Berg, Daniel A; Sun, Jiaqi; Ming, Guo-Li; Song, Hongjun

    2016-01-01

    Aided by advances in technology, recent studies of neural precursor identity and regulation have revealed various cell types as contributors to ongoing cell genesis in the adult mammalian brain. Here, we use stem-cell biology as a framework to highlight the diversity of adult neural precursor populations and emphasize their hierarchy, organization, and plasticity under physiological and pathological conditions. PMID:26988967

  4. Incorporation of nanoparticles within mammalian spermatozoa using in vitro capacitation

    Science.gov (United States)

    There is still much unknown about the journey of spermatozoa within the female genital tract. Recent studies have investigated mammalian spermatozoa labeling with fluorescent quantum dot nanoparticles (QD) for non-invasive imaging. Furthermore, the incorporation of these QD within the spermatozoa ma...

  5. ¿Con o sin ancestros?: vigencia de lo ancestral en la Amazonía peruana

    Directory of Open Access Journals (Sweden)

    Thomas Mouriès

    2014-06-01

    Full Text Available La existencia o no de ancestros en la Amazonía indígena ha sido objeto de importantes debates. Sin embargo, los líderes de la región no dudan en llamar ‘ancestrales’ sus saberes, normas o territorios, en un sentido que, desde un punto de vista académico, puede parecer enigmático. «Ancestrales, pero… ¿con o sin ancestros?», preguntaría entonces, confuso, el antropólogo. En este artículo propongo aportar elementos de respuesta a esta pregunta a través del caso peruano. Primero analizo cómo los líderes indígenas amazónicos, conectándose al circuito del derecho internacional, adoptan la noción jurídica de ‘posesión ancestral’ del territorio para adaptarla al ámbito político. Este planteamiento rinde cuenta de la generalización y uniformización reciente del vocablo ‘ancestral’ pero deja pendiente el problema de su eventual articulación con las cosmologías indígenas que pretende reflejar. Por eso, en la segunda parte, intento sondear sobre la pertinencia de la categoría de ‘ancestro’ en la Amazonía indígena, recordando brevemente el debate académico para ir definiendo en qué medida esta categoría puede cobrar sentido. A partir del testimonio de un experimentado líder awajún, la tercera parte permite, entonces, volver más explícitos los diferentes sentidos y planos referenciales que despliega la referencia a lo ancestral, mostrando cómo los indígenas amazónicos no solo adoptan elementos conceptuales y discursivos externos, sino que al mismo tiempo los transforman a partir de sus propias singularidades cosmológicas y perspectivas políticas.

  6. How difficult is inference of mammalian causal gene regulatory networks?

    Directory of Open Access Journals (Sweden)

    Djordje Djordjevic

    Full Text Available Gene regulatory networks (GRNs play a central role in systems biology, especially in the study of mammalian organ development. One key question remains largely unanswered: Is it possible to infer mammalian causal GRNs using observable gene co-expression patterns alone? We assembled two mouse GRN datasets (embryonic tooth and heart and matching microarray gene expression profiles to systematically investigate the difficulties of mammalian causal GRN inference. The GRNs were assembled based on > 2,000 pieces of experimental genetic perturbation evidence from manually reading > 150 primary research articles. Each piece of perturbation evidence records the qualitative change of the expression of one gene following knock-down or over-expression of another gene. Our data have thorough annotation of tissue types and embryonic stages, as well as the type of regulation (activation, inhibition and no effect, which uniquely allows us to estimate both sensitivity and specificity of the inference of tissue specific causal GRN edges. Using these unprecedented datasets, we found that gene co-expression does not reliably distinguish true positive from false positive interactions, making inference of GRN in mammalian development very difficult. Nonetheless, if we have expression profiling data from genetic or molecular perturbation experiments, such as gene knock-out or signalling stimulation, it is possible to use the set of differentially expressed genes to recover causal regulatory relationships with good sensitivity and specificity. Our result supports the importance of using perturbation experimental data in causal network reconstruction. Furthermore, we showed that causal gene regulatory relationship can be highly cell type or developmental stage specific, suggesting the importance of employing expression profiles from homogeneous cell populations. This study provides essential datasets and empirical evidence to guide the development of new GRN inference

  7. How difficult is inference of mammalian causal gene regulatory networks?

    Science.gov (United States)

    Djordjevic, Djordje; Yang, Andrian; Zadoorian, Armella; Rungrugeecharoen, Kevin; Ho, Joshua W K

    2014-01-01

    Gene regulatory networks (GRNs) play a central role in systems biology, especially in the study of mammalian organ development. One key question remains largely unanswered: Is it possible to infer mammalian causal GRNs using observable gene co-expression patterns alone? We assembled two mouse GRN datasets (embryonic tooth and heart) and matching microarray gene expression profiles to systematically investigate the difficulties of mammalian causal GRN inference. The GRNs were assembled based on > 2,000 pieces of experimental genetic perturbation evidence from manually reading > 150 primary research articles. Each piece of perturbation evidence records the qualitative change of the expression of one gene following knock-down or over-expression of another gene. Our data have thorough annotation of tissue types and embryonic stages, as well as the type of regulation (activation, inhibition and no effect), which uniquely allows us to estimate both sensitivity and specificity of the inference of tissue specific causal GRN edges. Using these unprecedented datasets, we found that gene co-expression does not reliably distinguish true positive from false positive interactions, making inference of GRN in mammalian development very difficult. Nonetheless, if we have expression profiling data from genetic or molecular perturbation experiments, such as gene knock-out or signalling stimulation, it is possible to use the set of differentially expressed genes to recover causal regulatory relationships with good sensitivity and specificity. Our result supports the importance of using perturbation experimental data in causal network reconstruction. Furthermore, we showed that causal gene regulatory relationship can be highly cell type or developmental stage specific, suggesting the importance of employing expression profiles from homogeneous cell populations. This study provides essential datasets and empirical evidence to guide the development of new GRN inference methods for

  8. Mammalian development does not recapitulate suspected key transformations in the evolutionary detachment of the mammalian middle ear.

    Science.gov (United States)

    Ramírez-Chaves, Héctor E; Wroe, Stephen W; Selwood, Lynne; Hinds, Lyn A; Leigh, Chris; Koyabu, Daisuke; Kardjilov, Nikolay; Weisbecker, Vera

    2016-01-13

    The ectotympanic, malleus and incus of the developing mammalian middle ear (ME) are initially attached to the dentary via Meckel's cartilage, betraying their origins from the primary jaw joint of land vertebrates. This recapitulation has prompted mostly unquantified suggestions that several suspected--but similarly unquantified--key evolutionary transformations leading to the mammalian ME are recapitulated in development, through negative allometry and posterior/medial displacement of ME bones relative to the jaw joint. Here we show, using µCT reconstructions, that neither allometric nor topological change is quantifiable in the pre-detachment ME development of six marsupials and two monotremes. Also, differential ME positioning in the two monotreme species is not recapitulated. This challenges the developmental prerequisites of widely cited evolutionary scenarios of definitive mammalian middle ear (DMME) evolution, highlighting the requirement for further fossil evidence to test these hypotheses. Possible association between rear molar eruption, full ME ossification and ME detachment in marsupials suggests functional divergence between dentary and ME as a trigger for developmental, and possibly also evolutionary, ME detachment. The stable positioning of the dentary and ME supports suggestions that a 'partial mammalian middle ear' as found in many mammaliaforms--probably with a cartilaginous Meckel's cartilage--represents the only developmentally plausible evolutionary DMME precursor. PMID:26763693

  9. Intermolecular recombination assay for mammalian cells that produces recombinants carrying both homologous and nonhomologous junctions.

    OpenAIRE

    Brouillette, S; Chartrand, P

    1987-01-01

    We present an intermolecular recombination assay for mammalian cells that does not involve the reconstitution of a selectable marker. It is based on the generation of a shuttle vector by recombination between a bacterial and a mammalian vector. The recombinants can thus be amplified in mammalian cells, isolated by plasmid rescue in an Escherichia coli RecA- host, and identified by in situ hybridization, by using mammalian vector sequences as probes. Since both parental molecules can share def...

  10. Was basking important in the evolution of mammalian endothermy?

    Science.gov (United States)

    Geiser, Fritz; Goodship, Nicola; Pavey, Chris

    2002-08-01

    The first mammals were small, nocturnal, and presumably had low metabolic rates and were therefore probably unable to maintain a constant high body temperature throughout cool nights. How these animals, without sufficient heat production for endogenous rewarming, were able to become warm and active again before the next activity period remains unresolved. However, we discovered that, similar to reptiles, the carnivorous marsupial mammal Pseudantechinus macdonnellensis (body mass 30.8+/-5.0 g) uses the morning sun to rewarm from low (26.3+/-4.5°C) body temperatures during torpor. Our findings provide the first evidence of basking during rewarming from torpor in mammals and may provide an alternative explanation as to how ancestral mammals could have become nocturnal to avoid diurnal predators despite their small size and a low endogenous heat production.

  11. Pre-and post-Missoula flood geomorphology of the Pre-Holocene ancestral Columbia River Valley in the Portland forearc basin, Oregon and Washington, USA

    Science.gov (United States)

    Peterson, Curt D.; Minor, Rick; Peterson, Gary L.; Gates, Edward B.

    2011-06-01

    Geomorphic landscape development in the pre-Holocene ancestral Columbia River Valley (1-5 km width) in the Portland forearc basin (~ 50 km length) is established from depositional sequences, which pre-date and post-date the glacial Lake Missoula floods. The sequences are observed from selected borehole logs (150 in number) and intact terrace soil profiles (56 in number) in backhoe trenches. Four sequences are widespread, including (1) a vertically aggraded Pleistocene alluvial plain, (2) a steep sided valley that is incised (125-150 m) into the Pleistocene gravel plain, (3) Missoula flood terraces (19-13 ka) abandoned on the sides of the ancestral valley, and (4) Holocene flooding surfaces (11-8 ka) buried at 70-30 m depth in the axial Columbia River Valley. Weathering rims and cementation are used for relative dating of incised Pleistocene gravel units. Soil development on the abandoned Missoula flood terraces is directly related to terrace deposit lithology, including thin Bw horizons in gravel, irregular podzols in sand, and multiple Bw horizons in thicker loess-capping layers. Radiocarbon dating of sand and mud alluvium in the submerged axial valley ties Holocene flooding surfaces to a local sea level curve and establishes Holocene sedimentation rates of 1.5 cm year- 1 during 11-9 ka and 0.3 cm year- 1 during 9-0 ka. The sequences of Pleistocene gravel aggradation, river valley incision, cataclysmic Missoula flooding, and Holocene submergence yield complex geomorphic landscapes in the ancestral lower Columbia River Valley.

  12. Personal and Social Transformation in the Health Area through Education: A Brief Journey from the Ancestral Indigenous Wisdom to the Modern Tyranny of Healthiness

    Directory of Open Access Journals (Sweden)

    Andrés de Muller

    2015-09-01

    Full Text Available This paper aims at claiming the ancestral wisdom of indigenous people in the health area. It analyzes how health has been commodified in the interest of large companies (particularly those related to the pharmaceutical industry to the detriment of a holistic definition of wellness through education. Furthermore, the concept of health as a right disagrees with such commodification or sale to the highest bidder, which prompts dehumanization of health services and public misinformation. The abundance of self-proclaimed gurus or healers who appeal to autosuggestion contributes both to confusion and to an unhealthy cult of healthiness.

  13. New time constraints for the age of metamorphism at the ancestral Pacific Gondwana margin of southern Chile (42-52°S)

    OpenAIRE

    Stuart N. Thomson; Francisco Hervé

    2002-01-01

    Fission-track (FT) analysis was performed on ten samples of detrital zircons from several pre-Late Jurassic metamorphic accretionary complexes at the ancestral Pacific margin of Gondwana in southern Chile (42-52°S) previously dated by U-Pb SHRIMP. Post-metamorphic zircon FT cooling ages combined with published U-Pb provenance ages allow the estimation of the following maximum and minimum ages of deposition and metamorphism: the Eastern Andes metamorphic complex (EAMC), 364 to 250 Ma (Late Dev...

  14. The Influence of the Autoimmunity-Associated Ancestral HLA Haplotype AH8.1 on the Human Gut Microbiota: A Cross-Sectional Study

    OpenAIRE

    Hov, Johannes R; Zhong, Huanzi; Qin, Bingcai; Anmarkrud, Jarl Andreas; Holm, Kristian; Franke, Andre; Benedicte A Lie; Karlsen, Tom H.

    2015-01-01

    Multiple immune-related genes are encoded in the HLA complex on chromosome 6p21. The 8.1 ancestral haplotype (AH8.1) include the classical HLA alleles HLA-B*08:01 and HLA-DRB1*03:01, and has been associated with a large number of autoimmune diseases, but the underlying mechanisms for this association are largely unknown. Given the recently established links between the gut microbiota and inflammatory diseases, we hypothesized that the AH8.1 influences the host gut microbial community composit...

  15. Tracing the origin and geographic distribution of an ancestral form of the modern human Y chromosome Reconstrucción del origen y distribución geográfica de una forma ancestral del cromosoma Y del hombre moderno

    OpenAIRE

    Bravi, Claudio M.; GRACIELA BAILLIET; VERÓNICA L MARTÍNEZ-MARIGNAC; Bianchi, Nestor O.

    2001-01-01

    We screened a total of 841 Y chromosomes representing 36 human populations of wide geographical distribution for the presence of a Y-specific Alu insert (YAP+ chromosomes). The Alu element was found in 77 cases. We tested five biallelic and eight polyallelic markers in 70 out of the 77 YAP+ chromosomes. We could identify the existence of a hierarchical and chronological structuring of ancestral and derived YAP+ lineages giving rise to four haplogroups, 14 subhaplogroups and 60 haplotypes. Mor...

  16. The impact of Toxoplasma gondii on the mammalian genome.

    Science.gov (United States)

    Müller, Urs B; Howard, Jonathan C

    2016-08-01

    Nobody doubts that infections have imposed specialisations on the mammalian genome. However sufficient information is usually missing to attribute a specific genomic modification to pressure from a specific pathogen. Recent studies on mechanisms of mammalian resistance against the ubiquitous protozoan parasite, Toxoplasma gondii, have shown that the small rodents presumed to be largely responsible for transmission of the parasite to its definitive host, the domestic cat, possess distinctive recognition proteins, and interferon-inducible effector proteins (IRG proteins) that limit the potential virulence of the parasite. The phylogenetic association of the recognition proteins, TLR11 and TLR12, with T. gondii resistance is weak, but there is evidence for reciprocal polymorphism between parasite virulence proteins and host IRG proteins that strongly suggests current or recent coevolution. PMID:27128504

  17. Inhibition of mammalian mitochondrial protein synthesis by oxazolidinones.

    Science.gov (United States)

    McKee, E E; Ferguson, M; Bentley, A T; Marks, T A

    2006-06-01

    The effects of a variety of oxazolidinones, with different antibacterial potencies, including linezolid, on mitochondrial protein synthesis were determined in intact mitochondria isolated from rat heart and liver and rabbit heart and bone marrow. The results demonstrate that a general feature of the oxazolidinone class of antibiotics is the inhibition of mammalian mitochondrial protein synthesis. Inhibition was similar in mitochondria from all tissues studied. Further, oxazolidinones that were very potent as antibiotics were uniformly potent in inhibiting mitochondrial protein synthesis. These results were compared to the inhibitory profiles of other antibiotics that function by inhibiting bacterial protein synthesis. Of these, chloramphenicol and tetracycline were significant inhibitors of mammalian mitochondrial protein synthesis while the macrolides, lincosamides, and aminoglycosides were not. Development of future antibiotics from the oxazolidinone class will have to evaluate potential mitochondrial toxicity. PMID:16723564

  18. The evolution of gene expression levels in mammalian organs

    DEFF Research Database (Denmark)

    Brawand, David; Soumillon, Magali; Necsulea, Anamaria;

    2011-01-01

    Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across...... ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. We show that the rate of gene expression evolution varies among organs, lineages and...... chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation. Although gene expression evolution in mammals was strongly shaped by...

  19. Evolution of the mammalian middle ear: a historical review.

    Science.gov (United States)

    Maier, Wolfgang; Ruf, Irina

    2016-02-01

    Here we present a brief, historical review of research into the mammalian middle ear structures. Most of their essential homologies were established by embryologists, notably including Reichert, during the 19th century. The evolutionary dimension was confirmed by finds of fossil synapsids, mainly from the Karroo of South Africa. In 1913, Ernst Gaupp was the first to present a synthesis of the available embryological and paleontological data, but a number of morphological details remained to be solved, such as the origin of the tympanic membrane. Gaupp favoured an independent origin of the eardrum in anurans, sauropsids, and mammals; we support most of his ideas. The present review emphasizes the problem of how the mammalian middle ear structures that developed at the angle of the lower jaw were transferred to the basicranium; the ontogenesis of extant marsupials provides important information on this question. PMID:26397963

  20. Stability of resazurin in buffers and mammalian cell culture media

    DEFF Research Database (Denmark)

    Rasmussen, Eva; Nicolaisen, G.M.

    1999-01-01

    The utility of a ferricyanide/ferrocyanide system used in the AlamarBlue(TM) (Serotec, Oxford, UK) vital. dye to inhibit the reduction of resazurin by mammalian cell culture media is questioned. Resazurin was found to be relatively stable when dissolved in phosphate-buffered saline (PBS). The use...... of HEPES resulted in a huge immediate dye reduction, which was significantly enhanced by exposure to diffuse light from fluorescent tubes in the laboratory 8 h per day. The reduction of resazurin by various cell culture media was time and temperature dependent, and it was significantly enhanced by......'s nutrient mixture F-10 and F-12. Fetal calf serum (5-20%) slightly decreased resazurin reduction during the first 2 days of incubation. The reduction of resazurin by mammalian cell culture media do not appear to be problematic under normal culture conditions, and it is primarily dependent upon the presence...

  1. Cell type-specific transcriptome profiling in mammalian brains.

    Science.gov (United States)

    LoVerso, Peter R; Cui, Feng

    2016-01-01

    A mammalian brain contains numerous types of cells. Advances in neuroscience in the past decade allow us to identify and isolate neural cells of interest from mammalian brains. Recent developments in high-throughput technologies, such as microarrays and next-generation sequencing (NGS), provide detailed information on gene expression in pooled cells on a genomic scale. As a result, many novel genes have been found critical in cell type-specific transcriptional regulation. These differentially expressed genes can be used as molecular signatures, unique to a particular class of neural cells. Use of this gene expression-based approach can further differentiate neural cell types into subtypes, potentially linking some of them with neurological diseases. In this article, experimental techniques used to purify neural cells are described, followed by a review on recent microarray- or NGS-based transcriptomic studies of common neural cell types. The future prospects of cell type-specific research are also discussed. PMID:27100485

  2. Adult neural stem cells in the mammalian central nervous system

    Institute of Scientific and Technical Information of China (English)

    Dengke K Ma; Michael A Bonaguidi; Guo-li Ming; Hongjun Song

    2009-01-01

    Neural stem cells (NSCs) are present not only during the embryonic development but also in the adult brain of all mammalian species, including humans. Stem cell niche architecture in vivo enables adult NSCs to continuously generate functional neurons in specific brain regions throughout life. The adult neurogenesis process is subject to dynamic regulation by various physiological, pathological and pharmacological stimuli. Multipotent adult NSCs also appear to be intrinsically plastic, amenable to genetic programing during normal differentiation, and to epigenetic reprograming during de-differentiation into pluripotency. Increasing evidence suggests that adult NSCs significantly contribute to specialized neural functions under physiological and pathological conditions. Fully understanding the biology of adult NSCs will provide crucial insights into both the etiology and potential therapeutic interventions of major brain disorders. Here, we review recent progress on adult NSCs of the mammalian central nervous system, in-cluding topics on their identity, niche, function, plasticity, and emerging roles in cancer and regenerative medicine.

  3. Leadership in Mammalian Societies: Emergence, Distribution, Power, and Payoff.

    Science.gov (United States)

    Smith, Jennifer E; Gavrilets, Sergey; Mulder, Monique Borgerhoff; Hooper, Paul L; El Mouden, Claire; Nettle, Daniel; Hauert, Christoph; Hill, Kim; Perry, Susan; Pusey, Anne E; van Vugt, Mark; Smith, Eric Alden

    2016-01-01

    Leadership is an active area of research in both the biological and social sciences. This review provides a transdisciplinary synthesis of biological and social-science views of leadership from an evolutionary perspective, and examines patterns of leadership in a set of small-scale human and non-human mammalian societies. We review empirical and theoretical work on leadership in four domains: movement, food acquisition, within-group conflict mediation, and between-group interactions. We categorize patterns of variation in leadership in five dimensions: distribution (across individuals), emergence (achieved versus inherited), power, relative payoff to leadership, and generality (across domains). We find that human leadership exhibits commonalities with and differences from the broader mammalian pattern, raising interesting theoretical and empirical issues. PMID:26552515

  4. Report on Mammalian Fossils of Chinji Formation, Dhulian, Pakistan

    Directory of Open Access Journals (Sweden)

    Muhammad A. Khan

    2005-01-01

    Full Text Available Twenty mammalian fossil specimens of varying preservational state are described from the Chinji Formation of Dhulian, Pakistan. The remains described in this study are all teeth and represent the Proboscidea, Perissodactyla and Artiodactyla. All the dental specimens are new variants recorded here for the first time. Pliotriplopus dhulianensis is new to science having small size and absence of crista than Pliotriplopus chinjiensis. These findings extend the geographic distribution of this dentally highly derived Triplopinae, which was previously restricted to a single species, Pliotriplopus chinjiensis. Additional fossils of the three mammalian orders are necessary to shed new light on the phylogenetic relationships within the first representatives of the orders in Eurasia. A very important, deciduous tooth of the species Stegolophodon cautleyi hitherto unknown is described in this report.

  5. Biocompatibility assessment of fibrous nanomaterials in mammalian embryos.

    Science.gov (United States)

    Munk, Michele; Camargo, Luiz S A; Quintão, Carolina C R; Silva, Saulo R; Souza, Eliza D; Raposo, Nádia R B; Marconcini, Jose M; Jorio, Ado; Ladeira, Luiz O; Brandão, Humberto M

    2016-07-01

    Currently there is a growing interest in the use of nanotechnology in reproductive medicine and reproductive biology. However, their toxic effects on mammalian embryos remain poorly understood. In this work, we evaluate the biocompatibility of two fibrous nanomaterials (NMs): cotton cellulose nanofibers (CNF) and carboxylated multiwalled carbon nanotubes (MWCNT-COOH), by performing an investigation of the embryonic development, gene expression (biomarkers focused on cell stress, apoptosis and totipotency) and in situ apoptosis in bovine embryos. Exposure to NMs did not interfere in preimplantation development or in the incidence of apoptosis in the bovine embryo, but they did affect the gene expression. The results presented are important for an understanding of the toxicity of cotton CNF and MWCNT-COOH on mammalian embryos. To our knowledge, we report the first evaluation of biocompatibility between these NMs on preimplantation embryos, which may open a new window for reproductive biomedical applications. PMID:26949162

  6. Searching for Common Mammalian Retroviruses in Pediatric Idiopathic Diseases

    Directory of Open Access Journals (Sweden)

    Eric Jeziorski

    2016-03-01

    Full Text Available Mammalian retroviruses cause a variety of diseases in their hosts, including hematological and immunodeficiency disorders. Both human T-cell leukemia (HTLV and human immunodeficiency (HIV viruses originated from several independent zoonotic transmissions, indicating that cross-species transmissions from animal to humans may still occur. Thus, as the risk for retroviral transmissions from animals to humans increase, we investigated whether mammalian retroviruses are involved in selected pediatric idiopathic diseases whose symptoms evoke retroviral infections. Blood samples, sera, and synovial fluids, or bone marrow cells were collected from pediatric patients under 18 years of age with different autoimmune idiopathic diseases. Overall, we screened clinical samples from 110 children using sensitive nested and semi-nested PCR strategies targeting env genes, and a C-type retrovirus reverse transcriptase (RT activity kit. All clinical samples were free of retroviral signatures, indicating the unlikelihood of an etiological role of the retroviruses we assessed in the pediatric diseases we tested.

  7. Searching for Common Mammalian Retroviruses in Pediatric Idiopathic Diseases.

    Science.gov (United States)

    Jeziorski, Eric; Foulongne, Vincent; Ludwig, Catherine; Louhaem, Djamel; Rodiere, Michel; Sitbon, Marc; Courgnaud, Valérie

    2016-03-01

    Mammalian retroviruses cause a variety of diseases in their hosts, including hematological and immunodeficiency disorders. Both human T-cell leukemia (HTLV) and human immunodeficiency (HIV) viruses originated from several independent zoonotic transmissions, indicating that cross-species transmissions from animal to humans may still occur. Thus, as the risk for retroviral transmissions from animals to humans increase, we investigated whether mammalian retroviruses are involved in selected pediatric idiopathic diseases whose symptoms evoke retroviral infections. Blood samples, sera, and synovial fluids, or bone marrow cells were collected from pediatric patients under 18 years of age with different autoimmune idiopathic diseases. Overall, we screened clinical samples from 110 children using sensitive nested and semi-nested PCR strategies targeting env genes, and a C-type retrovirus reverse transcriptase (RT) activity kit. All clinical samples were free of retroviral signatures, indicating the unlikelihood of an etiological role of the retroviruses we assessed in the pediatric diseases we tested. PMID:27102168

  8. Energy deposition in selected-mammalian cell for several-MeV single-proton beam

    Science.gov (United States)

    Ding, K.; Yu, Z.

    2007-05-01

    The phenomena resulting from interaction between ion beam and mammalian cell pose important problems for biological applications. Classic Bethe-Bloch theory utilizing attached V79 mammalian cell has been conducted in order to establish the stopping powers of the mammalian cell for several-MeV single-proton microbeam. Based on the biological structure of the mammalian cell, a physical model is proposed which presumes that the attached cell is simple MWM model. According to this model and Monte Carlo simulation, we studied the energy deposition and its ratio on the selected attached mammalian cell for MeV proton implantation.

  9. A direct computer control concept for mammalian cell fermentation processes

    OpenAIRE

    Büntemeyer, Heino; Marzahl, Rainer; Lehmann, Jürgen

    1994-01-01

    In the last 10 years, new assignments and the special demands of mammalian cells to the culture conditions caused the development of complex small scale fermentation setups. The use of continuous fermentation and cell retention devices requires appropriate process control systems. An arrangement for control and data-acquisition of complex laboratory-scale bioreactors is presented. The fundamental idea was the usage of a standard personal computer, which is connected to pumps, valves and senso...

  10. Clotting of mammalian fibrinogens by papain: A re-examination

    OpenAIRE

    Doolittle, RF

    2014-01-01

    © 2014 American Chemical Society. Papain has long been known to cause the gelation of mammalian fibrinogens. It has also been reported that papain-fibrin is insoluble in dispersing solvents like strong urea or sodium bromide solutions, similar to what is observed with thrombin-generated clots in the presence of factor XIIIa and calcium. In those old studies, both the gelation and subsequent clot stabilization were attributed to papain, although the possibility that the second step might be du...

  11. Conservation of Sleep: Insights from Non-Mammalian Model Systems

    OpenAIRE

    Zimmerman, John E.; Naidoo, Nirinjini; Raizen, David M.; Pack, Allan I.

    2008-01-01

    The past ten years have seen new approaches to elucidating genetic pathways regulating sleep. The emerging theme is that sleep-like states are conserved in evolution, with similar signaling pathways playing a role in animals as distantly related as flies and humans. We review the evidence for the presence of sleep states in non-mammalian species including zebrafish (Danio rerio), fruit flies (Drosophila melanogaster), and round worms (Caenorhabditis elegans). We describe conserved sleep-regul...

  12. Filament proteins in central, cranial, and peripheral mammalian nerves

    OpenAIRE

    1981-01-01

    Several classes of 10-nm filaments have been reported in mammalian cells and they can be distinguished by the size of their protein subunit. We have studied the distribution of these filaments in nerves from calves and other mammals. From the display on polyacrylamide electrophoretic gels of proteins in extracts from fibroblast and central, cranial and peripheral nerves, we cut the appropriate stained bands and prepared iodinated peptide maps. The similarities between the respective maps prov...

  13. Mammalian fauna of the Temessos National Park, Turkey

    OpenAIRE

    Anna De Marinis; Marco Masseti

    2009-01-01

    The National Park of Termessos, Southern Turkey, is one of the Turkey’s biggest national park not only with its archeological richness but also with its great natural wild life. We provided a checklist of the mammalian fauna of the park on the base of direct observations, interviews and a comparative analysis of the available literature. Sixteen species have been reported in the park. Hedgehogs, hares, porcupines and Persian squirrels and, among flying mammals, Egyptian rousette and Mou...

  14. Dithiothreitol and the translocation of preprolactin across mammalian endoplasmic reticulum

    OpenAIRE

    1987-01-01

    The translocation mode of preprolactin (pPL) across mammalian endoplasmic reticulum was reinvestigated in light of recent findings that nascent secretory polypeptides synthesized in the presence of a highly reducing environment could be translocated posttranslationally and independently of their attachment to the ribosome (Maher, P. A., and S. J. Singer, 1986, Proc. Natl. Acad. Sci. USA, 83:9001-9005). The effects of the reducing agent dithiothreitol (DTT) on pPL synthesis and translocation w...

  15. High-efficiency transformation of mammalian cells by plasmid DNA.

    OpenAIRE

    Chen, C.; Okayama, H

    1987-01-01

    We describe a simple calcium phosphate transfection protocol and neo marker vectors that achieve highly efficient transformation of mammalian cells. In this protocol, the calcium phosphate-DNA complex is formed gradually in the medium during incubation with cells and precipitates on the cells. The crucial factors for obtaining efficient transformation are the pH (6.95) of the buffer used for the calcium phosphate precipitation, the CO2 level (3%) during the incubation of the DNA with the cell...

  16. New, small circular DNA in transfected mammalian cells.

    OpenAIRE

    Wiberg, F C; Sunnerhagen, P; Bjursell, G

    1986-01-01

    Circular DNA isolated by the Hirt procedure from transfected mammalian cells was examined by electron microscopy. Typically, the number of small (1- to 5-kilobase) DNA circles increased about fivefold even though DNA of larger size classes (5 to 15 kilobases) has been transferred. In one case, where extensive rearrangement of the transferred DNA was observed, the rearrangement products were cloned and analyzed. In most cases, however, no rearrangement could be detected, but the amount of smal...

  17. Mammalian cell retention devices for stirred perfusion bioreactors

    OpenAIRE

    Woodside, Steven M.; Bowen, Bruce D.; Piret, James M.

    1998-01-01

    Within the spectrum of current applications for cell culture technologies, efficient large-scale mammalian cell production processes are typically carried out in stirred fed-batch or perfusion bioreactors. The specific aspects of each individual process that can be considered when determining the method of choice are presented. A major challenge for perfusion reactor design and operation is the reliability of the cell retention device. Current retention systems include cross-flow membrane fil...

  18. Mammalian Pumilio 2 regulates dendrite morphogenesis and synaptic function

    OpenAIRE

    Vessey, John P.; Schoderboeck, Lucia; Gingl, Ewald; Luzi, Ettore; Riefler, Julia; Di Leva, Francesca; Karra, Daniela; Thomas, Sabine; Kiebler, Michael A.; Macchi, Paolo

    2010-01-01

    In Drosophila, Pumilio (Pum) is important for neuronal homeostasis as well as learning and memory. We have recently characterized a mammalian homolog of Pum, Pum2, which is found in discrete RNA-containing particles in the somatodendritic compartment of polarized neurons. In this study, we investigated the role of Pum2 in developing and mature neurons by RNA interference. In immature neurons, loss of Pum2 led to enhanced dendritic outgrowth and arborization. In mature neurons, Pum2 down-regul...

  19. CRISPR-Cas: Development and applications for mammalian genome editing

    OpenAIRE

    Ran, Fei Ann

    2014-01-01

    The ability to introduce targeted modifications into genomes and engineer model organisms holds enormous promise for biomedical and technological applications, and has driven the development of tools such as zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). To facilitate genome engineering in mammalian cells, we have engineered the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 programmable nuclease systems from Streptococcus p...

  20. Inhibition of Mammalian Mitochondrial Protein Synthesis by Oxazolidinones

    OpenAIRE

    McKee, E. E.; Ferguson, M; Bentley, A T; Marks, T. A.

    2006-01-01

    The effects of a variety of oxazolidinones, with different antibacterial potencies, including linezolid, on mitochondrial protein synthesis were determined in intact mitochondria isolated from rat heart and liver and rabbit heart and bone marrow. The results demonstrate that a general feature of the oxazolidinone class of antibiotics is the inhibition of mammalian mitochondrial protein synthesis. Inhibition was similar in mitochondria from all tissues studied. Further, oxazolidinones that wer...

  1. Toward an integrated evolutionary understanding of the mammalian placenta

    OpenAIRE

    Wildman, Derek E.

    2011-01-01

    The placenta is fundamentally important for the success of pregnancy. Disruptions outside the normal range for placenta function can result in pregnancy failure and other complications. The anatomy of the placenta varies greatly across mammals, as do key parameters in pregnancy such as neonatal body mass, length of gestation and number of offspring per pregnancy. An accurate understanding of the evolution of the mammalian placenta will require at minimum the integration of anatomical, develop...

  2. Measuring the Energetics of Membrane Protein Dimerization in Mammalian Membranes

    OpenAIRE

    Chen, Lirong; Novicky, Lawrence; Merzlyakov, Mikhail; Hristov, Tihomir; Hristova, Kalina

    2010-01-01

    Thus far, methods that give quantitative information about lateral interactions in membranes have been restricted peptides or simplified protein constructs studied in detergents, lipid vesicles or bacterial membranes. None of the available methods have been extended to complex or full length membrane proteins. Here we show how free energies of membrane protein dimerization can be measured in mammalian plasma membrane-derived vesicles. The measurements, performed in single vesicles, utilize th...

  3. Mammalian mitogenomic relationships and the root of the eutherian tree

    OpenAIRE

    Arnason, Ulfur; Adegoke, Joseph A.; Bodin, Kristina; Erik W Born; Esa, Yuzine B.; Gullberg, Anette; Nilsson, Maria; Short, Roger V.; Xu, Xiufeng; Janke, Axel

    2002-01-01

    The strict orthology of mitochondrial (mt) coding sequences has promoted their use in phylogenetic analyses at different levels. Here we present the results of a mitogenomic study (i.e., analysis based on the set of protein-coding genes from complete mt genomes) of 60 mammalian species. This number includes 11 new mt genomes. The sampling comprises all but one of the traditional eutherian orders. The previously unrepresented order Dermoptera (flying lemurs) fell within Primates as the sister ...

  4. Mammalian target of rapamycin inhibitors for treatment in tuberous sclerosis

    OpenAIRE

    Won Seop Kim

    2011-01-01

    Tuberous sclerosis complex (TSC) is a genetic multisystem disorder that results from mutations in the TSC1 or TSC2 genes, and is associated with hamartomas in several organs, including subependymal giant cell tumors. The neurological manifestations of TSC are particularly challenging and include infantile spasms, intractable epilepsy, cognitive disabilities, and autism. The TSC1- and TSC2-encoded proteins modulate cell function via the mammalian target of rapamycin (mTOR) signaling cascade, a...

  5. Plasma long-chain free fatty acids predict mammalian longevity

    OpenAIRE

    Mariona Jové; Alba Naudí; Juan Carlos Aledo; Rosanna Cabré; Victoria Ayala; Manuel Portero-Otin; Gustavo Barja; Reinald Pamplona

    2013-01-01

    Membrane lipid composition is an important correlate of the rate of aging of animals and, therefore, the determination of their longevity. In the present work, the use of high-throughput technologies allowed us to determine the plasma lipidomic profile of 11 mammalian species ranging in maximum longevity from 3.5 to 120 years. The non-targeted approach revealed a specie-specific lipidomic profile that accurately predicts the animal longevity. The regression analysis between lipid species and ...

  6. Expression of Rh Glycoproteins in the Mammalian Kidney

    OpenAIRE

    Han, Ki-Hwan; Kim, Hye-Young; Weiner, I. David

    2009-01-01

    Ammonia metabolism is a fundamental process in the maintenance of life in all living organisms. Recent studies have identified ammonia transporter family proteins in yeast (Mep), plants (Amt), and mammals (Rh glycoproteins). In mammalian kidneys, where ammonia metabolism and transport are critically important for the regulation of systemic acid-base homeostasis, basolateral Rh B glycoprotein and apical/basolateral Rh C glycoprotein are expressed along the distal nephron segments. Data from ex...

  7. Dolphin insula reflects minicolumnar organization of mammalian isocortex

    OpenAIRE

    Casanova, Manuel F.; Trippe, Juan; Tillquist, Christopher R; Switala, Andrew E.

    2010-01-01

    The brain of the bottlenose dolphin exhibits patterns of isocortical parcellation and cytoarchitecture distinct from those seen in primates, yet cell clusters in anterior insula are comparable in scale to module-like cell arrangements found throughout isocortex in other placental mammalian species with long divergent evolutionary histories. This similarity may be due to common ancestry, or to convergence as a result of selective constraints on organization of connections within such modules. ...

  8. Sequence conservation of linker histones between chicken and mammalian species

    OpenAIRE

    Bettina Sarg; Rita Lopez; Herbert Lindner; Inma Ponte; Pedro Suau; Alicia Roque

    2014-01-01

    The percent identity matrices of two sequence multiple alignments between linker histones from chicken and mammalian species are described. Linker histone protein sequences for chicken, mouse, rat and humans, available on public databases were used. This information is related to the research article entitled “Identification of novel post-translational modifications in linker histones from chicken erythrocytes”published in the Journal of Proteomics [1].

  9. Characterization of nonconservative homologous junctions in mammalian cells.

    OpenAIRE

    Desautels, L; Brouillette, S; Wallenburg, J; Belmaaza, A; Gusew, N; Trudel, P; Chartrand, P

    1990-01-01

    Homologous recombination in mammalian cells between extrachromosomal molecules, as well as between episomes and chromosomes, can be mediated by a nonconservative mechanism. It has been proposed that the key steps in this process are the generation (by double-strand cleavage) of overlapping homologous ends, the creation of complementary single-strand ends (either by strand-specific exonuclease degradation or by unwinding of the DNA helix), and finally the creation of heteroduplex DNA by the an...

  10. Photothermal nanoblade for large cargo delivery into mammalian cells

    OpenAIRE

    Wu, Ting-Hsiang; Teslaa, Tara; Kalim, Sheraz; French, Christopher T; Maghadam, Shahriar; Wall, Randolph; Miller, Jeffery F.; Witte, Owen N.; Teitell, Michael A.; Chiou, Pei-Yu

    2011-01-01

    It is difficult to achieve controlled cutting of elastic, mechanically fragile, and rapidly resealing mammalian cell membranes. Here, we report a photothermal nanoblade that utilizes a metallic nanostructure to harvest short laser pulse energy and convert it into a highly localized explosive vapor bubble, which rapidly punctures a lightly-contacting cell membrane via high-speed fluidic flows and induced transient shear stress. The cavitation bubble pattern is controlled by the metallic struct...

  11. Expression of Tas1 taste receptors in mammalian spermatozoa

    OpenAIRE

    Meyer, Dorke; Voigt, Anja; Widmayer, Patricia; Borth, Heike; Huebner, Sandra; Breit, Andreas; Marschall, Susan; Hrabé de Angelis, Martin; Boehm, Ulrich; Meyerhof, Wolfgang; Gudermann, Thomas; Boekhoff, Ingrid

    2012-01-01

    Background: During their transit through the female genital tract, sperm have to recognize and discriminate numerous chemical compounds. However, our current knowledge of the molecular identity of appropriate chemosensory receptor proteins in sperm is still rudimentary. Considering that members of the Tas1r family of taste receptors are able to discriminate between a broad diversity of hydrophilic chemosensory substances, the expression of taste receptors in mammalian spermatozoa was examined...

  12. Studying non-mammalian models? Not a fool's ERRand!

    OpenAIRE

    Bardet, Pierre-Luc; Laudet, Vincent; Vanacker, Jean-Marc

    2006-01-01

    Through studies in mammalian model systems, the estrogen-receptor-related receptor (ERR) alpha, an orphan nuclear receptor, has been shown to interfere with estrogen signaling and might therefore be an interesting pharmaceutical target in estrogen-related diseases. ERRalpha is also involved in energy storage and consumption, and its modulation might be of relevance in the treatment of obesity and diabetes. Recent data have also been published on the effects of this receptor, as well as other ...

  13. Auditory hair cell precursors immortalized from the mammalian inner ear.

    OpenAIRE

    Rivolta, M.N.; Grix, N; Lawlor, P.; Ashmore, J. F.; Jagger, D J; Holley, M C

    1998-01-01

    Mammalian auditory hair cells are few in number, experimentally inaccessible, and do not proliferate postnatally or in vitro. Immortal cell lines with the potential to differentiate into auditory hair cells would substantially facilitate auditory research, drug development, and the isolation of critical molecules involved in hair cell biology. We have established two conditionally immortal cell lines that express at least five characteristic hair cell markers. These markers are the transcript...

  14. A wave dynamics criterion for optimization of mammalian cardiovascular system

    OpenAIRE

    Pahlevan, Niema M.; Gharib, Morteza

    2014-01-01

    The cardiovascular system in mammals follows various optimization criteria covering the heart, the vascular network, and the coupling of the two. Through a simple dimensional analysis we arrived at a non-dimensional number (wave condition number) that can predict the optimum wave state in which the left ventricular (LV) pulsatile power (LV workload) is minimized in a mammalian cardiovascular system. This number is also universal among all mammals independent of animal size maintaining a value...

  15. Nuclear organization of DNA replication in primary mammalian cells

    OpenAIRE

    Kennedy, Brian K.; Barbie, David A; Classon, Marie; Dyson, Nicholas; Harlow, Ed

    2000-01-01

    Using methods that conserve nuclear architecture, we have reanalyzed the spatial organization of the initiation of mammalian DNA synthesis. Contrary to the commonly held view that replication begins at hundreds of dispersed nuclear sites, primary fibroblasts initiate synthesis in a limited number of foci that contain replication proteins, surround the nucleolus, and overlap with previously identified internal lamin A/C structures. These foci are established in early G1-phase and also contain ...

  16. Imaging the Dynamics of Endocytosis in Live Mammalian Tissues

    OpenAIRE

    Weigert, Roberto

    2014-01-01

    In mammalian cells, endocytosis plays a pivotal role in regulating several basic cellular functions. Up to now, the dynamics and the organization of the endocytic pathways have been primarily investigated in reductionist model systems such as cell and organ cultures. Although these experimental models have been fully successful in unraveling the endocytic machinery at a molecular level, our understanding of the regulation and the role of endocytosis in vivo has been limited. Recently, advance...

  17. Early fluorescence signals detect transitions at mammalian serotonin transporters.

    OpenAIRE

    Li, Ming; Lester, Henry A.

    2002-01-01

    The mammalian serotonin transporters rSERT or hSERT were expressed in oocytes and labeled with sulforhodamine-MTS. The endogenous Cys-109 residue contributes most of the signal, and the labeled transporter shows normal function. The SERT fluorescence decreases in the presence of 5-HT and also depends on the inorganic substrates of SERT. The fluorescence also increases with membrane depolarization. During voltage-jump experiments, fluorescence relaxations show little inactivation or history de...

  18. Temperature as a universal resetting cue for mammalian circadian oscillators

    OpenAIRE

    Buhr, Ethan D.; Yoo, Seung-Hee; Takahashi, Joseph S.

    2010-01-01

    Environmental temperature cycles are a universal entraining cue for all circadian systems at the organismal level with the exception of homeothermic vertebrates. We report here that resistance to temperature entrainment is a property of the suprachiasmatic nucleus (SCN) network and is not a cell autonomous property of mammalian clocks. This differential sensitivity to temperature allows the SCN to drive circadian rhythms in body temperature which can then act as a universal cue for the entrai...

  19. The evolution of infanticide by males in mammalian societies

    OpenAIRE

    Lukas, D; Huchard, E.

    2014-01-01

    Male mammals may commonly kill conspecific offspring. The benefits of such infanticide to males, and its costs to females, likely vary across mammalian social and mating systems. Here we use comparative analyses to show that infanticide primarily evolves in social mammals where reproduction is monopolized by a minority of males. It has not promoted social counter-strategies such as female gregariousness, pair-living, or changes in group size and sex-ratio but is successfully prevented by fema...

  20. Mammalian sex determination—insights from humans and mice

    OpenAIRE

    Eggers, Stefanie; Sinclair, Andrew

    2012-01-01

    Disorders of sex development (DSD) are congenital conditions in which the development of chromosomal, gonadal, or anatomical sex is atypical. Many of the genes required for gonad development have been identified by analysis of DSD patients. However, the use of knockout and transgenic mouse strains have contributed enormously to the study of gonad gene function and interactions within the development network. Although the genetic basis of mammalian sex determination and differentiation has adv...

  1. Mechanism of reaction of chlorite with mammalian heme peroxidases

    OpenAIRE

    Jakopitsch, Christa; Pirker, Katharina F.; Flemmig, Jörg; Hofbauer, Stefan; Schlorke, Denise; Furtmüller, Paul G.; Arnhold, Jürgen; Obinger, Christian

    2014-01-01

    This study demonstrates that heme peroxidases from different superfamilies react differently with chlorite. In contrast to plant peroxidases, like horseradish peroxidase (HRP), the mammalian counterparts myeloperoxidase (MPO) and lactoperoxidase (LPO) are rapidly and irreversibly inactivated by chlorite in the micromolar concentration range. Chlorite acts as efficient one-electron donor for Compound I and Compound II of MPO and LPO and reacts with the corresponding ferric resting states in a ...

  2. Evolutionary dynamics of gene and isoform regulation in mammalian tissues*

    OpenAIRE

    Merkin, Jason; Russell, Caitlin; CHEN, PING; Burge, Christopher B.

    2012-01-01

    Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear. To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth. We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specifi...

  3. A hyperactive piggyBac transposase for mammalian applications

    OpenAIRE

    Yusa, K; Zhou, L.; Li, M. A.; Bradley, A; Craig, N. L.

    2011-01-01

    DNA transposons have been widely used for transgenesis and insertional mutagenesis in various organisms. Among the transposons active in mammalian cells, the moth-derived transposon piggyBac is most promising with its highly efficient transposition, large cargo capacity, and precise repair of the donor site. Here we report the generation of a hyperactive piggyBac transposase. The active transposition of piggyBac in multiple organisms allowed us to screen a transposase mutant library in yeast ...

  4. Regions of extreme synonymous codon selection in mammalian genes

    OpenAIRE

    Schattner, Peter; Diekhans, Mark

    2006-01-01

    Recently there has been increasing evidence that purifying selection occurs among synonymous codons in mammalian genes. This selection appears to be a consequence of either cis-regulatory motifs, such as exonic splicing enhancers (ESEs), or mRNA secondary structures, being superimposed on the coding sequence of the gene. We have developed a program to identify regions likely to be enriched for such motifs by searching for extended regions of extreme codon conservation between homologous genes...

  5. DNA repair and radiation sensitivity in mammalian cells

    International Nuclear Information System (INIS)

    Ionizing radiation induces various types of damage in mammalian cells including DNA single-strand breaks, DNA double-strand breaks (DSB), DNA-protein cross links, and altered DNA bases. Although human cells can repair many of these lesions there is little detailed knowledge of the nature of the genes and the encoded enzymes that control these repair processes. We report here on the cellular and genetic analyses of DNA double-strand break repair deficient mammalian cells. It has been well established that the DNA double-strand break is one of the major lesions induced by ionizing radiation. Utilizing rodent repair-deficient mutant, we have shown that the genes responsible for DNA double-strand break repair are also responsible for the cellular expression of radiation sensitivity. The molecular genetic analysis of DSB repair in rodent/human hybrid cells indicate that at least 6 different genes in mammalian cells are responsible for the repair of radiation-induced DNA double-strand breaks. Mapping and the prospect of cloning of human radiation repair genes are reviewed. Understanding the molecular and genetic basis of radiation sensitivity and DNA repair in man will provide a rational foundation to predict the individual risk associated with radiation exposure and to prevent radiation-induced genetic damage in the human population

  6. Origin and evolution of developmental enhancers in the mammalian neocortex.

    Science.gov (United States)

    Emera, Deena; Yin, Jun; Reilly, Steven K; Gockley, Jake; Noonan, James P

    2016-05-10

    Morphological innovations such as the mammalian neocortex may involve the evolution of novel regulatory sequences. However, de novo birth of regulatory elements active during morphogenesis has not been extensively studied in mammals. Here, we use H3K27ac-defined regulatory elements active during human and mouse corticogenesis to identify enhancers that were likely active in the ancient mammalian forebrain. We infer the phylogenetic origins of these enhancers and find that ∼20% arose in the mammalian stem lineage, coincident with the emergence of the neocortex. Implementing a permutation strategy that controls for the nonrandom variation in the ages of background genomic sequences, we find that mammal-specific enhancers are overrepresented near genes involved in cell migration, cell signaling, and axon guidance. Mammal-specific enhancers are also overrepresented in modules of coexpressed genes in the cortex that are associated with these pathways, notably ephrin and semaphorin signaling. Our results also provide insight into the mechanisms of regulatory innovation in mammals. We find that most neocortical enhancers did not originate by en bloc exaptation of transposons. Young neocortical enhancers exhibit smaller H3K27ac footprints and weaker evolutionary constraint in eutherian mammals than older neocortical enhancers. Based on these observations, we present a model of the enhancer life cycle in which neocortical enhancers initially emerge from genomic background as short, weakly constrained "proto-enhancers." Many proto-enhancers are likely lost, but some may serve as nucleation points for complex enhancers to evolve. PMID:27114548

  7. Non-linear leak currents affect mammalian neuron physiology

    Directory of Open Access Journals (Sweden)

    Shiwei Huang

    2015-11-01

    Full Text Available In their seminal works on squid giant axons, Hodgkin and Huxley approximated the membrane leak current as Ohmic, i.e. linear, since in their preparation, sub-threshold current rectification due to the influence of ionic concentration is negligible. Most studies on mammalian neurons have made the same, largely untested, assumption. Here we show that the membrane time constant and input resistance of mammalian neurons (when other major voltage-sensitive and ligand-gated ionic currents are discounted varies non-linearly with membrane voltage, following the prediction of a Goldman-Hodgkin-Katz-based passive membrane model. The model predicts that under such conditions, the time constant/input resistance-voltage relationship will linearize if the concentration differences across the cell membrane are reduced. These properties were observed in patch-clamp recordings of cerebellar Purkinje neurons (in the presence of pharmacological blockers of other background ionic currents and were more prominent in the sub-threshold region of the membrane potential. Model simulations showed that the non-linear leak affects voltage-clamp recordings and reduces temporal summation of excitatory synaptic input. Together, our results demonstrate the importance of trans-membrane ionic concentration in defining the functional properties of the passive membrane in mammalian neurons as well as other excitable cells.

  8. Superoxide radical and iron modulate aconitase activity in mammalian cells.

    Science.gov (United States)

    Gardner, P R; Raineri, I; Epstein, L B; White, C W

    1995-06-01

    Aconitase is a member of a family of iron-sulfur-containing (de)hydratases whose activities are modulated in bacteria by superoxide radical (O2-.)-mediated inactivation and iron-dependent reactivation. The inactivation-reactivation of aconitase(s) in cultured mammalian cells was explored since these reactions may impact important and diverse aconitase functions in the cytoplasm and mitochondria. Conditions which increase O2-. production including exposure to the redox-cycling agent phenazine methosulfate (PMS), inhibitors of mitochondrial ubiquinol-cytochrome c oxidoreductase, or hyperoxia inactivated aconitase in mammalian cells. Overproduction of mitochondrial Mn-superoxide dismutase protected aconitase from inactivation by PMS or inhibitors of ubiquinol-cytochrome c oxidoreductase, but not from normobaric hyperoxia. Aconitase activity was reactivated (t1/2 of 12 +/- 3 min) upon removal of PMS. The iron chelator deferoxamine impaired reactivation and increased net inactivation of aconitase by O2-.. The ability of ubiquinol-cytochrome c oxidoreductase-generated O2-. to inactivate aconitase in several cell types correlated with the fraction of the aconitase activity localized in mitochondria. Extracellular O2-. generated with xanthine oxidase did not affect aconitase activity nor did exogenous superoxide dismutase decrease aconitase inactivation by PMS. The results demonstrate a dynamic and cyclical O2-.-mediated inactivation and iron-dependent reactivation of the mammalian [4Fe-4S] aconitases under normal and stress conditions and provide further evidence for the membrane compartmentalization of O2-.. PMID:7768942

  9. Base Composition Characteristics of Mammalian miRNAs

    Directory of Open Access Journals (Sweden)

    Bin Wang

    2013-01-01

    Full Text Available MicroRNAs (miRNAs are short RNA sequences that repress protein synthesis by either inhibiting the translation of messenger RNA (mRNA or increasing mRNA degradation. Endogenous miRNAs have been found in various organisms, including animals, plants, and viruses. Mammalian miRNAs are evolutionarily conserved, are scattered throughout chromosomes, and play an important role in the immune response and the onset of cancer. For this study, the author explored the base composition characteristics of miRNA genes from the six mammalian species that contain the largest number of known miRNAs. It was found that mammalian miRNAs are evolutionarily conserved and GU-rich. Interestingly, in the miRNA sequences investigated, A residues are clearly the most frequent occupants of positions 2 and 3 of the 5′ end of miRNAs. Unlike G and U residues that may pair with C/U and A/G, respectively, A residues can only pair with U residues of target mRNAs, which may augment the recognition specificity of the 5′ seed region.

  10. Space radiation effects on plant and mammalian cells

    Science.gov (United States)

    Arena, C.; De Micco, V.; Macaeva, E.; Quintens, R.

    2014-11-01

    The study of the effects of ionizing radiation on organisms is related to different research aims. The current review emphasizes the studies on the effects of different doses of sparsely and densely ionizing radiation on living organisms, with the final purpose of highlighting specific and common effects of space radiation in mammals and plants. This topic is extremely relevant in the context of radiation protection from space environment. The response of different organisms to ionizing radiation depends on the radiation quality/dose and/or the intrinsic characteristics of the living system. Macromolecules, in particular DNA, are the critical targets of radiation, even if there is a strong difference between damages encountered by plant and mammalian cells. The differences in structure and metabolism between the two cell types are responsible for the higher resistance of the plant cell compared with its animal counterpart. In this review, we report some recent findings from studies performed in Space or on Earth, simulating space-like levels of radiation with ground-based facilities, to understand the effect of ionizing radiation on mammalian and plant cells. In particular, our attention is focused on genetic alterations and repair mechanisms in mammalian cells and on structures and mechanisms conferring radioresistance to plant cells.

  11. Review of Quantitative Structure - Activity Relationships for Acute Mammalian Toxicity

    Directory of Open Access Journals (Sweden)

    Iglika Lessigiarska

    2006-12-01

    Full Text Available This paper reviews Quantitative Structure-Activity Relationship (QSAR models for acute mammalian toxicity published in the last decade. A number of QSAR models based on cytotoxicity data from mammalian cell lines are also included because of their possible use as a surrogate system for predicting acute toxicity to mammals. On the basis of the review, the following conclusions can be made: i a relatively small number of models for in vivo toxicity are published in the literature. This is due to the nature of the endpoint - acute systemic toxicity is usually related to whole body phenomena and therefore is very complex. The complexity of the mechanisms involved leads to difficulties in the QSAR modelling; ii most QSAR models identify hydrophobicity as a parameter of high importance for the modelled toxicity. In addition, many models indicate the role of the electronic and steric effects; iii most of the literature-based models are restricted to single chemical classes. Models based on more heterogeneous data sets are those incorporated in expert systems. In general, the QSAR models for mammalian toxicity identified in this review are considered useful for investigating the mechanisms of toxicity of defined chemical classes. However, for predictive purposes in the regulatory assessment of chemicals most of the models require additional information to satisfy internationally agreed validation principles. In addition, the development of new models covering larger chemical domains would be useful for the regulatory assessment of chemicals.

  12. A vaccine grade of yeast Saccharomyces cerevisiae expressing mammalian myostatin

    Directory of Open Access Journals (Sweden)

    Zhang Tingting

    2012-12-01

    Full Text Available Abstract Background Yeast Saccharomyces cerevisiae is a widely-used system for protein expression. We previously showed that heat-killed whole recombinant yeast vaccine expressing mammalian myostatin can modulate myostatin function in mice, resulting in increase of body weight and muscle composition in these animals. Foreign DNA introduced into yeast cells can be lost soon unless cells are continuously cultured in selection media, which usually contain antibiotics. For cost and safety concerns, it is essential to optimize conditions to produce quality food and pharmaceutical products. Results We developed a simple but effective method to engineer a yeast strain stably expressing mammalian myostatin. This method utilized high-copy-number integration of myostatin gene into the ribosomal DNA of Saccharomyces cerevisiae. In the final step, antibiotic selection marker was removed using the Cre-LoxP system to minimize any possible side-effects for animals. The resulting yeast strain can be maintained in rich culture media and stably express mammalian myostatin for two years. Oral administration of the recombinant yeast was able to induce immune response to myostatin and modulated the body weight of mice. Conclusions Establishment of such yeast strain is a step further toward transformation of yeast cells into edible vaccine to improve meat production in farm animals and treat human muscle-wasting diseases in the future.

  13. δ-Conotoxin SuVIA suggests an evolutionary link between ancestral predator defence and the origin of fish-hunting behaviour in carnivorous cone snails.

    Science.gov (United States)

    Jin, Ai-Hua; Israel, Mathilde R; Inserra, Marco C; Smith, Jennifer J; Lewis, Richard J; Alewood, Paul F; Vetter, Irina; Dutertre, Sébastien

    2015-07-22

    Some venomous cone snails feed on small fishes using an immobilizing combination of synergistic venom peptides that target Kv and Nav channels. As part of this envenomation strategy, δ-conotoxins are potent ichtyotoxins that enhance Nav channel function. δ-Conotoxins belong to an ancient and widely distributed gene superfamily, but any evolutionary link from ancestral worm-eating cone snails to modern piscivorous species has not been elucidated. Here, we report the discovery of SuVIA, a potent vertebrate-active δ-conotoxin characterized from a vermivorous cone snail (Conus suturatus). SuVIA is equipotent at hNaV1.3, hNaV1.4 and hNaV1.6 with EC50s in the low nanomolar range. SuVIA also increased peak hNaV1.7 current by approximately 75% and shifted the voltage-dependence of activation to more hyperpolarized potentials from -15 mV to -25 mV, with little effect on the voltage-dependence of inactivation. Interestingly, the proximal venom gland expression and pain-inducing effect of SuVIA in mammals suggest that δ-conotoxins in vermivorous cone snails play a defensive role against higher order vertebrates. We propose that δ-conotoxins originally evolved in ancestral vermivorous cones to defend against larger predators including fishes have been repurposed to facilitate a shift to piscivorous behaviour, suggesting an unexpected underlying mechanism for this remarkable evolutionary transition. PMID:26156767

  14. The secreted proteins of Achlya hypogyna and Thraustotheca clavata identify the ancestral oomycete secretome and reveal gene acquisitions by horizontal gene transfer.

    Science.gov (United States)

    Misner, Ian; Blouin, Nic; Leonard, Guy; Richards, Thomas A; Lane, Christopher E

    2015-01-01

    Saprotrophic and parasitic microorganisms secrete proteins into the environment to breakdown macromolecules and obtain nutrients. The molecules secreted are collectively termed the "secretome" and the composition and function of this set of proteins varies depending on the ecology, life cycle, and environment of an organism. Beyond the function of nutrient acquisition, parasitic lineages must also secrete molecules to manipulate their host. Here, we use a combination of de novo genome and transcriptome sequencing and bioinformatic identification of signal peptides to identify the putative secreted proteome of two oomycetes, the facultative parasite Achlya hypogyna and free-living Thraustotheca clavata. By comparing the secretomes of these saprolegnialean oomycetes with that of eight other oomycetes, we were able to characterize the evolution of this protein set across the oomycete clade. These species span the last common ancestor of the two major oomycete families allowing us to identify the ancestral secretome. This putative ancestral secretome consists of at least 84 gene families. Only 11 of these gene families are conserved across all 10 secretomes analyzed and the two major branches in the oomycete radiation. Notably, we have identified expressed elicitin-like effector genes in the saprotrophic decomposer, T. clavata. Phylogenetic analyses show six novel horizontal gene transfers to the oomycete secretome from bacterial and fungal donor lineages, four of which are specific to the Saprolegnialeans. Comparisons between free-living and pathogenic taxa highlight the functional changes of oomycete secretomes associated with shifts in lifestyle. PMID:25527045

  15. Molecular evolutionary analysis of ABCB5: the ancestral gene is a full transporter with potentially deleterious single nucleotide polymorphisms.

    Directory of Open Access Journals (Sweden)

    Karobi Moitra

    Full Text Available BACKGROUND: ABCB5 is a member of the ABC protein superfamily, which includes the transporters ABCB1, ABCC1 and ABCG2 responsible for causing drug resistance in cancer patients and also several other transporters that have been linked to human disease. The ABCB5 full transporter (ABCB5.ts is expressed in human testis and its functional significance is presently unknown. Another variant of this transporter, ABCB5 beta possess a "half-transporter-like" structure and is expressed in melanoma stem cells, normal melanocytes, and other types of pigment cells. ABCB5 beta has important clinical implications, as it may be involved with multidrug resistance in melanoma stem cells, allowing these stem cells to survive chemotherapeutic regimes. METHODOLOGY/PRINCIPAL FINDINGS: We constructed and examined in detail topological structures of the human ABCB5 protein and determined in-silico the cSNPs (coding single nucleotide polymorphisms that may affect its function. Evolutionary analysis of ABCB5 indicated that ABCB5, ABCB1, ABCB4, and ABCB11 share a common ancestor, which began duplicating early in the evolutionary history of chordates. This suggests that ABCB5 has evolved as a full transporter throughout its evolutionary history. CONCLUSIONS/SIGNIFICANCE: From our in-silco analysis of cSNPs we found that a large number of non-synonymous cSNPs map to important functional regions of the protein suggesting that these SNPs if present in human populations may play a role in diseases associated with ABCB5. From phylogenetic analyses, we have shown that ABCB5 evolved as a full transporter throughout its evolutionary history with an absence of any major shifts in selection between the various lineages suggesting that the function of ABCB5 has been maintained during mammalian evolution. This finding would suggest that ABCB5 beta may have evolved to play a specific role in human pigment cells and/or melanoma cells where it is predominantly expressed.

  16. Estimating ancestral distributions of lineages with uncertain sister groups: a statistical approach to Dispersal-Vicariance Analysis and a case using Aesculus L. (Sapindaceae) including fossils

    Institute of Scientific and Technical Information of China (English)

    A.J. HARRIS; Qiu-Yun (Jenny) XIANG

    2009-01-01

    We propose a simple statistical approach for using Dispersal-Vicariance Analysis (DIVA) software to infer biogeographic histories without fully bifurcating trees. In this approach, ancestral ranges are first optimized for a sample of Bayesian trees. The probability P of an ancestral range r at a node is then calculated as P(rY)= Σnt=1 F(rY)tPt where Y is a node, and F(rY) is the frequency of range r among all the optimal solutions resulting from DIVA optimization at node Y, t is one of n topologies optimized, and Pt is the probability of topology t. Node Y is a hypothesized ancestor shared by a specific crown lineage and the sister of that lineage "x", where x may vary due to phylogenetic uncertainty (polytomies and nodes with posterior probability <100%). Using this method, the ancestral distribution at Y can be estimated to provide inference of the geographic origins of the specific crown group of interest. This approach takes into account phylogenetic uncertainty as well as uncertainty from DIVA optimization. It is an extension of the previously described method called Bayes-DIVA, which pairs Bayesian phylogenetic analysis with biogeographic analysis using DIVA. Further, we show that the probability P of an ancestral range at Y calculated using this method does not equate to pp* F(rY) on the Bayesian consensus tree when both variables are < 100%, where pp is the posterior probability and F(rY) is the frequency of range r for the node containing the specific crown group. We tested our DIVA-Bayes approach using Aesculus L., which has major lineages unresolved as a polytomy. We inferred the most probable geographic origins of the five traditional sections of Aesculus and ofAesculus californica Nutt. and examined range subdivisions at parental nodes of these lineages.Additionally, we used the DIVA-Bayes data from Aesculus to quantify the effects on biogeographic inference of including two wildcard fossil taxa in phylogenetic analysis. Our analysis resolved the

  17. Non-immune binding of human protein Fv to immunoglobulins from various mammalian and non-mammalian species.

    Science.gov (United States)

    Bouvet, J P; Pires, R; Charlemagne, J; Pillot, J; Iscaki, S

    1991-10-01

    Reactivity of the secretory protein Fv with immunoglobulins (Ig) from various species of vertebrates was investigated. Binding was observed throughout all taxonomic classes: mammalian, avian, reptilian, amphibian and fish. Contrasting with this wide spectrum, no significant binding was found with most mammalian ungulates, such as horse (Perissodactyl), cow, sheep and goat (Artiodactyls). Nevertheless, disruption of the hydrogen bonds of Ig allowed these non-reactive molecules to bind. Such a conserved reactivity during evolution, and our previous data on the effect of the cleavage of the intra-chain disulphide bonds, suggest that protein Fv recognizes a discontinuous framework structure involving both the FR1 and FR3 regions in the variable domain of the heavy chain of Ig. PMID:1925412

  18. Evolutionary history of mammalian sucking lice (Phthiraptera: Anoplura

    Directory of Open Access Journals (Sweden)

    Allen Julie M

    2010-09-01

    Full Text Available Abstract Background Sucking lice (Phthiraptera: Anoplura are obligate, permanent ectoparasites of eutherian mammals, parasitizing members of 12 of the 29 recognized mammalian orders and approximately 20% of all mammalian species. These host specific, blood-sucking insects are morphologically adapted for life on mammals: they are wingless, dorso-ventrally flattened, possess tibio-tarsal claws for clinging to host hair, and have piercing mouthparts for feeding. Although there are more than 540 described species of Anoplura and despite the potential economical and medical implications of sucking louse infestations, this study represents the first attempt to examine higher-level anopluran relationships using molecular data. In this study, we use molecular data to reconstruct the evolutionary history of 65 sucking louse taxa with phylogenetic analyses and compare the results to findings based on morphological data. We also estimate divergence times among anopluran taxa and compare our results to host (mammal relationships. Results This study represents the first phylogenetic hypothesis of sucking louse relationships using molecular data and we find significant conflict between phylogenies constructed using molecular and morphological data. We also find that multiple families and genera of sucking lice are not monophyletic and that extensive taxonomic revision will be necessary for this group. Based on our divergence dating analyses, sucking lice diversified in the late Cretaceous, approximately 77 Ma, and soon after the Cretaceous-Paleogene boundary (ca. 65 Ma these lice proliferated rapidly to parasitize multiple mammalian orders and families. Conclusions The diversification time of sucking lice approximately 77 Ma is in agreement with mammalian evolutionary history: all modern mammal orders are hypothesized to have diverged by 75 Ma thus providing suitable habitat for the colonization and radiation of sucking lice. Despite the concordant timing of

  19. Store-operated channels regulate intracellular calcium in mammalian rods.

    Science.gov (United States)

    Molnar, Tünde; Barabas, Peter; Birnbaumer, Lutz; Punzo, Claudio; Kefalov, Vladimir; Križaj, David

    2012-08-01

    Exposure to daylight closes cyclic nucleotide-gated (CNG) and voltage-operated Ca(2+) -permeable channels in mammalian rods. The consequent lowering of the cytosolic calcium concentration ([Ca(2+)](i)), if protracted, can contribute to light-induced damage and apoptosis in these cells. We here report that mouse rods are protected against prolonged lowering of [Ca(2+)](i) by store-operated Ca(2+) entry (SOCE). Ca(2+) stores were depleted in Ca(2+)-free saline supplemented with the endoplasmic reticulum (ER) sequestration blocker cyclopiazonic acid. Store depletion elicited [Ca(2+)](i) signals that exceeded baseline [Ca(2+)](i) by 5.9 ± 0.7-fold and were antagonized by an inhibitory cocktail containing 2-APB, SKF 96365 and Gd(3+). Cation influx through SOCE channels was sufficient to elicit a secondary activation of L-type voltage-operated Ca2+ entry. We also found that TRPC1, the type 1 canonical mammalian homologue of the Drosophila photoreceptor TRP channel, is predominantly expressed within the outer nuclear layer of the retina. Rod loss in Pde6b(rdl) (rd1), Chx10/Kip1(-/-rdl) and Elovl4(TG2) dystrophic models was associated with ∼70% reduction in Trpc1 mRNA content whereas Trpc1 mRNA levels in rodless cone-full Nrl(-/-) retinas were decreased by ∼50%. Genetic ablation of TRPC1 channels, however, had no effect on SOCE, the sensitivity of the rod phototransduction cascade or synaptic transmission at rod and cone synapses. Thus, we localized two new mechanisms, SOCE and TRPC1, to mammalian rods and characterized the contribution of SOCE to Ca(2+) homeostasis. By preventing the cytosolic [Ca(2+)](i) from dropping too low under sustained saturating light conditions, these signalling pathways may protect Ca(2+)-dependent mechanisms within the ER and the cytosol without affecting normal rod function. PMID:22674725

  20. Chemical radiation protection of sodium pump in mammalian skeletal muscle

    International Nuclear Information System (INIS)

    When male albino rats of the Wistar strain received wholebody gamma irradiation at a dose level of 8.5 Gy, 22N outward movement from the diaphragm muscle fibres slowed down, while its uptake was enhanced. When imidazole was intraperitoneally injected prior to irradiation both movements returned nearly to normal rates. Experiments carried out on the 7th day post irradiation, indicated that gamma irradiation had exerted some sort of damage upon the sodium pumping mechanism in mammalian skeletal muscle, and that imidazole injection prior to radiation exposure exerted a remarkable radioprotective effect on those vital biophysical processes. The results have been discussed in view of the relevant literature. (author)

  1. Engineering controlled mammalian type O-Glycosylation in plant cells

    DEFF Research Database (Denmark)

    Yang, Zhang; Drew, Damian Paul; Jørgensen, Bodil;

    2011-01-01

    Human mucins are large heavily O-glycosylated glycoproteins (>200 kDa), which account for the majority of proteins in mucus layers that e.g. hydrate, lubricate and protect cells from proteases as well as from pathogens. O-linked mucin glycans are truncated in many cancers, yielding truncated cancer...... specific glyco-peptide epitopes, such as the Tn epitope (GalNAc sugar attached to either Serine or Threonine), which are antigenic to the immune system. In the present study, we have identified plant cells as the only eukaryotic cells without mammalian type O-glycosylation or competing (for sites) O...

  2. Centriole Age Underlies Asynchronous Primary Cilium Growth in Mammalian Cells

    OpenAIRE

    Anderson, Charles T; Stearns, Tim

    2009-01-01

    Primary cilia are microtubule-based sensory organelles that are present in most mammalian tissues and play important roles in development and disease [1]. They are required for the Sonic hedgehog (Shh) [2-4] and PDGF [5] signalling pathways. Primary cilia grow from the older of the two centrioles of the centrosome, referred to as the mother centriole. In cycling cells the cilium typically grows in G1 and is lost before mitosis, but the regulation of its growth is poorly understood. Centriole ...

  3. Factors affecting the spontaneous mutational spectra in somatic mammalian cells

    Directory of Open Access Journals (Sweden)

    О.А. Ковальова

    2006-04-01

    Full Text Available  In our survey of references we are discussed the influence of factors biological origin on the spontaneous mutation specters in mammalian. Seasonal and age components influence on the frequence of cytogenetic anomalies. The immune and endocrinous systems are take part in control of the alteration of the spontaneous mutation specters. Genetical difference of sensibility in animal and human at the alteration of factors enviroment as and  genetical differences of repair systems activity are may influence on individual variation of spontaneous destabilization characters of chromosomal apparatus.

  4. Loss of the Mammalian DREAM Complex Deregulates Chondrocyte Proliferation

    OpenAIRE

    Forristal, Chantal; Henley, Shauna A; MacDonald, James I.; Bush, Jason R.; Ort, Carley; Daniel T. Passos; Talluri, Srikanth; Ishak, Charles A.; Thwaites, Michael J.; Norley, Chris J.; Litovchick, Larisa; DeCaprio, James A.; DiMattia, Gabriel; Holdsworth, David W.; Beier, Frank

    2014-01-01

    Mammalian DREAM is a conserved protein complex that functions in cellular quiescence. DREAM contains an E2F, a retinoblastoma (RB)-family protein, and the MuvB core (LIN9, LIN37, LIN52, LIN54, and RBBP4). In mammals, MuvB can alternatively bind to BMYB to form a complex that promotes mitotic gene expression. Because BMYB-MuvB is essential for proliferation, loss-of-function approaches to study MuvB have generated limited insight into DREAM function. Here, we report a gene-targeted mouse model...

  5. Robust expression of a bioactive mammalian protein in chlamydomonas chloroplast

    Science.gov (United States)

    Mayfield, Stephen P.

    2010-03-16

    Methods and compositions are disclosed to engineer chloroplast comprising heterologous mammalian genes via a direct replacement of chloroplast Photosystem II (PSII) reaction center protein coding regions to achieve expression of recombinant protein above 5% of total protein. When algae is used, algal expressed protein is produced predominantly as a soluble protein where the functional activity of the peptide is intact. As the host algae is edible, production of biologics in this organism for oral delivery or proteins/peptides, especially gut active proteins, without purification is disclosed.

  6. Robust expression of a bioactive mammalian protein in Chlamydomonas chloroplast

    Energy Technology Data Exchange (ETDEWEB)

    Mayfield, Stephen P

    2015-01-13

    Methods and compositions are disclosed to engineer chloroplast comprising heterologous mammalian genes via a direct replacement of chloroplast Photosystem II (PSII) reaction center protein coding regions to achieve expression of recombinant protein above 5% of total protein. When algae is used, algal expressed protein is produced predominantly as a soluble protein where the functional activity of the peptide is intact. As the host algae is edible, production of biologics in this organism for oral delivery of proteins/peptides, especially gut active proteins, without purification is disclosed.

  7. Equipment for large-scale mammalian cell culture.

    Science.gov (United States)

    Ozturk, Sadettin S

    2014-01-01

    This chapter provides information on commonly used equipment in industrial mammalian cell culture, with an emphasis on bioreactors. The actual equipment used in the cell culture process can vary from one company to another, but the main steps remain the same. The process involves expansion of cells in seed train and inoculation train processes followed by cultivation of cells in a production bioreactor. Process and equipment options for each stage of the cell culture process are introduced and examples are provided. Finally, the use of disposables during seed train and cell culture production is discussed. PMID:24429549

  8. Strategies to discover regulatory circuits of the mammalian immune system

    Science.gov (United States)

    Amit, Ido; Regev, Aviv; Hacohen, Nir

    2013-01-01

    Recent advances in technologies for genome- and proteome-scale measurements and perturbations promise to accelerate discovery in every aspect of biology and medicine. Although such rapid technological progress provides a tremendous opportunity, it also demands that we learn how to use these tools effectively. One application with great potential to enhance our understanding of biological systems is the unbiased reconstruction of genetic and molecular networks. Cells of the immune system provide a particularly useful model for developing and applying such approaches. Here, we review approaches for the reconstruction of signalling and transcriptional networks, with a focus on applications in the mammalian innate immune system. PMID:22094988

  9. Extreme variability among mammalian V1R gene families

    OpenAIRE

    Janet M Young; Massa, Hillary F.; Hsu, Li; Trask, Barbara J

    2010-01-01

    We report an evolutionary analysis of the V1R gene family across 37 mammalian genomes. V1Rs comprise one of three chemosensory receptor families expressed in the vomeronasal organ, and contribute to pheromone detection. We first demonstrate that Trace Archive data can be used effectively to determine V1R family sizes and to obtain sequences of most V1R family members. Analyses of V1R sequences from trace data and genome assemblies show that species-specific expansions previously observed in o...

  10. Caffeine, cyclic AMP and postreplication repair of mammalian DNA

    International Nuclear Information System (INIS)

    The methylxanthines, caffeine and theophylline, inhibit postreplication repair of DNA in mammalian cells. Because they also inhibit cyclic AMP phosphodiesterase, it was thought that there might be some connection between concentrations of cyclic AMP and postreplication repair. This possibility was tested by performing DNA sedimentation experiments with a cyclic AMP-resistant mouse lymphoma cell mutant and its wild-type counterpart. The results show that there is no connection between cellular cyclic AMP concentrations and the rate of postreplication repair. Therefore, it is more likely that caffeine and theophylline inhibit postreplication repair by some other means, such as by binding to DNA

  11. Detection of "punctuated equilibrium" by bayesian estimation of speciation and extinction rates, ancestral character states, and rates of anagenetic and cladogenetic evolution on a molecular phylogeny.

    Science.gov (United States)

    Bokma, Folmer

    2008-11-01

    Algorithms are presented to simultaneously estimate probabilities of speciation and extinction, rates of anagenetic and cladogenetic phenotypic evolution, as well as ancestral character states, from a complete ultrametric species-level phylogeny with dates assigned to all bifurcations and one or more phenotypes in three or more extant species, using Metropolis-Hastings Markov Chain Monte Carlo sampling. The algorithms also estimate missing phenotypes of extant species and numbers of speciation events that occurred on all branches of the phylogeny. The algorithms are discussed and their performance is evaluated using simulated data. That evaluation shows that precise estimation of rates of evolution of one or a few phenotypes requires large phylogenies. Estimation accuracy improves with the number of species on the phylogeny. PMID:18752617

  12. Mating animals by minimising the covariance between ancestral contributions generates less inbreeding without compromising genetic gain in breeding schemes with truncation selection

    DEFF Research Database (Denmark)

    Henryon, M; Berg, P; Sørensen, A C

    2009-01-01

    they can be achieved without extra costs or practical constraints. MCAC mating merely uses pedigree information to pair the animals more appropriately and is clearly a worthy alternative to minimum-coancestry mating and probably any other mating criterion. We believe, therefore, that MCAC mating should......We reasoned that mating animals by minimising the covariance between ancestral contributions (MCAC mating) will generate less inbreeding and at least as much genetic gain as minimum-coancestry mating in breeding schemes where the animals are truncation-selected. We tested this hypothesis...... by stochastic simulation and compared the mating criteria in hierarchical and factorial breeding schemes, where the animals were selected based on breeding values predicted by animal-model BLUP. Random mating was included as a reference-mating criterion. We found that MCAC mating generated 4% to 8% less...

  13. 济南市闵子骞祠堂东汉墓%Eastern Han Tomb in the Min Ziqian Ancestral Temple in Jinan City

    Institute of Scientific and Technical Information of China (English)

    济南市考古研究所

    2004-01-01

    In 2000, the Jinan Municipal Institute of Archaeology carried out a rescuing excavation to explore a tomb in the Min Ziqian ancestral temple, Jinan City. The grave is built of brick and stone, consists of an anterior, a middle, a back and two side rooms, and has a "凸"-shaped plan. It has been seriously robbed, but still above 60 pottery objects and copper coins are left over from the grave goods. Among them pottery domestic fowls and animals come first in number, and four pictorial stones remain in the tomb. The tomb shape, the features of the objects and those of the pictorial stones suggest that the burial belongs to the late Eastern Han period.

  14. X-Ray Crystal Structure of the Ancestral 3-Ketosteroid Receptor-Progesterone-Mifepristone Complex Shows Mifepristone Bound at the Coactivator Binding Interface

    Energy Technology Data Exchange (ETDEWEB)

    Colucci, Jennifer K.; Ortlund, Eric A. [Emory-MED

    2013-12-12

    Steroid receptors are a subfamily of nuclear receptors found throughout all metazoans. They are highly important in the regulation of development, inflammation, and reproduction and their misregulation has been implicated in hormone insensitivity syndromes and cancer. Steroid binding to SRs drives a conformational change in the ligand binding domain that promotes nuclear localization and subsequent interaction with coregulator proteins to affect gene regulation. SRs are important pharmaceutical targets, yet most SR-targeting drugs have off-target pharmacology leading to unwanted side effects. A better understanding of the structural mechanisms dictating ligand specificity and the evolution of the forces that created the SR-hormone pairs will enable the design of better pharmaceutical ligands. In order to investigate this relationship, we attempted to crystallize the ancestral 3-ketosteroid receptor (ancSR2) with mifepristone, a SR antagonist. Here, we present the x-ray crystal structure of the ancestral 3-keto steroid receptor (ancSR2)-progesterone complex at a resolution of 2.05 Å. This improves upon our previously reported structure of the ancSR2-progesterone complex, permitting unambiguous assignment of the ligand conformation within the binding pocket. Surprisingly, we find mifepristone, fortuitously docked at the protein surface, poised to interfere with coregulator binding. Recent attention has been given to generating pharmaceuticals that block the coregulator binding site in order to obstruct coregulator binding and achieve tissue-specific SR regulation independent of hormone binding. Mifepristone’s interaction with the coactivator cleft of this SR suggests that it may be a useful molecular scaffold for further coactivator binding inhibitor development.

  15. Comparison with ancestral diets suggests dense acellular carbohydrates promote an inflammatory microbiota, and may be the primary dietary cause of leptin resistance and obesity.

    Science.gov (United States)

    Spreadbury, Ian

    2012-01-01

    A novel hypothesis of obesity is suggested by consideration of diet-related inflammation and evolutionary medicine. The obese homeostatically guard their elevated weight. In rodent models of high-fat diet-induced obesity, leptin resistance is seen initially at vagal afferents, blunting the actions of satiety mediators, then centrally, with gastrointestinal bacterial-triggered SOCS3 signaling implicated. In humans, dietary fat and fructose elevate systemic lipopolysaccharide, while dietary glucose also strongly activates SOCS3 signaling. Crucially however, in humans, low-carbohydrate diets spontaneously decrease weight in a way that low-fat diets do not. Furthermore, nutrition transition patterns and the health of those still eating diverse ancestral diets with abundant food suggest that neither glycemic index, altered fat, nor carbohydrate intake can be intrinsic causes of obesity, and that human energy homeostasis functions well without Westernized foods containing flours, sugar, and refined fats. Due to being made up of cells, virtually all "ancestral foods" have markedly lower carbohydrate densities than flour- and sugar-containing foods, a property quite independent of glycemic index. Thus the "forgotten organ" of the gastrointestinal microbiota is a prime candidate to be influenced by evolutionarily unprecedented postprandial luminal carbohydrate concentrations. The present hypothesis suggests that in parallel with the bacterial effects of sugars on dental and periodontal health, acellular flours, sugars, and processed foods produce an inflammatory microbiota via the upper gastrointestinal tract, with fat able to effect a "double hit" by increasing systemic absorption of lipopolysaccharide. This model is consistent with a broad spectrum of reported dietary phenomena. A diet of grain-free whole foods with carbohydrate from cellular tubers, leaves, and fruits may produce a gastrointestinal microbiota consistent with our evolutionary condition, potentially

  16. The impact of ancestral heath management on soils and landscapes. A reconstruction based on paleoecological analyses of soil records in the middle and southeast Netherlands.

    Science.gov (United States)

    van Mourik, Jan; Doorenbosch, Marieke

    2016-04-01

    The evolution of heath lands during the Holocene has been registered in various soil records . Paleoecological analyses of these records enable to reconstruct the changing economic and cultural management of heaths and the consequences for landscape and soils. Heaths are characteristic components of cultural landscape mosaics on sandy soils in the Netherlands. The natural habitat of heather species was moorland. At first, natural events like forest fires and storms caused small-scale forest degradation, in addition on the forest degradation accelerated due to cultural activities like forest grazing, wood cutting and shifting cultivation. Heather plants invaded on degraded forest soils and heaths developed. People learned to use the heaths for economic and cultural purposes. The impact of the heath management on landscape and soils was registered in soil records of barrows, drift sand sequences and plaggic Anthrosols. Based on pollen diagrams of such records we could reconstruct that heaths were developed and used for cattle grazing before the Bronze Age. During the Late Neolithic, the Bronze Age and Iron Age, people created the barrow landscape on the ancestral heaths. After the Iron Age people probably continued with cattle grazing on the heaths and plaggic agriculture until the Early Middle Ages. After 1000 AD two events affected the heaths. At first deforestation for the sale of wood resulted in the first regional extension of sand drifting and heath degradation. After that the introduction of the deep stable economy and heath sods digging resulted in acceleration of the rise of plaggic horizons, severe heath degradation and the second extension of sand drifting. At the end of the 19th century the heath lost its economic value due to the introduction of chemical fertilizers. The heaths were transformed into 'new' arable fields and forests and due to deep ploughing most soil archives were destroyed. Since 1980 AD, the remaining relicts of the ancestral heaths are

  17. Clusters of ancestrally related genes that show paralogy in whole or in part are a major feature of the genomes of humans and other species.

    Directory of Open Access Journals (Sweden)

    Michael B Walker

    Full Text Available Arrangements of genes along chromosomes are a product of evolutionary processes, and we can expect that preferable arrangements will prevail over the span of evolutionary time, often being reflected in the non-random clustering of structurally and/or functionally related genes. Such non-random arrangements can arise by two distinct evolutionary processes: duplications of DNA sequences that give rise to clusters of genes sharing both sequence similarity and common sequence features and the migration together of genes related by function, but not by common descent. To provide a background for distinguishing between the two, which is important for future efforts to unravel the evolutionary processes involved, we here provide a description of the extent to which ancestrally related genes are found in proximity.Towards this purpose, we combined information from five genomic datasets, InterPro, SCOP, PANTHER, Ensembl protein families, and Ensembl gene paralogs. The results are provided in publicly available datasets (http://cgd.jax.org/datasets/clustering/paraclustering.shtml describing the extent to which ancestrally related genes are in proximity beyond what is expected by chance (i.e. form paraclusters in the human and nine other vertebrate genomes, as well as the D. melanogaster, C. elegans, A. thaliana, and S. cerevisiae genomes. With the exception of Saccharomyces, paraclusters are a common feature of the genomes we examined. In the human genome they are estimated to include at least 22% of all protein coding genes. Paraclusters are far more prevalent among some gene families than others, are highly species or clade specific and can evolve rapidly, sometimes in response to environmental cues. Altogether, they account for a large portion of the functional clustering previously reported in several genomes.

  18. Conserved intron positions in FGFR genes reflect the modular structure of FGFR and reveal stepwise addition of domains to an already complex ancestral FGFR.

    Science.gov (United States)

    Rebscher, Nicole; Deichmann, Christina; Sudhop, Stefanie; Fritzenwanker, Jens Holger; Green, Stephen; Hassel, Monika

    2009-10-01

    We have analyzed the evolution of fibroblast growth factor receptor (FGFR) tyrosine kinase genes throughout a wide range of animal phyla. No evidence for an FGFR gene was found in Porifera, but we tentatively identified an FGFR gene in the placozoan Trichoplax adhaerens. The gene encodes a protein with three immunoglobulin-like domains, a single-pass transmembrane, and a split tyrosine kinase domain. By superimposing intron positions of 20 FGFR genes from Placozoa, Cnidaria, Protostomia, and Deuterostomia over the respective protein domain structure, we identified ten ancestral introns and three conserved intron groups. Our analysis shows (1) that the position of ancestral introns correlates to the modular structure of FGFRs, (2) that the acidic domain very likely evolved in the last common ancestor of triploblasts, (3) that splicing of IgIII was enabled by a triploblast-specific insertion, and (4) that IgI is subject to substantial loss or duplication particularly in quickly evolving genomes. Moreover, intron positions in the catalytic domain of FGFRs map to the borders of protein subdomains highly conserved in other serine/threonine kinases. Nevertheless, these introns were introduced in metazoan receptor tyrosine kinases exclusively. Our data support the view that protein evolution dating back to the Cambrian explosion took place in such a short time window that only subtle changes in the domain structure are detectable in extant representatives of animal phyla. We propose that the first multidomain FGFR originated in the last common ancestor of Placozoa, Cnidaria, and Bilateria. Additional domains were introduced mainly in the ancestor of triploblasts and in the Ecdysozoa. PMID:20016912

  19. Proteasome Inhibitors Enhance Bacteriophage Lambda (λ) Mediated Gene Transfer in Mammalian Cells

    OpenAIRE

    Volcy, Ketna; Dewhurst, Stephen

    2008-01-01

    Bacteriophage lambda vectors can transfer their genomes into mammalian cells, resulting in expression of phage-encoded genes. However, this process is inefficient. Experiments were therefore conducted to delineate the rate limiting step(s) involved, using a phage vector that contains a mammalian luciferase reporter gene cassette. The efficiency of phage-mediated gene transfer in mammalian cells was quantitated, in the presence or absence of pharmacologic inhibitors of cell uptake and degradat...

  20. Efflux-mediated multidrug resistance in Bacillus subtilis: similarities and dissimilarities with the mammalian system.

    OpenAIRE

    Neyfakh, A A; Bidnenko, V E; L. B. CHEN

    1991-01-01

    Bacillus subtilis cells selected for their resistance to rhodamine 6G demonstrated a multidrug-resistance (MDR) phenotype resembling that of mammalian MDR cells. Like MDR in mammalian cells, MDR in bacteria was mediated by the efflux of the drugs from the cells. The bacterial multidrug efflux system transported similar drugs and was sensitive to similar inhibitors as the mammalian multidrug transporter, P-glycoprotein. The gene coding for the bacterial multidrug transporter, like the P-glycop...

  1. Tick-induced allergies: mammalian meat allergy, tick anaphylaxis and their significance

    OpenAIRE

    van Nunen, Sheryl

    2015-01-01

    Serious tick-induced allergies comprise mammalian meat allergy following tick bites and tick anaphylaxis. Mammalian meat allergy is an emergent allergy, increasingly prevalent in tick-endemic areas of Australia and the United States, occurring worldwide where ticks are endemic. Sensitisation to galactose-α-1,3-galactose (α-Gal) has been shown to be the mechanism of allergic reaction in mammalian meat allergy following tick bite. Whilst other carbohydrate allergens have been identified, this a...

  2. Carbamazepine induces mitotic arrest in mammalian Vero cells

    International Nuclear Information System (INIS)

    We reported recently that the anticonvulsant drug carbamazepine, at supratherapeutic concentrations, exerts antiproliferative effects in mammalian Vero cells, but the underlying mechanism has not been elucidated. This motivates us to examine rigorously whether growth arrest was associated with structural changes in cellular organization during mitosis. In the present work, we found that exposure of the cells to carbamazepine led to an increase in mitotic index, mainly due to the sustained block at the metaphase/anaphase boundary, with the consequent inhibition of cell proliferation. Indirect immunofluorescence, using antibodies directed against spindle apparatus proteins, revealed that mitotic arrest was associated with formation of monopolar spindles, caused by impairment of centrosome separation. The final consequence of the spindle defects induced by carbamazepine, depended on the duration of cell cycle arrest. Following the time course of accumulation of metaphase and apoptotic cells during carbamazepine treatments, we observed a causative relationship between mitotic arrest and induction of cell death. Conversely, cells released from the block of metaphase by removal of the drug, continued to progress through mitosis and resume normal proliferation. Our results show that carbamazepine shares a common antiproliferative mechanism with spindle-targeted drugs and contribute to a better understanding of the cytostatic activity previously described in Vero cells. Additional studies are in progress to extend these initial findings that define a novel mode of action of carbamazepine in cultured mammalian cells

  3. CRISPR Technology for Genome Activation and Repression in Mammalian Cells.

    Science.gov (United States)

    Du, Dan; Qi, Lei S

    2016-01-01

    Targeted modulation of transcription is necessary for understanding complex gene networks and has great potential for medical and industrial applications. CRISPR is emerging as a powerful system for targeted genome activation and repression, in addition to its use in genome editing. This protocol describes how to design, construct, and experimentally validate the function of sequence-specific single guide RNAs (sgRNAs) for sequence-specific repression (CRISPRi) or activation (CRISPRa) of transcription in mammalian cells. In this technology, the CRISPR-associated protein Cas9 is catalytically deactivated (dCas9) to provide a general platform for RNA-guided DNA targeting of any locus in the genome. Fusion of dCas9 to effector domains with distinct regulatory functions enables stable and efficient transcriptional repression or activation in mammalian cells. Delivery of multiple sgRNAs further enables activation or repression of multiple genes. By using scaffold RNAs (scRNAs), different effectors can be recruited to different genes for simultaneous activation of some and repression of others. The CRISPRi and CRISPRa methods provide powerful tools for sequence-specific control of gene expression on a genome-wide scale to aid understanding gene functions and for engineering genetic regulatory systems. PMID:26729910

  4. Network scaling reveals consistent fractal pattern in hierarchical mammalian societies.

    Science.gov (United States)

    Hill, Russell A; Bentley, R Alexander; Dunbar, Robin I M

    2008-12-23

    Recent studies have demonstrated that human societies are hierarchically structured with a consistent scaling ratio across successive layers of the social network; each layer of the network is between three and four times the size of the preceding (smaller) grouping level. Here we show that similar relationships hold for four mammalian taxa living in multi-level social systems. For elephant (Loxodonta africana), gelada (Theropithecus gelada) and hamadryas (Papio hamadryas hamadryas) baboon, successive layers of social organization have a scaling ratio of almost exactly 3, indicating that such branching ratios may be a consistent feature of all hierarchically structured societies. Interestingly, the scaling ratio for orca (Orcinus orca) was 3.8, which might mean that aquatic environments place different constraints on the organization of social hierarchies. However, circumstantial evidence from a range of other species suggests that scaling ratios close to 3 may apply widely, even in species where hierarchical social structures have not traditionally been identified. These results identify the origin of the hierarchical, fractal-like organization of mammalian social systems as a fundamental question. PMID:18765349

  5. Characterization of mammalian glucose transport proteins using photoaffinity labeling techniques

    International Nuclear Information System (INIS)

    A carrier-free radioiodinated phenylazide derivative of forskolin, 3-iodo-4-azidophenethylamido-7-O-succinyl-deacetyl-forskolin ([125I]IAPS-forskolin), has been shown to be a highly selective photoaffinity probe for the human erythrocyte glucose transported and the glucose transport proteins found in several mammalian tissues and cultured cells where the glucose transport protein is present at a low concentration. The photoincorporation of [125I]IAPS-forskolin into these glucose transporters was blocked by D- (but not L-) glucose, cytochalasin B, and forskolin. In addition to labeling the mammalian glucose transport proteins, [125I]IAPS-forskolin also labeled the L-arabinose transporter from E. coli. In muscle and adipose tissues, glucose transport is markedly increased in response to insulin. [125I]IAPS-forskolin was shown to selectivity tag the glucose transporter in membranes derived from these cells. In addition, the covalent derivatization of the transport protein in subcellular fractions of the adipocyte has provided a means to study the hormonal regulation of glucose transport. [125I]IAPS-forskolin has also been used to label the purified human erythrocyte glucose transporter. The site of insertion has therefore been localized by analysis of the radiolabeled peptides which were produced following chemical and proteolytic digestion of the labeled transport protein

  6. Characterization of mammalian glucose transport proteins using photoaffinity labeling techniques

    Energy Technology Data Exchange (ETDEWEB)

    Wadzinski, B.E.

    1989-01-01

    A carrier-free radioiodinated phenylazide derivative of forskolin, 3-iodo-4-azidophenethylamido-7-O-succinyl-deacetyl-forskolin (({sup 125}I)IAPS-forskolin), has been shown to be a highly selective photoaffinity probe for the human erythrocyte glucose transported and the glucose transport proteins found in several mammalian tissues and cultured cells where the glucose transport protein is present at a low concentration. The photoincorporation of ({sup 125}I)IAPS-forskolin into these glucose transporters was blocked by D- (but not L-) glucose, cytochalasin B, and forskolin. In addition to labeling the mammalian glucose transport proteins, ({sup 125}I)IAPS-forskolin also labeled the L-arabinose transporter from E. coli. In muscle and adipose tissues, glucose transport is markedly increased in response to insulin. ({sup 125}I)IAPS-forskolin was shown to selectivity tag the glucose transporter in membranes derived from these cells. In addition, the covalent derivatization of the transport protein in subcellular fractions of the adipocyte has provided a means to study the hormonal regulation of glucose transport. ({sup 125}I)IAPS-forskolin has also been used to label the purified human erythrocyte glucose transporter. The site of insertion has therefore been localized by analysis of the radiolabeled peptides which were produced following chemical and proteolytic digestion of the labeled transport protein.

  7. Recombinant genomes which express chloramphenicol acetyltransferase in mammalian cells

    Energy Technology Data Exchange (ETDEWEB)

    Gorman, C.M.; Moffat, L.F.; Howard, B.H.

    1982-09-01

    The authors constructed a series of recombinant genomes which directed expression of the enzyme chloramphenicol acetyltransferase (CAT) in mammalian cells. The prototype recombinant in this series, pSV2-cat, consisted of the beta-lactamase gene and origin of replication from pBR322 coupled to a simian virus 40 (SV40) early transcription region into which CAT coding sequences were inserted. Readily measured levels of CAT accumulated within 48 h after the introduction of pSV2-cat DNA into African green monkey kidney CV-1 cells. Because endogenous CAT activity is not present in CV-1 or other mammalian cells, and because rapid, sensitive assays for CAT activity are available, these recombinants provided a uniquely convenient system for monitoring the expression of foreign DNAs in tissue culture cells. To demonstrate the usefulness of this system, we constructed derivatives of pSV2-cat from which part or all of the SV 40 promoter region was removed. Deletion of one copy of the 72-base-pair repeat sequence in the SV40 promoter caused no significant decrease in CAT synthesis in monkey kidney CV-1 cells; however, an additional deletion of 50 base pairs from the second copy of the repeats reduced CAT synthesis to 11% of its level in the wild type. They also constructed a recombinant, pSVO-cat, in which the entire SV40 promoter region was removed and a unique HindIII site was substituted for the insertion of other promoter sequences.

  8. Colour as a signal for entraining the mammalian circadian clock.

    Directory of Open Access Journals (Sweden)

    Lauren Walmsley

    2015-04-01

    Full Text Available Twilight is characterised by changes in both quantity ("irradiance" and quality ("colour" of light. Animals use the variation in irradiance to adjust their internal circadian clocks, aligning their behaviour and physiology with the solar cycle. However, it is currently unknown whether changes in colour also contribute to this entrainment process. Using environmental measurements, we show here that mammalian blue-yellow colour discrimination provides a more reliable method of tracking twilight progression than simply measuring irradiance. We next use electrophysiological recordings to demonstrate that neurons in the mouse suprachiasmatic circadian clock display the cone-dependent spectral opponency required to make use of this information. Thus, our data show that some clock neurons are highly sensitive to changes in spectral composition occurring over twilight and that this input dictates their response to changes in irradiance. Finally, using mice housed under photoperiods with simulated dawn/dusk transitions, we confirm that spectral changes occurring during twilight are required for appropriate circadian alignment under natural conditions. Together, these data reveal a new sensory mechanism for telling time of day that would be available to any mammalian species capable of chromatic vision.

  9. Mammalian designer cells: Engineering principles and biomedical applications.

    Science.gov (United States)

    Xie, Mingqi; Fussenegger, Martin

    2015-07-01

    Biotechnology is a widely interdisciplinary field focusing on the use of living cells or organisms to solve established problems in medicine, food production and agriculture. Synthetic biology, the science of engineering complex biological systems that do not exist in nature, continues to provide the biotechnology industry with tools, technologies and intellectual property leading to improved cellular performance. One key aspect of synthetic biology is the engineering of deliberately reprogrammed designer cells whose behavior can be controlled over time and space. This review discusses the most commonly used techniques to engineer mammalian designer cells; while control elements acting on the transcriptional and translational levels of target gene expression determine the kinetic and dynamic profiles, coupling them to a variety of extracellular stimuli permits their remote control with user-defined trigger signals. Designer mammalian cells with novel or improved biological functions not only directly improve the production efficiency during biopharmaceutical manufacturing but also open the door for cell-based treatment strategies in molecular and translational medicine. In the future, the rational combination of multiple sets of designer cells could permit the construction and regulation of higher-order systems with increased complexity, thereby enabling the molecular reprogramming of tissues, organisms or even populations with highest precision. PMID:26010998

  10. cDNA expression cloning in mammalian cells.

    Science.gov (United States)

    Hoffman, B J

    2001-05-01

    This unit contains protocols for expression cloning in mammalian cells. Either calcium phosphate- or liposome-mediated transfection of mammalian cells, or virus infection and liposome-mediated transfection are used to screen pools derived from a cDNA library. cDNA pools are prepared for cloning from library-transformed E. coli grown in liquid culture medium or on antibiotic-containing selection plates. Results of screening assays for expression can be detected using autoradiography of dishes of cultured cells to identify clones, direct visualization of radiolabeled cells on emulsion-coated and developed chamber slides, detection and quantification of gene activity by a functional (transport) assay with scintillation counting, or detection using a filter-based assay for binding of radioligand to membranes or whole cells. The most critical step of any cDNA cloning project is the establishment of the screening protocol. Therefore, the bioassay for the gene product must be established prior to executing any of these protocols, including construction of the cDNA library. PMID:18428491

  11. Stochastic mRNA synthesis in mammalian cells.

    Science.gov (United States)

    Raj, Arjun; Peskin, Charles S; Tranchina, Daniel; Vargas, Diana Y; Tyagi, Sanjay

    2006-10-01

    Individual cells in genetically homogeneous populations have been found to express different numbers of molecules of specific proteins. We investigated the origins of these variations in mammalian cells by counting individual molecules of mRNA produced from a reporter gene that was stably integrated into the cell's genome. We found that there are massive variations in the number of mRNA molecules present in each cell. These variations occur because mRNAs are synthesized in short but intense bursts of transcription beginning when the gene transitions from an inactive to an active state and ending when they transition back to the inactive state. We show that these transitions are intrinsically random and not due to global, extrinsic factors such as the levels of transcriptional activators. Moreover, the gene activation causes burst-like expression of all genes within a wider genomic locus. We further found that bursts are also exhibited in the synthesis of natural genes. The bursts of mRNA expression can be buffered at the protein level by slow protein degradation rates. A stochastic model of gene activation and inactivation was developed to explain the statistical properties of the bursts. The model showed that increasing the level of transcription factors increases the average size of the bursts rather than their frequency. These results demonstrate that gene expression in mammalian cells is subject to large, intrinsically random fluctuations and raise questions about how cells are able to function in the face of such noise. PMID:17048983

  12. Loss of the mammalian DREAM complex deregulates chondrocyte proliferation.

    Science.gov (United States)

    Forristal, Chantal; Henley, Shauna A; MacDonald, James I; Bush, Jason R; Ort, Carley; Passos, Daniel T; Talluri, Srikanth; Ishak, Charles A; Thwaites, Michael J; Norley, Chris J; Litovchick, Larisa; DeCaprio, James A; DiMattia, Gabriel; Holdsworth, David W; Beier, Frank; Dick, Frederick A

    2014-06-01

    Mammalian DREAM is a conserved protein complex that functions in cellular quiescence. DREAM contains an E2F, a retinoblastoma (RB)-family protein, and the MuvB core (LIN9, LIN37, LIN52, LIN54, and RBBP4). In mammals, MuvB can alternatively bind to BMYB to form a complex that promotes mitotic gene expression. Because BMYB-MuvB is essential for proliferation, loss-of-function approaches to study MuvB have generated limited insight into DREAM function. Here, we report a gene-targeted mouse model that is uniquely deficient for DREAM complex assembly. We have targeted p107 (Rbl1) to prevent MuvB binding and combined it with deficiency for p130 (Rbl2). Our data demonstrate that cells from these mice preferentially assemble BMYB-MuvB complexes and fail to repress transcription. DREAM-deficient mice show defects in endochondral bone formation and die shortly after birth. Micro-computed tomography and histology demonstrate that in the absence of DREAM, chondrocytes fail to arrest proliferation. Since DREAM requires DYRK1A (dual-specificity tyrosine phosphorylation-regulated protein kinase 1A) phosphorylation of LIN52 for assembly, we utilized an embryonic bone culture system and pharmacologic inhibition of (DYRK) kinase to demonstrate a similar defect in endochondral bone growth. This reveals that assembly of mammalian DREAM is required to induce cell cycle exit in chondrocytes. PMID:24710275

  13. Loss of the Mammalian DREAM Complex Deregulates Chondrocyte Proliferation

    Science.gov (United States)

    Forristal, Chantal; Henley, Shauna A.; MacDonald, James I.; Bush, Jason R.; Ort, Carley; Passos, Daniel T.; Talluri, Srikanth; Ishak, Charles A.; Thwaites, Michael J.; Norley, Chris J.; Litovchick, Larisa; DeCaprio, James A.; DiMattia, Gabriel; Holdsworth, David W.; Beier, Frank

    2014-01-01

    Mammalian DREAM is a conserved protein complex that functions in cellular quiescence. DREAM contains an E2F, a retinoblastoma (RB)-family protein, and the MuvB core (LIN9, LIN37, LIN52, LIN54, and RBBP4). In mammals, MuvB can alternatively bind to BMYB to form a complex that promotes mitotic gene expression. Because BMYB-MuvB is essential for proliferation, loss-of-function approaches to study MuvB have generated limited insight into DREAM function. Here, we report a gene-targeted mouse model that is uniquely deficient for DREAM complex assembly. We have targeted p107 (Rbl1) to prevent MuvB binding and combined it with deficiency for p130 (Rbl2). Our data demonstrate that cells from these mice preferentially assemble BMYB-MuvB complexes and fail to repress transcription. DREAM-deficient mice show defects in endochondral bone formation and die shortly after birth. Micro-computed tomography and histology demonstrate that in the absence of DREAM, chondrocytes fail to arrest proliferation. Since DREAM requires DYRK1A (dual-specificity tyrosine phosphorylation-regulated protein kinase 1A) phosphorylation of LIN52 for assembly, we utilized an embryonic bone culture system and pharmacologic inhibition of (DYRK) kinase to demonstrate a similar defect in endochondral bone growth. This reveals that assembly of mammalian DREAM is required to induce cell cycle exit in chondrocytes. PMID:24710275

  14. Identification of chikungunya virus interacting proteins in mammalian cells

    Indian Academy of Sciences (India)

    Mandar S Paingankar; Vidya A Arankalle

    2014-06-01

    Identification and characterization of virus host interactions is an essential step for the development of novel antiviral strategies. Very few studies have been targeted towards identification of chikungunya virus (CHIKV) interacting host proteins. In current study, virus overlay protein binding assay (VOPBA) and matrix-assisted laser desorption/ionization time of flight analysis (MALDI TOF/TOF) were employed for the identification of CHIKV binding proteins in mammalian cells. HSP70 and actin were identified as virus binding proteins in HEK-293T and Vero-E6 cells, whereas STAT-2 was identified as an additional protein in Vero-E6 cells. Pre-incubation with anti-HSP70 antibody and miRNA silencing of HSP70 significantly reduced the CHIKV production in HEK-293T and Vero-E6 cells at early time points. These results suggest that CHIKV exploits the housekeeping molecules such as actin, HSP70 and STAT-2 to establish infection in the mammalian cells.

  15. Carbamazepine induces mitotic arrest in mammalian Vero cells

    Energy Technology Data Exchange (ETDEWEB)

    Perez Martin, J.M.; Fernandez Freire, P.; Labrador, V. [Departamento de Biologia, Facultad de Ciencias, Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain); Hazen, M.J. [Departamento de Biologia, Facultad de Ciencias, Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain)], E-mail: mariajose.hazen@uam.es

    2008-01-01

    We reported recently that the anticonvulsant drug carbamazepine, at supratherapeutic concentrations, exerts antiproliferative effects in mammalian Vero cells, but the underlying mechanism has not been elucidated. This motivates us to examine rigorously whether growth arrest was associated with structural changes in cellular organization during mitosis. In the present work, we found that exposure of the cells to carbamazepine led to an increase in mitotic index, mainly due to the sustained block at the metaphase/anaphase boundary, with the consequent inhibition of cell proliferation. Indirect immunofluorescence, using antibodies directed against spindle apparatus proteins, revealed that mitotic arrest was associated with formation of monopolar spindles, caused by impairment of centrosome separation. The final consequence of the spindle defects induced by carbamazepine, depended on the duration of cell cycle arrest. Following the time course of accumulation of metaphase and apoptotic cells during carbamazepine treatments, we observed a causative relationship between mitotic arrest and induction of cell death. Conversely, cells released from the block of metaphase by removal of the drug, continued to progress through mitosis and resume normal proliferation. Our results show that carbamazepine shares a common antiproliferative mechanism with spindle-targeted drugs and contribute to a better understanding of the cytostatic activity previously described in Vero cells. Additional studies are in progress to extend these initial findings that define a novel mode of action of carbamazepine in cultured mammalian cells.

  16. A genetic time-delay circuitry in mammalian cells.

    Science.gov (United States)

    Weber, Wilfried; Kramer, Beat P; Fussenegger, Martin

    2007-11-01

    Gene expression circuitries with time-delayed expression profiles regulate key events, such as oscillating systems, noise elimination, and coordinated multi-step processes, in all organisms from bacteria to mammalian cells. We present the rational synthesis of a genetic circuit displaying time-delayed expression in silico and in mammalian cells. The network is based on a time-delay circuit, where the tetracycline-responsive transactivator (tTA) induces expression of the pristinamycin-responsive repressor PIP-KRAB, which silences expression of the terminal human placental secreted alkaline phosphatase (SEAP). While the addition of pristinamycin I inactivates PIP-KRAB and results in the immediate resumption of SEAP expression, addition of tetracycline abolishes PIP-KRAB synthesis. Consequently, SEAP production remains repressed until the PIP-KRAB buffer in the cell is eliminated. We characterized in silico and in vivo the time-delayed expression properties and analyzed the impact of the size and stability of the PIP-KRAB buffer on fine-tuning of the response kinetics. This tunable time-delay circuitry represents a biologic building block for emulating a fundamental circuit topology in integrated artificial synthetic gene networks for the design of tailor-made cell types and organisms. PMID:17461420

  17. Garcinielliptone FC: antiparasitic activity without cytotoxicity to mammalian cells.

    Science.gov (United States)

    Silva, Ana P; Silva, Marcos P; Oliveira, Cristiano G; Monteiro, Daniela C; Pinto, Pedro L; Mendonça, Ronaldo Z; Costa Júnior, Joaquim S; Freitas, Rivelilson M; de Moraes, Josué

    2015-06-01

    Garcinielliptone FC (GFC) is a natural prenylated benzophenone found in the seeds of Platonia insignis Mart. (Clusiaceae), a native Brazilian plant. It has been chemically characterized and it is known that GFC has several biological activities such as antioxidant and vasorelaxant properties. In this study, we report the in vitro effect of GFC against the blood fluke Schistosoma mansoni, the parasite responsible for schistosomiasis mansoni. The anti-S. mansoni activity and cytotoxicity toward mammalian cells were determined for the compound. GFC⩾6.25 μM showed antischistosomal activity and confocal laser scanning microscopy analysis demonstrated several morphological alterations on the tegument of worms, and a correlation between viability and tegumental damage was observed. In addition, at sub-lethal concentrations of GFC (⩽3.125 μM), the number of S. mansoni eggs was reduced. More importantly, GFC exhibited no activity toward mammalian cells and, therefore, there is an appreciable selectivity of this compound against the helminths. In conclusion, these findings indicate the potential of GFC as an antiparasitic agent. PMID:25553916

  18. Secondary instabilities modulate cortical complexity in the mammalian brain

    Science.gov (United States)

    Budday, Silvia; Steinmann, Paul; Kuhl, Ellen

    2015-10-01

    Disclosing the origin of convolutions in the mammalian brain remains a scientific challenge. Primary folds form before we are born: they are static, well defined and highly preserved across individuals. Secondary folds occur and disappear throughout our entire lifetime: they are dynamic, irregular and highly variable among individuals. While extensive research has improved our understanding of primary folding in the mammalian brain, secondary folding remains understudied and poorly understood. Here, we show that secondary instabilities can explain the increasing complexity of our brain surface as we age. Using the nonlinear field theories of mechanics supplemented by the theory of finite growth, we explore the critical conditions for secondary instabilities. We show that with continuing growth, our brain surface continues to bifurcate into increasingly complex morphologies. Our results suggest that even small geometric variations can have a significant impact on surface morphogenesis. Secondary bifurcations, and with them morphological changes during childhood and adolescence, are closely associated with the formation and loss of neuronal connections. Understanding the correlation between neuronal connectivity, cortical thickness, surface morphology and ultimately behaviour, could have important implications on the diagnostics, classification and treatment of neurological disorders.

  19. MCM9 Is Required for Mammalian DNA Mismatch Repair.

    Science.gov (United States)

    Traver, Sabine; Coulombe, Philippe; Peiffer, Isabelle; Hutchins, James R A; Kitzmann, Magali; Latreille, Daniel; Méchali, Marcel

    2015-09-01

    DNA mismatch repair (MMR) is an evolutionarily conserved process that corrects DNA polymerase errors during replication to maintain genomic integrity. In E. coli, the DNA helicase UvrD is implicated in MMR, yet an analogous helicase activity has not been identified in eukaryotes. Here, we show that mammalian MCM9, a protein involved in replication and homologous recombination, forms a complex with MMR initiation proteins (MSH2, MSH3, MLH1, PMS1, and the clamp loader RFC) and is essential for MMR. Mcm9-/- cells display microsatellite instability and MMR deficiency. The MCM9 complex has a helicase activity that is required for efficient MMR since wild-type but not helicase-dead MCM9 restores MMR activity in Mcm9-/- cells. Moreover, MCM9 loading onto chromatin is MSH2-dependent, and in turn MCM9 stimulates the recruitment of MLH1 to chromatin. Our results reveal a role for MCM9 and its helicase activity in mammalian MMR. PMID:26300262

  20. Development of a monoclonal antibody specific to cooked mammalian meats.

    Science.gov (United States)

    Hsieh, Y H; Sheu, S C; Bridgman, R C

    1998-04-01

    Detection of species adulteration in ground meat products is important for consumer protection and food-labeling law enforcement. This study was conducted to develop monoclonal antibodies (MAbs) that can be used in an enzyme-linked immunosorbent assay (ELISA) for rapid detection of any cooked mammalian meats in cooked poultry products. Soluble muscle proteins extracted from cooked pork (heated at 100 degrees C for 15 min) were used as the antigen to immunized mice for developing the MAb. One that was developed, MAb 2F8 (IgG2b class), strongly reacted with cooked meat of five mammalian species (beef cattle, hogs, sheep, horse, and deer) but did not react with any cooked poultry (chicken, turkey, and duck) or raw meats. At least 0.5% by weight of pork, beef, lamb, and horse meats in a chicken-based mixture could not detect using the indirect ELISA with MAb 2F8. The MAb 2F8 is useful in a single initial screening test to detect the presence of five nonpoultry meat adulterants in cooked poultry products. PMID:9709213

  1. Radioimmunoassay for mammalian type C viral reverse transcriptase

    International Nuclear Information System (INIS)

    Radioimmunological techniques were applied to the analysis of reverse transcriptases of mammalian type C RNA viruses. The polymerase of Rauscher mouse leukemia virus was purified by ion exchange and sequential affinity chromatography. Radioimmunoassays that utilized the viral enzyme as a probe detected as little as 1 ng of purified polymerase. No cross-reactivity could be demonstrated between the reverse transcriptase and other known virus-coded proteins. By comparing the immunological reactivity of the purified enzyme with the reactivity of detergent-disrupted virions, Rauscher mouse leukemia virus was shown to contain the antigenic equivalent of 40 molecules of reverse transcriptase. In a homologous competition immunoassay, the Rauscher viral enzyme demonstrated type-specific antigenic determinants, which distinguish it from other mouse type C viral polymerases. In a broadly reactive interspecies immunoassay, the reverse transcriptases of a number of mammalian type C viruses were cross-reactive, indicating their shared antigenic determinants. Various treatments that inhibited or inactivated DNA polymerase activity had little or no effect on the immunological properties of the enzyme. Thus, radioimmunoassays should be useful in the search for type C viral reverse transcriptase as a marker of subviral expression

  2. Mechanisms Underlying Mammalian Hybrid Sterility in Two Feline Interspecies Models.

    Science.gov (United States)

    Davis, Brian W; Seabury, Christopher M; Brashear, Wesley A; Li, Gang; Roelke-Parker, Melody; Murphy, William J

    2015-10-01

    The phenomenon of male sterility in interspecies hybrids has been observed for over a century, however, few genes influencing this recurrent phenotype have been identified. Genetic investigations have been primarily limited to a small number of model organisms, thus limiting our understanding of the underlying molecular basis of this well-documented "rule of speciation." We utilized two interspecies hybrid cat breeds in a genome-wide association study employing the Illumina 63 K single-nucleotide polymorphism array. Collectively, we identified eight autosomal genes/gene regions underlying associations with hybrid male sterility (HMS) involved in the function of the blood-testis barrier, gamete structural development, and transcriptional regulation. We also identified several candidate hybrid sterility regions on the X chromosome, with most residing in close proximity to complex duplicated regions. Differential gene expression analyses revealed significant chromosome-wide upregulation of X chromosome transcripts in testes of sterile hybrids, which were enriched for genes involved in chromatin regulation of gene expression. Our expression results parallel those reported in Mus hybrids, supporting the "Large X-Effect" in mammalian HMS and the potential epigenetic basis for this phenomenon. These results support the value of the interspecies feline model as a powerful tool for comparison to rodent models of HMS, demonstrating unique aspects and potential commonalities that underpin mammalian reproductive isolation. PMID:26006188

  3. Autosomal location of genes from the conserved mammalian X in the platypus (Ornithorhynchus anatinus): implications for mammalian sex chromosome evolution.

    Science.gov (United States)

    Waters, Paul D; Delbridge, Margaret L; Deakin, Janine E; El-Mogharbel, Nisrine; Kirby, Patrick J; Carvalho-Silva, Denise R; Graves, Jennifer A Marshall

    2005-01-01

    Mammalian sex chromosomes evolved from an ancient autosomal pair. Mapping of human X- and Y-borne genes in distantly related mammals and non-mammalian vertebrates has proved valuable to help deduce the evolution of this unique part of the genome. The platypus, a monotreme mammal distantly related to eutherians and marsupials, has an extraordinary sex chromosome system comprising five X and five Y chromosomes that form a translocation chain at male meiosis. The largest X chromosome (X1), which lies at one end of the chain, has considerable homology to the human X. Using comparative mapping and the emerging chicken database, we demonstrate that part of the therian X chromosome, previously thought to be conserved across all mammals, was lost from the platypus X1 to an autosome. This region included genes flanking the XIST locus, and also genes with Y-linked homologues that are important to male reproduction in therians. Since these genes lie on the X in marsupials and eutherians, and also on the homologous region of chicken chromosome 4, this represents a loss from the monotreme X rather than an additional evolutionary stratum of the human X. PMID:15973504

  4. The mammalian PYHIN gene family: Phylogeny, evolution and expression

    Directory of Open Access Journals (Sweden)

    Cridland Jasmyn A

    2012-08-01

    Full Text Available Abstract Background Proteins of the mammalian PYHIN (IFI200/HIN-200 family are involved in defence against infection through recognition of foreign DNA. The family member absent in melanoma 2 (AIM2 binds cytosolic DNA via its HIN domain and initiates inflammasome formation via its pyrin domain. AIM2 lies within a cluster of related genes, many of which are uncharacterised in mouse. To better understand the evolution, orthology and function of these genes, we have documented the range of PYHIN genes present in representative mammalian species, and undertaken phylogenetic and expression analyses. Results No PYHIN genes are evident in non-mammals or monotremes, with a single member found in each of three marsupial genomes. Placental mammals show variable family expansions, from one gene in cow to four in human and 14 in mouse. A single HIN domain appears to have evolved in the common ancestor of marsupials and placental mammals, and duplicated to give rise to three distinct forms (HIN-A, -B and -C in the placental mammal ancestor. Phylogenetic analyses showed that AIM2 HIN-C and pyrin domains clearly diverge from the rest of the family, and it is the only PYHIN protein with orthology across many species. Interestingly, although AIM2 is important in defence against some bacteria and viruses in mice, AIM2 is a pseudogene in cow, sheep, llama, dolphin, dog and elephant. The other 13 mouse genes have arisen by duplication and rearrangement within the lineage, which has allowed some diversification in expression patterns. Conclusions The role of AIM2 in forming the inflammasome is relatively well understood, but molecular interactions of other PYHIN proteins involved in defence against foreign DNA remain to be defined. The non-AIM2 PYHIN protein sequences are very distinct from AIM2, suggesting they vary in effector mechanism in response to foreign DNA, and may bind different DNA structures. The PYHIN family has highly varied gene composition between

  5. Quantum Mechanics, Pattern Recognition, and the Mammalian Brain

    Science.gov (United States)

    Chapline, George

    2008-10-01

    Although the usual way of representing Markov processes is time asymmetric, there is a way of describing Markov processes, due to Schrodinger, which is time symmetric. This observation provides a link between quantum mechanics and the layered Bayesian networks that are often used in automated pattern recognition systems. In particular, there is a striking formal similarity between quantum mechanics and a particular type of Bayesian network, the Helmholtz machine, which provides a plausible model for how the mammalian brain recognizes important environmental situations. One interesting aspect of this relationship is that the "wake-sleep" algorithm for training a Helmholtz machine is very similar to the problem of finding the potential for the multi-channel Schrodinger equation. As a practical application of this insight it may be possible to use inverse scattering techniques to study the relationship between human brain wave patterns, pattern recognition, and learning. We also comment on whether there is a relationship between quantum measurements and consciousness.

  6. Effects of exposure to electromagnetic fields (microwaves) on mammalian pregnancy

    International Nuclear Information System (INIS)

    Women soldiers account now for nearly 10 % of the NATO forces. Some studies have alleged that exposure to microwaves may result in pregnancy mishaps. We have tried to assess what was the risk. A lot of studies were conducted on non mammalian species: birds, sea urchins, worms and insects. Extrapolation to the mammals is subject to caution due to the protective effect of intrauterine development. We reviewed the literature dealing only with mammals. Even if some discrepancy persists, it seems that the presence or the absence of thermic effect is essential in order to estimate the risk. Reduced birth weight and increased rate of miscarriage were the most common findings when the exposure reached a thermic effect. In the majority of the studies, non thermic exposure had no impact on pregnancy outcome. (authors)

  7. Interactions of cryptosin with mammalian cardiac beta-adrenoceptors

    International Nuclear Information System (INIS)

    Cryptosin - a new cardenolide from the leaves of Cryptolepis buchanani R ampersand S was found to be a potent positive inotropic agent. In experiments with dog heart ex vivo, the rise in the cardiac rate associated with an increase in dP/dtmax and left ventricular pressure (LVP) correlated with changes in the beta-adrenoceptor densities as measured by the binding of 3H-Dihydroalprenolol (DHA). A significant change in the beta-adrenoceptor densities was observed when cryptosin was incubated with guinea pig and dog heart sarcolemmal membranes in vitro. Analysis of the binding of 3H-DHA in post-cryptosin treated membranes indicated a non-specific type of interaction of cryptosin with mammalian cardiac beta-adrenoceptors

  8. Crystal structure of the mammalian Grb2 adaptor.

    Science.gov (United States)

    Maignan, S; Guilloteau, J P; Fromage, N; Arnoux, B; Becquart, J; Ducruix, A

    1995-04-14

    The mammalian growth factor receptor-binding protein Grb2 is an adaptor that mediates activation of guanine nucleotide exchange on Ras. Grb2 binds to the receptor through its SH2 domain and to the carboxyl-terminal domain of Son of sevenless through its two SH3 domains. It is thus a key element in the signal transduction pathway. The crystal structure of Grb2 was determined to 3.1 angstrom resolution. The asymmetric unit is composed of an embedded dimer. The interlaced junctions between the SH2 and SH3 domains bring the two adjacent faces of the SH3 domains in van der Waals contact but leave room for the binding of proline-rich peptides. PMID:7716522

  9. Retinoic Acid Stimulates Regeneration of Mammalian Auditory Hair Cells

    Science.gov (United States)

    Lefebvre, Philippe P.; Malgrange, Brigitte; Staecker, Hinrich; Moonen, Gustave; van de Water, Thomas R.

    1993-04-01

    Sensorineural hearing loss resulting from the loss of auditory hair cells is thought to be irreversible in mammals. This study provides evidence that retinoic acid can stimulate the regeneration in vitro of mammalian auditory hair cells in ototoxic-poisoned organ of Corti explants in the rat. In contrast, treatment with retinoic acid does not stimulate the formation of extra hair cells in control cultures of Corti's organ. Retinoic acid-stimulated hair cell regeneration can be blocked by cytosine arabinoside, which suggests that a period of mitosis is required for the regeneration of auditory hair cells in this system. These results provide hope for a recovery of hearing function in mammals after auditory hair cell damage.

  10. Differential requirements for actin during yeast and mammalian endocytosis.

    Science.gov (United States)

    Aghamohammadzadeh, Soheil; Ayscough, Kathryn R

    2009-08-01

    Key features of clathrin-mediated endocytosis have been conserved across evolution. However, endocytosis in Saccharomyces cerevisiae is completely dependent on a functional actin cytoskeleton, whereas actin appears to be less critical in mammalian cell endocytosis. We reveal that the fundamental requirement for actin in the early stages of yeast endocytosis is to provide a strong framework to support the force generation needed to direct the invaginating plasma membrane into the cell against turgor pressure. By providing osmotic support, pressure differences across the plasma membrane were removed and this reduced the requirement for actin-bundling proteins in normal endocytosis. Conversely, increased turgor pressure in specific yeast mutants correlated with a decreased rate of endocytic patch invagination. PMID:19597484

  11. Pedigree analysis of proliferation kinetics in cultured mammalian cells

    International Nuclear Information System (INIS)

    Quantitative analysis of proliferation kinetics in cultured mammalian cells was given an outline by extremely low speed photography (pedigree method). Photographing method of this analysis, camera used in this analysis, cultivation method and apparatus for cultivation, and film analysis were explained. As to changes of generation time by this analysis, relationship of each stage of cell cycle to colony formation or to proliferation capacity were explained in non-irradiated cells and irradiated cells. On abnormal cell division in time of large dose irradiation, a condition from cell fusion to cell death via multipolar division was explained. Mechanisms of proliferation death and interphase death were explained by analysis of pedigree data on radiation injuries in time of division and by mentioning division probability. Some information about inhibition of cell proliferation by radiation and lethal effect of radiation was described. (Kanao, N.)

  12. Presence of abscisic acid, a phytohormone, in the mammalian brain

    International Nuclear Information System (INIS)

    This paper reports the presence of abscisic acid, one of the most important phytohormones, in the central nervous system of pigs and rats. The identification of this hormone in brain was made after extensive purification by using a radioimmunoassay that is very specific for (+)-cis-abscisic acid. The final product of purification from mammalian brain has the same properties as authentic abscisic acid: it crossreacts in the radioimmunoassay for the phytohormone and it has the same retention properties and the same gas chromatography/mass spectrometry characteristics. Moreover, like (+)-cis-abscisic acid itself, the brain factor inhibits stomatal apertures of abaxial epidermis strips of Setcreasea purpurea Boom (Commelinaceae). The presence of abscisic acid conjugates that are present in plants has also been identified in brain

  13. Presence of abscisic acid, a phytohormone, in the mammalian brain

    Energy Technology Data Exchange (ETDEWEB)

    Le Page-Degivry, M.T.; Bidard, J.N.; Rouvier, E.; Bulard, C.; Lazdunski, M.

    1986-02-01

    This paper reports the presence of abscisic acid, one of the most important phytohormones, in the central nervous system of pigs and rats. The identification of this hormone in brain was made after extensive purification by using a radioimmunoassay that is very specific for (+)-cis-abscisic acid. The final product of purification from mammalian brain has the same properties as authentic abscisic acid: it crossreacts in the radioimmunoassay for the phytohormone and it has the same retention properties and the same gas chromatography/mass spectrometry characteristics. Moreover, like (+)-cis-abscisic acid itself, the brain factor inhibits stomatal apertures of abaxial epidermis strips of Setcreasea purpurea Boom (Commelinaceae). The presence of abscisic acid conjugates that are present in plants has also been identified in brain.

  14. Mammalian target of rapamycin inhibitors for treatment in tuberous sclerosis

    Directory of Open Access Journals (Sweden)

    Won Seop Kim

    2013-06-01

    Full Text Available Korean J Pediatr 2011;54:241-5. &lt;a href='http://dx.doi.org/10.3345/kjp.2011.54.6.241'&gt;http://dx.doi.org/10.3345/kjp.2011.54.6.241&lt;/a&gt;. PMID: 21949518 [PubMed] &lt;div style="border-top:1px solid #0092C8"&gt;&lt;/div&gt; The following article&lt;sup&gt;1&lt;/sup&gt; is being retracted as a part of the manuscript was plagiarized. Yeong-Ho Rha, MD, PhD Editor-in-Chief, Korean J Pediatr 1.Kim WS. Mammalian target of rapamycin inhibitors for treatment in tuberous sclerosis. Korean J Pediatr 2011;54:241-5.

  15. Mottled Mice and Non-Mammalian Models of Menkes Disease

    DEFF Research Database (Denmark)

    Lenartowicz, Małgorzata; Krzeptowski, Wojciech; Lipiński, Paweł;

    2015-01-01

    Menkes disease is a multi-systemic copper metabolism disorder caused by mutations in the X-linked ATP7A gene and characterized by progressive neurodegeneration and severe connective tissue defects. The ATP7A protein is a copper (Cu)-transporting ATPase expressed in all tissues and plays a critical...... synaptogenesis and axonal development. In cells, ATP7A participates in the incorporation of copper into Cu-dependent enzymes during the course of its maturation in the secretory pathway. There is a high degree of homology (>80%) between the human ATP7A and murine Atp7a genes. Mice with mutations in the Atp7a......-mammalian models of Menkes disease, Drosophila melanogaster and Danio rerio mutants were used in experiments which would be technically difficult to carry out in mammals....

  16. Genetic variability, individuality and the evolution of the mammalian brain.

    Science.gov (United States)

    Lipp, H P

    1995-12-01

    The neo-Darwinian theory of evolution has difficulty in explaining the rapid evolution of mammalian brain and behavior. I shall argue that the plasticity mechanisms of the brain (i.e., system homeostasis, developmental reorganization, structural adult plasticity, and cognition and learning) have evolved primarily as genetic buffer systems which protect subtle mutations influencing brain structures from natural selection. These buffer systems permit accumulation of genetic variation in the higher system levels of the brain (simply defined as structures with late differentiation), while low-level systems are kept constant by natural selection. The organization of this intrinsic genetic buffering system provides several features facilitating neo-Darwinian evolution: In conclusion, the evolutionary appearance of cognition and intelligence is an ordinary biological mechanism compensating evolutionary drags such as long lifespans and fewer offspring. The concept has heuristic value for identifying gene-brain-behavior relationships and for explaining behavioral consequences of artifical gene deletions. PMID:24896017

  17. Mammalian cell viability in electrospun composite nanofiber structures.

    Science.gov (United States)

    Canbolat, Mehmet Fatih; Tang, Christina; Bernacki, Susan H; Pourdeyhimi, Behnam; Khan, Saad

    2011-10-10

    Incorporation of mammalian cells into nanofibers (cell electrospinning) and multilayered cell-nanofiber structures (cell layering) via electrospinning are promising techniques for tissue engineering applications. We investigate the viability of 3T3-L1 mouse fibroblasts after incorporation into poly(vinyl alcohol) nanofibers and multilayering with poly(caprolactone) nanofibers and analyze the possible factors that affect cell viability. We observe that cells do not survive cell electrospinning but survive cell layering. Assessing the factors involved in cell electrospinning, we find that dehydration and fiber stretching are the main causes of cell death. In cell layering, the choice of solvent is critical, as residual solvent in the electrospun fibers could be detrimental to the cells. PMID:21984502

  18. Possible detection of mammalian metallothionein in higher plant tissue

    International Nuclear Information System (INIS)

    Metallothionein (MT) is a low molecular weight, cysteine rick, heavy metal binding protein found in animals, Neurospora and fusion yeast but not in fission yeast or higher plants so far. Recently, however, it has been reported that wheat-germ Ec protein may be a Zn containing MT. The present paper provides some evidence showing that higher plants produce MT similar to rat MT under either heavy metal stress or normal conditions by RIA and SDS-PAGE of proteins extracted from plant tissues. It was also found that wheat germ did not contain this MT. Moreover, this plant-produced MT was confirmed by studying the immunohistochemistry of MT through an indirect immunoperoxidase technique using antibody of rat MT. The intense immuno-stain of MT was detected in the specific location of normal legume plant tissue whereas wheat-germ showed a negative staining. These results suggest possibly higher plants produce mammalian MT

  19. Mammalian mitogenomic relationships and the root of the eutherian tree.

    Science.gov (United States)

    Arnason, Ulfur; Adegoke, Joseph A; Bodin, Kristina; Born, Erik W; Esa, Yuzine B; Gullberg, Anette; Nilsson, Maria; Short, Roger V; Xu, Xiufeng; Janke, Axel

    2002-06-11

    The strict orthology of mitochondrial (mt) coding sequences has promoted their use in phylogenetic analyses at different levels. Here we present the results of a mitogenomic study (i.e., analysis based on the set of protein-coding genes from complete mt genomes) of 60 mammalian species. This number includes 11 new mt genomes. The sampling comprises all but one of the traditional eutherian orders. The previously unrepresented order Dermoptera (flying lemurs) fell within Primates as the sister group of Anthropoidea, making Primates paraphyletic. This relationship was strongly supported. Lipotyphla ("insectivores") split into three distinct lineages: Erinaceomorpha, Tenrecomorpha, and Soricomorpha. Erinaceomorpha was the basal eutherian lineage. Sirenia (dugong) and Macroscelidea (elephant shrew) fell within the African clade. Pholidota (pangolin) joined the Cetferungulata as the sister group of Carnivora. The analyses identified monophyletic Pinnipedia with Otariidae (sea lions, fur seals) and Odobenidae (walruses) as sister groups to the exclusion of Phocidae (true seals). PMID:12034869

  20. Computing in mammalian cells with nucleic acid strand exchange

    Science.gov (United States)

    Groves, Benjamin; Chen, Yuan-Jyue; Zurla, Chiara; Pochekailov, Sergii; Kirschman, Jonathan L.; Santangelo, Philip J.; Seelig, Georg

    2016-03-01

    DNA strand displacement has been widely used for the design of molecular circuits, motors, and sensors in cell-free settings. Recently, it has been shown that this technology can also operate in biological environments, but capabilities remain limited. Here, we look to adapt strand displacement and exchange reactions to mammalian cells and report DNA circuitry that can directly interact with a native mRNA. We began by optimizing the cellular performance of fluorescent reporters based on four-way strand exchange reactions and identified robust design principles by systematically varying the molecular structure, chemistry and delivery method. Next, we developed and tested AND and OR logic gates based on four-way strand exchange, demonstrating the feasibility of multi-input logic. Finally, we established that functional siRNA could be activated through strand exchange, and used native mRNA as programmable scaffolds for co-localizing gates and visualizing their operation with subcellular resolution.

  1. Transport of an intact oligopeptide across adult mammalian jejunum

    Energy Technology Data Exchange (ETDEWEB)

    Takaori, K.; Burton, J.; Donowitz, M.

    1986-06-13

    The passage of an intact nonapeptide across adult rabbit jejunum mounted in an Ussing Chamber is demonstrated with an HPLC system which resolves the renin inhibitor Pro-His-Pro-Phe-His-Leu-Phe-Val-(/sup 3/H)Phe from all labelled proteolytic cleavage products. Permeability of the peptide (0.016 cm hr/sup -1/) is approximately one-seventh that observed for the actively transported 3-9-methyl glucose (0.104 cm hr/sup -1/). Flux of the peptide is not changed by the absence of sodium. This study shows that adult mammalian intestine can transport intact oligopeptides and suggests that it will be feasible to develop orally active peptide drugs.

  2. Noncoding RNAs: Regulators of the Mammalian Transcription Machinery.

    Science.gov (United States)

    Eidem, Tess M; Kugel, Jennifer F; Goodrich, James A

    2016-06-19

    Transcription by RNA polymerase II (Pol II) is required to produce mRNAs and some noncoding RNAs (ncRNAs) within mammalian cells. This coordinated process is precisely regulated by multiple factors, including many recently discovered ncRNAs. In this perspective, we will discuss newly identified ncRNAs that facilitate DNA looping, regulate transcription factor binding, mediate promoter-proximal pausing of Pol II, and/or interact with Pol II to modulate transcription. Moreover, we will discuss new roles for ncRNAs, as well as a novel Pol II RNA-dependent RNA polymerase activity that regulates an ncRNA inhibitor of transcription. As the multifaceted nature of ncRNAs continues to be revealed, we believe that many more ncRNA species and functions will be discovered. PMID:26920110

  3. Transient transfection of mammalian cells using a violet diode laser

    Science.gov (United States)

    Torres-Mapa, Maria Leilani; Angus, Liselotte; Ploschner, Martin; Dholakia, Kishan; Gunn-Moore, Frank J.

    2010-07-01

    We demonstrate the first use of the violet diode laser for transient mammalian cell transfection. In contrast to previous studies, which showed the generation of stable cell lines over a few weeks, we develop a methodology to transiently transfect cells with an efficiency of up to ~40%. Chinese hamster ovary (CHO-K1) and human embryonic kidney (HEK293) cells are exposed to a tightly focused 405-nm laser in the presence of plasmid DNA encoding for a mitochondrial targeted red fluorescent protein. We report transfection efficiencies as a function of laser power and exposure time for our system. We also show, for the first time, that a continuous wave laser source can be successfully applied to selective gene silencing experiments using small interfering RNA. This work is a major step towards an inexpensive and portable phototransfection system.

  4. A wave dynamics criterion for optimization of mammalian cardiovascular system.

    Science.gov (United States)

    Pahlevan, Niema M; Gharib, Morteza

    2014-05-01

    The cardiovascular system in mammals follows various optimization criteria covering the heart, the vascular network, and the coupling of the two. Through a simple dimensional analysis we arrived at a non-dimensional number (wave condition number) that can predict the optimum wave state in which the left ventricular (LV) pulsatile power (LV workload) is minimized in a mammalian cardiovascular system. This number is also universal among all mammals independent of animal size maintaining a value of around 0.1. By utilizing a unique in vitro model of human aorta, we tested our hypothesis against a wide range of aortic compliance (pulse wave velocity). We concluded that the optimum value of the wave condition number remains to be around 0.1 for a wide range of aorta compliance that we could simulate in our in-vitro system. PMID:24642352

  5. Mammalian comparative sequence analysis of the Agrp locus.

    Directory of Open Access Journals (Sweden)

    Christopher B Kaelin

    Full Text Available Agouti-related protein encodes a neuropeptide that stimulates food intake. Agrp expression in the brain is restricted to neurons in the arcuate nucleus of the hypothalamus and is elevated by states of negative energy balance. The molecular mechanisms underlying Agrp regulation, however, remain poorly defined. Using a combination of transgenic and comparative sequence analysis, we have previously identified a 760 bp conserved region upstream of Agrp which contains STAT binding elements that participate in Agrp transcriptional regulation. In this study, we attempt to improve the specificity for detecting conserved elements in this region by comparing genomic sequences from 10 mammalian species. Our analysis reveals a symmetrical organization of conserved sequences upstream of Agrp, which cluster into two inverted repeat elements. Conserved sequences within these elements suggest a role for homeodomain proteins in the regulation of Agrp and provide additional targets for functional evaluation.

  6. Hematologic syndrome in man modeled from mammalian lethality

    International Nuclear Information System (INIS)

    Data on acute radiation lethality due to failure of the hematologic system in rats, mice, dogs, swine, monkeys and man are analyzed. Based on the available data, the mortality incidences for 1-100% levels can be computed directly if one has only an estimate of the dose lethal to 50% of the population (LD50) for the mammalian strain and radiation environment of interest. The sole restriction is that the dose profile to the marrow be moderately uniform. If an LD50 for any exposure situation has been measured, then one can readily scale to any desired situation through implicit-biological and empirical-physical relationships. The LD50 for man, exposed to an isotropic cloud of photons, and knowledge of the bone-marrow dose profiles readily permit evaluation of the model for other levels of human mortality from different irradiating particles, partial body irradiation and spatially dependent and/or mixed radiation environments. (author)

  7. Methods for the Detection of Autophagy in Mammalian Cells.

    Science.gov (United States)

    Zhang, Ziyan; Singh, Rajat; Aschner, Michael

    2016-01-01

    Macroautophagy (hereafter referred to as autophagy) is a degradation pathway that delivers cytoplasmic materials to lysosomes via double-membraned vesicles designated autophagosomes. Cytoplasmic constituents are sequestered into autophagosomes, which subsequently fuse with lysosomes, where the cargo is degraded. Autophagy is a crucial mechanism involved in many aspects of cell function, including cellular metabolism and energy balance; alterations in autophagy have been linked to various human pathological processes. Thus, methods that accurately measure autophagic activity are necessary. In this unit, we introduce several approaches to analyze autophagy in mammalian cells, including immunoblotting analysis of LC3 and p62, detection of autophagosome formation by fluorescence microscopy, and monitoring autophagosome maturation by tandem mRFP-GFP fluorescence microscopy. Overall, we recommend a combined use of multiple methods to accurately assess the autophagic activity in any given biological setting. © 2016 by John Wiley & Sons, Inc. PMID:27479363

  8. Regulation of mammalian pre-mRNA splicing

    Institute of Scientific and Technical Information of China (English)

    HUI JingYi

    2009-01-01

    In eukaryotes, most protein-coding genes contain introns which are removed by precursor messenger RNA (pre-mRNA) splicing. Alternative splicing is a process by which multiple messenger RNAs (mRNAs) are generated from a single pre-mRNA, resulting in functionally distinct proteins. Recent genome-wide analyses of alternative splicing indicated that in higher eukaryotes alternative splicing is an important mechanism that generates proteomic complexity and regulates gene expression. Mis-regulation of splicing causes a wide range of human diseases. This review describes the current understanding of pre-mRNA splicing and the mechanisms that regulate mammalian pre-mRNA splicing. It also discusses emerging directions in the field of alternative splicing.

  9. Regulation of mammalian pre-mRNA splicing

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    In eukaryotes,most protein-coding genes contain introns which are removed by precursor messenger RNA(pre-mRNA) splicing.Alternative splicing is a process by which multiple messenger RNAs(mRNAs) are generated from a single pre-mRNA,resulting in functionally distinct proteins.Recent genome-wide analyses of alternative splicing indicated that in higher eukaryotes alternative splicing is an important mechanism that generates proteomic complexity and regulates gene expression.Mis-regulation of splicing causes a wide range of human diseases.This review describes the current understanding of pre-mRNA splicing and the mechanisms that regulate mammalian pre-mRNA splicing.It also discusses emerging directions in the field of alternative splicing.

  10. The calming effect of maternal carrying in different mammalian species.

    Science.gov (United States)

    Esposito, Gianluca; Setoh, Peipei; Yoshida, Sachine; Kuroda, Kumi O

    2015-01-01

    Attachment theory postulates that mothers and their infants possess some basic physiological mechanisms that favor their dyadic interaction and bonding. Many studies have focused on the maternal physiological mechanisms that promote attachment (e.g., mothers' automatic responses to infant faces and/or cries), and relatively less have examined infant physiology. Thus, the physiological mechanisms regulating infant bonding behaviors remain largely undefined. This review elucidates some of the neurobiological mechanisms governing social bonding and cooperation in humans by focusing on maternal carrying and its beneficial effect on mother-infant interaction in mammalian species (e.g., in humans, big cats, and rodents). These studies show that infants have a specific calming response to maternal carrying. A human infant carried by his/her walking mother exhibits a rapid heart rate decrease, and immediately stops voluntary movement and crying compared to when he/she is held in a sitting position. Furthermore, strikingly similar responses were identified in mouse rodents, who exhibit immobility, diminished ultra-sonic vocalizations and heart rate. In general, the studies described in the current review demonstrate the calming effect of maternal carrying to be comprised of a complex set of behavioral and physiological components, each of which has a specific postnatal time window and is orchestrated in a well-matched manner with the maturation of the infants. Such reactions could have been evolutionarily adaptive in mammalian mother-infant interactions. The findings have implications for parenting practices in developmentally normal populations. In addition, we propose that infants' physiological response may be useful in clinical assessments as we discuss possible implications on early screening for child psychopathology (e.g., autism spectrum disorders and perinatal brain disorders). PMID:25932017

  11. Short latency compound action potentials from mammalian gravity receptor organs

    Science.gov (United States)

    Jones, T. A.; Jones, S. M.

    1999-01-01

    Gravity receptor function was characterized in four mammalian species using far-field vestibular evoked potentials (VsEPs). VsEPs are compound action potentials of the vestibular nerve and central relays that are elicited by linear acceleration ramps applied to the cranium. Rats, mice, guinea pigs, and gerbils were studied. In all species, response onset occurred within 1.5 ms of the stimulus onset. Responses persisted during intense (116 dBSPL) wide-band (50 to 50 inverted question mark omitted inverted question mark000 Hz) forward masking, whereas auditory responses to intense clicks (112 dBpeSPL) were eliminated under the same conditions. VsEPs remained after cochlear extirpation but were eliminated following bilateral labyrinthectomy. Responses included a series of positive and negative peaks that occurred within 8 ms of stimulus onset (range of means at +6 dBre: 1.0 g/ms: P1=908 to 1062 micros, N1=1342 to 1475 micros, P2=1632 to 1952 micros, N2=2038 to 2387 micros). Mean response amplitudes at +6 dBre: 1.0 g/ms ranged from 0.14 to 0.99 microV. VsEP input/output functions revealed latency slopes that varied across peaks and species ranging from -19 to -51 micros/dB. Amplitude-intensity slopes also varied ranging from 0.04 to 0.08 microV/dB for rats and mice. Latency values were comparable to those of birds although amplitudes were substantially smaller in mammals. VsEP threshold values were considerably higher in mammals compared to birds and ranged from -8.1 to -10.5 dBre 1.0 g/ms across species. These results support the hypothesis that mammalian gravity receptors are less sensitive to dynamic stimuli than are those of birds.

  12. The calming effect of maternal carrying in different mammalian species

    Science.gov (United States)

    Esposito, Gianluca; Setoh, Peipei; Yoshida, Sachine; Kuroda, Kumi O.

    2015-01-01

    Attachment theory postulates that mothers and their infants possess some basic physiological mechanisms that favor their dyadic interaction and bonding. Many studies have focused on the maternal physiological mechanisms that promote attachment (e.g., mothers’ automatic responses to infant faces and/or cries), and relatively less have examined infant physiology. Thus, the physiological mechanisms regulating infant bonding behaviors remain largely undefined. This review elucidates some of the neurobiological mechanisms governing social bonding and cooperation in humans by focusing on maternal carrying and its beneficial effect on mother–infant interaction in mammalian species (e.g., in humans, big cats, and rodents). These studies show that infants have a specific calming response to maternal carrying. A human infant carried by his/her walking mother exhibits a rapid heart rate decrease, and immediately stops voluntary movement and crying compared to when he/she is held in a sitting position. Furthermore, strikingly similar responses were identified in mouse rodents, who exhibit immobility, diminished ultra-sonic vocalizations and heart rate. In general, the studies described in the current review demonstrate the calming effect of maternal carrying to be comprised of a complex set of behavioral and physiological components, each of which has a specific postnatal time window and is orchestrated in a well-matched manner with the maturation of the infants. Such reactions could have been evolutionarily adaptive in mammalian mother–infant interactions. The findings have implications for parenting practices in developmentally normal populations. In addition, we propose that infants’ physiological response may be useful in clinical assessments as we discuss possible implications on early screening for child psychopathology (e.g., autism spectrum disorders and perinatal brain disorders). PMID:25932017

  13. Phylogenetic analysis of mammalian maximal oxygen consumption during exercise.

    Science.gov (United States)

    Dlugosz, Elizabeth M; Chappell, Mark A; Meek, Thomas H; Szafranska, Paulina A; Zub, Karol; Konarzewski, Marek; Jones, James H; Bicudo, J Eduardo P W; Nespolo, Roberto F; Careau, Vincent; Garland, Theodore

    2013-12-15

    We compiled published values of mammalian maximum oxygen consumption during exercise ( ) and supplemented these data with new measurements of for the largest rodent (capybara), 20 species of smaller-bodied rodents, two species of weasels and one small marsupial. Many of the new data were obtained with running-wheel respirometers instead of the treadmill systems used in most previous measurements of mammalian . We used both conventional and phylogenetically informed allometric regression models to analyze of 77 'species' (including subspecies or separate populations within species) in relation to body size, phylogeny, diet and measurement method. Both body mass and allometrically mass-corrected showed highly significant phylogenetic signals (i.e. related species tended to resemble each other). The Akaike information criterion corrected for sample size was used to compare 27 candidate models predicting (all of which included body mass). In addition to mass, the two best-fitting models (cumulative Akaike weight=0.93) included dummy variables coding for three species previously shown to have high (pronghorn, horse and a bat), and incorporated a transformation of the phylogenetic branch lengths under an Ornstein-Uhlenbeck model of residual variation (thus indicating phylogenetic signal in the residuals). We found no statistical difference between wheel- and treadmill-elicited values, and diet had no predictive ability for . Averaged across all models, the allometric scaling exponent was 0.839, with 95% confidence limits of 0.795 and 0.883, which does not provide support for a scaling exponent of 0.67, 0.75 or unity. PMID:24031059

  14. Studies of copper transport in mammalian cells using copper radioisotopes

    Energy Technology Data Exchange (ETDEWEB)

    Camakaris, J.; Voskoboinik, I.; Brooks, H.; Greenough, M. [University of Melbourne, Parkville, VIC (Australia). Department of Genetics; Smith, S. [Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia). Radiopharmaceuticals Division; Mercer, J. [Deakin University, Clayton, VIC (Australia). Centre of Cellular and Molecular Biology

    1998-12-31

    The trace element copper poses a major problem for all organisms. It is essential as a number of vital enzymes require it. Copper deficiency can lead to neurological disorders, osteoporosis and weakening of arteries. However Cu is also highly toxic and homeostatic mechanisms have evolved to maintain Cu at levels which satisfy requirements but do not cause toxicity. Toxicity is mediated by the oxidative capacity of Cu and its ability to generate toxic free radicals. There are several acquired and inherited diseases due to either Cu toxicity or Cu deficiency. The study of these diseases facilitates identification of genes and proteins involved in copper homeostasis, and this in turn will provide rational therapeutic approaches. Using the copper radioisotopes {sup 64}Cu (t1/2 = 12.8 hr) and {sup 67}Cu (t1/2 = 61 hr) we have developed a number of systems for studying copper transport in mammalian cells. These include investigation of copper uptake, copper efflux and ligand blot assays for Cu-binding proteins. Our studies have focused on Menkes disease which is an inherited and usually lethal copper deficiency disorder in humans. We have demonstrated that the Menkes protein is directly involved as a copper efflux pump in mammalian cells. Using cells overexpressing the Menkes protein we have provided the first biochemical evidence that this functions as a Cu translocating (across the membrane) P-type ATPase (Voskoboinik et al., FEBS Letters, in press). These studies were carried out using purified plasma membrane vesicles. We are now carrying out structure- function studies on this protein using targeted mutations and assaying using the radiocopper vesicle assay. Recently we have commenced studies on the role of amyloid precursor protein (APP) in copper transport and relationship of this to Alzheimers disease

  15. Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis

    NARCIS (Netherlands)

    Berezikov, Eugene; van Tetering, Geert; Verheul, Mark; van de Belt, Jose; van Laake, Linda; Vos, Joost; Verloop, Robert; van de Wetering, Marc; Guryev, Victor; Takada, Shuji; van Zonneveld, Anton Jan; Mano, Hiroyuki; Plasterk, Ronald; Cuppen, Edwin

    2006-01-01

    MicroRNAs are 20- to 23-nucleotide RNA molecules that can regulate gene expression. Currently > 400 microRNAs have been experimentally identified in mammalian genomes, whereas estimates go up to 1000 and beyond. Here we show that many more mammalian microRNAs exist. We discovered novel microRNA cand

  16. Dual-function vector for protein expression in both mammalian cells and Xenopus laevis oocytes

    DEFF Research Database (Denmark)

    Jespersen, Thomas; Grunnet, M; Angelo, K;

    2002-01-01

    and oocytes. To address this problem, we have constructed a plasmid vector, pXOOM, that can function as a template for expression in both oocytes and mammalian cells. By including all the necessary RNA stability elements for oocyte expression in a standard mammalian expression vector, we have obtained...

  17. Molecular dissection of the roles of the SOD genes in mammalian response to low dose irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Li, Chuan-Yaun

    2009-01-27

    “Molecular dissection of the roles of the SOD genes in mammalian response to low dose irradiation " was started on 09/01/03 and ended on 08/31/07. The primary objective of the project was to carry out mechanistic studies of the roles of the anti-oxidant SOD genes in mammalian cellular response to low dose ionizing radiation.

  18. Gelation, oxygen permeability and mechanical properties of mammalian and fish gelatin films

    Science.gov (United States)

    The objective of this study was to evaluate the gelation, thermal, mechanical and oxygen permeability properties of different mammalian, warm- and cold-water fish gelatin solutions and films. Mammalian gelatin solutions had the highest gel set temperatures, followed by warm-water fish and then cold-...

  19. 40 CFR 798.5385 - In vivo mammalian bone marrow cytogenetics tests: Chromosomal analysis.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 31 2010-07-01 2010-07-01 true In vivo mammalian bone marrow... PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT (CONTINUED) HEALTH EFFECTS TESTING GUIDELINES Genetic Toxicity § 798.5385 In vivo mammalian bone marrow cytogenetics tests: Chromosomal analysis....

  20. 40 CFR 798.5395 - In vivo mammalian bone marrow cytogenetics tests: Micronucleus assay.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 31 2010-07-01 2010-07-01 true In vivo mammalian bone marrow... PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT (CONTINUED) HEALTH EFFECTS TESTING GUIDELINES Genetic Toxicity § 798.5395 In vivo mammalian bone marrow cytogenetics tests: Micronucleus assay....

  1. The impact of ancestral heath management on soils and landscapes: a reconstruction based on paleoecological analyses of soil records in the central and southeastern Netherlands

    Science.gov (United States)

    Doorenbosch, Marieke; van Mourik, Jan M.

    2016-07-01

    The evolution of heathlands during the Holocene has been registered in various soil records. Paleoecological analyses of these records enable reconstruction of the changing economic and cultural management of heaths and the consequences for landscape and soils. Heaths are characteristic components of cultural landscape mosaics on sandy soils in the Netherlands. The natural habitat of heather species was moorland. At first, natural events like forest fires and storms caused small-scale forest degradation; in addition on that, the forest degradation accelerated due to cultural activities like forest grazing, wood cutting, and shifting cultivation. Heather plants invaded degraded forest soils, and heaths developed. People learned to use the heaths for economic and cultural purposes. The impact of the heath management on landscape and soils was registered in soil records of barrows, drift sand sequences, and plaggic Anthrosols. Based on pollen diagrams of such records we could reconstruct that heaths were developed and used for cattle grazing before the Bronze Age. During the late Neolithic, the Bronze Age, and Iron Age, people created the barrow landscape on the ancestral heaths. After the Iron Age, people probably continued with cattle grazing on the heaths and plaggic agriculture until the early Middle Ages. Severe forest degradation by the production of charcoal for melting iron during the Iron Age till the 6th-7th century and during the 11th-13th century for the trade of wood resulted in extensive sand drifting, a threat to the valuable heaths. The introduction of the deep, stable economy and heath sods digging in the course of the 18th century resulted in acceleration of the rise of plaggic horizons, severe heath degradation, and again extension of sand drifting. At the end of the 19th century heath lost its economic value due to the introduction of chemical fertilizers. The heaths were transformed into "new" arable fields and forests, and due to deep ploughing

  2. Comparison with ancestral diets suggests dense acellular carbohydrates promote an inflammatory microbiota, and may be the primary dietary cause of leptin resistance and obesity

    Directory of Open Access Journals (Sweden)

    Spreadbury I

    2012-07-01

    Full Text Available Ian SpreadburyGastrointestinal Diseases Research Unit, Queen's University, Kingston, Ontario, CanadaAbstract: A novel hypothesis of obesity is suggested by consideration of diet-related inflammation and evolutionary medicine. The obese homeostatically guard their elevated weight. In rodent models of high-fat diet-induced obesity, leptin resistance is seen initially at vagal afferents, blunting the actions of satiety mediators, then centrally, with gastrointestinal bacterial-triggered SOCS3 signaling implicated. In humans, dietary fat and fructose elevate systemic lipopolysaccharide, while dietary glucose also strongly activates SOCS3 signaling. Crucially however, in humans, low-carbohydrate diets spontaneously decrease weight in a way that low-fat diets do not. Furthermore, nutrition transition patterns and the health of those still eating diverse ancestral diets with abundant food suggest that neither glycemic index, altered fat, nor carbohydrate intake can be intrinsic causes of obesity, and that human energy homeostasis functions well without Westernized foods containing flours, sugar, and refined fats. Due to being made up of cells, virtually all "ancestral foods" have markedly lower carbohydrate densities than flour- and sugar-containing foods, a property quite independent of glycemic index. Thus the "forgotten organ" of the gastrointestinal microbiota is a prime candidate to be influenced by evolutionarily unprecedented postprandial luminal carbohydrate concentrations. The present hypothesis suggests that in parallel with the bacterial effects of sugars on dental and periodontal health, acellular flours, sugars, and processed foods produce an inflammatory microbiota via the upper gastrointestinal tract, with fat able to effect a "double hit" by increasing systemic absorption of lipopolysaccharide. This model is consistent with a broad spectrum of reported dietary phenomena. A diet of grain-free whole foods with carbohydrate from cellular

  3. Transposon-mediated death of an ancestral A-23-like allele: evolution of TCR-positioning motifs in the HLA-A lineage.

    Science.gov (United States)

    Murray, Joseph S

    2015-08-01

    HLA-A alleles are characterized by tandem arginine and histidine/arginine motifs (i.e., R65 and H151R motifs) present on the α1- and α2-helix, respectively. In crystallographic structures, α/β T-cell receptors (TCR) contact both motifs and appear to be geometrically positioned for alloreactivity. Herein, bioinformatics of "dual-motif" MHC A-like alleles were investigated across phylogeny. While A-like alleles with the R65 motif are widespread, the H151R motif has segregated out of most species. Surprisingly, an uncharacterized orf in tarsiers (Loc-103275158) encodes R151 within a truncated A-23-like gene, which is in frame with short footprints of Tc5 and Tigger transposons (TE); the extant tarsier A-23 allele is totally missing exon-3 and part of exon-4; together, suggesting TE-mediated inactivation of an intact/ancestral A-23 allele. Since the only other (non-human) dual-motif A-like alleles are in gorilla, chimpanzee, and the Florida manatee, we speculate that dual-motif A alleles first emerged in the Afrotherian lineage and reappeared during the evolution of higher primates. PMID:26063599

  4. A recurrent laminin 5 mutation in British patients with lethal (Herlitz) junctional epidermolysis bullosa: evidence for a mutational hotspot rather than propagation of an ancestral allele.

    Science.gov (United States)

    Ashton, G H; Mellerio, J E; Dunnill, M G; Pulkkinen, L; Christiano, A M; Uitto, J; Eady, R A; McGrath, J A

    1997-05-01

    The three genes (LAMA3, LAB3 and LAMC2) that encode the anchoring filament protein, laminin 5, may all harbour pathogenetic mutations in the autosomal recessive blistering skin disorder, junctional epidermolysis bullosa (JEB). Recently, one particular mutation, R635X in the LAMB3 gene, has been found to account for approximately 40% of all JEB laminin 5 mutations (Kivirikko et al., Hum Mol Genet 1996; 5: 231-7). In this study, we assessed the frequency of this mutation in 12 British patients with lethal (Herlitz) JEB using PCR amplification of genomic DNA and restriction endonuclease digestion. The mutation R635X was fond in seven of 24 (29%) mutant alleles, confirming its relative frequency within the British gene pool. In addition, haplotype analysis using intragenic polymorphisms showed that the mutation arose on at least four different haplotype backgrounds, suggesting it represents a mutational hotspot rather than propagation of a common British ancestral allele. These findings support the hypermutable nature of this CpG dinucleotide and have implications in screening for laminin 5 gene mutations in British and other patients with JEB. PMID:9205497

  5. New time constraints for the age of metamorphism at the ancestral Pacific Gondwana margin of southern Chile (42-52°S

    Directory of Open Access Journals (Sweden)

    Stuart N. Thomson

    2002-12-01

    Full Text Available Fission-track (FT analysis was performed on ten samples of detrital zircons from several pre-Late Jurassic metamorphic accretionary complexes at the ancestral Pacific margin of Gondwana in southern Chile (42-52°S previously dated by U-Pb SHRIMP. Post-metamorphic zircon FT cooling ages combined with published U-Pb provenance ages allow the estimation of the following maximum and minimum ages of deposition and metamorphism: the Eastern Andes metamorphic complex (EAMC, 364 to 250 Ma (Late Devonian to Permian/Triassic boundary; the Duque de York flysch of the Madre de Dios accretionary complex (MDAC, 234 to 195 Ma (Middle Triassic to Early Jurassic; and the Chonos/Chiloé metamorphic complex (CMC, 213 to 198 Ma (Late Triassic to Early Jurassic. The implications of these results are (1 they verify that deposition, accretion and metamorphism of most of the EAMC took place well before continentally derived flysch in the complexes west of the Patagonian batholith (MDAC and CMC was deposited, accreted, and metamorphosed, supporting either a punctuated evolution of accretion along the ancestral Pacific Gondwana margin or the existence two distinct basement terranes and (2 that the continentally derived flysch of the CMC and MDAC share an equivalent depositional and metamorphic history indicative of widespread accretion in Late Triassic to Early Jurassic times. Mixed post-metamorphic zircon FT single grain ages and an apatite FT age from the island of Chiloé (43°S reveal a previously unknown Late Cretaceous (109-60 Ma phase of reheating in these rocks, most likely linked to plutonic activity of this age described in other parts of the CMCNuevas limitaciones temporales a la edad del metamorfismo, en el margen ancestral pacífico de Gondwana, sur de Chile (42-52°S. La datación por trazas de fisión (FT fue realizado en circones detríticos previamente datados por U-Pb SHRIMP, pertenecientes a distintos complejos metamórficos del sur de Chile (42-52

  6. Migration of the Pee Dee River system inferred from ancestral paleochannels underlying the South Carolina Grand Strand and Long Bay inner shelf

    Science.gov (United States)

    Baldwin, W.E.; Morton, R.A.; Putney, T.R.; Katuna, M.P.; Harris, M.S.; Gayes, P.T.; Driscoll, N.W.; Denny, J.F.; Schwab, W.C.

    2006-01-01

    Several generations of the ancestral Pee Dee River system have been mapped beneath the South Carolina Grand Strand coastline and adjacent Long Bay inner shelf. Deep boreholes onshore and high-resolution seismic-reflection data offshore allow for reconstruction of these paleochannels, which formed during glacial lowstands, when the Pee Dee River system incised subaerially exposed coastal-plain and continental-shelf strata. Paleochannel groups, representing different generations of the system, decrease in age to the southwest, where the modern Pee Dee River merges with several coastal-plain tributaries at Winyah Bay, the southern terminus of Long Bay. Positions of the successive generational groups record a regional, southwestward migration of the river system that may have initiated during the late Pliocene. The migration was primarily driven by barrier-island deposition, resulting from the interaction of fluvial and shoreline processes during eustatic highstands. Structurally driven, subsurface paleotopography associated with the Mid-Carolina Platform High has also indirectly assisted in forcing this migration. These results provide a better understanding of the evolution of the region and help explain the lack of mobile sediment on the Long Bay inner shelf. Migration of the river system caused a profound change in sediment supply during the late Pleistocene. The abundant fluvial source that once fed sand-rich barrier islands was cut off and replaced with a limited source, supplied by erosion and reworking of former coastal deposits exposed at the shore and on the inner shelf.

  7. Distribution of KIR genes in the population of unrelated individuals homozygous for ancestral haplotype AH8.1 (HLA-A1B8DR3).

    Science.gov (United States)

    Jindra, P; Venigová, P; Lysák, D; Steinerova, K; Koza, V

    2010-09-01

    Despite the independent segregation of genes encoding killer immunoglobulin-like receptor (KIR) and human leukocyte antigen (HLA), there is some evidence of some kind of co-evolution. Therefore, one could expect reduced KIR diversity within the HLA restricted population. A total of 41 unrelated individuals homozygous for ancestral HLA haplotype AH8.1 (HLA-A*0101-Cw*0701-B*0801-DRB1*0301-DQB1*0201) were genotyped for KIRs. Over all, 14 different genotypes were identified. The KIR genes and genotypes repertoire generally mirror the published frequencies in Caucasians. Except for KIR2DS4, all activating genes presented frequencies below 50%. KIR2DS5 was the least frequent among activating genes (17%), whereas KIR2DL5 (37%) among inhibitory ones. The most frequent (39%) was AA genotype. Twenty-two individuals (54%) had a copy of KIR haplotypes A and B (AB genotype), whereas three (7%) were homozygous for B (BB genotype). Nine of fourteen reported genotypes occurred only in one individual. Five genotypes were reported in less than twenty individuals worldwide and one genotype was reported so far only once. Conversely, the three most frequent genotypes account for 68% of all detected genotypes. The results show the unrestricted KIR diversity in this HLA uniform group and support the fact that the driving force for KIR evolution is not exclusively a major histocompatibility complex. PMID:20492596

  8. Travelling in time with networks: Revealing present day hybridization versus ancestral polymorphism between two species of brown algae, Fucus vesiculosus and F. spiralis

    Directory of Open Access Journals (Sweden)

    Pearson Gareth A

    2011-01-01

    Full Text Available Abstract Background Hybridization or divergence between sympatric sister species provides a natural laboratory to study speciation processes. The shared polymorphism in sister species may either be ancestral or derive from hybridization, and the accuracy of analytic methods used thus far to derive convincing evidence for the occurrence of present day hybridization is largely debated. Results Here we propose the application of network analysis to test for the occurrence of present day hybridization between the two species of brown algae Fucus spiralis and F. vesiculosus. Individual-centered networks were analyzed on the basis of microsatellite genotypes from North Africa to the Pacific American coast, through the North Atlantic. Two genetic distances integrating different time steps were used, the Rozenfeld (RD; based on alleles divergence and the Shared Allele (SAD; based on alleles identity distances. A diagnostic level of genotype divergence and clustering of individuals from each species was obtained through RD while screening for exchanges through putative hybridization was facilitated using SAD. Intermediate individuals linking both clusters on the RD network were those sampled at the limits of the sympatric zone in Northwest Iberia. Conclusion These results suggesting rare hybridization were confirmed by simulation of hybrids and F2 with directed backcrosses. Comparison with the Bayesian method STRUCTURE confirmed the usefulness of both approaches and emphasized the reliability of network analysis to unravel and study hybridization

  9. The footprint of metabolism in the organization of mammalian genomes

    Directory of Open Access Journals (Sweden)

    Berná Luisa

    2012-05-01

    Full Text Available Abstract Background At present five evolutionary hypotheses have been proposed to explain the great variability of the genomic GC content among and within genomes: the mutational bias, the biased gene conversion, the DNA breakpoints distribution, the thermal stability and the metabolic rate. Several studies carried out on bacteria and teleostean fish pointed towards the critical role played by the environment on the metabolic rate in shaping the base composition of genomes. In mammals the debate is still open, and evidences have been produced in favor of each evolutionary hypothesis. Human genes were assigned to three large functional categories (as well as to the corresponding functional classes according to the KOG database: (i information storage and processing, (ii cellular processes and signaling, and (iii metabolism. The classification was extended to the organisms so far analyzed performing a reciprocal Blastp and selecting the best reciprocal hit. The base composition was calculated for each sequence of the whole CDS dataset. Results The GC3 level of the above functional categories was increasing from (i to (iii. This specific compositional pattern was found, as footprint, in all mammalian genomes, but not in frog and lizard ones. Comparative analysis of human versus both frog and lizard functional categories showed that genes involved in the metabolic processes underwent the highest GC3 increment. Analyzing the KOG functional classes of genes, again a well defined intra-genomic pattern was found in all mammals. Not only genes of metabolic pathways, but also genes involved in chromatin structure and dynamics, transcription, signal transduction mechanisms and cytoskeleton, showed an average GC3 level higher than that of the whole genome. In the case of the human genome, the genes of the aforementioned functional categories showed a high probability to be associated with the chromosomal bands. Conclusions In the light of different

  10. Evolutionary patterns of RNA-based duplication in non-mammalian chordates.

    Directory of Open Access Journals (Sweden)

    Ming Chen

    Full Text Available The role of RNA-based duplication, or retroposition, in the evolution of new gene functions in mammals, plants, and Drosophila has been widely reported. However, little is known about RNA-based duplication in non-mammalian chordates. In this study, we screened ten non-mammalian chordate genomes for retrocopies and investigated their evolutionary patterns. We identified numerous retrocopies in these species. Examination of the age distribution of these retrocopies revealed no burst of young retrocopies in ancient chordate species. Upon comparing these non-mammalian chordate species to the mammalian species, we observed that a larger fraction of the non-mammalian retrocopies was under strong evolutionary constraints than mammalian retrocopies are, as evidenced by signals of purifying selection and expression profiles. For the Western clawed frog, Medaka, and Sea squirt, many retrogenes have evolved gonad and brain expression patterns, similar to what was observed in human. Testing of retrogene movement in the Medaka genome, where the nascent sex chrosomes have been well assembled, did not reveal any significant gene movement. Taken together, our analyses demonstrate that RNA-based duplication generates many functional genes and can make a significant contribution to the evolution of non-mammalian genomes.

  11. A molecular determinant of phosphoinositide affinity in mammalian TRPV channels.

    Science.gov (United States)

    Velisetty, Phanindra; Borbiro, Istvan; Kasimova, Marina A; Liu, Luyu; Badheka, Doreen; Carnevale, Vincenzo; Rohacs, Tibor

    2016-01-01

    Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is an important cofactor for ion channels. Affinity for this lipid is a major determinant of channel inhibition by depletion of PI(4,5)P2 upon phospholipase C (PLC) activation. Little is known about what determines PI(4,5)P2 affinity in mammalian ion channels. Here we report that two members of the Transient Receptor Potential Vanilloid (TRPV) ion channel family, TRPV5 and TRPV6 lack a positively charged residue in the TM4-TM5 loop that was shown to interact with PI(4,5)P2 in TRPV1, which shows high affinity for this lipid. When this positively charged residue was introduced to either TRPV6 or TRPV5, they displayed markedly higher affinities for PI(4,5)P2, and were largely resistant to inhibition by PI(4,5)P2 depletion. Furthermore, Ca(2+)-induced inactivation of TRPV6 was essentially eliminated in the G488R mutant, showing the importance of PLC-mediated PI(4,5)P2 depletion in this process. Computational modeling shows that the introduced positive charge interacts with PI(4,5)P2 in TRPV6. PMID:27291418

  12. Mammalian fauna of the Temessos National Park, Turkey

    Directory of Open Access Journals (Sweden)

    Anna De Marinis

    2009-12-01

    Full Text Available The National Park of Termessos, Southern Turkey, is one of the Turkey’s biggest national park not only with its archeological richness but also with its great natural wild life. We provided a checklist of the mammalian fauna of the park on the base of direct observations, interviews and a comparative analysis of the available literature. Sixteen species have been reported in the park. Hedgehogs, hares, porcupines and Persian squirrels and, among flying mammals, Egyptian rousette and Mouse-eared bat have been recorded. Carnivores are represented by Golden jackal, Wolf, Red fox, Stone marten, Badger, Otter and Wild cat. Very recently (2005 the presence of the Caracal in the park has been confirmed, whereas no signs of the presence of the Lynx were detected. The last Anatolian leopards seems to have definitively disappeared from the region. The occurrence in the area of striped hyaenas and brown bears is documented up to a few decades ago. The Park is regarded as the only geographical range in the whole world where the European or Common fallow deer has persisted as a native form. Other ungulates too, such as Wild goat and Wild boar are dispersed within the boundary of the park. Management implications are discussed.

  13. Toward a detailed computational model for the mammalian circadian clock

    Science.gov (United States)

    Leloup, Jean-Christophe; Goldbeter, Albert

    2003-06-01

    We present a computational model for the mammalian circadian clock based on the intertwined positive and negative regulatory loops involving the Per, Cry, Bmal1, Clock, and Rev-Erb genes. In agreement with experimental observations, the model can give rise to sustained circadian oscillations in continuous darkness, characterized by an antiphase relationship between Per/Cry/Rev-Erb and Bmal1 mRNAs. Sustained oscillations correspond to the rhythms autonomously generated by suprachiasmatic nuclei. For other parameter values, damped oscillations can also be obtained in the model. These oscillations, which transform into sustained oscillations when coupled to a periodic signal, correspond to rhythms produced by peripheral tissues. When incorporating the light-induced expression of the Per gene, the model accounts for entrainment of the oscillations by light-dark cycles. Simulations show that the phase of the oscillations can then vary by several hours with relatively minor changes in parameter values. Such a lability of the phase could account for physiological disorders related to circadian rhythms in humans, such as advanced or delayed sleep phase syndrome, whereas the lack of entrainment by light-dark cycles can be related to the non-24h sleep-wake syndrome. The model uncovers the possible existence of multiple sources of oscillatory behavior. Thus, in conditions where the indirect negative autoregulation of Per and Cry expression is inoperative, the model indicates the possibility that sustained oscillations might still arise from the negative autoregulation of Bmal1 expression.

  14. Dimerization of mammalian kinesin-3 motors results in superprocessive motion.

    Science.gov (United States)

    Soppina, Virupakshi; Norris, Stephen R; Dizaji, Aslan S; Kortus, Matt; Veatch, Sarah; Peckham, Michelle; Verhey, Kristen J

    2014-04-15

    The kinesin-3 family is one of the largest among the kinesin superfamily and its members play important roles in a wide range of cellular transport activities, yet the molecular mechanisms of kinesin-3 regulation and cargo transport are largely unknown. We performed a comprehensive analysis of mammalian kinesin-3 motors from three different subfamilies (KIF1, KIF13, and KIF16). Using Forster resonance energy transfer microscopy in live cells, we show for the first time to our knowledge that KIF16B motors undergo cargo-mediated dimerization. The molecular mechanisms that regulate the monomer-to-dimer transition center around the neck coil (NC) segment and its ability to undergo intramolecular interactions in the monomer state versus intermolecular interactions in the dimer state. Regulation of NC dimerization is unique to the kinesin-3 family and in the case of KIF13A and KIF13B requires the release of a proline-induced kink between the NC and subsequent coiled-coil 1 segments. We show that dimerization of kinesin-3 motors results in superprocessive motion, with average run lengths of ∼10 μm, and that this property is intrinsic to the dimeric kinesin-3 motor domain. This finding opens up studies on the mechanistic basis of motor processivity. Such high processivity has not been observed for any other motor protein and suggests that kinesin-3 motors are evolutionarily adapted to serve as the marathon runners of the cellular world. PMID:24706892

  15. Isolation and characterization of three mammalian orthoreoviruses from European bats.

    Directory of Open Access Journals (Sweden)

    Claudia Kohl

    Full Text Available In recent years novel human respiratory disease agents have been described in South East Asia and Australia. The causative pathogens were classified as pteropine orthoreoviruses with strong phylogenetic relationship to orthoreoviruses of flying foxes inhabiting these regions. Subsequently, a zoonotic bat-to-human transmission has been assumed. We report the isolation of three novel mammalian orthoreoviruses (MRVs from European bats, comprising bat-borne orthoreovirus outside of South East Asia and Australia and moreover detected in insectivorous bats (Microchiroptera. MRVs are well known to infect a broad range of mammals including man. Although they are associated with rather mild and clinically unapparent infections in their hosts, there is growing evidence of their ability to also induce more severe illness in dogs and man. In this study, eight out of 120 vespertilionid bats proved to be infected with one out of three novel MRV isolates, with a distinct organ tropism for the intestine. One isolate was analyzed by 454 genome sequencing. The obtained strain T3/Bat/Germany/342/08 had closest phylogenetic relationship to MRV strain T3D/04, isolated from a dog. These novel reoviruses provide a rare chance of gaining insight into possible transmission events and of tracing the evolution of bat viruses.

  16. Mammalian Pumilio 2 regulates dendrite morphogenesis and synaptic function.

    Science.gov (United States)

    Vessey, John P; Schoderboeck, Lucia; Gingl, Ewald; Luzi, Ettore; Riefler, Julia; Di Leva, Francesca; Karra, Daniela; Thomas, Sabine; Kiebler, Michael A; Macchi, Paolo

    2010-02-16

    In Drosophila, Pumilio (Pum) is important for neuronal homeostasis as well as learning and memory. We have recently characterized a mammalian homolog of Pum, Pum2, which is found in discrete RNA-containing particles in the somatodendritic compartment of polarized neurons. In this study, we investigated the role of Pum2 in developing and mature neurons by RNA interference. In immature neurons, loss of Pum2 led to enhanced dendritic outgrowth and arborization. In mature neurons, Pum2 down-regulation resulted in a significant reduction in dendritic spines and an increase in elongated dendritic filopodia. Furthermore, we observed an increase in excitatory synapse markers along dendritic shafts. Electrophysiological analysis of synaptic function of neurons lacking Pum2 revealed an increased miniature excitatory postsynaptic current frequency. We then identified two specific mRNAs coding for a known translational regulator, eIF4E, and for a voltage-gated sodium channel, Scn1a, which interacts with Pum2 in immunoprecipitations from brain lysates. Finally, we show that Pum2 regulates translation of the eIF4E mRNA. Taken together, our data reveal a previously undescribed role for Pum2 in dendrite morphogenesis, synapse function, and translational control. PMID:20133610

  17. Effects of Tetrodotoxin on the Mammalian Cardiovascular System

    Directory of Open Access Journals (Sweden)

    Thomas Zimmer

    2010-03-01

    Full Text Available The human genome encodes nine functional voltage-gated Na+ channels. Three of them, namely Nav1.5, Nav1.8, and Nav1.9, are resistant to nanomolar concentrations of tetrodotoxin (TTX; IC50 ≥ 1 μM. The other isoforms, which are predominantly expressed in the skeletal muscle and nervous system, are highly sensitive to TTX (IC50 ~ 10 nM. During the last two decades, it has become evident that in addition to the major cardiac isoform Nav1.5, several of those TTX sensitive isoforms are expressed in the mammalian heart. Whereas immunohistochemical and electrophysiological methods demonstrated functional expression in various heart regions, the physiological importance of those isoforms for cardiac excitation in higher mammals is still debated. This review summarizes our knowledge on the systemic cardiovascular effects of TTX in animals and humans, with a special focus on cardiac excitation and performance at lower concentrations of this marine drug. Altogether, these data strongly suggest that TTX sensitive Na+ channels, detected more recently in various heart tissues, are not involved in excitation phenomena in the healthy adult heart of higher mammals.

  18. [Using inter-SINE-PCR to study mammalian phylogeny].

    Science.gov (United States)

    Bannikova, A A; Matveev, V A; Kramerov, D A

    2002-06-01

    Results of the use of the fingerprinting method related to short interspersed elements (SINEs), inter-SINE-PCR, in the study of phylogenetic and taxonomic relationship in mammals from orders Chiroptera (family Vespertilionidae) and Lipotyphla (family Erinaceidae) are reported. The inter-SINE-PCR method is based on the amplification of fragments situated between copies of SINEs, which are short retroposons spaced 100 to 1000 bp apart. Specifically selected primers were used, which are complementary to consensus sequences of two short retroposons: the mammalian interspersed repeat (MIR), which is typical of all mammals and some other vertebrates, was used in the cases of bats and Erinaceidae, and the ERI-1 element recently isolated from the genome of the Daurian hedgehog was used in the case of Erinaceidae. The results support the current view on phylogenetic relationship between hedgehogs belonging to genera Erinaceus, Hemiechinus, and Paraechinus (but not the genus Atelerix). In bats, the phylogenetic reconstruction revealed a statistically valid topology only at lower taxonomic levels, whereas the topology for the genus and supragenus ranks was unresolved and fan-shaped. The benefits and limitations of the inter-SINE-PCR method are discussed. PMID:12138785

  19. Antineoplastic effects of mammalian target of rapamycine inhibitors.

    Science.gov (United States)

    Salvadori, Maurizio

    2012-10-24

    Cancer after transplantation is the third cause of death and one of the more relevant comorbidities. Aim of this review is to verify the role of different pathogenetic mechanisms in cancer development in transplant patients and in general population as well. In particular has been outlined the different role exerted by two different families of drug as calcineurin inhibitor and mammalian target of rapamycin (mTOR) inhibitor. The role of mTOR pathways in cell homeostasis is complex but enough clear. As a consequence the mTOR pathway deregulation is involved in the genesis of several cancers. Hence the relevant role of mTOR inhibitors. The authors review the complex mechanism of action of mTOR inhibitors, not only for what concerns the immune system but also other cells as endothelial, smooth muscle and epithelial cells. The mechanism of action is still now not completely defined and understood. It implies the inhibition of mTOR pathway at different levels, but mainly at level of the phosphorylation of several intracellular kinases that contribute to activate mTOR complex. Many prospective and retrospective studies in transplant patients document the antineoplastic role of mTOR inhibition. More recently mTOR inhibitors proven to be effective in the treatment of some cancers also in general population. Kidney cancers, neuroendocrine tumors and liver cancers seem to be the most sensitive to these drugs. Best results are obtained with a combination treatment, targeting the mTOR pathway at different levels. PMID:24175199

  20. Mammalian target of rapamycin inhibitors for treatment in tuberous sclerosis

    Directory of Open Access Journals (Sweden)

    Won Seop Kim

    2011-06-01

    Full Text Available Tuberous sclerosis complex (TSC is a genetic multisystem disorder that results from mutations in the TSC1 or TSC2 genes, and is associated with hamartomas in several organs, including subependymal giant cell tumors. The neurological manifestations of TSC are particularly challenging and include infantile spasms, intractable epilepsy, cognitive disabilities, and autism. The TSC1- and TSC2-encoded proteins modulate cell function via the mammalian target of rapamycin (mTOR signaling cascade, and are key factors in the regulation of cell growth and proliferation. The mTOR pathway provides an intersection for an intricate network of protein cascades that respond to cellular nutrition, energy levels, and growth factor stimulation. In the brain, TSC1 and TSC2 have been implicated in cell body size, dendritic arborization, axonal outgrowth and targeting, neuronal migration, cortical lamination, and spine formation. The mTOR pathway represents a logical candidate for drug targeting, because mTOR regulates multiple cellular functions that may contribute to epileptogenesis, including protein synthesis, cell growth and proliferation, and synaptic plasticity. Antagonism of the mTOR pathway with rapamycin and related compounds may provide new therapeutic options for TSC patients.

  1. RNA gymnastics in mammalian signal recognition particle assembly.

    Science.gov (United States)

    Wild, Klemens; Sinning, Irmgard

    2014-01-01

    More than one third of the cellular proteome is destined for incorporation into cell membranes or export from the cell. In all domains of life, the signal recognition particle (SRP) delivers these proteins to the membrane and protein traffic falls apart without SRP logistics. With the aid of a topogenic transport signal, SRP retrieves its cargo right at the ribosome, from where they are sorted to the translocation channel. Mammalian SRP is a ribonucleoprotein complex consisting of an SRP RNA of 300 nucleotides and 6 proteins bound to it. Assembly occurs in a hierarchical manner mainly in the nucleolus and only SRP54, which recognizes the signal sequence and regulates the targeting process, is added as the last component in the cytosol. Here we present an update on recent insights in the structure, function and dynamics of SRP RNA in SRP assembly with focus on the S domain, and present SRP as an example for the complex biogenesis of a rather small ribonucleoprotein particle. PMID:25692231

  2. Epigenetic control of mammalian LINE-1 retrotransposon by retinoblastoma proteins

    International Nuclear Information System (INIS)

    Long interspersed nuclear elements (LINEs or L1 elements) are targeted for epigenetic silencing during early embryonic development and remain inactive in most cells and tissues. Here we show that E2F-Rb family complexes participate in L1 elements epigenetic regulation via nucleosomal histone modifications and recruitment of histone deacetylases (HDACs) HDAC1 and HDAC2. Our experiments demonstrated that (i) Rb and E2F interact with human and mouse L1 elements, (ii) L1 elements are deficient in both heterochromatin-associated histone marks H3 tri methyl K9 and H4 tri methyl K20 in Rb family triple knock out (Rb, p107, and p130) fibroblasts (TKO), (iii) L1 promoter exhibits increased histone H3 acetylation in the absence of HDAC1 and HDAC2 recruitment, (iv) L1 expression in TKO fibroblasts is upregulated compared to wild type counterparts, (v) L1 expression increases in the presence of the HDAC inhibitor TSA. On the basis of these findings we propose a model in which L1 sequences throughout the genome serve as centers for heterochromatin formation in an Rb family-dependent manner. As such, Rb proteins and L1 elements may play key roles in heterochromatin formation beyond pericentromeric chromosomal regions. These findings describe a novel mechanism of L1 reactivation in mammalian cells mediated by failure of corepressor protein recruitment by Rb, loss of histone epigenetic marks, heterochromatin formation, and increased histone H3 acetylation.

  3. Mammalian cadherins DCHS1-FAT4 affect functional cerebral architecture.

    Science.gov (United States)

    Beste, Christian; Ocklenburg, Sebastian; von der Hagen, Maja; Di Donato, Nataliya

    2016-06-01

    Cortical development is a complex process where a multitude of factors, including cadherins, plays an important role and where disruptions are known to have far reaching effects in neural development and cortical patterning. Cadherins play a central role in structural left-right differentiation during brain and body development, but their effect on a functional level remains elusive. We addressed this question by examining functional cerebral asymmetries in a patient with Van Maldergem Syndrome (VMS) (MIM#601390), which is caused by mutations in DCHS1-FAT4 cadherins, using a dichotic listening task. Using neurophysiological (EEG) data, we show that when key regulators during mammalian cerebral cortical development are disrupted due to DCHS1-FAT4 mutations, functional cerebral asymmetries are stronger. Basic perceptual processing of biaurally presented auditory stimuli was unaffected. This suggests that the strength and emergence of functional cerebral asymmetries is a direct function of proliferation and differentiation of neuronal stem cells. Moreover, these results support the recent assumption that the molecular mechanisms establishing early left-right differentiation are an important factor in the ontogenesis of functional lateralization. PMID:25930014

  4. Epigenetic control of mammalian LINE-1 retrotransposon by retinoblastoma proteins

    Energy Technology Data Exchange (ETDEWEB)

    Montoya-Durango, Diego E. [Department of Biochemistry and Molecular Biology and Center for Genetics and Molecular Medicine, University of Louisville School of Medicine Health Sciences Center, Louisville, KY 40202 (United States); Liu, Yongqing [James Graham Brown Cancer Center and Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine Health Sciences Center, Louisville, KY 40202 (United States); Teneng, Ivo; Kalbfleisch, Ted; Lacy, Mary E.; Steffen, Marlene C. [Department of Biochemistry and Molecular Biology and Center for Genetics and Molecular Medicine, University of Louisville School of Medicine Health Sciences Center, Louisville, KY 40202 (United States); Ramos, Kenneth S., E-mail: kenneth.ramos@louisville.edu [Department of Biochemistry and Molecular Biology and Center for Genetics and Molecular Medicine, University of Louisville School of Medicine Health Sciences Center, Louisville, KY 40202 (United States)

    2009-06-01

    Long interspersed nuclear elements (LINEs or L1 elements) are targeted for epigenetic silencing during early embryonic development and remain inactive in most cells and tissues. Here we show that E2F-Rb family complexes participate in L1 elements epigenetic regulation via nucleosomal histone modifications and recruitment of histone deacetylases (HDACs) HDAC1 and HDAC2. Our experiments demonstrated that (i) Rb and E2F interact with human and mouse L1 elements, (ii) L1 elements are deficient in both heterochromatin-associated histone marks H3 tri methyl K9 and H4 tri methyl K20 in Rb family triple knock out (Rb, p107, and p130) fibroblasts (TKO), (iii) L1 promoter exhibits increased histone H3 acetylation in the absence of HDAC1 and HDAC2 recruitment, (iv) L1 expression in TKO fibroblasts is upregulated compared to wild type counterparts, (v) L1 expression increases in the presence of the HDAC inhibitor TSA. On the basis of these findings we propose a model in which L1 sequences throughout the genome serve as centers for heterochromatin formation in an Rb family-dependent manner. As such, Rb proteins and L1 elements may play key roles in heterochromatin formation beyond pericentromeric chromosomal regions. These findings describe a novel mechanism of L1 reactivation in mammalian cells mediated by failure of corepressor protein recruitment by Rb, loss of histone epigenetic marks, heterochromatin formation, and increased histone H3 acetylation.

  5. Observation of Mammalian Similarity Through Allometric Scaling Laws

    CERN Document Server

    Kokshenev, V B

    2002-01-01

    We discuss the problem of observation of natural similarity in skeletal evolution of terrestrial mammals. Analysis is given by means of testing of the power scaling laws established in long bone allometry, which describe development of bones (of length $L$ and diameter $D$) with body mass in terms of the growth exponents, \\QTR{it}{e.g.} $\\lambda =d\\log L/d\\log D$ . The bone-size evolution scenario given three decades ago by McMahon was quiet explicit on the geometrical-shape and mechanical-force constraints that predicted $\\lambda =2/3$. This remains too far from the mammalian allometric exponent $\\lambda ^{(\\exp)}=0.80\\pm 0.2$, recently revised by Christiansen, that is a chief puzzle in long bone allometry. We give therefore new insights into McMagon's constraints and report on the first observation of the critical-elastic-force, bending-deformation, muscle-induced mechanism found with $\\lambda =0.80\\pm 0.3$. This mechanism governs the bone-size evolution with avoiding skeletal fracture caused by muscle-indu...

  6. Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses

    International Nuclear Information System (INIS)

    Plus strand RNA viruses that replicate in the cytoplasm face challenges in supporting the numerous biosynthetic functions required for replication and propagation. Most of these viruses are genetically simple and rely heavily on co-opting cellular proteins, particularly cellular RNA-binding proteins, into new roles for support of virus infection at the level of virus-specific translation, and building RNA replication complexes. In the course of infectious cycles many nuclear-cytoplasmic shuttling proteins of mostly nuclear distribution are detained in the cytoplasm by viruses and re-purposed for their own gain. Many mammalian viruses hijack a common group of the same factors. This review summarizes recent gains in our knowledge of how cytoplasmic RNA viruses use these co-opted host nuclear factors in new functional roles supporting virus translation and virus RNA replication and common themes employed between different virus groups. - Highlights: • Nuclear shuttling host proteins are commonly hijacked by RNA viruses to support replication. • A limited group of ubiquitous RNA binding proteins are commonly hijacked by a broad range of viruses. • Key virus proteins alter roles of RNA binding proteins in different stages of virus replication

  7. Evolution and function of mammalian binder of sperm proteins.

    Science.gov (United States)

    Plante, Geneviève; Prud'homme, Bruno; Fan, Jinjiang; Lafleur, Michel; Manjunath, Puttaswamy

    2016-01-01

    Binder of sperm (BSP) proteins are ubiquitous among mammals and have been extensively investigated over the last three decades. They were first characterized in bull seminal plasma and have now been identified in more than 15 different mammalian species where they represent a superfamily. In addition to sharing a common structure, BSP proteins share many characteristics. They are expressed by seminal vesicles and epididymides, interact with similar ligands and bind to the outer leaflet of sperm membranes via an interaction with choline phospholipids. In addition to playing a major role in sperm capacitation, they are implicated as molecular chaperones in sperm motility and viability, in the formation of the oviductal sperm reservoir, in the regulation of cell volume and possibly in the interaction between sperm and oocytes, making them crucial multifunctional proteins. Furthermore, BSP proteins can bind to egg yolk low-density lipoproteins and milk components, an interaction important for the protection of sperm during semen preservation in liquid or frozen state. Our current knowledge of BSP proteins strongly emphasizes their fundamental importance in male fertility and in the optimization of semen preservation techniques. Much work is still ahead in order to fully understand all the mysteries of BSP proteins. PMID:26386584

  8. Noncanonical Sites of Adult Neurogenesis in the Mammalian Brain.

    Science.gov (United States)

    Feliciano, David M; Bordey, Angélique; Bonfanti, Luca

    2015-10-01

    Two decades after the discovery that neural stem cells (NSCs) populate some regions of the mammalian central nervous system (CNS), deep knowledge has been accumulated on their capacity to generate new neurons in the adult brain. This constitutive adult neurogenesis occurs throughout life primarily within remnants of the embryonic germinal layers known as "neurogenic sites." Nevertheless, some processes of neurogliogenesis also occur in the CNS parenchyma commonly considered as "nonneurogenic." This "noncanonical" cell genesis has been the object of many claims, some of which turned out to be not true. Indeed, it is often an "incomplete" process as to its final outcome, heterogeneous by several measures, including regional location, progenitor identity, and fate of the progeny. These aspects also strictly depend on the animal species, suggesting that persistent neurogenic processes have uniquely adapted to the brain anatomy of different mammals. Whereas some examples of noncanonical neurogenesis are strictly parenchymal, others also show stem cell niche-like features and a strong link with the ventricular cavities. This work will review results obtained in a research field that expanded from classic neurogenesis studies involving a variety of areas of the CNS outside of the subventricular zone (SVZ) and subgranular zone (SGZ). It will be highlighted how knowledge concerning noncanonical neurogenic areas is still incomplete owing to its regional and species-specific heterogeneity, and to objective difficulties still hampering its full identification and characterization. PMID:26384869

  9. Special Delivery: Distributing Iron in the Cytosol of Mammalian cells

    Directory of Open Access Journals (Sweden)

    Caroline C Philpott

    2014-07-01

    Full Text Available Eukaryotic cells contain hundreds of proteins that require iron cofactors for activity. These iron enzymes are located in essentially every subcellular compartment; thus, iron cofactors must travel to every compartment in the cell. Iron cofactors exist in three basic forms: Heme, iron-sulfur clusters, and simple iron ions (also called non-heme iron. Iron ions taken up by the cell initially enter a kinetically labile, exchangeable pool that is referred to as the labile iron pool. The majority of the iron in this pool is delivered to mitochondria, where it is incorporated into heme and iron-sulfur clusters, as well as non-heme iron enzymes. These cofactors must then be distributed to nascent proteins in the mitochondria, cytosol, and membrane-bound organelles. Emerging evidence suggests that specific systems exist for the distribution of iron cofactors within the cell. These systems include membrane transporters, protein chaperones, specialized carriers, and small molecules. This review focuses on the distribution of iron ions in the cytosol and will highlight differences between the iron distribution systems of simple eukaryotes and mammalian cells.

  10. Engineering Mammalian Mucin-type O-Glycosylation in Plants

    DEFF Research Database (Denmark)

    Yang, Zhang; Drew, Damian P; Jørgensen, Bodil;

    2012-01-01

    -glycans are attached to proteins, and which structures are formed, difficult. Because plants are devoid of GalNAc-type O-glycosylation, we have assessed requirements for establishing human GalNAc O-glycosylation de novo in plants with the aim of developing cell systems with custom-designed O...... of MUC1 was glycosylated with up to three and five GalNAc residues when co-expressed with GalNAc-T2 and a combination of GalNAc-T2 and GalNAc-T4, respectively, as determined by mass spectrometry. O-Glycosylation was furthermore demonstrated on a tandem repeat of MUC16 and interferon a2b. In plants......, prolines in certain classes of proteins are hydroxylated and further substituted with plant-specific O-glycosylation; unsubstituted hydroxyprolines were identified in our MUC1 construct. In summary, this study demonstrates that mammalian type O-glycosylation can be established in plants and that plants may...

  11. The landscape of accessible chromatin in mammalian preimplantation embryos.

    Science.gov (United States)

    Wu, Jingyi; Huang, Bo; Chen, He; Yin, Qiangzong; Liu, Yang; Xiang, Yunlong; Zhang, Bingjie; Liu, Bofeng; Wang, Qiujun; Xia, Weikun; Li, Wenzhi; Li, Yuanyuan; Ma, Jing; Peng, Xu; Zheng, Hui; Ming, Jia; Zhang, Wenhao; Zhang, Jing; Tian, Geng; Xu, Feng; Chang, Zai; Na, Jie; Yang, Xuerui; Xie, Wei

    2016-06-30

    In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion. We show that despite extensive parental asymmetry in DNA methylomes, the chromatin accessibility between the parental genomes is globally comparable after major zygotic genome activation (ZGA). Accessible chromatin in early embryos is widely shaped by transposable elements and overlaps extensively with putative cis-regulatory sequences. Unexpectedly, accessible chromatin is also found near the transcription end sites of active genes. By integrating the maps of cis-regulatory elements and single-cell transcriptomes, we construct the regulatory network of early development, which helps to identify the key modulators for lineage specification. Finally, we find that the activities of cis-regulatory elements and their associated open chromatin diminished before major ZGA. Surprisingly, we observed many loci showing non-canonical, large open chromatin domains over the entire transcribed units in minor ZGA, supporting the presence of an unusually permissive chromatin state. Together, these data reveal a unique spatiotemporal chromatin configuration that accompanies early mammalian development. PMID:27309802

  12. Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses

    Energy Technology Data Exchange (ETDEWEB)

    Lloyd, Richard E., E-mail: rlloyd@bcm.edu

    2015-05-15

    Plus strand RNA viruses that replicate in the cytoplasm face challenges in supporting the numerous biosynthetic functions required for replication and propagation. Most of these viruses are genetically simple and rely heavily on co-opting cellular proteins, particularly cellular RNA-binding proteins, into new roles for support of virus infection at the level of virus-specific translation, and building RNA replication complexes. In the course of infectious cycles many nuclear-cytoplasmic shuttling proteins of mostly nuclear distribution are detained in the cytoplasm by viruses and re-purposed for their own gain. Many mammalian viruses hijack a common group of the same factors. This review summarizes recent gains in our knowledge of how cytoplasmic RNA viruses use these co-opted host nuclear factors in new functional roles supporting virus translation and virus RNA replication and common themes employed between different virus groups. - Highlights: • Nuclear shuttling host proteins are commonly hijacked by RNA viruses to support replication. • A limited group of ubiquitous RNA binding proteins are commonly hijacked by a broad range of viruses. • Key virus proteins alter roles of RNA binding proteins in different stages of virus replication.

  13. Exogenous phospholipase C permeabilizes mammalian cells to proteins

    International Nuclear Information System (INIS)

    Mammalian cells treated with low concentrations of phospholipase C become permeable to the protein toxin alpha-sarcin. A similar permeabilization is not induced upon treatment with other lipases such as phospholipase A2, sphingomyelinase, or cholesterol esterase. Concentrations of 10 micrograms/ml alpha-sarcin almost completely blocked translation in HeLa cells treated with 0.3 U/ml phospholipase C (PL-C) for 1 h. In contrast, 200 micrograms/ml of alpha-sarcin had no effect at all on protein synthesis in untreated cells. Other macromolecules such as horseradish peroxidase and luciferase also enter into cells if they are treated with phospholipase C. This permeabilization method is fully reversible. As soon as 5 min after PL-C removal, the cells become impermeable to alpha-sarcin. Other metabolites such as uridine nucleotides are partially released after PL-C incubation, whereas the content of 86Rb+ remains at control levels, probably because the Na+/K+ ATPase activity increases

  14. Proton production, regulation and pathophysiological roles in the mammalian brain

    Institute of Scientific and Technical Information of China (English)

    Wei-Zheng Zeng; Tian-Le Xu

    2012-01-01

    The recent demonstration of proton signaling in C elegans muscle contraction suggests a novel mechanism for proton-based intercellular communication and has stimulated enthusiasm for exploring proton signaling in higher organisms.Emerging evidence indicates that protons are produced and regulated in localized space and time.Furthermore,identification of proton regulators and sensors in the brain leads to the speculation that proton production and regulation may be of major importance for both physiological and pathological functions ranging from nociception to learning and memory.Extracellular protons may play a role in signal transmission by not only acting on adjacent cells but also affecting the cell from which they were released.In this review,we summarize the upstream and downstream pathways of proton production and regulation in the mammalian brain,with special emphasis on the proton extruders and sensors that are critical in the homeostatic regulation of pH,and discuss their potential roles in proton signaling under normal and pathophysiological conditions.

  15. Transcriptional regulation of mammalian autophagy at a glance.

    Science.gov (United States)

    Füllgrabe, Jens; Ghislat, Ghita; Cho, Dong-Hyung; Rubinsztein, David C

    2016-08-15

    Macroautophagy, hereafter referred to as autophagy, is a catabolic process that results in the lysosomal degradation of cytoplasmic contents ranging from abnormal proteins to damaged cell organelles. It is activated  under diverse conditions, including nutrient deprivation and hypoxia. During autophagy, members of the core autophagy-related (ATG) family of proteins mediate membrane rearrangements, which lead to the engulfment and degradation of cytoplasmic cargo. Recently, the nuclear regulation of autophagy, especially by transcription factors and histone modifiers, has gained increased attention. These factors are not only involved in rapid responses to autophagic stimuli, but also regulate the long-term outcome of autophagy. Now there are more than 20 transcription factors that have been shown to be linked to the autophagic process. However, their interplay and timing appear enigmatic as several have been individually shown to act as major regulators of autophagy. This Cell Science at a Glance article and the accompanying poster highlights the main cellular regulators of transcription involved in mammalian autophagy and their target genes. PMID:27528206

  16. Structural comparison of human mammalian ste20-like kinases.

    Directory of Open Access Journals (Sweden)

    Christopher J Record

    Full Text Available BACKGROUND: The serine/threonine mammalian Ste-20 like kinases (MSTs are key regulators of apoptosis, cellular proliferation as well as polarization. Deregulation of MSTs has been associated with disease progression in prostate and colorectal cancer. The four human MSTs are regulated differently by C-terminal regions flanking the catalytic domains. PRINCIPAL FINDINGS: We have determined the crystal structure of kinase domain of MST4 in complex with an ATP-mimetic inhibitor. This is the first structure of an inactive conformation of a member of the MST kinase family. Comparison with active structures of MST3 and MST1 revealed a dimeric association of MST4 suggesting an activation loop exchanged mechanism of MST4 auto-activation. Together with a homology model of MST2 we provide a comparative analysis of the kinase domains for all four members of the human MST family. SIGNIFICANCE: The comparative analysis identified new structural features in the MST ATP binding pocket and has also defined the mechanism for autophosphorylation. Both structural features may be further explored for inhibitors design. ENHANCED VERSION: This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

  17. Telomere homeostasis in mammalian germ cells: a review.

    Science.gov (United States)

    Reig-Viader, Rita; Garcia-Caldés, Montserrat; Ruiz-Herrera, Aurora

    2016-06-01

    Telomeres protect against genome instability and participate in chromosomal movements during gametogenesis, especially in meiosis. Thus, maintaining telomere structure and telomeric length is essential to both cell integrity and the production of germ cells. As a result, alteration of telomere homeostasis in the germ line may result in the generation of aneuploid gametes or gametogenesis disruption, triggering fertility problems. In this work, we provide an overview on fundamental aspects of the literature regarding the organization of telomeres in mammalian germ cells, paying special attention to telomere structure and function, as well as the maintenance of telomeric length during gametogenesis. Moreover, we discuss the different roles recently described for telomerase and TERRA in maintaining telomere functionality. Finally, we review how new findings in the field of reproductive biology underscore the role of telomere homeostasis as a potential biomarker for infertility. Overall, we anticipate that the study of telomere stability and equilibrium will contribute to improve diagnoses of patients; assess the risk of infertility in the offspring; and in turn, find new treatments. PMID:26525972

  18. Role of cysteines in mammalian VDAC isoforms' function.

    Science.gov (United States)

    De Pinto, Vito; Reina, Simona; Gupta, Ankit; Messina, Angela; Mahalakshmi, Radhakrishnan

    2016-08-01

    In this mini-review, we analyze the influence of cysteines in the structure and activity of mitochondrial outer membrane mammalian VDAC isoforms. The three VDAC isoforms show conserved sequences, similar structures and the same gene organization. The meaning of three proteins encoded in different chromosomes must thus be searched for subtle differences at the amino acid level. Among others, cysteine content is noticeable. In humans, VDAC1 has 2, VDAC2 has 9 and VDAC3 has 6 cysteines. Recent works have shown that, at variance from VDAC1, VDAC2 and VDAC3 exhibit cysteines predicted to protrude towards the intermembrane space, making them a preferred target for oxidation by ROS. Mass spectrometry in VDAC3 revealed that a disulfide bridge can be formed and other cysteine oxidations are also detectable. Both VDAC2 and VDAC3 cysteines were mutagenized to highlight their role in vitro and in complementation assays in Δporin1 yeast. Chemico-physical techniques revealed an important function of cysteines in the structural stabilization of the pore. In conclusion, the works available on VDAC cysteines support the notion that the three proteins are paralogs with a similar pore-function and slightly different, but important, ancillary biological functions. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi. PMID:26947058

  19. Quantitative live imaging of endogenous DNA replication in mammalian cells.

    Directory of Open Access Journals (Sweden)

    Andrew Burgess

    Full Text Available Historically, the analysis of DNA replication in mammalian tissue culture cells has been limited to static time points, and the use of nucleoside analogues to pulse-label replicating DNA. Here we characterize for the first time a novel Chromobody cell line that specifically labels endogenous PCNA. By combining this with high-resolution confocal time-lapse microscopy, and with a simplified analysis workflow, we were able to produce highly detailed, reproducible, quantitative 4D data on endogenous DNA replication. The increased resolution allowed accurate classification and segregation of S phase into early-, mid-, and late-stages based on the unique subcellular localization of endogenous PCNA. Surprisingly, this localization was slightly but significantly different from previous studies, which utilized over-expressed GFP tagged forms of PCNA. Finally, low dose exposure to Hydroxyurea caused the loss of mid- and late-S phase localization patterns of endogenous PCNA, despite cells eventually completing S phase. Taken together, these results indicate that this simplified method can be used to accurately identify and quantify DNA replication under multiple and various experimental conditions.

  20. Identification of Mammalian orthoreovirus type 3 in Italian bats.

    Science.gov (United States)

    Lelli, D; Moreno, A; Lavazza, A; Bresaola, M; Canelli, E; Boniotti, M B; Cordioli, P

    2013-02-01

    Summary This study describes the isolation and molecular characterization of Mammalian orthoreovirus (MRV) in microbats. Faecal samples and dead individuals available from rehabilitation centres or collected from known roost sites were virologically tested. In total, 112 carcasses of bats found dead, and 44 faecal samples were analysed. Nineteen viral strains were isolated by in vitro cell culture from faecal and tissue samples of different bat species (Pipistrellus khulii, Tadarida teniotis, Rhinolophus hipposideros and Vespertilio murinus), and they were morphologically identified as reoviruses by negative staining electron microscopy observation. The definitive assignment of all isolates to MRV was confirmed by RT-PCR assays targeting the L1 gene. Through a multiplex RT-PCR assay targeting the S1 gene, we typed 15 of 19 isolates as MRV type 3. Partial L1 (416 bp) and complete S1 (1416 bp) sequences of the isolates were analysed and compared with those of reference strains obtained from GenBank, belonging to the three serotypes. Molecular analysis of the S1 gene revealed that the amino acid residues associated with neurotropism (198-204NLAIRLP, 249I, 350D and 419E) were highly conserved among the Italian bat strains. These results suggest that potentially neurotropic MRV type 3 strains are widespread among Italian bats. Furthermore, the identification of MRV type 3 in bat species such as Pipistrellus Khulii, which is common in urban areas and known for its close contact with humans, underlines the need for vigilance. PMID:22931153