Random ancestor trees

International Nuclear Information System (INIS)

Ben-Naim, E; Krapivsky, P L

2010-01-01

We investigate a network growth model in which the genealogy controls the evolution. In this model, a new node selects a random target node and links either to this target node, or to its parent, or to its grandparent, etc; all nodes from the target node to its most ancient ancestor are equiprobable destinations. The emerging random ancestor tree is very shallow: the fraction g n of nodes at distance n from the root decreases super-exponentially with n, g n = e −1 /(n − 1)!. We find that a macroscopic hub at the root coexists with highly connected nodes at higher generations. The maximal degree of a node at the nth generation grows algebraically as N 1/β n , where N is the system size. We obtain the series of nontrivial exponents which are roots of transcendental equations: β 1 ≅1.351 746, β 2 ≅1.682 201, etc. As a consequence, the fraction p k of nodes with degree k has an algebraic tail, p k ∼ k −γ , with γ = β 1 + 1 = 2.351 746

Correction to: A sophisticated, differentiated Golgi in the ancestor of eukaryotes.

Science.gov (United States)

Barlow, Lael D; Nývltová, Eva; Aguilar, Maria; Tachezy, Jan; Dacks, Joel B

2018-03-28

Upon publication of the original article, Barlow et al. [1], the authors noticed that Fig. 4b contained an inaccuracy when additional data is taken into account. We inferred a loss of GRASP in the common ancestor of cryptophytes and archaeplastids, based on the absence of identified homologues in the data from taxa that we analyzed, which include Cyanidioschyzon merolae as the single representative of red algae.

RNase MRP and the RNA processing cascade in the eukaryotic ancestor.

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Woodhams, Michael D; Stadler, Peter F; Penny, David; Collins, Lesley J

2007-02-08

Within eukaryotes there is a complex cascade of RNA-based macromolecules that process other RNA molecules, especially mRNA, tRNA and rRNA. An example is RNase MRP processing ribosomal RNA (rRNA) in ribosome biogenesis. One hypothesis is that this complexity was present early in eukaryotic evolution; an alternative is that an initial simpler network later gained complexity by gene duplication in lineages that led to animals, fungi and plants. Recently there has been a rapid increase in support for the complexity-early theory because the vast majority of these RNA-processing reactions are found throughout eukaryotes, and thus were likely to be present in the last common ancestor of living eukaryotes, herein called the Eukaryotic Ancestor. We present an overview of the RNA processing cascade in the Eukaryotic Ancestor and investigate in particular, RNase MRP which was previously thought to have evolved later in eukaryotes due to its apparent limited distribution in fungi and animals and plants. Recent publications, as well as our own genomic searches, find previously unknown RNase MRP RNAs, indicating that RNase MRP has a wide distribution in eukaryotes. Combining secondary structure and promoter region analysis of RNAs for RNase MRP, along with analysis of the target substrate (rRNA), allows us to discuss this distribution in the light of eukaryotic evolution. We conclude that RNase MRP can now be placed in the RNA-processing cascade of the Eukaryotic Ancestor, highlighting the complexity of RNA-processing in early eukaryotes. Promoter analyses of MRP-RNA suggest that regulation of the critical processes of rRNA cleavage can vary, showing that even these key cellular processes (for which we expect high conservation) show some species-specific variability. We present our consensus MRP-RNA secondary structure as a useful model for further searches.

Dewey Called Them Utopians, I Call Them Ancestors

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Kulago, Hollie A.

2018-01-01

In this article, I will describe how the Utopians whom John Dewey once referenced are possibly the ancestors of Indigenous peoples, in this case, ancestors of the Diné. I will describe a Diné philosophy of education through the Kinaaldá ceremony which was the first ceremony created by the Holy People of the Diné to ensure the survival of the…

THE WHITE BLOOD ANCESTOR?

OpenAIRE

M.Arulmani; V.R.Hema Latha

2014-01-01

This scientific research article focus that “Red colour blood” of human shall be considered as the 3rd generation Blood and the Human on origin shall be considered having white colour Blood. The white colour blood of human Ancestor shall be considered composed of only ions of Photon, Electron, Proton and free from Hydrogen, Carbon, Nitrogen, Ozone.

Phylogenetic rooting using minimal ancestor deviation.

Science.gov (United States)

Tria, Fernando Domingues Kümmel; Landan, Giddy; Dagan, Tal

2017-06-19

Ancestor-descendent relations play a cardinal role in evolutionary theory. Those relations are determined by rooting phylogenetic trees. Existing rooting methods are hampered by evolutionary rate heterogeneity or the unavailability of auxiliary phylogenetic information. Here we present a rooting approach, the minimal ancestor deviation (MAD) method, which accommodates heterotachy by using all pairwise topological and metric information in unrooted trees. We demonstrate the performance of the method, in comparison to existing rooting methods, by the analysis of phylogenies from eukaryotes and prokaryotes. MAD correctly recovers the known root of eukaryotes and uncovers evidence for the origin of cyanobacteria in the ocean. MAD is more robust and consistent than existing methods, provides measures of the root inference quality and is applicable to any tree with branch lengths.

The galaxy ancestor problem

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Disney, M. J.; Lang, R. H.

2012-11-01

The Hubble Space Telescope (HST) findsgalaxies whose Tolman dimming exceeds 10 mag. Could evolution alone explain these as our ancestor galaxies or could they be representatives of quite a different dynasty whose descendants are no longer prominent today? We explore the latter hypothesis and argue that surface brightness selection effects naturally bring into focus quite different dynasties from different redshifts. Thus, the HST z = 7 galaxies could be examples of galaxies whose descendants are both too small and too choked with dust to be recognizable in our neighbourhood easily today. Conversely, the ancestors of the Milky Way and its obvious neighbours would have completely sunk below the sky at z > 1.2, unless they were more luminous in the past, although their diffused light could account for the missing re-ionization flux. This Succeeding Prominent Dynasties Hypothesis (SPDH) fits the existing observations both naturally and well even without evolution, including the bizarre distributions of galaxy surface brightness found in deep fields, the angular size ˜(1 + z)-1 law, 'downsizing' which turns out to be an 'illusion' in the sense that it does not imply evolution, 'infant mortality', that is, the discrepancy between stars born and stars seen, the existence of 'red nuggets', and finally the recently discovered and unexpected excess of quasar absorption line damped Lyα systems at high redshift. If galaxies were not significantly brighter in the past and the SPDH were true, then a large proportion of galaxies could remain sunk from sight, possibly at all redshifts, and these sunken galaxies could supply the missing re-ionization flux. We show that fishing these sunken galaxies out of the sky by their optical emissions alone is practically impossible, even when they are nearby. More ingenious methods are needed to detect them. It follows that disentangling galaxy evolution through studying ever higher redshift galaxies may be a forlorn hope because one could

The Five Ancestors--Book 1: Tiger

Science.gov (United States)

Stone, Jeff

2004-01-01

Losing a job is an awfully low point--until it turns into the opportunity to pursue writing full time, and a book like "The Five Ancestors: Tiger" results. Jeff Stone looks back to his own experience as a young reader and taps that experience to help frame his own writing. An intriguing snapshot of his new book follows.

A molecular clock dates the common ancestor of European-type porcine reproductive and respiratory syndrome virus at more than 10 years before the emergence of disease

DEFF Research Database (Denmark)

Forsberg, Roald; Oleksiewicz, Martin B.; Krabbe Petersen, Anne Mette

2001-01-01

an accurate molecular clock for the European PRRSV ORF 3 gene, place the root in the genealogy, estimate the rate of nucleotide substitution, and date the most recent common viral ancestor of the data set to 1979; more than 10 years before the onset of the European epidemic. Based on these findings, we...... conclude that PRRSV virus most likely entered the pig population some time before the epidemic emergence of the virus, and hence, that emergence of European-type PRRSV is not the result of a recent species transmission event. Together, our results show that ORF3 sequencing is a valuable epidemiologic tool...... for examining the emergence and spread of PRRSV in Europe. As such, the panel of well-characterized and highly divergent ORF3 sequences described in this study provides a reference point for future molecular epidemiologic studies....

Apparatus Named after Our Academic Ancestors, III

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Greenslade, Thomas B., Jr.

2014-01-01

My academic ancestors in physics have called on me once more to tell you about the apparatus that they devised, and that many of you have used in your demonstrations and labs. This article is about apparatus named after François Arago, Heinrich Helmholtz, Leon Foucault, and James Watt.

Ancestors protocol for scalable key management

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Dieter Gollmann

2010-06-01

Full Text Available Group key management is an important functional building block for secure multicast architecture. Thereby, it has been extensively studied in the literature. The main proposed protocol is Adaptive Clustering for Scalable Group Key Management (ASGK. According to ASGK protocol, the multicast group is divided into clusters, where each cluster consists of areas of members. Each cluster uses its own Traffic Encryption Key (TEK. These clusters are updated periodically depending on the dynamism of the members during the secure session. The modified protocol has been proposed based on ASGK with some modifications to balance the number of affected members and the encryption/decryption overhead with any number of the areas when a member joins or leaves the group. This modified protocol is called Ancestors protocol. According to Ancestors protocol, every area receives the dynamism of the members from its parents. The main objective of the modified protocol is to reduce the number of affected members during the leaving and joining members, then 1 affects n overhead would be reduced. A comparative study has been done between ASGK protocol and the modified protocol. According to the comparative results, it found that the modified protocol is always outperforming the ASGK protocol.

Vacuum fluctuations in an ancestor vacuum: A possible dark energy candidate

Science.gov (United States)

Aoki, Hajime; Iso, Satoshi; Lee, Da-Shin; Sekino, Yasuhiro; Yeh, Chen-Pin

2018-02-01

We consider an open universe created by bubble nucleation, and study possible effects of our "ancestor vacuum," a de Sitter space in which bubble nucleation occurred, on the present universe. We compute vacuum expectation values of the energy-momentum tensor for a minimally coupled scalar field, carefully taking into account the effect of the ancestor vacuum by the Euclidean prescription. We pay particular attention to the so-called supercurvature mode, a non-normalizable mode on a spatial slice of the open universe, which has been known to exist for sufficiently light fields. This mode decays in time most slowly, and may leave residual effects of the ancestor vacuum, potentially observable in the present universe. We point out that the vacuum energy of the quantum field can be regarded as dark energy if mass of the field is of order the present Hubble parameter or smaller. We obtain preliminary results for the dark energy equation of state w (z ) as a function of the redshift.

The Ancestor Project: Aboriginal Computer Education through Storytelling

Science.gov (United States)

Weston, Marla; Biin, Dianne

2013-01-01

The goal of the ANCESTOR program is to use digital storytelling as a means of promoting an interest in technology careers for Aboriginal learners, as well as increasing cultural literacy. A curriculum was developed and first tested with Aboriginal students at the LÁU,WELNEW Tribal School near Victoria, British Columbia, Canada. Based on feedback…

Graves, Ancestors and Cement in Land disputes in Acholi and Ikland, Uganda

DEFF Research Database (Denmark)

Meinert, Lotte; Willerslev, Rane; Seebach, Sophie Hooge

2017-01-01

graves are made concrete and increasingly cemented indices of belonging in wrangles over land. Belonging is often justified through the presence of ancestor graves on land. The cementing of graves turns them into more concrete and durable proofs of ownership, and the reburial of relatives to disputed......The paper explores the roles of graves, ancestors and concrete pillars in disputes over land across different land-systems, -conflicts, and territory making in northern Uganda by comparing extended cases between Acholi in Gulu district and Ik in Kaabong district . In the post-conflict Acholi region...

Is Ancestor veneration the most universal of all world religions? A critique of modernist cosmological bias

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Thomas Reuter

2015-07-01

Full Text Available Research by anthropologists engaged with the Comparative Austronesia Project (Australian National University has amassed an enormous data set for ethnological comparison between the religions of Austronesian-speaking societies, a language group to which nearly all Indonesian societies also belong. Comparative analysis reveals that ancestor veneration is a key-shared feature among “Austronesian” religious cosmologies; a feature that also resonates strongly with the ancestor-focused religions characteristic of East Asia. Characteristically, the religions of Austronesian-speaking societies focus on the core idea of a sacred time and place of ancestral origin and the continuous flow of life that is issuing forth from this source. Present-day individuals connect with the place and time of origin though ritual acts of retracing a historical path of migration to its source. What can this seemingly exotic notion of a flow of life reveal about the human condition writ large? Is it merely a curiosity of the ethnographic record of this region, a traditional religious insight forgotten even by many of the people whose traditional religion this is, but who have come under the influence of so-called world religions? Or is there something of great importance to be learnt from the Austronesian approach to life? Such questions have remained unasked until now, I argue, because a systematic cosmological bias within western thought has largely prevented us from taking Ancestor Religion and other forms of “traditional knowledge” seriously as an alternative truth claim. While I have discussed elsewhere the significance of Ancestor Religion in reference to my own research in highland Bali, I will attempt in this paper to remove this bias by its roots. I do so by contrasting two modes of thought: the “incremental dualism” of precedence characteristic of Austronesian cultures and their Ancestor Religions, and the “transcendental dualism” of mind and

Algal ancestor of land plants was preadapted for symbiosis.

Science.gov (United States)

Delaux, Pierre-Marc; Radhakrishnan, Guru V; Jayaraman, Dhileepkumar; Cheema, Jitender; Malbreil, Mathilde; Volkening, Jeremy D; Sekimoto, Hiroyuki; Nishiyama, Tomoaki; Melkonian, Michael; Pokorny, Lisa; Rothfels, Carl J; Sederoff, Heike Winter; Stevenson, Dennis W; Surek, Barbara; Zhang, Yong; Sussman, Michael R; Dunand, Christophe; Morris, Richard J; Roux, Christophe; Wong, Gane Ka-Shu; Oldroyd, Giles E D; Ané, Jean-Michel

2015-10-27

Colonization of land by plants was a major transition on Earth, but the developmental and genetic innovations required for this transition remain unknown. Physiological studies and the fossil record strongly suggest that the ability of the first land plants to form symbiotic associations with beneficial fungi was one of these critical innovations. In angiosperms, genes required for the perception and transduction of diffusible fungal signals for root colonization and for nutrient exchange have been characterized. However, the origin of these genes and their potential correlation with land colonization remain elusive. A comprehensive phylogenetic analysis of 259 transcriptomes and 10 green algal and basal land plant genomes, coupled with the characterization of the evolutionary path leading to the appearance of a key regulator, a calcium- and calmodulin-dependent protein kinase, showed that the symbiotic signaling pathway predated the first land plants. In contrast, downstream genes required for root colonization and their specific expression pattern probably appeared subsequent to the colonization of land. We conclude that the most recent common ancestor of extant land plants and green algae was preadapted for symbiotic associations. Subsequent improvement of this precursor stage in early land plants through rounds of gene duplication led to the acquisition of additional pathways and the ability to form a fully functional arbuscular mycorrhizal symbiosis.

The Waikato river: Changing properties of a living Māori ancestor

NARCIS (Netherlands)

Meijl, A.H.M. van

2015-01-01

In Māori cosmology, rivers and other waterways are conceptualised as living ancestors, who have their own life force and spiritual strength. The special status of rivers in Māori society also explains why they are sometimes separated from other Māori claims to natural resources of which they were

The phylogenomic analysis of the anaphase promoting complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes

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Brochier-Armanet Céline

2011-09-01

Full Text Available Abstract Background The Anaphase Promoting Complex or Cyclosome (APC/C is the largest member of the ubiquitin ligase [E3] family. It plays a crucial role in the control of the cell cycle and cell proliferation by mediating the proteolysis of key components by the proteasome. APC/C is made of a dozen subunits that assemble into a large complex of ~1.5 MDa, which interacts with various cofactors and targets. Results Using comparative genomic and phylogenetic approaches, we showed that 24 out of 37 known APC/C subunits, adaptors/co-activators and main targets, were already present in the Last Eukaryotic Common Ancestor (LECA and were well conserved to a few exceptions in all present-day eukaryotic lineages. The phylogenetic analysis of the 24 components inferred to be present in LECA showed that they contain a reliable phylogenetic signal to reconstruct the phylogeny of the domain Eucarya. Conclusions Taken together our analyses indicated that LECA had a complex and highly controlled modern-like cell cycle. Moreover, we showed that, despite what is generally assumed, proteins involved in housekeeping cellular functions may be a good complement to informational genes to study the phylogeny of eukaryotes.

Windmills: Ancestors of the wind power generation

Institute of Scientific and Technical Information of China (English)

Cesare ROSSI; Flavio RUSSO; Sergio SAVINO

2017-01-01

A brief description of the windmills from the second millennium BC to the Renaissance is presented.This survey is a part of several studies conducted by the authors on technology in the ancient world.The windmills are the first motor,other than human muscles,and are the ancestors of the modem wind turbines.Some authors' virtual reconstructions of old windmills are also presented.The paper shows that the operating principle of many modem machines had already been conceived in the ancient times by using a technology that was more advanced than expected,but with two main differences,as follows:Similar tasks were accomplished by using much less energy;and the environmental impact was nil or very low.Modem designers should sometimes consider simplicity rather than the use of a large amount of energy.

Windmills: Ancestors of the wind power generation

Science.gov (United States)

Rossi, Cesare; Russo, Flavio; Savino, Sergio

2017-09-01

A brief description of the windmills from the second millennium BC to the Renaissance is presented. This survey is a part of several studies conducted by the authors on technology in the ancient world. The windmills are the first motor, other than human muscles, and are the ancestors of the modern wind turbines. Some authors' virtual reconstructions of old windmills are also presented. The paper shows that the operating principle of many modern machines had already been conceived in the ancient times by using a technology that was more advanced than expected, but with two main differences, as follows: Similar tasks were accomplished by using much less energy; and the environmental impact was nil or very low. Modern designers should sometimes consider simplicity rather than the use of a large amount of energy.

Heterokont predator Develorapax marinus gen. et sp. nov. – a model of the ochrophyte ancestor

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Vladimir V. Aleoshin

2016-08-01

Full Text Available Heterotrophic lineages of Heterokonta (or stramenopiles, in contrast to a single monophyletic group of autotrophs, Ochrophyta, form several clades that independently branch off the heterokont stem lineage. The nearest neighbors of Ochrophyta in the phylogenetic tree appear to be almost exclusively bacterivorous, whereas the hypothesis of plastid acquisition by the ancestors of the ochrophyte lineage suggests an ability to engulf eukaryotic alga. In line with this hypothesis, the heteretrophic predator at the base of the ochrophyte lineage may be regarded as a model for the ochrophyte ancestor. Here we present a new genus and species of marine free-living heterotrophic heterokont Develorapax marinus, which falls into an isolated heterokont cluster, along with the marine flagellate Developayella elegans, and is able to engulf eukaryotic cells. Together with environmental sequences D. marinus and D. elegans form a class-level clade Developea nom. nov. represented by species adapted to different environmental conditions and with a wide geographical distribution. The position of Developea among Heterokonta in large-scale phylogenetic tree is discussed. We propose that members of the Developea clade represent a model for transition from bacterivory to a predatory feeding mode by selection for larger prey. Presumably, such transition in the grazing strategy is possible in the presence of bacterial biofilms, and has likely occured in the ochrophyte ancestor.

Healing and coping with life within challenges of spiritual insecurity: Juxtaposed consideration of Christ’s sinlessness and African ancestors in pastoral guidance

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Vhumani Magezi

2017-04-01

Full Text Available Spiritual insecurity among African Christians is a huge challenge. The insecurity among other things arises from African people’s former traditional African ancestral world view of ancestral veneration. The ancestors promote or hinder African Christians’ reliance on Christ because they have presupposedly acquired the supernatural power that enables them to provide diagnoses and solutions to life challenges. The inherent problem in the ancestral world view, however, is that the ancestors are both respected and feared by their descendants because they can either bless or harm depending on the state of the relationship between the surviving human beings and the ancestors. The basis of the unpredictable influence of ancestors lies in the fact that they (ancestors are considered as human beings who carry their human qualities to the spiritual world. In light of this situation, one constructive approach that can be advanced to address the challenges of African Christians’ spiritual insecurity is a proper understanding of Christ as a sinless representative of humanity. This approach maintains that healing and coping with life within the challenge of African spirituality in the context of threatening life issues can be addressed by an appropriate understanding of Christ’s sinlessness. The article argues for the foundational status of Christ as a sinless representative of humanity as the controlling framework. In doing so, Christ’s sinlessness and the sinfulness of natural ancestors are juxtaposed to compare the two ontologies in order to draw some pastoral guidelines for African Christians. This approach pays close attention to the factors and mindset that sustain people who adhere to ancestral worship and assess them through a lens of Christology focusing on Christ’s sinlessness as an exemplary doctrine.

Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants.

Science.gov (United States)

Butzin, Nicholas C; Lapierre, Pascal; Green, Anna G; Swithers, Kristen S; Gogarten, J Peter; Noll, Kenneth M

2013-01-01

The bacterial genomes of Thermotoga species show evidence of significant interdomain horizontal gene transfer from the Archaea. Members of this genus acquired many genes from the Thermococcales, which grow at higher temperatures than Thermotoga species. In order to study the functional history of an interdomain horizontally acquired gene we used ancestral sequence reconstruction to examine the thermal characteristics of reconstructed ancestral proteins of the Thermotoga lineage and its archaeal donors. Several ancestral sequence reconstruction methods were used to determine the possible sequences of the ancestral Thermotoga and Archaea myo-inositol-3-phosphate synthase (MIPS). These sequences were predicted to be more thermostable than the extant proteins using an established sequence composition method. We verified these computational predictions by measuring the activities and thermostabilities of purified proteins from the Thermotoga and the Thermococcales species, and eight ancestral reconstructed proteins. We found that the ancestral proteins from both the archaeal donor and the Thermotoga most recent common ancestor recipient were more thermostable than their descendants. We show that there is a correlation between the thermostability of MIPS protein and the optimal growth temperature (OGT) of its host, which suggests that the OGT of the ancestors of these species of Archaea and the Thermotoga grew at higher OGTs than their descendants.

Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants.

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Nicholas C Butzin

Full Text Available The bacterial genomes of Thermotoga species show evidence of significant interdomain horizontal gene transfer from the Archaea. Members of this genus acquired many genes from the Thermococcales, which grow at higher temperatures than Thermotoga species. In order to study the functional history of an interdomain horizontally acquired gene we used ancestral sequence reconstruction to examine the thermal characteristics of reconstructed ancestral proteins of the Thermotoga lineage and its archaeal donors. Several ancestral sequence reconstruction methods were used to determine the possible sequences of the ancestral Thermotoga and Archaea myo-inositol-3-phosphate synthase (MIPS. These sequences were predicted to be more thermostable than the extant proteins using an established sequence composition method. We verified these computational predictions by measuring the activities and thermostabilities of purified proteins from the Thermotoga and the Thermococcales species, and eight ancestral reconstructed proteins. We found that the ancestral proteins from both the archaeal donor and the Thermotoga most recent common ancestor recipient were more thermostable than their descendants. We show that there is a correlation between the thermostability of MIPS protein and the optimal growth temperature (OGT of its host, which suggests that the OGT of the ancestors of these species of Archaea and the Thermotoga grew at higher OGTs than their descendants.

Comparative symbiotic plasmid analysis indicates that symbiosis gene ancestor type affects plasmid genetic evolution.

Science.gov (United States)

Wang, X; Zhao, L; Zhang, L; Wu, Y; Chou, M; Wei, G

2018-07-01

Rhizobial symbiotic plasmids play vital roles in mutualistic symbiosis with legume plants by executing the functions of nodulation and nitrogen fixation. To explore the gene composition and genetic constitution of rhizobial symbiotic plasmids, comparison analyses of 24 rhizobial symbiotic plasmids derived from four rhizobial genera was carried out. Results illustrated that rhizobial symbiotic plasmids had higher proportion of functional genes participating in amino acid transport and metabolism, replication; recombination and repair; carbohydrate transport and metabolism; energy production and conversion and transcription. Mesorhizobium amorphae CCNWGS0123 symbiotic plasmid - pM0123d had similar gene composition with pR899b and pSNGR234a. All symbiotic plasmids shared 13 orthologous genes, including five nod and eight nif/fix genes which participate in the rhizobia-legume symbiosis process. These plasmids contained nod genes from four ancestors and fix genes from six ancestors. The ancestral type of pM0123d nod genes was similar with that of Rhizobium etli plasmids, while the ancestral type of pM0123d fix genes was same as that of pM7653Rb. The phylogenetic trees constructed based on nodCIJ and fixABC displayed different topological structures mainly due to nodCIJ and fixABC ancestral type discordance. The study presents valuable insights into mosaic structures and the evolution of rhizobial symbiotic plasmids. This study compared 24 rhizobial symbiotic plasmids that included four genera and 11 species, illuminating the functional gene composition and symbiosis gene ancestor types of symbiotic plasmids from higher taxonomy. It provides valuable insights into mosaic structures and the evolution of symbiotic plasmids. © 2018 The Society for Applied Microbiology.

Convergent evolution of Hawaiian and Australo-Pacific honeyeaters from distant songbird ancestors.

Science.gov (United States)

Fleischer, Robert C; James, Helen F; Olson, Storrs L

2008-12-23

The Hawaiian "honeyeaters," five endemic species of recently extinct, nectar-feeding songbirds in the genera Moho and Chaetoptila, looked and acted like Australasian honeyeaters (Meliphagidae), and no taxonomist since their discovery on James Cook's third voyage has classified them as anything else. We obtained DNA sequences from museum specimens of Moho and Chaetoptila collected in Hawaii 115-158 years ago. Phylogenetic analysis of these sequences supports monophyly of the two Hawaiian genera but, surprisingly, reveals that neither taxon is a meliphagid honeyeater, nor even in the same part of the songbird radiation as meliphagids. Instead, the Hawaiian species are divergent members of a passeridan group that includes deceptively dissimilar families of songbirds (Holarctic waxwings, neotropical silky flycatchers, and palm chats). Here we designate them as a new family, the Mohoidae. A nuclear-DNA rate calibration suggests that mohoids diverged from their closest living ancestor 14-17 mya, coincident with the estimated earliest arrival in Hawaii of a bird-pollinated plant lineage. Convergent evolution, the evolution of similar traits in distantly related taxa because of common selective pressures, is illustrated well by nectar-feeding birds, but the morphological, behavioral, and ecological similarity of the mohoids to the Australasian honeyeaters makes them a particularly striking example of the phenomenon.

Before the dawn recovering the lost history of our ancestors

CERN Document Server

Wade, Nicholas

2007-01-01

Nicholas Wade’s articles are a major reason why the science section has become the most popular, nationwide, in the New York Times. In his groundbreaking Before the Dawn, Wade reveals humanity’s origins as never before—a journey made possible only recently by genetic science, whose incredible findings have answered such questions as: What was the first human language like? How large were the first societies, and how warlike were they? When did our ancestors first leave Africa, and by what route did they leave? By eloquently solving these and numerous other mysteries, Wade offers nothing less than a uniquely complete retelling of a story that began 500 centuries ago.

Outgroup, alignment and modelling improvements indicate that two TNFSF13-like genes existed in the vertebrate ancestor.

Science.gov (United States)

Redmond, Anthony K; Pettinello, Rita; Dooley, Helen

2017-03-01

The molecular machinery required for lymphocyte development and differentiation appears to have emerged concomitantly with distinct B- and T-like lymphocyte subsets in the ancestor of all vertebrates. The TNFSF superfamily (TNFSF) members BAFF (TNFSF13/Blys) and APRIL (TNFSF13) are key regulators of B cell development survival, and activation in mammals, but the temporal emergence of these molecules, and their precise relationship to the newly identified TNFSF gene BALM (BAFF and APRIL-like molecule), have not yet been elucidated. Here, to resolve the early evolutionary history of this family, we improved outgroup sampling and alignment quality, and applied better fitting substitution models compared to past studies. Our analyses reveal that BALM is a definitive TNFSF13 family member, which split from BAFF in the gnathostome (jawed vertebrate) ancestor. Most importantly, however, we show that both the APRIL and BAFF lineages existed in the ancestors of all extant vertebrates. This implies that APRIL has been lost, or is yet to be found, in cyclostomes (jawless vertebrates). Our results suggest that lineage-specific gene duplication and loss events have caused lymphocyte regulation, despite shared origins, to become secondarily distinct between gnathostomes and cyclostomes. Finally, the structure of lamprey BAFF-like, and its phylogenetic placement as sister to BAFF and BALM, but not the more slowly evolving APRIL, indicates that the primordial lymphocyte regulator was more APRIL-like than BAFF-like.

“Ancestors We Didn’t Even Know We Had”: Alice Walker, Asian Religion, and Ethnic Authenticity

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Kyle Garton-Gundling

2015-03-01

Full Text Available Recent debates about the ethics of identity in a global age have dealt with how to prioritize conflicting local and global allegiances. Guided by these concerns, the fiction of Alice Walker develops a distinctive view of how local cultures and global movements can fruitfully interact. This vision depends on concepts from Asian religions, a major influence that critics of Walker have largely overlooked. Walker promotes Hindu and Buddhist meditation in a context of widespread African American skepticism toward Asian religions. According to widespread notions of cultural authenticity, Asian religions cannot nourish an African American connection to ethnic roots. In response to this challenge, Alice Walker’s fiction portrays Hindu and Buddhist mystics as African Americans’ ancestors, thus positioning these faiths as authentically black. By creatively enfolding Asian religions into her sense of African American heritage, Walker builds a spiritual cosmopolitanism that relies on claims of ancestral affiliation even when these claims are not literal. This strategy is Walker’s effort to create a new paradigm of cultural authenticity, one that allows individuals and groups to choose their ancestors. Walker’s approach seeks to incorporate disparate global influences while still valorizing the figure of the ancestor. This innovative approach places Walker at the forefront of a growing number of African American artists and intellectuals who promote Asian religions to American minorities. Walker’s work vividly dramatizes larger concerns in transnational American Studies: Eastern philosophy’s relevance to identity politics, the tensions between universal ideals and cultural specifics, and the ethics of cross-cultural appropriation.

Wild mallards have more "goose-like" bills than their ancestors: a case of anthropogenic influence?

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Pär Söderquist

Full Text Available Wild populations of the world's most common dabbling duck, the mallard (Anas platyrhynchos, run the risk of genetic introgression by farmed conspecifics released for hunting purposes. We tested whether bill morphology of free-living birds has changed since large-scale releases of farmed mallards started. Three groups of mallards from Sweden, Norway and Finland were compared: historical wild (before large-scale releases started, present-day wild, and present-day farmed. Higher density of bill lamellae was observed in historical wild mallards (only males. Farmed mallards had wider bills than present-day and historical wild ones. Present-day wild and farmed mallards also had higher and shorter bills than historical wild mallards. Present-day mallards thus tend to have more "goose-like" bills (wider, higher, and shorter than their ancestors. Our study suggests that surviving released mallards affect morphological traits in wild population by introgression. We discuss how such anthropogenic impact may lead to a maladapted and genetically compromised wild mallard population. Our study system has bearing on other taxa where large-scale releases of conspecifics with 'alien genes' may cause a cryptic invasive process that nevertheless has fitness consequences for individual birds.

Extensive intron gain in the ancestor of placental mammals

Science.gov (United States)

2011-01-01

Background Genome-wide studies of intron dynamics in mammalian orthologous genes have found convincing evidence for loss of introns but very little for intron turnover. Similarly, large-scale analysis of intron dynamics in a few vertebrate genomes has identified only intron losses and no gains, indicating that intron gain is an extremely rare event in vertebrate evolution. These studies suggest that the intron-rich genomes of vertebrates do not allow intron gain. The aim of this study was to search for evidence of de novo intron gain in domesticated genes from an analysis of their exon/intron structures. Results A phylogenomic approach has been used to analyse all domesticated genes in mammals and chordates that originated from the coding parts of transposable elements. Gain of introns in domesticated genes has been reconstructed on well established mammalian, vertebrate and chordate phylogenies, and examined as to where and when the gain events occurred. The locations, sizes and amounts of de novo introns gained in the domesticated genes during the evolution of mammals and chordates has been analyzed. A significant amount of intron gain was found only in domesticated genes of placental mammals, where more than 70 cases were identified. De novo gained introns show clear positional bias, since they are distributed mainly in 5' UTR and coding regions, while 3' UTR introns are very rare. In the coding regions of some domesticated genes up to 8 de novo gained introns have been found. Intron densities in Eutheria-specific domesticated genes and in older domesticated genes that originated early in vertebrates are lower than those for normal mammalian and vertebrate genes. Surprisingly, the majority of intron gains have occurred in the ancestor of placentals. Conclusions This study provides the first evidence for numerous intron gains in the ancestor of placental mammals and demonstrates that adequate taxon sampling is crucial for reconstructing intron evolution. The

Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors.

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Shah, Firoz; Nicolás, César; Bentzer, Johan; Ellström, Magnus; Smits, Mark; Rineau, Francois; Canbäck, Björn; Floudas, Dimitrios; Carleer, Robert; Lackner, Gerald; Braesel, Jana; Hoffmeister, Dirk; Henrissat, Bernard; Ahrén, Dag; Johansson, Tomas; Hibbett, David S; Martin, Francis; Persson, Per; Tunlid, Anders

2016-03-01

Ectomycorrhizal fungi are thought to have a key role in mobilizing organic nitrogen that is trapped in soil organic matter (SOM). However, the extent to which ectomycorrhizal fungi decompose SOM and the mechanism by which they do so remain unclear, considering that they have lost many genes encoding lignocellulose-degrading enzymes that are present in their saprotrophic ancestors. Spectroscopic analyses and transcriptome profiling were used to examine the mechanisms by which five species of ectomycorrhizal fungi, representing at least four origins of symbiosis, decompose SOM extracted from forest soils. In the presence of glucose and when acquiring nitrogen, all species converted the organic matter in the SOM extract using oxidative mechanisms. The transcriptome expressed during oxidative decomposition has diverged over evolutionary time. Each species expressed a different set of transcripts encoding proteins associated with oxidation of lignocellulose by saprotrophic fungi. The decomposition 'toolbox' has diverged through differences in the regulation of orthologous genes, the formation of new genes by gene duplications, and the recruitment of genes from diverse but functionally similar enzyme families. The capacity to oxidize SOM appears to be common among ectomycorrhizal fungi. We propose that the ancestral decay mechanisms used primarily to obtain carbon have been adapted in symbiosis to scavenge nutrients instead. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Ontogeny of the maxilla in Neanderthals and their ancestors.

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Lacruz, Rodrigo S; Bromage, Timothy G; O'Higgins, Paul; Arsuaga, Juan-Luis; Stringer, Chris; Godinho, Ricardo Miguel; Warshaw, Johanna; Martínez, Ignacio; Gracia-Tellez, Ana; de Castro, José María Bermúdez; Carbonell, Eudald

2015-12-07

Neanderthals had large and projecting (prognathic) faces similar to those of their putative ancestors from Sima de los Huesos (SH) and different from the retracted modern human face. When such differences arose during development and the morphogenetic modifications involved are unknown. We show that maxillary growth remodelling (bone formation and resorption) of the Devil's Tower (Gibraltar 2) and La Quina 18 Neanderthals and four SH hominins, all sub-adults, show extensive bone deposition, whereas in modern humans extensive osteoclastic bone resorption is found in the same regions. This morphogenetic difference is evident by ∼5 years of age. Modern human faces are distinct from those of the Neanderthal and SH fossils in part because their postnatal growth processes differ markedly. The growth remodelling identified in these fossil hominins is shared with Australopithecus and early Homo but not with modern humans suggesting that the modern human face is developmentally derived.

The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammals

Directory of Open Access Journals (Sweden)

Andrésdóttir Valgerdur

2008-11-01

Full Text Available Abstract Background APOBEC3 (A3 proteins deaminate DNA cytosines and block the replication of retroviruses and retrotransposons. Each A3 gene encodes a protein with one or two conserved zinc-coordinating motifs (Z1, Z2 or Z3. The presence of one A3 gene in mice (Z2–Z3 and seven in humans, A3A-H (Z1a, Z2a-Z1b, Z2b, Z2c-Z2d, Z2e-Z2f, Z2g-Z1c, Z3, suggests extraordinary evolutionary flexibility. To gain insights into the mechanism and timing of A3 gene expansion and into the functional modularity of these genes, we analyzed the genomic sequences, expressed cDNAs and activities of the full A3 repertoire of three artiodactyl lineages: sheep, cattle and pigs. Results Sheep and cattle have three A3 genes, A3Z1, A3Z2 and A3Z3, whereas pigs only have two, A3Z2 and A3Z3. A comparison between domestic and wild pigs indicated that A3Z1 was deleted in the pig lineage. In all three species, read-through transcription and alternative splicing also produced a catalytically active double domain A3Z2-Z3 protein that had a distinct cytoplasmic localization. Thus, the three A3 genes of sheep and cattle encode four conserved and active proteins. These data, together with phylogenetic analyses, indicated that a similar, functionally modular A3 repertoire existed in the common ancestor of artiodactyls and primates (i.e., the ancestor of placental mammals. This mammalian ancestor therefore possessed the minimal A3 gene set, Z1-Z2-Z3, required to evolve through a remarkable series of eight recombination events into the present day eleven Z domain human repertoire. Conclusion The dynamic recombination-filled history of the mammalian A3 genes is consistent with the modular nature of the locus and a model in which most of these events (especially the expansions were selected by ancient pathogenic retrovirus infections.

PARTIAL REPRODUCTIVE ISOLATION OF A RECENTLY DERIVED RESIDENT-FRESHWATER POPULATION OF THREESPINE STICKLEBACK (GASTEROSTEUS ACULEATUS) FROM ITS PUTATIVE ANADROMOUS ANCESTOR

Science.gov (United States)

Furin, Christoff G.; Von Hippel, Frank A.; Bell, Michael A.

2012-01-01

We used no-choice mating trials to test for assortative mating between a newly derived resident-freshwater population (8 – 22 generations since founding) of threespine stickleback (Gasterosteus aculeatus) in Loberg Lake, Alaska and its putative anadromous ancestor as well as a morphologically convergent but distantly related resident-freshwater population. Partial reproductive isolation has evolved between the Loberg Lake population and its ancestor within a remarkably short time period. However, Loberg stickleback readily mate with morphologically similar, but distantly related resident-freshwater stickleback. Partial pre-mating isolation is asymmetrical; anadromous females and smaller, resident-freshwater males from Loberg Lake readily mate, but the anadromous males and smaller Loberg females do not. Our results indicate that pre-mating isolation can begin to evolve in allopatry within a few generations after isolation as a correlated effect of evolution of reduced body size. PMID:23025615

The viral transmembrane superfamily: possible divergence of Arenavirus and Filovirus glycoproteins from a common RNA virus ancestor

Directory of Open Access Journals (Sweden)

Buchmeier Michael J

2001-02-01

Full Text Available Abstract Background Recent studies of viral entry proteins from influenza, measles, human immunodeficiency virus, type 1 (HIV-1, and Ebola virus have shown, first with molecular modeling, and then X-ray crystallographic or other biophysical studies, that these disparate viruses share a coiled-coil type of entry protein. Results Structural models of the transmembrane glycoproteins (GP-2 of the Arenaviruses, lymphochoriomeningitis virus (LCMV and Lassa fever virus, are presented, based on consistent structural propensities despite variation in the amino acid sequence. The principal features of the model, a hydrophobic amino terminus, and two antiparallel helices separated by a glycosylated, antigenic apex, are common to a number of otherwise disparate families of enveloped RNA viruses. Within the first amphipathic helix, demonstrable by circular dichroism of a peptide fragment, there is a highly conserved heptad repeat pattern proposed to mediate multimerization by coiled-coil interactions. The amino terminal 18 amino acids are 28% identical and 50% highly similar to the corresponding region of Ebola, a member of the Filovirus family. Within the second, charged helix just prior to membrane insertion there is also high similarity over the central 18 amino acids in corresponding regions of Lassa and Ebola, which may be further related to the similar region of HIV-1 defining a potent antiviral peptide analogue. Conclusions These findings indicate a common pattern of structure and function among viral transmembrane fusion proteins from a number of virus families. Such a pattern may define a viral transmembrane superfamily that evolved from a common precursor eons ago.

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

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Galperin Michael Y

2003-01-01

Full Text Available Abstract Background Comparative analysis of sequenced genomes reveals numerous instances of apparent horizontal gene transfer (HGT, at least in prokaryotes, and indicates that lineage-specific gene loss might have been even more common in evolution. This complicates the notion of a species tree, which needs to be re-interpreted as a prevailing evolutionary trend, rather than the full depiction of evolution, and makes reconstruction of ancestral genomes a non-trivial task. Results We addressed the problem of constructing parsimonious scenarios for individual sets of orthologous genes given a species tree. The orthologous sets were taken from the database of Clusters of Orthologous Groups of proteins (COGs. We show that the phyletic patterns (patterns of presence-absence in completely sequenced genomes of almost 90% of the COGs are inconsistent with the hypothetical species tree. Algorithms were developed to reconcile the phyletic patterns with the species tree by postulating gene loss, COG emergence and HGT (the latter two classes of events were collectively treated as gene gains. We prove that each of these algorithms produces a parsimonious evolutionary scenario, which can be represented as mapping of loss and gain events on the species tree. The distribution of the evolutionary events among the tree nodes substantially depends on the underlying assumptions of the reconciliation algorithm, e.g. whether or not independent gene gains (gain after loss after gain are permitted. Biological considerations suggest that, on average, gene loss might be a more likely event than gene gain. Therefore different gain penalties were used and the resulting series of reconstructed gene sets for the last universal common ancestor (LUCA of the extant life forms were analysed. The number of genes in the reconstructed LUCA gene sets grows as the gain penalty increases. However, qualitative examination of the LUCA versions reconstructed with different gain penalties

Longest Common Extensions via Fingerprinting

DEFF Research Database (Denmark)

Bille, Philip; Gørtz, Inge Li; Kristensen, Jesper

2012-01-01

query time, no extra space and no preprocessing achieves significantly better average case performance. We show a new algorithm, Fingerprint k , which for a parameter k, 1 ≤ k ≤ [log n], on a string of length n and alphabet size σ, gives O(k n1/k) query time using O(k n) space and O(k n + sort......(n,σ)) preprocessing time, where sort(n,σ) is the time it takes to sort n numbers from σ. Though this solution is asymptotically strictly worse than the asymptotically best previously known algorithms, it outperforms them in practice in average case and is almost as fast as the simple linear time algorithm. On worst....... The LCE problem can be solved in linear space with constant query time and a preprocessing of sorting complexity. There are two known approaches achieving these bounds, which use nearest common ancestors and range minimum queries, respectively. However, in practice a much simpler approach with linear...

Ancestor-descendant relationships in evolution: origin of the extant pygmy right whale, Caperea marginata.

Science.gov (United States)

Tsai, Cheng-Hsiu; Fordyce, R Ewan

2015-01-01

Ancestor-descendant relationships (ADRs), involving descent with modification, are the fundamental concept in evolution, but are usually difficult to recognize. We examined the cladistic relationship between the only reported fossil pygmy right whale, †Miocaperea pulchra, and its sole living relative, the enigmatic pygmy right whale Caperea marginata, the latter represented by both adult and juvenile specimens. †Miocaperea is phylogenetically bracketed between juvenile and adult Caperea marginata in morphologically based analyses, thus suggesting a possible ADR-the first so far identified within baleen whales (Cetacea: Mysticeti). The †Miocaperea-Caperea lineage may show long-term morphological stasis and, in turn, punctuated equilibrium. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae.

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Barker, Michael S; Li, Zheng; Kidder, Thomas I; Reardon, Chris R; Lai, Zhao; Oliveira, Luiz O; Scascitelli, Moira; Rieseberg, Loren H

2016-07-01

Like many other flowering plants, members of the Compositae (Asteraceae) have a polyploid ancestry. Previous analyses found evidence for an ancient duplication or possibly triplication in the early evolutionary history of the family. We sought to better place this paleopolyploidy in the phylogeny and assess its nature. We sequenced new transcriptomes for Barnadesia, the lineage sister to all other Compositae, and four representatives of closely related families. Using a recently developed algorithm, MAPS, we analyzed nuclear gene family phylogenies for evidence of paleopolyploidy. We found that the previously recognized Compositae paleopolyploidy is also in the ancestry of the Calyceraceae. Our phylogenomic analyses uncovered evidence for a successive second round of genome duplication among all sampled Compositae except Barnadesia. Our analyses of new samples with new tools provide a revised view of paleopolyploidy in the Compositae. Together with results from a high density Lactuca linkage map, our results suggest that the Compositae and Calyceraceae have a common paleotetraploid ancestor and that most Compositae are descendants of a paleohexaploid. Although paleohexaploids have been previously identified, this is the first example where the paleotetraploid and paleohexaploid lineages have survived over tens of millions of years. The complex polyploidy in the ancestry of the Compositae and Calyceraceae represents a unique opportunity to study the long-term evolutionary fates and consequences of different ploidal levels. © 2016 Botanical Society of America.

Integrating Horizontal Gene Transfer and Common Descent to Depict Evolution and Contrast It with “Common Design”1

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GUILLERMO PAZ-Y-MIÑO-C; ESPINOSA, AVELINA

2016-01-01

Horizontal gene transfer (HGT) and common descent interact in space and time. Because events of HGT co-occur with phylogenetic evolution, it is difficult to depict evolutionary patterns graphically. Tree-like representations of life’s diversification are useful, but they ignore the significance of HGT in evolutionary history, particularly of unicellular organisms, ancestors of multicellular life. Here we integrate the reticulated-tree model, ring of life, symbiogenesis whole-organism model, and eliminative pattern pluralism to represent evolution. Using Entamoeba histolytica alcohol dehydrogenase 2 (EhADH2), a bifunctional enzyme in the glycolytic pathway of amoeba, we illustrate how EhADH2 could be the product of both horizontally acquired features from ancestral prokaryotes (i.e. aldehyde dehydrogenase [ALDH] and alcohol dehydrogenase [ADH]), and subsequent functional integration of these enzymes into EhADH2, which is now inherited by amoeba via common descent. Natural selection has driven the evolution of EhADH2 active sites, which require specific amino acids (cysteine 252 in the ALDH domain; histidine 754 in the ADH domain), iron- and NAD+ as cofactors, and the substrates acetyl-CoA for ALDH and acetaldehyde for ADH. Alternative views invoking “common design” (i.e. the non-naturalistic emergence of major taxa independent from ancestry) to explain the interaction between horizontal and vertical evolution are unfounded. PMID:20021546

In pursuit of our ancestors' hand laterality.

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Bargalló, Amèlia; Mosquera, Marina; Lozano, Sergi

2017-10-01

The aim of this paper is to apply a previously published method (Bargalló and Mosquera, 2014) to the archaeological record, allowing us to identify the hand laterality of our ancestors and determine when and how this feature, which is exhibited most strongly in humans, appeared in our evolutionary history. The method focuses on identifying handedness by looking at the technical features of the flakes produced by a single knapper, and discovering how many flakes are required to ascertain their hand preference. This method can potentially be applied to the majority of archaeological sites, since flakes are the most abundant stone tools, and stone tools are the most widespread and widely-preserved remains from prehistory. For our study, we selected two Spanish sites: Gran Dolina-TD10.1 (Atapuerca) and Abric Romaní (Barcelona), which were occupied by pre-Neanderthal and Neanderthal populations, respectively. Our analyses indicate that a minimum number of eight flakes produced by the same knapper is required to ascertain their hand preference. Even though this figure is relatively low, it is quite difficult to obtain from many archaeological sites. In addition, there is no single technical feature that provides information about handedness, instead there is a combination of eight technical features, localised on the striking platforms and ventral surfaces. The raw material is not relevant where good quality rocks are used, in this case quartzite and flint, since most of them retain the technical features required for the analysis. Expertise is not an issue either, since the technical features analysed here only correlate with handedness (Bargalló and Mosquera, 2014). Our results allow us to tentatively identify one right-handed knapper among the pre-Neanderthals of level TD10.1 at Gran Dolina (Atapuerca), while four of the five Neanderthals analysed from Abric Romaní were right-handed. The hand preference of the fifth knapper from that location (AR5) remains unclear

Large number of ultraconserved elements were already present in the jawed vertebrate ancestor.

KAUST Repository

Wang, Jianli; Lee, Alison P; Kodzius, Rimantas; Brenner, Sydney; Venkatesh, Byrappa

2009-01-01

Stephen (2008) identified 13,736 ultraconserved elements (UCEs) in placental mammals and investigated their evolution in opossum, chicken, frog, and fugu. They found that there was a massive expansion of UCEs during tetrapod evolution and the substitution rate in UCEs showed a significant decline in tetrapods compared with fugu, suggesting they were exapted in tetrapods. They considered it unlikely that these elements are ancient but evolved at a higher rate in teleost fishes. In this study, we investigated the evolution of UCEs in a cartilaginous fish, the elephant shark and show that nearly half the UCEs were present in the jawed vertebrate ancestor. The substitution rate in UCEs is higher in fugu than in elephant shark, and approximately one-third of ancient UCEs have diverged beyond recognition in teleost fishes. These data indicate that UCEs have evolved at a higher rate in teleost fishes, which may have implications for their vast diversity and evolutionary success.

Large number of ultraconserved elements were already present in the jawed vertebrate ancestor.

KAUST Repository

Wang, Jianli

2009-03-01

Stephen (2008) identified 13,736 ultraconserved elements (UCEs) in placental mammals and investigated their evolution in opossum, chicken, frog, and fugu. They found that there was a massive expansion of UCEs during tetrapod evolution and the substitution rate in UCEs showed a significant decline in tetrapods compared with fugu, suggesting they were exapted in tetrapods. They considered it unlikely that these elements are ancient but evolved at a higher rate in teleost fishes. In this study, we investigated the evolution of UCEs in a cartilaginous fish, the elephant shark and show that nearly half the UCEs were present in the jawed vertebrate ancestor. The substitution rate in UCEs is higher in fugu than in elephant shark, and approximately one-third of ancient UCEs have diverged beyond recognition in teleost fishes. These data indicate that UCEs have evolved at a higher rate in teleost fishes, which may have implications for their vast diversity and evolutionary success.

The backbone of the post-synaptic density originated in a unicellular ancestor of choanoflagellates and metazoans

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Manuel Michaël

2010-02-01

Full Text Available Abstract Background Comparative genomics of the early diverging metazoan lineages and of their unicellular sister-groups opens new window to reconstructing the genetic changes which preceded or accompanied the evolution of multicellular body plans. A recent analysis found that the genome of the nerve-less sponges encodes the homologues of most vertebrate post-synaptic proteins. In vertebrate excitatory synapses, these proteins assemble to form the post-synaptic density, a complex molecular platform linking membrane receptors, components of their signalling pathways, and the cytoskeleton. Newly available genomes from Monosiga brevicollis (a member of Choanoflagellata, the closest unicellular relatives of animals and Trichoplax adhaerens (a member of Placozoa: besides sponges, the only nerve-less metazoans offer an opportunity to refine our understanding of post-synaptic protein evolution. Results Searches for orthologous proteins and reconstruction of gene gains/losses based on the taxon phylogeny indicate that post-synaptic proteins originated in two main steps. The backbone scaffold proteins (Shank, Homer, DLG and some of their partners were acquired in a unicellular ancestor of choanoflagellates and metazoans. A substantial additional set appeared in an exclusive ancestor of the Metazoa. The placozoan genome contains most post-synaptic genes but lacks some of them. Notably, the master-scaffold protein Shank might have been lost secondarily in the placozoan lineage. Conclusions The time of origination of most post-synaptic proteins was not concomitant with the acquisition of synapses or neural-like cells. The backbone of the scaffold emerged in a unicellular context and was probably not involved in cell-cell communication. Based on the reconstructed protein composition and potential interactions, its ancestral function could have been to link calcium signalling and cytoskeleton regulation. The complex later became integrated into the evolving

The proteomic complexity and rise of the primordial ancestor of diversified life

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Kim Kyung

2011-05-01

Full Text Available Abstract Background The last universal common ancestor represents the primordial cellular organism from which diversified life was derived. This urancestor accumulated genetic information before the rise of organismal lineages and is considered to be either a simple 'progenote' organism with a rudimentary translational apparatus or a more complex 'cenancestor' with almost all essential biological processes. Recent comparative genomic studies support the latter model and propose that the urancestor was similar to modern organisms in terms of gene content. However, most of these studies were based on molecular sequences, which are fast evolving and of limited value for deep evolutionary explorations. Results Here we engage in a phylogenomic study of protein domain structure in the proteomes of 420 free-living fully sequenced organisms. Domains were defined at the highly conserved fold superfamily (FSF level of structural classification and an iterative phylogenomic approach was used to reconstruct max_set and min_set FSF repertoires as upper and lower bounds of the urancestral proteome. While the functional make up of the urancestral sets was complex, they represent only 5-11% of the 1,420 FSFs of extant proteomes and their make up and reuse was at least 5 and 3 times smaller than proteomes of free-living organisms, repectively. Trees of proteomes reconstructed directly from FSFs or from molecular functions, which included the max_set and min_set as articial taxa, showed that urancestors were always placed at their base and rooted the tree of life in Archaea. Finally, a molecular clock of FSFs suggests the min_set reflects urancestral genetic make up more reliably and confirms diversified life emerged about 2.9 billion years ago during the start of planet oxygenation. Conclusions The minimum urancestral FSF set reveals the urancestor had advanced metabolic capabilities, was especially rich in nucleotide metabolism enzymes, had pathways for the

CERN and ESA’s common roots to fly into space

CERN Multimedia

Antonella Del Rosso

2012-01-01

ESA has named a space ferry after Edoardo Amaldi, one of the founding fathers of CERN but also of ESRO, the ancestor of ESA. Although they have developed in different ways, the three large European scientific organisations – CERN, ESO and ESA – have common roots. A webcast on the day of the launch of the spaceship from Kourou (French Guiana) will celebrate this fact with historic recollections and the participation of members of the Amaldi family.   The ESA’s Automated Transfer Vehicle (ATV) number three will fly a document which has a very clear title: “Edoardo Amaldi, an ESA pioneer”. Given the fact that Edoardo Amaldi was also one of the founding fathers of CERN and that CERN gave birth to ESO, the idea to mark the event with a common action came quite naturally. The live webcast will take place on 23 March at 3 p.m. with the participation of Ugo Amaldi, CERN physicist and son of Edoardo Amaldi, Arturo Russo, historian and author with John...

Cytomolecular analysis of ribosomal DNA evolution in a natural allotetraploid Brachypodium hybridum and its putative ancestors – dissecting complex repetitive structure of intergenic spacers

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Natalia Borowska-Zuchowska

2016-10-01

Full Text Available Nucleolar dominance is an epigenetic phenomenon associated with nuclear 35S rRNA genes and consists in selective suppression of gene loci inherited from one of the progenitors in the allopolyploid. Our understanding of the exact mechanisms that determine this process is still fragmentary, especially in case of the grass species. This study aimed to shed some light on the molecular basis of this genome-specific inactivation of 35S rDNA loci in an allotetraploid Brachypodium hybridum (2n=30, which arose from the interspecific hybridization between two diploid ancestors that were very similar to modern B. distachyon (2n=10 and B. stacei (2n=20. Using fluorescence in situ hybridization with 25S rDNA and chromosome-specific BAC clones as probes we revealed that the nucleolar dominance is present not only in meristematic root-tip cells but also in differentiated cell fraction of B. hybridum. Additionally, the intergenic spacers (IGSs from both of the putative ancestors and the allotetraploid were sequenced and analyzed. The presumptive transcription initiation sites, spacer promoters and repeated elements were identified within the IGSs. Two different length variants, 2.3 kb and 3.5 kb, of IGSs were identified in B. distachyon and B. stacei, respectively, however only the IGS that had originated from B. distachyon-like ancestor was present in the allotetraploid. The amplification pattern of B. hybridum IGSs suggests that some genetic changes occurred in inactive B. stacei-like rDNA loci during the evolution of the allotetraploid. We hypothesize that their preferential silencing is an effect of structural changes in the sequence rather than just the result of the sole inactivation at the epigenetic level.

Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six Geobacteraceae species

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Lovley Derek R

2009-03-01

Full Text Available Abstract Background The anaerobic degradation of organic matter in natural environments, and the biotechnical use of anaerobes in energy production and remediation of subsurface environments, both require the cooperative activity of a diversity of microorganisms in different metabolic niches. The Geobacteraceae family contains members with three important anaerobic metabolisms: fermentation, syntrophic degradation of fermentation intermediates, and anaerobic respiration. Results In order to learn more about the evolution of anaerobic microbial communities, the genome sequences of six Geobacteraceae species were analyzed. The results indicate that the last common Geobacteraceae ancestor contained sufficient genes for anaerobic respiration, completely oxidizing organic compounds with the reduction of external electron acceptors, features that are still retained in modern Geobacter and Desulfuromonas species. Evolution of specialization for fermentative growth arose twice, via distinct lateral gene transfer events, in Pelobacter carbinolicus and Pelobacter propionicus. Furthermore, P. carbinolicus gained hydrogenase genes and genes for ferredoxin reduction that appear to permit syntrophic growth via hydrogen production. The gain of new physiological capabilities in the Pelobacter species were accompanied by the loss of several key genes necessary for the complete oxidation of organic compounds and the genes for the c-type cytochromes required for extracellular electron transfer. Conclusion The results suggest that Pelobacter species evolved parallel strategies to enhance their ability to compete in environments in which electron acceptors for anaerobic respiration were limiting. More generally, these results demonstrate how relatively few gene changes can dramatically transform metabolic capabilities and expand the range of environments in which microorganisms can compete.

Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor

KAUST Repository

Refregier, Guislaine; Abadia, Edgar; Matsumoto, Tomoshige; Ano, Hiromi; Takashima, Tetsuya; Tsuyuguchi, Izuo; Aktas, Elif; Cö mert, Fü sun; Gomgnimbou, Michel Kireopori; Panaiotov, Stefan; Phelan, Jody; Coll, Francesc; Mcnerney, Ruth; Pain, Arnab; Clark, Taane G.; Sola, Christophe

2016-01-01

Altogether, this study definitively proves a strong genetic link between Turkish and Japanese tuberculosis. It provides a first hypothesis for calibrating TB Euro-American lineage molecular clock; additional studies are needed to reliably date events corresponding to intermediate depths in tuberculosis phylogeny.

Chasing ghosts: allopolyploid origin of Oxyria sinensis (Polygonaceae) from its only diploid congener and an unknown ancestor.

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Luo, Xin; Hu, Quanjun; Zhou, Pingping; Zhang, Dan; Wang, Qian; Abbott, Richard J; Liu, Jianquan

2017-06-01

Reconstructing the origin of a polyploid species is particularly challenging when an ancestor has become extinct. Under such circumstances, the extinct donor of a genome found in the polyploid may be treated as a 'ghost' species in that its prior existence is recognized through the presence of its genome in the polyploid. In this study, we aimed to determine the polyploid origin of Oxyria sinensis (2n = 40) for which only one congeneric species is known, that is diploid O. digyna (2n = 14). Genomic in situ hybridization (GISH), transcriptome, phylogenetic and demographic analyses, and ecological niche modelling were conducted for this purpose. GISH revealed that O. sinensis comprised 14 chromosomes from O. digyna and 26 chromosomes from an unknown ancestor. Transcriptome analysis indicated that following divergence from O. digyna, involving genome duplication around 12 million years ago (Ma), a second genome duplication occurred approximately 6 Ma to give rise to O. sinensis. Oxyria sinensis was shown to contain homologous gene sequences divergent from those present in O. digyna in addition to a set that clustered with those in O. digyna. Coalescent simulations indicated that O. sinensis expanded its distribution approximately 6-7 Ma, possibly following the second polyploidization event, whereas O. digyna expanded its range much later. It was also indicated that the distributions of both species contracted and re-expanded during the Pleistocene climatic oscillations. Ecological niche modelling similarly suggested that both species experienced changes in their distributional ranges in response to Quaternary climatic changes. The extinction of the unknown 'ghost' tetraploid species implicated in the origin of O. sinensis could have resulted from superior adaptation of O. sinensis to repeated climatic changes in the region where it now occurs. © 2017 John Wiley & Sons Ltd.

The hominins: a very conservative tribe? Last common ancestors, plasticity and ecomorphology in Hominidae. Or, What's in a name?

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Crompton, Robin Huw

2016-04-01

In the early 20th century the dominant paradigm for the ecological context of the origins of human bipedalism was arboreal suspension. In the 1960s, however, with recognition of the close genetic relationship of humans, chimpanzees and bonobos, and with the first field studies of mountain gorillas and common chimpanzees, it was assumed that locomotion similar to that of common chimpanzees and mountain gorillas, which appeared to be dominated by terrestrial knuckle-walking, must have given rise to human bipedality. This paradigm has been popular, if not universally dominant, until very recently. However, evidence that neither the knuckle-walking or vertical climbing of these apes is mechanically similar to human bipedalism, as well as the hand-assisted bipedality and orthograde clambering of orang-utans, has cast doubt on this paradigm. It now appears that the dominance of terrestrial knuckle-walking in mountain gorillas is an artefact seen only in the extremes of their range, and that both mountain and lowland gorillas have a generalized orthogrady similar to that seen in orang-utans. These data, together with evidence for continued arboreal competence in humans, mesh well with an increasing weight of fossil evidence suggesting that a mix of orang-utan and gorilla-like arboreal locomotion and upright terrestrial bipedalism characterized most australopiths. The late split date of the panins, corresponding to dates for separation of Homo and Australopithecus, leads to the speculation that competition with chimpanzees, as appears to exist today with gorillas, may have driven ecological changes in hominins and perhaps cladogenesis. However, selection for ecological plasticity and morphological conservatism is a core characteristic of Hominidae as a whole, including Hominini. © 2015 Anatomical Society.

Reconstructing a B-cell clonal lineage. I. Statistical inference of unobserved ancestors [v1; ref status: indexed, http://f1000r.es/z6

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Thomas B Kepler

2013-04-01

Full Text Available One of the key phenomena in the adaptive immune response to infection and immunization is affinity maturation, during which antibody genes are mutated and selected, typically resulting in a substantial increase in binding affinity to the eliciting antigen. Advances in technology on several fronts have made it possible to clone large numbers of heavy-chain light-chain pairs from individual B cells and thereby identify whole sets of clonally related antibodies. These collections could provide the information necessary to reconstruct their own history - the sequence of changes introduced into the lineage during the development of the clone - and to study affinity maturation in detail. But the success of such a program depends entirely on accurately inferring the founding ancestor and the other unobserved intermediates. Given a set of clonally related immunoglobulin V-region genes, the method described here allows one to compute the posterior distribution over their possible ancestors, thereby giving a thorough accounting of the uncertainty inherent in the reconstruction. I demonstrate the application of this method on heavy-chain and light-chain clones, assess the reliability of the inference, and discuss the sources of uncertainty.

Buoyancy differences among two deepwater ciscoes from the Great Lakes and their putative ancestor

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Krause, A.E.; Eshenroder, R.L.; Begnoche, L.J.

2002-01-01

We analyzed buoyancy in two deepwater ciscoes, Coregonus hoyi and C. kiyi, and in C. artedi, their putative ancestor, and also analyzed how variations in fish weight, water content, and lipid content affected buoyancy. Buoyancy was significantly different among the three species (p < 0.0001). Estimates of percent buoyancy (neutral buoyancy = 0.0%) were: kiyi, 3.8%; hoyi, 4.7%; and artedi, 5.7%. Buoyancy did not change with fish weight alone (p = 0.38). Fish weight was negatively related to water content for all three species (p = 0.037). Lipid content was not significantly different between hoyi and kiyi, but artedi had significantly fewer lipids than hoyi and kiyi (p < 0.10). When artedi was removed from the analysis, fish weight and lipids accounted for 48% of the variation in buoyancy (p = 0.003), fatter hoyi were less dense than leaner hoyi, but fatter and leaner kiyi were no different in density. Our findings provide additional evidence that buoyancy regulation was a speciating mechanism in deepwater ciscoes and that kiyi is more specialized than hoyi for diel-vertical migration in deep water.

Population genetics of foxtail millet and its wild ancestor

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Wang Yongfang

2010-10-01

Full Text Available Abstract Background Foxtail millet (Setaria italica (L. P. Beauv., one of the most ancient domesticated crops, is becoming a model system for studying biofuel crops and comparative genomics in the grasses. However, knowledge on the level of genetic diversity and linkage disequilibrium (LD is very limited in this crop and its wild ancestor, green foxtail (Setaria viridis (L. P. Beauv.. Such information would help us to understand the domestication process of cultivated species and will allow further research in these species, including association mapping and identification of agricultural significant genes involved in domestication. Results In this study, we surveyed DNA sequence for nine loci across 50 accessions of cultivated foxtail millet and 34 of its wild progenitor. We found a low level of genetic diversity in wild green foxtail (θ = 0.0059, θ means Watterson's estimator of θ. Despite of a 55% loss of its wild diversity, foxtail millet still harbored a considerable level of diversity (θ = 0.0027 when compared to rice and sorghum (θ = 0.0024 and 0.0034, respectively. The level of LD in the domesticated foxtail millet extends to 1 kb, while it decayed rapidly to a negligible level within 150 bp in wild green foxtail. Using coalescent simulation, we estimated the bottleneck severity at k = 0.6095 when ρ/θ = 1. These results indicated that the domestication bottleneck of foxtail millet was more severe than that of maize but slightly less pronounced than that of rice. Conclusions The results in this study establish a general framework for the domestication history of foxtail millet. The low level of genetic diversity and the increased level of LD in foxtail millet are mainly caused by a population bottleneck, although gene flow from foxtail millet to green foxtail is another factor that may have shaped the pattern of genetic diversity of these two related gene pools. The knowledge provided in this study will benefit future population

"While we are questioning we are progressing"—A Reply to the Ancestors of Qualitative Research

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Monika Götsch

2009-07-01

Full Text Available REICHERTZ' reflections on the development of qualitative research during the Berlin Meeting on Qualitative Research Methods in 2009 (http://www.berliner-methodentreffen.de/ have led to the following central questions: Are we facing the end of critical social research? Is this possible end correlated with an uncritical mass of young scientists? In their reply to the ancestors of qualitative research the present authors advocate the abolition of a bipolar thinking about the issues and support a hybrid turn, standing the test through a fundamentally open-minded, reflexive, and deconstructive researcher`s attitude. Using the example of ethnography and gender studies we show that there are indeed opportunities for the future of critical social research: This approach would take place beyond the slaves of market-controlled contract research and ahead of the characters of the eternal hall of fame of social research. URN: urn:nbn:de:0114-fqs0903306

The evolution of air resonance power efficiency in the violin and its ancestors.

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Nia, Hadi T; Jain, Ankita D; Liu, Yuming; Alam, Mohammad-Reza; Barnas, Roman; Makris, Nicholas C

2015-03-08

The fact that acoustic radiation from a violin at air-cavity resonance is monopolar and can be determined by pure volume change is used to help explain related aspects of violin design evolution. By determining the acoustic conductance of arbitrarily shaped sound holes, it is found that air flow at the perimeter rather than the broader sound-hole area dominates acoustic conductance, and coupling between compressible air within the violin and its elastic structure lowers the Helmholtz resonance frequency from that found for a corresponding rigid instrument by roughly a semitone. As a result of the former, it is found that as sound-hole geometry of the violin's ancestors slowly evolved over centuries from simple circles to complex f-holes, the ratio of inefficient, acoustically inactive to total sound-hole area was decimated, roughly doubling air-resonance power efficiency. F-hole length then slowly increased by roughly 30% across two centuries in the renowned workshops of Amati, Stradivari and Guarneri, favouring instruments with higher air-resonance power, through a corresponding power increase of roughly 60%. By evolution-rate analysis, these changes are found to be consistent with mutations arising within the range of accidental replication fluctuations from craftsmanship limitations with subsequent selection favouring instruments with higher air-resonance power.

Molecular evolution of the endosperm starch synthesis pathway genes in rice (Oryza sativa L.) and its wild ancestor, O. rufipogon L.

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Yu, Guoqin; Olsen, Kenneth M; Schaal, Barbara A

2011-01-01

The evolution of metabolic pathways is a fundamental but poorly understood aspect of evolutionary change. One approach for understanding the complexity of pathway evolution is to examine the molecular evolution of genes that together comprise an integrated metabolic pathway. The rice endosperm starch biosynthetic pathway is one of the most thoroughly characterized metabolic pathways in plants, and starch is a trait that has evolved in response to strong selection during rice domestication. In this study, we have examined six key genes (AGPL2, AGPS2b, SSIIa, SBEIIb, GBSSI, ISA1) in the rice endosperm starch biosynthesis pathway to investigate the evolution of these genes before and after rice domestication. Genome-wide sequence tagged sites data were used as a neutral reference to overcome the problems of detecting selection in species with complex demographic histories such as rice. Five variety groups of Oryza sativa (aus, indica, tropical japonica, temperate japonica, aromatic) and its wild ancestor (O. rufipogon) were sampled. Our results showed evidence of purifying selection at AGPL2 in O. rufipogon and strong evidence of positive selection at GBSSI in temperate japonica and tropical japonica varieties and at GBSSI and SBEIIb in aromatic varieties. All the other genes showed a pattern consistent with neutral evolution in both cultivated rice and its wild ancestor. These results indicate the important role of positive selection in the evolution of starch genes during rice domestication. We discuss the role of SBEIIb and GBSSI in the evolution of starch quality during rice domestication and the power and limitation of detecting selection using genome-wide data as a neutral reference.

Modeling the genealogy of a cultural trait.

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Aguilar, Elliot; Ghirlanda, Stefano

2015-05-01

The mathematical study of genealogies has yielded important insights in population biology, such as the ability to estimate the time to the most recent common ancestor (MRCA) of a sample of genetic sequences or of a group of individuals. Here we introduce a model of cultural genealogies that is a step toward answering similar questions for cultural traits. In our model individuals can inherit from a variable, potentially large number of ancestors, rather than from a fixed, small number of ancestors (one or two) as is typical of genetic evolution. We first show that, given a sample of individuals, a cultural common ancestor does not necessarily exist. We then introduce a related concept: the most recent unique ancestor (MRUA), i.e., the most recent single individual who is the earliest cultural ancestor of the sample. We show that, under neutral evolution, the time to the MRUA can be staggeringly larger than the time to MRCA in a single ancestor model, except when the average number of learning opportunities per individuals is small. Our results point out that the properties of cultural genealogies may be very different from those of genetic genealogies, with potential implications for reconstructing the histories of cultural traits. Copyright © 2014 Elsevier Inc. All rights reserved.

Evidence for a single loss of mineralized teeth in the common avian ancestor

DEFF Research Database (Denmark)

Meredith, Robert W.; Zhang, Guojie; Gilbert, M. Thomas P.

2014-01-01

Edentulism, the absence of teeth, has evolved convergently among vertebrates, including birds, turtles, and several lineages of mammals. Instead of teeth, modern birds (Neornithes) use a horny beak (rhamphotheca) and a muscular gizzard to acquire and process food.We performed comparative genomic ...

Genetic variability in common wheat germplasm based on coefficients of parentage

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Fernanda Bered

2002-01-01

Full Text Available The characterization of genetic variability and an estimate of the genetic relationship among varieties are essential to any breeding program, because artificial crosses among less similar parents allow a larger segregation and the combination of different favorable alleles. Genetic variability can be evaluated in different ways, including the Coefficient of Parentage (COP, which estimates the probability of two alleles in two different individuals being identical by descent. In this study, we evaluated the degree of genetic relationship among 53 wheat genotypes, and identified the ancestor genotypes which contributed the most to the current wheat germplasm, as a prediction of the width of the genetic base of this cereal. The results revealed a mean COP of 0.07 and the formation of 22 similarity groups. The ancestor genotypes Ciano 67 and Mentana were those which contributed the most to the current wheat germplasm. According to the COP analyses, the genetic base of wheat rests on a small number of ancestral genotypes.

SARS-Coronavirus ancestor's foot-prints in South-East Asian bat colonies and the refuge theory.

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Gouilh, Meriadeg Ar; Puechmaille, Sébastien J; Gonzalez, Jean-Paul; Teeling, Emma; Kittayapong, Pattamaporn; Manuguerra, Jean-Claude

2011-10-01

phylogeny and the host/pathogen ecological interactions in the description and the understanding of pathogen emergence. The host's phylogeny, biogeography and behaviour, combined with already described roles of pathogen plasticity and anthropic changes are likely to be co-factors of disease emergence. Elucidating the common ancestor of Hipposideridae and Rhinolophidae is key to understanding the evolutionary history of actual betacoronaviruses and therefore to get an insight of the deep origin of SARS-CoV. Copyright © 2011 Elsevier B.V. All rights reserved.

Common themes and cell type specific variations of higher order chromatin arrangements in the mouse

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Cremer Thomas

2005-12-01

Full Text Available Abstract Background Similarities as well as differences in higher order chromatin arrangements of human cell types were previously reported. For an evolutionary comparison, we now studied the arrangements of chromosome territories and centromere regions in six mouse cell types (lymphocytes, embryonic stem cells, macrophages, fibroblasts, myoblasts and myotubes with fluorescence in situ hybridization and confocal laser scanning microscopy. Both species evolved pronounced differences in karyotypes after their last common ancestors lived about 87 million years ago and thus seem particularly suited to elucidate common and cell type specific themes of higher order chromatin arrangements in mammals. Results All mouse cell types showed non-random correlations of radial chromosome territory positions with gene density as well as with chromosome size. The distribution of chromosome territories and pericentromeric heterochromatin changed during differentiation, leading to distinct cell type specific distribution patterns. We exclude a strict dependence of these differences on nuclear shape. Positional differences in mouse cell nuclei were less pronounced compared to human cell nuclei in agreement with smaller differences in chromosome size and gene density. Notably, the position of chromosome territories relative to each other was very variable. Conclusion Chromosome territory arrangements according to chromosome size and gene density provide common, evolutionary conserved themes in both, human and mouse cell types. Our findings are incompatible with a previously reported model of parental genome separation.

Evolution of bidirectional sex change and gonochorism in fishes of the gobiid genera Trimma, Priolepis, and Trimmatom

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Sunobe, Tomoki; Sado, Tetsuya; Hagiwara, Kiyoshi; Manabe, Hisaya; Suzuki, Toshiyuki; Kobayashi, Yasuhisa; Sakurai, Makoto; Dewa, Shin-ichi; Matsuoka, Midori; Shinomiya, Akihiko; Fukuda, Kazuya; Miya, Masaki

2017-04-01

Size-advantage and low-density models have been used to explain how mating systems favor hermaphroditism or gonochorism. However, these models do not indicate historical transitions in sexuality. Here, we investigate the evolution of bidirectional sex change and gonochorism by phylogenetic analysis using the mitochondrial gene of the gobiids Trimma (31 species), Priolepis (eight species), and Trimmatom (two species). Trimma and Priolepis formed a clade within the sister group Trimmatom. Gonadal histology and rearing experiments revealed that Trimma marinae, Trimma nasa, and Trimmatom spp. were gonochoric, whereas all other Trimma and Priolepis spp. were bidirectional sex changers or inferred ones. A maximum-likelihood reconstruction analysis demonstrated that the common ancestor of the three genera was gonochoristic. Bidirectional sex change probably evolved from gonochorism in a common ancestor of Trimma and Priolepis. As the gonads of bidirectional sex changers simultaneously contain mature ovarian and immature testicular components or vice versa, individuals are always potentially capable of functioning as females or males, respectively. Monogamy under low-density conditions may have been the ecological condition for the evolution of bidirectional sex change in a common ancestor. As T. marinae and T. nasa are a monophyletic group, gonochorism should have evolved from bidirectional sex change in a common ancestor.

The cult of amphioxus in German Darwinism; or, our gelatinous ancestors in Naples' blue and balmy bay.

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Hopwood, Nick

2015-01-01

Biologists having rediscovered amphioxus, also known as the lancelet or Branchiostoma, it is time to reassess its place in early Darwinist debates over vertebrate origins. While the advent of the ascidian-amphioxus theory and challenges from various competitors have been, documented, this article offers a richer account of the public appeal of amphioxus as a primitive ancestor. The focus is on how the 'German Darwin' Ernst Haeckel persuaded general magazine and newspaper readers to revere this "flesh of our flesh and blood of our blood", and especially on Das neue Laienbrevier des Haeckelismus (The new lay breviary of Haeckelism) by Moritz Reymond with cartoons by Fritz Steub. From the late 1870s these successful little books of verse introduced the Neapolitan discoveries that made the animal's name and satirized Haeckel's rise as high priest of its cult. One song is reproduced and translated here, with a contemporary "imitation" by the Canadian palaeontologist Edward John Chapman, and extracts from others. Predating the American "It's a long way from amphioxus" by decades, these rhymes dramatize neglected 'species politics' of Darwinism and highlight the roles of humour in negotiating evolution.

Deconstructing Jaco: genetic heritage of an Afrikaner.

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Greeff, J M

2007-09-01

It is often assumed that Afrikaners stem from a small number of Dutch immigrants. As a result they should be genetically homogeneous, show founder effects and be rather inbred. By disentangling my own South African pedigree, that is on average 12 generations deep, I try to quantify the genetic heritage of an Afrikaner. As much as 6% of my genes have been contributed by slaves from Africa, Madagascar and India, and a woman from China. This figure compares well to other genetic and genealogical estimates. Seventy three percent of my lineages coalesce into common founders, and I am related in excess of 10 times to 20 founder ancestors (30 times to Willem Schalk van der Merwe). Significant founder effects are thus possible. The overrepresentation of certain founder ancestors is in part explained by the fact that they had more children. This is remarkable given that they lived more than 300 years (or 12 generations) ago. DECONSTRUCT, a new program for pedigree analysis, identified 125 common ancestors in my pedigree. However, these common ancestors are so distant from myself, paths of between 16 and 25 steps in length, that my inbreeding coefficient is not unusually high (f approximately 0.0019).

Functional study of the Hap4-like genes suggests that the key regulators of carbon metabolism HAP4 and oxidative stress response YAP1 in yeast diverged from a common ancestor.

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Nataliya Petryk

Full Text Available The transcriptional regulator HAP4, induced by respiratory substrates, is involved in the balance between fermentation and respiration in S. cerevisiae. We identified putative orthologues of the Hap4 protein in all ascomycetes, based only on a conserved sixteen amino acid-long motif. In addition to this motif, some of these proteins contain a DNA-binding motif of the bZIP type, while being nonetheless globally highly divergent. The genome of the yeast Hansenula polymorpha contains two HAP4-like genes encoding the protein HpHap4-A which, like ScHap4, is devoid of a bZIP motif, and HpHap4-B which contains it. This species has been chosen for a detailed examination of their respective properties. Based mostly on global gene expression studies performed in the S. cerevisiae HAP4 disruption mutant (ScΔhap4, we show here that HpHap4-A is functionally equivalent to ScHap4, whereas HpHap4-B is not. Moreover HpHAP4-B is able to complement the H2O2 hypersensitivity of the ScYap1 deletant, YAP1 being, in S. cerevisiae, the main regulator of oxidative stress. Finally, a transcriptomic analysis performed in the ScΔyap1 strain overexpressing HpHAP4-B shows that HpHap4-B acts both on oxidative stress response and carbohydrate metabolism in a manner different from both ScYap1 and ScHap4. Deletion of these two genes in their natural host, H. polymorpha, confirms that HpHAP4-A participates in the control of the fermentation/respiration balance, while HpHAP4-B is involved in oxidative stress since its deletion leads to hypersensitivity to H2O2. These data, placed in an evolutionary context, raise new questions concerning the evolution of the HAP4 transcriptional regulation function and suggest that Yap1 and Hap4 have diverged from a unique regulatory protein in the fungal ancestor.

Intravarietal polymorphisms reveal possible common ancestor of native Schinus terebinthifolius Raddi populations in Brazil.

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Pinto, J V C; Crispim, B A; Vasconcelos, A A; Geelen, D; Grisolia, A B; Vieira, M C

2016-01-08

Schinus terebinthifolius Raddi is a perennial native from Atlantic forest. It is of high ecological plasticity and is used in traditional medicine. Based on promising reports concerning its bioactivity, it was included as a species of great interest for distribution through the National Health System. A number of agronomic studies to guide its crop production are therefore underway. This study examined diversity and phylogenetic relationships among native S. terebinthifolius populations from different Brazilian ecosystems: Cerrado; sandbanks; dense rainforest; and deciduous forest. The intergenic regions rpl20-5'rps12, trnH-psbA, and trnS-trnG were sequenced from cpDNA and aligned using BLASTn. There were few fragments for comparison in GenBank and so only region trnS-trnG was informative. There were variations among and within populations with intravarietal polymorphisms and three distinct haplotypes (HpSM, HpDDO, HpNE), once populations from NE (sandbanks and rainforest) clustered together. Sequences from HpSM, HpNE, and HpDDO returned greater similarity to haplotypes A (AY928398.1), B (AY928399.1), and C (AY928400.1), respectively. A network, built by median-joining among native haplotypes and 10 available on GenBank, revealed HpSM as the origin of all other haplogroups. HpDDO showed the most mutations and was closely related to haplogroups from Argentina. While this could indicate hybridization, we believe that the polymorphisms resulted from adaptation to events such as deforestation, fire, rising temperature, and seasonal drought during the transition from Atlantic forest to Cerrado. While more detailed phylogeographical studies are needed, these results indicate eligible groups for distinct climates as an important step for pre-breeding programs before field propagation.

The Complete Chloroplast Genome of a Key Ancestor of Modern Roses, Rosa chinensis var. spontanea, and a Comparison with Congeneric Species

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Hong-Ying Jian

2018-02-01

Full Text Available Rosa chinensis var. spontanea, an endemic and endangered plant of China, is one of the key ancestors of modern roses and a source for famous traditional Chinese medicines against female diseases, such as irregular menses and dysmenorrhea. In this study, the complete chloroplast (cp genome of R. chinensis var. spontanea was sequenced, analyzed, and compared to congeneric species. The cp genome of R. chinensis var. spontanea is a typical quadripartite circular molecule of 156,590 bp in length, including one large single copy (LSC region of 85,910 bp and one small single copy (SSC region of 18,762 bp, separated by two inverted repeat (IR regions of 25,959 bp. The GC content of the whole genome is 37.2%, while that of LSC, SSC, and IR is 42.8%, 35.2% and 31.2%, respectively. The genome encodes 129 genes, including 84 protein-coding genes (PCGs, 37 transfer RNA (tRNA genes, and eight ribosomal RNA (rRNA genes. Seventeen genes in the IR regions were found to be duplicated. Thirty-three forward and five inverted repeats were detected in the cp genome of R. chinensis var. spontanea. The genome is rich in SSRs. In total, 85 SSRs were detected. A genome comparison revealed that IR contraction might be the reason for the relatively smaller cp genome size of R. chinensis var. spontanea compared to other congeneric species. Sequence analysis revealed that the LSC and SSC regions were more divergent than the IR regions within the genus Rosa and that a higher divergence occurred in non-coding regions than in coding regions. A phylogenetic analysis showed that the sampled species of the genus Rosa formed a monophyletic clade and that R. chinensis var. spontanea shared a more recent ancestor with R. lichiangensis of the section Synstylae than with R. odorata var. gigantea of the section Chinenses. This information will be useful for the conservation genetics of R. chinensis var. spontanea and for the phylogenetic study of the genus Rosa, and it might also

The Complete Chloroplast Genome of a Key Ancestor of Modern Roses, Rosa chinensis var. spontanea, and a Comparison with Congeneric Species.

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Jian, Hong-Ying; Zhang, Yong-Hong; Yan, Hui-Jun; Qiu, Xian-Qin; Wang, Qi-Gang; Li, Shu-Bin; Zhang, Shu-Dong

2018-02-12

Rosa chinensis var. spontanea , an endemic and endangered plant of China, is one of the key ancestors of modern roses and a source for famous traditional Chinese medicines against female diseases, such as irregular menses and dysmenorrhea. In this study, the complete chloroplast (cp) genome of R. chinensis var. spontanea was sequenced, analyzed, and compared to congeneric species. The cp genome of R. chinensis var. spontanea is a typical quadripartite circular molecule of 156,590 bp in length, including one large single copy (LSC) region of 85,910 bp and one small single copy (SSC) region of 18,762 bp, separated by two inverted repeat (IR) regions of 25,959 bp. The GC content of the whole genome is 37.2%, while that of LSC, SSC, and IR is 42.8%, 35.2% and 31.2%, respectively. The genome encodes 129 genes, including 84 protein-coding genes (PCGs), 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Seventeen genes in the IR regions were found to be duplicated. Thirty-three forward and five inverted repeats were detected in the cp genome of R. chinensis var. spontanea. The genome is rich in SSRs. In total, 85 SSRs were detected. A genome comparison revealed that IR contraction might be the reason for the relatively smaller cp genome size of R. chinensis var. spontanea compared to other congeneric species. Sequence analysis revealed that the LSC and SSC regions were more divergent than the IR regions within the genus Rosa and that a higher divergence occurred in non-coding regions than in coding regions. A phylogenetic analysis showed that the sampled species of the genus Rosa formed a monophyletic clade and that R. chinensis var. s pontanea shared a more recent ancestor with R. lichiangensis of the section Synstylae than with R. odorata var. gigantea of the section Chinenses . This information will be useful for the conservation genetics of R. chinensis var. spontanea and for the phylogenetic study of the genus Rosa , and it might also facilitate the

GRtoGR: a system for mapping GO relations to gene relations.

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Taha, Kamal

2013-12-01

We introduce in this paper a biological search engine called GRtoGR. Given a set of S genes, GRtoGR would determine from GO graph the most significant Lowest Common Ancestor (LCA) of the GO terms annotating the set S. This significant LCA annotates the genes that are the most semantically related to the set S. The framework of GRtoGR refines the concept of LCA by introducing the concepts of Relevant Lowest Common Ancestor (RLCA) and Semantically Relevant Lowest Common Ancestor (SRLCA). A SRLCA is the most significant LCA of the GO terms annotating the set S. We observe that the existence of the GO terms annotating the set S is dependent on the existence of this SRLCA in GO graph. That is, the terms annotating a given set of genes usually have existence dependency relationships with the SRLCA of these terms. We evaluated GRtoGR experimentally and compared it with nine other methods. Results showed marked improvement.

A shared promoter region suggests a common ancestor for the human VCX/Y, SPANX, and CSAG gene families and the murine CYPT family

DEFF Research Database (Denmark)

Hansen, Martin A; Nielsen, John E; Retelska, Dorota

2008-01-01

, sequences corresponding to the shared promoter region of the CYPT family were identified at 39 loci. Most loci were located immediately upstream of genes belonging to the VCX/Y, SPANX, or CSAG gene families. Sequence comparison of the loci revealed a conserved CYPT promoter-like (CPL) element featuring TATA...... cell types. The genomic regions harboring the gene families were rich in direct and inverted segmental duplications (SD), which may facilitate gene conversion and rapid evolution. The conserved CPL and the common expression profiles suggest that the human VCX/Y, SPANX, and CSAG2 gene families together......Many testis-specific genes from the sex chromosomes are subject to rapid evolution, which can make it difficult to identify murine genes in the human genome. The murine CYPT gene family includes 15 members, but orthologs were undetectable in the human genome. However, using refined homology search...

Complete chloroplast genome sequence of common bermudagrass (Cynodon dactylon (L.) Pers.) and comparative analysis within the family Poaceae.

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Huang, Ya-Yi; Cho, Shu-Ting; Haryono, Mindia; Kuo, Chih-Horng

2017-01-01

Common bermudagrass (Cynodon dactylon (L.) Pers.) belongs to the subfamily Chloridoideae of the Poaceae family, one of the most important plant families ecologically and economically. This grass has a long connection with human culture but its systematics is relatively understudied. In this study, we sequenced and investigated the chloroplast genome of common bermudagrass, which is 134,297 bp in length with two single copy regions (LSC: 79,732 bp; SSC: 12,521 bp) and a pair of inverted repeat (IR) regions (21,022 bp). The annotation contains a total of 128 predicted genes, including 82 protein-coding, 38 tRNA, and 8 rRNA genes. Additionally, our in silico analyses identified 10 sets of repeats longer than 20 bp and predicted the presence of 36 RNA editing sites. Overall, the chloroplast genome of common bermudagrass resembles those from other Poaceae lineages. Compared to most angiosperms, the accD gene and the introns of both clpP and rpoC1 genes are missing. Additionally, the ycf1, ycf2, ycf15, and ycf68 genes are pseudogenized and two genome rearrangements exist. Our phylogenetic analysis based on 47 chloroplast protein-coding genes supported the placement of common bermudagrass within Chloridoideae. Our phylogenetic character mapping based on the parsimony principle further indicated that the loss of the accD gene and clpP introns, the pseudogenization of four ycf genes, and the two rearrangements occurred only once after the most recent common ancestor of the Poaceae diverged from other monocots, which could explain the unusual long branch leading to the Poaceae when phylogeny is inferred based on chloroplast sequences.

tRNA-dependent cysteine biosynthetic pathway represents a strategy to increase cysteine contents by preventing it from thermal degradation: thermal adaptation of methanogenic archaea ancestor.

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Qu, Ge; Wang, Wei; Chen, Ling-Ling; Qian, Shao-Song; Zhang, Hong-Yu

2009-10-01

Although cysteine (Cys) is beneficial to stabilize protein structures, it is not prevalent in thermophiles. For instance, the Cys contents in most thermophilic archaea are only around 0.7%. However, methanogenic archaea, no matter thermophilic or not, contain relatively abundant Cys, which remains elusive for a long time. Recently, Klipcan et al. correlated this intriguing property of methanogenic archaea with their unique tRNA-dependent Cys biosynthetic pathway. But, the deep reasons underlying the correlation are ambiguous. Considering the facts that free Cys is thermally labile and the tRNA-dependent Cys biosynthesis avoids the use of free Cys, we speculate that the unique Cys biosynthetic pathway represents a strategy to increase Cys contents by preventing it from thermal degradation, which may be relevant to the thermal adaptation of methanogenic archaea ancestor.

[Genetic aspects of genealogy].

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Tetushkin, E Iu

2011-11-01

The supplementary historical discipline genealogy is also a supplementary genetic discipline. In its formation, genetics borrowed from genealogy some methods of pedigree analysis. In the 21th century, it started receiving contribution from computer-aided genealogy and genetic (molecular) genealogy. The former provides novel tools for genetics, while the latter, which employing genetic methods, enriches genetics with new evidence. Genealogists formulated three main laws ofgenealogy: the law of three generations, the law of doubling the ancestry number, and the law of declining ancestry. The significance and meaning of these laws can be fully understood only in light of genetics. For instance, a controversy between the exponential growth of the number of ancestors of an individual, i.e., the law of doubling the ancestry number, and the limited number of the humankind is explained by the presence of weak inbreeding because of sibs' interference; the latter causes the pedigrees' collapse, i.e., explains also the law of diminishing ancestry number. Mathematic modeling of pedigrees' collapse presented in a number of studies showed that the number of ancestors of each individual attains maximum in a particular generation termed ancestry saturated generation. All representatives of this and preceding generation that left progeny are common ancestors of all current members of the population. In subdivided populations, these generations are more ancient than in panmictic ones, whereas in small isolates and social strata with limited numbers of partners, they are younger. The genealogical law of three generations, according to which each hundred years contain on average three generation intervals, holds for generation lengths for Y-chromosomal DNA, typically equal to 31-32 years; for autosomal and mtDNA, this time is somewhat shorter. Moving along ascending lineas, the number of genetically effective ancestors transmitting their DNA fragment to descendants increases far

Health and Ancestors: The Case of South Africa and Beyond

African Journals Online (AJOL)

denise

The IPJP is a joint project of the Humanities Faculty of the University of Johannesburg (South Africa) and Edith Cowan ... This work is licensed to the publisher under the Creative Commons Attributions License 3.0 .... that can be successful without the guidance and co- .... the failure by the family to perform a certain ritual.

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

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Wolf Yuri I

2012-12-01

Full Text Available Abstract Background Collections of Clusters of Orthologous Genes (COGs provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs. Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. Results The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of archaeal ancestral forms and gene gain and loss events in archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria, acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major ‘highways’ of horizontal gene transfer. Conclusions The updated collection

Comparative genomics analysis of rice and pineapple contributes to understand the chromosome number reduction and genomic changes in grasses

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Jinpeng Wang

2016-10-01

Full Text Available Rice is one of the most researched model plant, and has a genome structure most resembling that of the grass common ancestor after a grass common tetraploidization ~100 million years ago. There has been a standing controversy whether there had been 5 or 7 basic chromosomes, before the tetraploidization, which were tackled but could not be well solved for the lacking of a sequenced and assembled outgroup plant to have a conservative genome structure. Recently, the availability of pineapple genome, which has not been subjected to the grass-common tetraploidization, provides a precious opportunity to solve the above controversy and to research into genome changes of rice and other grasses. Here, we performed a comparative genomics analysis of pineapple and rice, and found solid evidence that grass-common ancestor had 2n =2x =14 basic chromosomes before the tetraploidization and duplicated to 2n = 4x = 28 after the event. Moreover, we proposed that enormous gene missing from duplicated regions in rice should be explained by an allotetraploid produced by prominently divergent parental lines, rather than gene losses after their divergence. This means that genome fractionation might have occurred before the formation of the allotetraploid grass ancestor.

Adaptation to environmental temperature is a major determinant of molecular evolutionary rates in archaea.

Science.gov (United States)

Groussin, Mathieu; Gouy, Manolo

2011-09-01

Methods to infer the ancestral conditions of life are commonly based on geological and paleontological analyses. Recently, several studies used genome sequences to gain information about past ecological conditions taking advantage of the property that the G+C and amino acid contents of bacterial and archaeal ribosomal DNA genes and proteins, respectively, are strongly influenced by the environmental temperature. The adaptation to optimal growth temperature (OGT) since the Last Universal Common Ancestor (LUCA) over the universal tree of life was examined, and it was concluded that LUCA was likely to have been a mesophilic organism and that a parallel adaptation to high temperature occurred independently along the two lineages leading to the ancestors of Bacteria on one side and of Archaea and Eukarya on the other side. Here, we focus on Archaea to gain a precise view of the adaptation to OGT over time in this domain. It has been often proposed on the basis of indirect evidence that the last archaeal common ancestor was a hyperthermophilic organism. Moreover, many results showed the influence of environmental temperature on the evolutionary dynamics of archaeal genomes: Thermophilic organisms generally display lower evolutionary rates than mesophiles. However, to our knowledge, no study tried to explain the differences of evolutionary rates for the entire archaeal domain and to investigate the evolution of substitution rates over time. A comprehensive archaeal phylogeny and a non homogeneous model of the molecular evolutionary process allowed us to estimate ancestral base and amino acid compositions and OGTs at each internal node of the archaeal phylogenetic tree. The last archaeal common ancestor is predicted to have been hyperthermophilic and adaptations to cooler environments can be observed for extant mesophilic species. Furthermore, mesophilic species present both long branches and high variation of nucleotide and amino acid compositions since the last archaeal

Physical mapping of a large plant genome using global high-information-content-fingerprinting: the distal region of the wheat ancestor Aegilops tauschii chromosome 3DS

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You Frank M

2010-06-01

Full Text Available Abstract Background Physical maps employing libraries of bacterial artificial chromosome (BAC clones are essential for comparative genomics and sequencing of large and repetitive genomes such as those of the hexaploid bread wheat. The diploid ancestor of the D-genome of hexaploid wheat (Triticum aestivum, Aegilops tauschii, is used as a resource for wheat genomics. The barley diploid genome also provides a good model for the Triticeae and T. aestivum since it is only slightly larger than the ancestor wheat D genome. Gene co-linearity between the grasses can be exploited by extrapolating from rice and Brachypodium distachyon to Ae. tauschii or barley, and then to wheat. Results We report the use of Ae. tauschii for the construction of the physical map of a large distal region of chromosome arm 3DS. A physical map of 25.4 Mb was constructed by anchoring BAC clones of Ae. tauschii with 85 EST on the Ae. tauschii and barley genetic maps. The 24 contigs were aligned to the rice and B. distachyon genomic sequences and a high density SNP genetic map of barley. As expected, the mapped region is highly collinear to the orthologous chromosome 1 in rice, chromosome 2 in B. distachyon and chromosome 3H in barley. However, the chromosome scale of the comparative maps presented provides new insights into grass genome organization. The disruptions of the Ae. tauschii-rice and Ae. tauschii-Brachypodium syntenies were identical. We observed chromosomal rearrangements between Ae. tauschii and barley. The comparison of Ae. tauschii physical and genetic maps showed that the recombination rate across the region dropped from 2.19 cM/Mb in the distal region to 0.09 cM/Mb in the proximal region. The size of the gaps between contigs was evaluated by comparing the recombination rate along the map with the local recombination rates calculated on single contigs. Conclusions The physical map reported here is the first physical map using fingerprinting of a complete

Identification, genealogical structure and population genetics of S-alleles in Malus sieversii, the wild ancestor of domesticated apple.

Science.gov (United States)

Ma, X; Cai, Z; Liu, W; Ge, S; Tang, L

2017-09-01

The self-incompatibility (SI) gene that is specifically expressed in pistils encodes the SI-associated ribonuclease (S-RNase), functioning as the female-specificity determinant of a gametophytic SI system. Despite extensive surveys in Malus domestica, the S-alleles have not been fully investigated for Malus sieversii, the primary wild ancestor of the domesticated apple. Here we screened the M. sieversii S-alleles via PCR amplification and sequencing, and identified 14 distinct alleles in this species. By contrast, nearly 40 are present in its close wild relative, Malus sylvestris. We further sequenced 8 nuclear genes to provide a neutral reference, and investigated the evolution of S-alleles via genealogical and population genetic analyses. Both shared ancestral polymorphism and an excess of non-synonymous substitution were detected in the S-RNases of the tribe Maleae in Rosaceae, indicating the action of long-term balancing selection. Approximate Bayesian Computations based on the reference neutral loci revealed a severe bottleneck in four of the six studied M. sieversii populations, suggesting that the low number of S-alleles found in this species is mainly the result of diversity loss due to a drastic population contraction. Such a bottleneck may lead to ambiguous footprints of ongoing balancing selection detected at the S-locus. This study not only elucidates the constituents and number of S-alleles in M. sieversii but also illustrates the potential utility of S-allele number shifts in demographic inference for self-incompatible plant species.

Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome.

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Jonathan L Gordon

2009-05-01

Full Text Available Comparative genomics can be used to infer the history of genomic rearrangements that occurred during the evolution of a species. We used the principle of parsimony, applied to aligned synteny blocks from 11 yeast species, to infer the gene content and gene order that existed in the genome of an extinct ancestral yeast about 100 Mya, immediately before it underwent whole-genome duplication (WGD. The reconstructed ancestral genome contains 4,703 ordered loci on eight chromosomes. The reconstruction is complete except for the subtelomeric regions. We then inferred the series of rearrangement steps that led from this ancestor to the current Saccharomyces cerevisiae genome; relative to the ancestral genome we observe 73 inversions, 66 reciprocal translocations, and five translocations involving telomeres. Some fragile chromosomal sites were reused as evolutionary breakpoints multiple times. We identified 124 genes that have been gained by S. cerevisiae in the time since the WGD, including one that is derived from a hAT family transposon, and 88 ancestral loci at which S. cerevisiae did not retain either of the gene copies that were formed by WGD. Sites of gene gain and evolutionary breakpoints both tend to be associated with tRNA genes and, to a lesser extent, with origins of replication. Many of the gained genes in S. cerevisiae have functions associated with ethanol production, growth in hypoxic environments, or the uptake of alternative nutrient sources.

Developing Multi-Level Institutions from Top-Down Ancestors

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Martha Dowsley

2007-11-01

Full Text Available The academic literature contains numerous examples of the failures of both top-down and bottom-up common pool resource management frameworks. Many authors agree that management regimes instead need to utilize a multi-level governance approach to meet diverse objectives in management. However, many currently operating systems do not have that history. This paper explores the conversion of ancestral top-down regimes to complex systems involving multiple scales, levels and objectives through the management of the polar bear (Ursus maritimus in its five range countries. The less successful polar bear management systems continue to struggle with the challenges of developing institutions with the capacity to learn and change, addressing multiple objectives while recognizing the conservation backbone to management, and matching the institutional scale with biophysical, economic and social scales. The comparatively successful institutions incorporate these features, but reveal on-going problems with vertical links that are partially dealt with through the creation of links to other groups.

In-frame seven amino-acid duplication in AIP arose over the last 3000 years, disrupts protein interaction and stability and is associated with gigantism.

Science.gov (United States)

Salvatori, Roberto; Radian, Serban; Diekmann, Yoan; Iacovazzo, Donato; David, Alessia; Gabrovska, Plamena; Grassi, Giorgia; Bussell, Anna-Marie; Stals, Karen; Weber, Astrid; Quinton, Richard; Crowne, Elizabeth C; Corazzini, Valentina; Metherell, Lou; Kearney, Tara; Du Plessis, Daniel; Sinha, Ajay Kumar; Baborie, Atik; Lecoq, Anne-Lise; Chanson, Philippe; Ansorge, Olaf; Ellard, Sian; Trainer, Peter J; Balding, David; Thomas, Mark G; Korbonits, Márta

2017-09-01

Mutations in the aryl hydrocarbon receptor-interacting protein ( AIP ) gene are associated with pituitary adenoma, acromegaly and gigantism. Identical alleles in unrelated pedigrees could be inherited from a common ancestor or result from recurrent mutation events. Observational, inferential and experimental study, including: AIP mutation testing; reconstruction of 14 AIP -region (8.3 Mbp) haplotypes; coalescent-based approximate Bayesian estimation of the time to most recent common ancestor (tMRCA) of the derived allele; forward population simulations to estimate current number of allele carriers; proposal of mutation mechanism; protein structure predictions; co-immunoprecipitation and cycloheximide chase experiments. Nine European-origin, unrelated c.805_825dup-positive pedigrees (four familial, five sporadic from the UK, USA and France) included 16 affected (nine gigantism/four acromegaly/two non-functioning pituitary adenoma patients and one prospectively diagnosed acromegaly patient) and nine unaffected carriers. All pedigrees shared a 2.79 Mbp haploblock around AIP with additional haploblocks privately shared between subsets of the pedigrees, indicating the existence of an evolutionarily recent common ancestor, the 'English founder', with an estimated median tMRCA of 47 generations (corresponding to 1175 years) with a confidence interval (9-113 generations, equivalent to 225-2825 years). The mutation occurred in a small tandem repeat region predisposed to slipped strand mispairing. The resulting seven amino-acid duplication disrupts interaction with HSP90 and leads to a marked reduction in protein stability. The c.805_825dup allele, originating from a common ancestor, associates with a severe clinical phenotype and a high frequency of gigantism. The mutation is likely to be the result of slipped strand mispairing and affects protein-protein interactions and AIP protein stability. © 2017 The authors.

The NBS-LRR architectures of plant R-proteins and metazoan NLRs evolved in independent events.

Science.gov (United States)

Urbach, Jonathan M; Ausubel, Frederick M

2017-01-31

There are intriguing parallels between plants and animals, with respect to the structures of their innate immune receptors, that suggest universal principles of innate immunity. The cytosolic nucleotide binding site-leucine rich repeat (NBS-LRR) resistance proteins of plants (R-proteins) and the so-called NOD-like receptors of animals (NLRs) share a domain architecture that includes a STAND (signal transduction ATPases with numerous domains) family NTPase followed by a series of LRRs, suggesting inheritance from a common ancestor with that architecture. Focusing on the STAND NTPases of plant R-proteins, animal NLRs, and their homologs that represent the NB-ARC (nucleotide-binding adaptor shared by APAF-1, certain R gene products and CED-4) and NACHT (named for NAIP, CIIA, HET-E, and TEP1) subfamilies of the STAND NTPases, we analyzed the phylogenetic distribution of the NBS-LRR domain architecture, used maximum-likelihood methods to infer a phylogeny of the NTPase domains of R-proteins, and reconstructed the domain structure of the protein containing the common ancestor of the STAND NTPase domain of R-proteins and NLRs. Our analyses reject monophyly of plant R-proteins and NLRs and suggest that the protein containing the last common ancestor of the STAND NTPases of plant R-proteins and animal NLRs (and, by extension, all NB-ARC and NACHT domains) possessed a domain structure that included a STAND NTPase paired with a series of tetratricopeptide repeats. These analyses reject the hypothesis that the domain architecture of R-proteins and NLRs was inherited from a common ancestor and instead suggest the domain architecture evolved at least twice. It remains unclear whether the NBS-LRR architectures were innovations of plants and animals themselves or were acquired by one or both lineages through horizontal gene transfer.

Nicolae Milescu Spătarul - ancestor of a Nobel Laureate - Ilia I. Mecinikov. Part I. Nicolae Milescu-Spătarul’s secular European impact; 1st of June 2011 - 375 years since the birth of the European erudite

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Dan RIGA

2011-01-01

Full Text Available The culture of tradition and patrimony is an act of civilization, as well as one of identitaryeducation. This is why the promotion of restitution comprises all areas of progress and humancreation.Nicolae Milescu-Spătarul (b. 1636 in Moldavia - d. 1708 in Russia was an eruditehumanist scholar, an encyclopaedist, a theologist, diplomat, historian, geographer, ethnographer,translator, memorialist and a polyglot (Romanian, ancient and modern Greek, Latin, Turkish andSlavonic-Russian. Commemorating and honouring this figure, of European and Eurasianimportance alike, is a debt of honour: 1958 – 250 years since death; 2011 – 375 years since birth.At this time, the need to fully publish his work arises, as a large part of it is still kept in libraries,archives and European private collections in the form of manuscripts. Nicolae Milescu-Spătarulwas the ancestor of the Nobel Laureate (1908, scientist Ilia I. Mecinikov (1845-1916.The work reveals the great scholar’s (eastern, but also western, European and Asiancultural, scientific and diplomatic impact – at that moment and throughout time – but also theSorin Riga, Dan Riga, Vasile Man - Nicolae Milescu Spătarul - ancestor of a Nobel Laureate - Ilia I. Mecinikov impact of his vast work. The remarkable monograph The Description of China (58 chapters was published in Romanian only in 1958.

The environmental context of human evolutionary history in Eurasia and Africa.

Science.gov (United States)

Elton, Sarah

2008-04-01

This review has three main aims: (1) to make specific predictions about the habitat of the hypothetical last common ancestor of the chimpanzee/bonobo-human clade; (2) to outline the major trends in environments between 8-6 Ma and the late Pleistocene; and (3) to pinpoint when, and in some cases where, human ancestors evolved to cope with the wide range of habitats they presently tolerate. Several lines of evidence indicate that arboreal environments, particularly woodlands, were important habitats for late Miocene hominids and hominins, and therefore possibly for the last common ancestor of the chimpanzee/bonobo-human clade. However, as there is no clear candidate for this last common ancestor, and because the sampling of fossils and past environments is inevitably patchy, this prediction remains a working hypothesis at best. Nonetheless, as a primate, it is expected that the last common ancestor was ecologically dependent on trees in some form. Understanding past environments is important, as palaeoenvironmental reconstructions provide the context for human morphological and behavioural evolution. Indeed, the impact of climate on the evolutionary history of our species has long been debated. Since the mid-Miocene, the Earth has been experiencing a general cooling trend accompanied by aridification, which intensified during the later Pliocene and Pleistocene. Numerous climatic fluctuations, as well as local, regional and continental geography that influenced weather patterns and vegetation, created hominin environments that were dynamic in space and time. Behavioural flexibility and cultural complexity were crucial aspects of hominin expansion into diverse environments during the Pleistocene, but the ability to exploit varied and varying habitats was established much earlier in human evolutionary history. The development of increasingly complex tool technology facilitated re-expansion into tropical forests. These environments are difficult for obligate bipeds to

Rosaceous Chamaebatiaria-like foliage from the Paleogene of western North America

Science.gov (United States)

Wolfe, Jack A.; Wehr, Wesley

1988-01-01

Chamaebatiaria and Chamaebatia, two characteristic genera of the Californian floristic province, are traditionally placed in different subfamilies of Rosaceae, Spiraeoideae and Rosoideae, respectively. Analysis of the foliar and reproductive characters of the extant species of these genera indicates that the two genera could be closely related and the assignment of Chamaebatia to Rosoideae invalid. Fossil leaves of lineages of both genera occur in the Paleogene montane floras of the Rocky Mountain region and provide evidence that the two lineages diverged from a common ancestor in the Eocene. The common ancestor probably was adapted to sunny habitats in mesic coniferous forest, and, during the post-Eocene, the two lineages were able to adapt to progressively drier climates. A third extant genus, the east Asian Sorbaria, also appears to be closely related to the California genera and to have been derived from the same common ancestor. New taxa and combinations proposed are: St onebergia columbiana. n. gen. and n. sp.; Salmonensea prefoliolosa (R. W. Br.), n. gen. and n. comb.; Stockeya creedensis (R. W. Br.), n. gen. and n. comb.; Stockeya montana, n. sp.; and Sorbaria wahrhaftigii, n. sp.

Assessment of Flagellate Diversity at Deep-Sea Hydrothermal Vents Using the Combined Approach of Culture-Dependent and Culture-Independent Methods

National Research Council Canada - National Science Library

Atkins, Michael

2000-01-01

.... Molecular and ultrastructural evidence point to one of the isolates. Ancyromonas, as a plausible candidate for the closest relative to the common ancestor of Metazoans, Fungi, and Choanoglagellates...

Common approach to common interests

Energy Technology Data Exchange (ETDEWEB)

NONE

2001-06-01

In referring to issues confronting the energy field in this region and options to be exercised in the future, I would like to mention the fundamental condition of the utmost importance. That can be summed up as follows: any subject in energy area can never be solved by one country alone, given the geographical and geopolitical characteristics intrinsically possessed by energy. So, a regional approach is needed and it is especially necessary for the main players in the region to jointly address problems common to them. Though it may be a matter to be pursued in the distant future, I am personally dreaming a 'Common Energy Market for Northeast Asia,' in which member countries' interests are adjusted so that the market can be integrated and the region can become a most economically efficient market, thus formulating an effective power to encounter the outside. It should be noted that Europe needed forty years to integrate its market as the unified common market. It is necessary for us to follow a number of steps over the period to eventually materialize our common market concept, too. Now is the time for us to take a first step to lay the foundation for our descendants to enjoy prosperity from such a common market.

Common Courses for Common Purposes:

DEFF Research Database (Denmark)

Schaub Jr, Gary John

2014-01-01

(PME)? I suggest three alternative paths that increased cooperation in PME at the level of the command and staff course could take: a Nordic Defence College, standardized national command and staff courses, and a core curriculum of common courses for common purposes. I conclude with a discussion of how...

Cell-Specific Expression of Homospermidine Synthase, the Entry Enzyme of the Pyrrolizidine Alkaloid Pathway in Senecio vernalis, in Comparison with Its Ancestor, Deoxyhypusine Synthase1

Science.gov (United States)

Moll, Stefanie; Anke, Sven; Kahmann, Uwe; Hänsch, Robert; Hartmann, Thomas; Ober, Dietrich

2002-01-01

Pyrrolizidine alkaloids (PAs) are constitutive plant defense compounds with a sporadic taxonomic occurrence. The first committed step in PA biosynthesis is catalyzed by homospermidine synthase (HSS). Recent evidence confirmed that HSS evolved by gene duplication from deoxyhypusine synthase (DHS), an enzyme involved in the posttranslational activation of the eukaryotic translation initiation factor 5A. To better understand the evolutionary relationship between these two enzymes, which are involved in completely different biological processes, we studied their tissue-specific expression. RNA-blot analysis, reverse transcriptase-PCR, and immunolocalization techniques demonstrated that DHS is constitutively expressed in shoots and roots of Senecio vernalis (Asteraceae), whereas HSS expression is root specific and restricted to distinct groups of endodermis and neighboring cortex cells located opposite to the phloem. All efforts to detect DHS by immunolocalization failed, but studies with promoter-β-glucuronidase fusions confirmed a general expression pattern, at least in young seedlings of tobacco (Nicotiana tabacum). The expression pattern for HSS differs completely from its ancestor DHS due to the adaptation of HSS to the specific requirements of PA biosynthesis. PMID:12226485

Phylogenomic analysis of Odyssella thessalonicensis fortifies the common origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana mitochondrion.

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Kalliopi Georgiades

Full Text Available BACKGROUND: The evolution of the Alphaproteobacteria and origin of the mitochondria are topics of considerable debate. Most studies have placed the mitochondria ancestor within the Rickettsiales order. Ten years ago, the bacterium Odyssella thessalonicensis was isolated from Acanthamoeba spp., and the 16S rDNA phylogeny placed it within the Rickettsiales. Recently, the whole genome of O. thessalonicensis has been sequenced, and 16S rDNA phylogeny and more robust and accurate phylogenomic analyses have been performed with 65 highly conserved proteins. METHODOLOGY/PRINCIPAL FINDINGS: The results suggested that the O. thessalonicensis emerged between the Rickettsiales and other Alphaproteobacteria. The mitochondrial proteins of the Reclinomonas americana have been used to locate the phylogenetic position of the mitochondrion ancestor within the Alphaproteobacteria tree. Using the K tree score method, nine mitochondrion-encoded proteins, whose phylogenies were congruent with the Alphaproteobacteria phylogenomic tree, have been selected and concatenated for Bayesian and Maximum Likelihood phylogenies. The Reclinomonas americana mitochondrion is a sister taxon to the free-living bacteria Candidatus Pelagibacter ubique, and together, they form a clade that is deeply rooted in the Rickettsiales clade. CONCLUSIONS/SIGNIFICANCE: The Reclinomonas americana mitochondrion phylogenomic study confirmed that mitochondria emerged deeply in the Rickettsiales clade and that they are closely related to Candidatus Pelagibacter ubique.

Fido, a novel AMPylation domain common to fic, doc, and AvrB.

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Lisa N Kinch

2009-06-01

Full Text Available The Vibrio parahaemolyticus type III secreted effector VopS contains a fic domain that covalently modifies Rho GTPase threonine with AMP to inhibit downstream signaling events in host cells. The VopS fic domain includes a conserved sequence motif (HPFx[D/E]GN[G/K]R that contributes to AMPylation. Fic domains are found in a variety of species, including bacteria, a few archaea, and metazoan eukaryotes.We show that the AMPylation activity extends to a eukaryotic fic domain in Drosophila melanogaster CG9523, and use sequence and structure based computational methods to identify related domains in doc toxins and the type III effector AvrB. The conserved sequence motif that contributes to AMPylation unites fic with doc. Although AvrB lacks this motif, its structure reveals a similar topology to the fic and doc folds. AvrB binds to a peptide fragment of its host virulence target in a similar manner as fic binds peptide substrate. AvrB also orients a phosphate group from a bound ADP ligand near the peptide-binding site and in a similar position as a bound fic phosphate.The demonstrated eukaryotic fic domain AMPylation activity suggests that the VopS effector has exploited a novel host posttranslational modification. Fic domain-related structures give insight to the AMPylation active site and to the VopS fic domain interaction with its host GTPase target. These results suggest that fic, doc, and AvrB stem from a common ancestor that has evolved to AMPylate protein substrates.

Positively selected sites in cetacean myoglobins contribute to protein stability

DEFF Research Database (Denmark)

Dasmeh, Pouria; Serohijos, Adrian W R; Kepp, Kasper P

2013-01-01

Since divergence ∼50 Ma ago from their terrestrial ancestors, cetaceans underwent a series of adaptations such as a ∼10-20 fold increase in myoglobin (Mb) concentration in skeletal muscle, critical for increasing oxygen storage capacity and prolonging dive time. Whereas the O2-binding affinity...... between Mb folding stability and protein abundance, suggesting that a selection pressure for stability acts proportionally to higher expression. We also identify a major divergence event leading to the common ancestor of whales, during which major stabilization occurred. Most of the positively selected...

Horizontal transfer of a subtilisin gene from plants into an ancestor of the plant pathogenic fungal genus Colletotrichum.

Science.gov (United States)

Armijos Jaramillo, Vinicio Danilo; Vargas, Walter Alberto; Sukno, Serenella Ana; Thon, Michael R

2013-01-01

The genus Colletotrichum contains a large number of phytopathogenic fungi that produce enormous economic losses around the world. The effect of horizontal gene transfer (HGT) has not been studied yet in these organisms. Inter-Kingdom HGT into fungal genomes has been reported in the past but knowledge about the HGT between plants and fungi is particularly limited. We describe a gene in the genome of several species of the genus Colletotrichum with a strong resemblance to subtilisins typically found in plant genomes. Subtilisins are an important group of serine proteases, widely distributed in all of the kingdoms of life. Our hypothesis is that the gene was acquired by Colletotrichum spp. through (HGT) from plants to a Colletotrichum ancestor. We provide evidence to support this hypothesis in the form of phylogenetic analyses as well as a characterization of the similarity of the subtilisin at the primary, secondary and tertiary structural levels. The remarkable level of structural conservation of Colletotrichum plant-like subtilisin (CPLS) with plant subtilisins and the differences with the rest of Colletotrichum subtilisins suggests the possibility of molecular mimicry. Our phylogenetic analysis indicates that the HGT event would have occurred approximately 150-155 million years ago, after the divergence of the Colletotrichum lineage from other fungi. Gene expression analysis shows that the gene is modulated during the infection of maize by C. graminicola suggesting that it has a role in plant disease. Furthermore, the upregulation of the CPLS coincides with the downregulation of several plant genes encoding subtilisins. Based on the known roles of subtilisins in plant pathogenic fungi and the gene expression pattern that we observed, we postulate that the CPLSs have an important role in plant infection.

Innexin gap junctions in nerve cells coordinate spontaneous contractile behavior in Hydra polyps

KAUST Repository

Takaku, Yasuharu; Hwang, Jung Shan; Wolf, Alexander; Bö ttger, Angelika; Shimizu, Hiroshi; David, Charles N.; Gojobori, Takashi

2014-01-01

Nerve cells and spontaneous coordinated behavior first appeared near the base of animal evolution in the common ancestor of cnidarians and bilaterians. Experiments on the cnidarian Hydra have demonstrated that nerve cells are essential

Genealogies in simple models of evolution

International Nuclear Information System (INIS)

Brunet, Éric; Derrida, Bernard

2013-01-01

We review the statistical properties of the genealogies of a few models of evolution. In the asexual case, selection leads to coalescence times which grow logarithmically with the size of the population, in contrast with the linear growth of the neutral case. Moreover for a whole class of models, the statistics of the genealogies are those of the Bolthausen–Sznitman coalescent rather than the Kingman coalescent in the neutral case. For sexual reproduction in the neutral case, the time to reach the first common ancestors for the whole population and the time for all individuals to have all their ancestors in common are also logarithmic in the population size, as predicted by Chang in 1999. We discuss how these times are modified by introducing selection in a simple way. (paper)

De novo Transcriptome Assembly of Common Wild Rice (Oryza rufipogon Griff.) and Discovery of Drought-Response Genes in Root Tissue Based on Transcriptomic Data.

Science.gov (United States)

Tian, Xin-Jie; Long, Yan; Wang, Jiao; Zhang, Jing-Wen; Wang, Yan-Yan; Li, Wei-Min; Peng, Yu-Fa; Yuan, Qian-Hua; Pei, Xin-Wu

2015-01-01

The perennial O. rufipogon (common wild rice), which is considered to be the ancestor of Asian cultivated rice species, contains many useful genetic resources, including drought resistance genes. However, few studies have identified the drought resistance and tissue-specific genes in common wild rice. In this study, transcriptome sequencing libraries were constructed, including drought-treated roots (DR) and control leaves (CL) and roots (CR). Using Illumina sequencing technology, we generated 16.75 million bases of high-quality sequence data for common wild rice and conducted de novo assembly and annotation of genes without prior genome information. These reads were assembled into 119,332 unigenes with an average length of 715 bp. A total of 88,813 distinct sequences (74.42% of unigenes) significantly matched known genes in the NCBI NT database. Differentially expressed gene (DEG) analysis showed that 3617 genes were up-regulated and 4171 genes were down-regulated in the CR library compared with the CL library. Among the DEGs, 535 genes were expressed in roots but not in shoots. A similar comparison between the DR and CR libraries showed that 1393 genes were up-regulated and 315 genes were down-regulated in the DR library compared with the CR library. Finally, 37 genes that were specifically expressed in roots were screened after comparing the DEGs identified in the above-described analyses. This study provides a transcriptome sequence resource for common wild rice plants and establishes a digital gene expression profile of wild rice plants under drought conditions using the assembled transcriptome data as a reference. Several tissue-specific and drought-stress-related candidate genes were identified, representing a fully characterized transcriptome and providing a valuable resource for genetic and genomic studies in plants.

The Socio-Cultural Significance of the Kakube Festival of the ...

African Journals Online (AJOL)

This paper generally explores the importance of local events such as the festivals which bring people together to celebrate a common heritage. It finally narrowed in on the people of Nandom who trace their roots to a common ancestor and as such make feverish attempts aimed at ensuring that an annual affair (Kakube) ...

Evolution of the fish rhabdovirus viral haemorrhagic septicaemia virus

DEFF Research Database (Denmark)

Einer-Jensen, Katja; Ahrens, Peter; Forsberg, Roald

2004-01-01

of free-living marine fish species. To study the genetic evolution of VHSV, the entire G gene from 74 isolates was analysed. VHSV from wild marine species caught in the Baltic Sea, Skagerrak, Kattegat, North Sea, and English Channel and European freshwater isolates, appeared to share a recent common...... ancestor. Based on the estimated nucleotide substitution rate, the ancestor of the European fresh water isolates was dated some 50 years ago. This finding fits with the initial reports in the 1950s on clinical observations of VHS in Danish freshwater rainbow trout farms. The study also indicates...

Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs

KAUST Repository

Alam, Tanvir; Alazmi, Meshari; Naser, Rayan Mohammad Mahmoud; Huser, Franceline; Momin, Afaque Ahmad Imtiyaz; Walkiewicz, Katarzyna Wiktoria; Canlas, Christian; Huser, Raphaë l; Ali, Amal J.; Merzaban, Jasmeen; Bajic, Vladimir B.; Gao, Xin; Arold, Stefan T.

2018-01-01

and migration, and revealed a new type of inverse LD motif consensus. Our evolutionary analysis suggested that LD motif signalling originated in the common unicellular ancestor of opisthokonts and amoebozoa by co-opting nuclear export sequences. Inter

A SNP-Based Molecular Barcode for Characterization of Common Wheat.

Directory of Open Access Journals (Sweden)

LiFeng Gao

Full Text Available Wheat is grown as a staple crop worldwide. It is important to develop an effective genotyping tool for this cereal grain both to identify germplasm diversity and to protect the rights of breeders. Single-nucleotide polymorphism (SNP genotyping provides a means for developing a practical, rapid, inexpensive and high-throughput assay. Here, we investigated SNPs as robust markers of genetic variation for typing wheat cultivars. We identified SNPs from an array of 9000 across a collection of 429 well-known wheat cultivars grown in China, of which 43 SNP markers with high minor allele frequency and variations discriminated the selected wheat varieties and their wild ancestors. This SNP-based barcode will allow for the rapid and precise identification of wheat germplasm resources and newly released varieties and will further assist in the wheat breeding program.

Comparative genomics of the apicomplexan parasites Toxoplasma gondii and neospora caninum: Coccidia differing in host range and transmission strategy

KAUST Repository

Reid, Adam James; Vermont, Sarah J.; Cotton, James A.; Harris, David; Hill-Cawthorne, Grant A.; Kö nen-Waisman, Stephanie; Latham, Sophia M.; Mourier, Tobias; Norton, Rebecca; Quail, Michael A.; Sanders, Mandy; Shanmugam, Dhanasekaran; Sohal, Amandeep; Wasmuth, James D.; Brunk, Brian; Grigg, Michael E.; Howard, Jonathan C.; Parkinson, John; Roos, David S.; Trees, Alexander J.; Berriman, Matthew; Pain, Arnab; Wastling, Jonathan M.

2012-01-01

and transcriptomics analysis. We estimate that these organisms diverged from their common ancestor around 28 million years ago and find that both genomes and gene expression are remarkably conserved. However, in N. caninum we identified an unexpected expansion

From the Cult of the “Self” to the Ancestor Cult: Trilogy The Cult of the Self by Maurice Barrés

Directory of Open Access Journals (Sweden)

Vera V. Shervashidze

2016-09-01

Full Text Available The debut of Maurice Barrès, his trilogy The Cult of the Self immediately won the reader’s attention. In the 1890s, his works evoked increasing interest. His contemporaries read them as a fascinating narrative about the drama of European consciousness and the attempts to overcome this drama. However, after the author’s death, the interest of readers and researchers to his works decreased that may be explained by his fascination with ideas of nationalism, or boulangisme, especially during the war. The writer was accused of nationalism, however his nationalism was but a “replica” of his early ideas about the “culture” of “the self.” According to Barrès, all major themes of his work were reflected in the first trilogy of The Cult of the Self. Later in his career, revealing the typological similarity of the processes taking place in the inner “self” and within the nation, he wrote about degradation of the “self” and degradation of the nation in parallel. Portraying “the disease of the century” and seeking its recovery, Barrès introduced the theme of the ancestor cult as a means of moral redemption in his late work. The present study of linguistic, cultural, and historical properties of Barrès’s work intends to introduce one of the greatest turn-of-the-century writers into the Russian academic context.

Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications.

Science.gov (United States)

Onimaru, Koh; Kuraku, Shigehiro

2018-03-16

Inferring the phenotype of the last common ancestor of living vertebrates is a challenging problem because of several unresolvable factors. They include the lack of reliable out-groups of living vertebrates, poor information about less fossilizable organs and specialized traits of phylogenetically important species, such as lampreys and hagfishes (e.g. secondary loss of vertebrae in adult hagfishes). These factors undermine the reliability of ancestral reconstruction by traditional character mapping approaches based on maximum parsimony. In this article, we formulate an approach to hypothesizing ancestral vertebrate phenotypes using information from the phylogenetic and functional properties of genes duplicated by genome expansions in early vertebrate evolution. We named the conjecture as 'chronological reconstruction of ohnolog functions (CHROF)'. This CHROF conjecture raises the possibility that the last common ancestor of living vertebrates may have had more complex traits than currently thought.

Evolution of dinosaur epidermal structures.

Science.gov (United States)

Barrett, Paul M; Evans, David C; Campione, Nicolás E

2015-06-01

Spectacularly preserved non-avian dinosaurs with integumentary filaments/feathers have revolutionized dinosaur studies and fostered the suggestion that the dinosaur common ancestor possessed complex integumentary structures homologous to feathers. This hypothesis has major implications for interpreting dinosaur biology, but has not been tested rigorously. Using a comprehensive database of dinosaur skin traces, we apply maximum-likelihood methods to reconstruct the phylogenetic distribution of epidermal structures and interpret their evolutionary history. Most of these analyses find no compelling evidence for the appearance of protofeathers in the dinosaur common ancestor and scales are usually recovered as the plesiomorphic state, but results are sensitive to the outgroup condition in pterosaurs. Rare occurrences of ornithischian filamentous integument might represent independent acquisitions of novel epidermal structures that are not homologous with theropod feathers. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Conflation of Short Identity-by-Descent Segments Bias Their Inferred Length Distribution

Directory of Open Access Journals (Sweden)

Charleston W. K. Chiang

2016-05-01

Full Text Available Identity-by-descent (IBD is a fundamental concept in genetics with many applications. In a common definition, two haplotypes are said to share an IBD segment if that segment is inherited from a recent shared common ancestor without intervening recombination. Segments several cM long can be efficiently detected by a number of algorithms using high-density SNP array data from a population sample, and there are currently efforts to detect shorter segments from sequencing. Here, we study a problem of identifiability: because existing approaches detect IBD based on contiguous segments of identity-by-state, inferred long segments of IBD may arise from the conflation of smaller, nearby IBD segments. We quantified this effect using coalescent simulations, finding that significant proportions of inferred segments 1–2 cM long are results of conflations of two or more shorter segments, each at least 0.2 cM or longer, under demographic scenarios typical for modern humans for all programs tested. The impact of such conflation is much smaller for longer (> 2 cM segments. This biases the inferred IBD segment length distribution, and so can affect downstream inferences that depend on the assumption that each segment of IBD derives from a single common ancestor. As an example, we present and analyze an estimator of the de novo mutation rate using IBD segments, and demonstrate that unmodeled conflation leads to underestimates of the ages of the common ancestors on these segments, and hence a significant overestimate of the mutation rate. Understanding the conflation effect in detail will make its correction in future methods more tractable.

Genome digging: insight into the mitochondrial genome of Homo.

Directory of Open Access Journals (Sweden)

Igor V Ovchinnikov

2010-12-01

Full Text Available A fraction of the Neanderthal mitochondrial genome sequence has a similarity with a 5,839-bp nuclear DNA sequence of mitochondrial origin (numt on the human chromosome 1. This fact has never been interpreted. Although this phenomenon may be attributed to contamination and mosaic assembly of Neanderthal mtDNA from short sequencing reads, we explain the mysterious similarity by integration of this numt (mtAncestor-1 into the nuclear genome of the common ancestor of Neanderthals and modern humans not long before their reproductive split.Exploiting bioinformatics, we uncovered an additional numt (mtAncestor-2 with a high similarity to the Neanderthal mtDNA and indicated that both numts represent almost identical replicas of the mtDNA sequences ancestral to the mitochondrial genomes of Neanderthals and modern humans. In the proteins, encoded by mtDNA, the majority of amino acids distinguishing chimpanzees from humans and Neanderthals were acquired by the ancestral hominins. The overall rate of nonsynonymous evolution in Neanderthal mitochondrial protein-coding genes is not higher than in other lineages. The model incorporating the ancestral hominin mtDNA sequences estimates the average divergence age of the mtDNAs of Neanderthals and modern humans to be 450,000-485,000 years. The mtAncestor-1 and mtAncestor-2 sequences were incorporated into the nuclear genome approximately 620,000 years and 2,885,000 years ago, respectively.This study provides the first insight into the evolution of the mitochondrial DNA in hominins ancestral to Neanderthals and humans. We hypothesize that mtAncestor-1 and mtAncestor-2 are likely to be molecular fossils of the mtDNAs of Homo heidelbergensis and a stem Homo lineage. The d(N/d(S dynamics suggests that the effective population size of extinct hominins was low. However, the hominin lineage ancestral to humans, Neanderthals and H. heidelbergensis, had a larger effective population size and possessed genetic diversity

Comparative genetic mapping reveals synteny and collinearity between the American cranberry and diploid blueberry genomes

Science.gov (United States)

Cranberry (section Oxcycoccus) and blueberry (section Cyanococcus), are closely related and recently domesticated fruit crops in the genus Vaccinium (family Ericaceae). Both the Oxycoccus and Cyanococcus sections are presumed to have an American origin and likely evolved from a common ancestor; howe...

LUCA, or just a conserved Archaeon?: Comments on Xue et al. (2003)

Czech Academy of Sciences Publication Activity Database

Čejchan, Petr

2004-01-01

Roč. 333, Supplement (2004), s. 47-50 ISSN 0378-1119 R&D Projects: GA ČR(CZ) GA205/03/1124 Keywords : Last universal common ancestor * universal tree * phylogeny Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.705, year: 2004

The Function and Evolution of the Halloween Genes; the Pathway to the Arthropod Molting Hormone. In Ecdysone, Structures and Functions

DEFF Research Database (Denmark)

Gilbert, Lawrence; Rewitz, Kim

2009-01-01

, Coleoptera, Hymenoptera and other Diptera allowed the development of a phylogenetic scheme for this gene family and suggests that the Halloween genes and vertebrate steroidogenic P450s originated from common ancestors that were perhaps destined for steroidogenesis, and arose before the deuterostome...

Unseen and unsung heroes: The microbes

Digital Repository Service at National Institute of Oceanography (India)

Raghukumar, S.

Fungi are larger microorganisms and their bodies are mostly filamentous, the filaments being called hyphae. It is now believed that fungi evolved from an ancestor that was also common to animals. The width of the fungal hyphae is just about 3 to 5...

The Ancestor as Subtext

Directory of Open Access Journals (Sweden)

Sabine Broeck

2009-06-01

Full Text Available This text has grown out of my love of and respect for Toni Morrison's work. It is supposed to be−however much it might take the shape of a critical reading−very much my homage to the work of a writer who has made some of the most articulate and publicly visible moves to satisfy a communal desire for the African-American memory, and to create, if sites of stone and marble have been lacking, fictional spaces as "monuments" to the black diaspora in the New World. It is also a piece of work that ...

ATLAS (Automatic Tool for Local Assembly Structures) - A Comprehensive Infrastructure for Assembly, Annotation, and Genomic Binning of Metagenomic and Metaranscripomic Data

Energy Technology Data Exchange (ETDEWEB)

White, Richard A.; Brown, Joseph M.; Colby, Sean M.; Overall, Christopher C.; Lee, Joon-Yong; Zucker, Jeremy D.; Glaesemann, Kurt R.; Jansson, Georg C.; Jansson, Janet K.

2017-03-02

ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multiomics data analysis pipeline that is massively parallel and scalable. ATLAS contains a modular analysis pipeline for assembly, annotation, quantification and genome binning of metagenomics and metatranscriptomics data and a framework for reference metaproteomic database construction. ATLAS transforms raw sequence data into functional and taxonomic data at the microbial population level and provides genome-centric resolution through genome binning. ATLAS provides robust taxonomy based on majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS provides robust taxonomy based on majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS is user-friendly, easy install through bioconda maintained as open-source on GitHub, and is implemented in Snakemake for modular customizable workflows.

Auditory opportunity and visual constraint enabled the evolution of echolocation in bats.

Science.gov (United States)

Thiagavel, Jeneni; Cechetto, Clément; Santana, Sharlene E; Jakobsen, Lasse; Warrant, Eric J; Ratcliffe, John M

2018-01-08

Substantial evidence now supports the hypothesis that the common ancestor of bats was nocturnal and capable of both powered flight and laryngeal echolocation. This scenario entails a parallel sensory and biomechanical transition from a nonvolant, vision-reliant mammal to one capable of sonar and flight. Here we consider anatomical constraints and opportunities that led to a sonar rather than vision-based solution. We show that bats' common ancestor had eyes too small to allow for successful aerial hawking of flying insects at night, but an auditory brain design sufficient to afford echolocation. Further, we find that among extant predatory bats (all of which use laryngeal echolocation), those with putatively less sophisticated biosonar have relatively larger eyes than do more sophisticated echolocators. We contend that signs of ancient trade-offs between vision and echolocation persist today, and that non-echolocating, phytophagous pteropodid bats may retain some of the necessary foundations for biosonar.

Evidence for a common toolbox based on necrotrophy in a fungal lineage spanning necrotrophs, biotrophs, endophytes, host generalists and specialists.

Directory of Open Access Journals (Sweden)

Marion Andrew

Full Text Available The Sclerotiniaceae (Ascomycotina, Leotiomycetes is a relatively recently evolved lineage of necrotrophic host generalists, and necrotrophic or biotrophic host specialists, some latent or symptomless. We hypothesized that they inherited a basic toolbox of genes for plant symbiosis from their common ancestor. Maintenance and evolutionary diversification of symbiosis could require selection on toolbox genes or on timing and magnitude of gene expression. The genes studied were chosen because their products have been previously investigated as pathogenicity factors in the Sclerotiniaceae. They encode proteins associated with cell wall degradation: acid protease 1 (acp1, aspartyl protease (asps, and polygalacturonases (pg1, pg3, pg5, pg6, and the oxalic acid (OA pathway: a zinc finger transcription factor (pac1, and oxaloacetate acetylhydrolase (oah, catalyst in OA production, essential for full symptom production in Sclerotinia sclerotiorum. Site-specific likelihood analyses provided evidence for purifying selection in all 8 pathogenicity-related genes. Consistent with an evolutionary arms race model, positive selection was detected in 5 of 8 genes. Only generalists produced large, proliferating disease lesions on excised Arabidopsis thaliana leaves and oxalic acid by 72 hours in vitro. In planta expression of oah was 10-300 times greater among the necrotrophic host generalists than necrotrophic and biotrophic host specialists; pac1 was not differentially expressed. Ability to amplify 6/8 pathogenicity related genes and produce oxalic acid in all genera are consistent with the common toolbox hypothesis for this gene sample. That our data did not distinguish biotrophs from necrotrophs is consistent with 1 a common toolbox based on necrotrophy and 2 the most conservative interpretation of the 3-locus housekeeping gene phylogeny--a baseline of necrotrophy from which forms of biotrophy emerged at least twice. Early oah overexpression likely expands the

Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes.

Science.gov (United States)

Novák, Lukáš; Zubáčová, Zuzana; Karnkowska, Anna; Kolisko, Martin; Hroudová, Miluše; Stairs, Courtney W; Simpson, Alastair G B; Keeling, Patrick J; Roger, Andrew J; Čepička, Ivan; Hampl, Vladimír

2016-10-06

Multiple prokaryotic lineages use the arginine deiminase (ADI) pathway for anaerobic energy production by arginine degradation. The distribution of this pathway among eukaryotes has been thought to be very limited, with only two specialized groups living in low oxygen environments (Parabasalia and Diplomonadida) known to possess the complete set of all three enzymes. We have performed an extensive survey of available sequence data in order to map the distribution of these enzymes among eukaryotes and to reconstruct their phylogenies. We have found genes for the complete pathway in almost all examined representatives of Metamonada, the anaerobic protist group that includes parabasalids and diplomonads. Phylogenetic analyses indicate the presence of the complete pathway in the last common ancestor of metamonads and heterologous transformation experiments suggest its cytosolic localization in the metamonad ancestor. Outside Metamonada, the complete pathway occurs rarely, nevertheless, it was found in representatives of most major eukaryotic clades. Phylogenetic relationships of complete pathways are consistent with the presence of the Archaea-derived ADI pathway in the last common ancestor of all eukaryotes, although other evolutionary scenarios remain possible. The presence of the incomplete set of enzymes is relatively common among eukaryotes and it may be related to the fact that these enzymes are involved in other cellular processes, such as the ornithine-urea cycle. Single protein phylogenies suggest that the evolutionary history of all three enzymes has been shaped by frequent gene losses and horizontal transfers, which may sometimes be connected with their diverse roles in cellular metabolism.

Cenozoic climate change shaped the evolutionary ecophysiology of the Cupressaceae conifers.

Science.gov (United States)

Pittermann, Jarmila; Stuart, Stephanie A; Dawson, Todd E; Moreau, Astrid

2012-06-12

The Cupressaceae clade has the broadest diversity in habitat and morphology of any conifer family. This clade is characterized by highly divergent physiological strategies, with deciduous swamp-adapted genera-like Taxodium at one extreme, and evergreen desert genera-like Cupressus at the other. The size disparity within the Cupressaceae is equally impressive, with members ranging from 5-m-tall juniper shrubs to 100-m-tall redwood trees. Phylogenetic studies demonstrate that despite this variation, these taxa all share a single common ancestor; by extension, they also share a common ancestral habitat. Here, we use a common-garden approach to compare xylem and leaf-level physiology in this family. We then apply comparative phylogenetic methods to infer how Cenozoic climatic change shaped the morphological and physiological differences between modern-day members of the Cupressaceae. Our data show that drought-resistant crown clades (the Cupressoid and Callitroid clades) most likely evolved from drought-intolerant Mesozoic ancestors, and that this pattern is consistent with proposed shifts in post-Eocene paleoclimates. We also provide evidence that within the Cupressaceae, the evolution of drought-resistant xylem is coupled to increased carbon investment in xylem tissue, reduced xylem transport efficiency, and at the leaf level, reduced photosynthetic capacity. Phylogenetically based analyses suggest that the ancestors of the Cupressaceae were dependent upon moist habitats, and that drought-resistant physiology developed along with increasing habitat aridity from the Oligocene onward. We conclude that the modern biogeography of the Cupressaceae conifers was shaped in large part by their capacity to adapt to drought.

The amphioxus genome illuminates vertebrate origins and cephalochordate biology

OpenAIRE

Holland, Linda Z.; Albalat, Ricard; Azumi, Kaoru; Benito-Gutiérrez, Èlia; Blow, Matthew J.; Bronner-Fraser, Marianne; Brunet, Frederic; Butts, Thomas; Candiani, Simona; Dishaw, Larry J.; Ferrier, David E.K.; Garcia-Fernàndez, Jordi; Gibson-Brown, Jeremy J.; Gissi, Carmela; Godzik, Adam

2008-01-01

Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets. Special attention was given to homeobox genes, opsin genes, genes involved in neural crest development,...

Contemporary temperature-driven divergence in a Nordic freshwater fish under conditions commonly thought to hinder adaptation

Directory of Open Access Journals (Sweden)

Gregersen Finn

2010-11-01

Full Text Available Abstract Background Evaluating the limits of adaptation to temperature is important given the IPCC-predicted rise in global temperatures. The rate and scope of evolutionary adaptation can be limited by low genetic diversity, gene flow, and costs associated with adaptive change. Freshwater organisms are physically confined to lakes and rivers, and must therefore deal directly with climate variation and change. In this study, we take advantage of a system characterised by low genetic variation, small population size, gene flow and between-trait trade-offs to study how such conditions affect the ability of a freshwater fish to adapt to climate change. We test for genetically-based differences in developmental traits indicating local adaptation, by conducting a common-garden experiment using embryos and larvae from replicate pairs of sympatric grayling demes that spawn and develop in natural cold and warm water, respectively. These demes have common ancestors from a colonization event 22 generations ago. Consequently, we explore if diversification may occur under severely constraining conditions. Results We found evidence for divergence in ontogenetic rates. The divergence pattern followed adaptation predictions as cold-deme individuals displayed higher growth rates and yolk conversion efficiency than warm-deme individuals at the same temperature. The cold-deme embryos had a higher rate of muscle mass development. Most of the growth- and development differences occurred prior to hatch. The divergence was probably not caused by genetic drift as there was a strong degree of parallelism in the divergence pattern and because phenotypic differentiation (QST was larger than estimated genetic drift levels (microsatellite FST between demes from different temperature groups. We also document that these particular grayling populations cannot develop successfully at temperatures above 12°C, whereas other European populations can, and that increasing the

A trophic framework for animal origins

DEFF Research Database (Denmark)

Mills, D. B.; Canfield, D. E.

2017-01-01

Metazoans emerged in a microbial world and play a unique role in the biosphere as the only complex multicellular eukaryotes capable of phagocytosis. While the bodyplan and feeding mode of the last common metazoan ancestor remain unresolved, the earliest multicellular stem-metazoans likely subsist...

The Amborella Genome and the Evolution of Flowering Plants

DEFF Research Database (Denmark)

Albert, Victor A.; Barbazuk, W. Bradley; dePamphilis, Claude W.

2013-01-01

Amborella trichopoda is strongly supported as the single living species of the sister lineage to all other extant flowering plants, providing a unique reference for inferring the genome content and structure of the most recent common ancestor (MRCA) of living angiosperms. Sequencing the Amborella...

The Physiology of Phagocytosis in the Context of Mitochondrial Origin

NARCIS (Netherlands)

Martin, William F; Tielens, Aloysius G M; Mentel, Marek; Garg, Sriram G; Gould, Sven B

How mitochondria came to reside within the cytosol of their host has been debated for 50 years. Though current data indicate that the last eukaryote common ancestor possessed mitochondria and was a complex cell, whether mitochondria or complexity came first in eukaryotic evolution is still

The impact of 'anthropotechnology’ on human evolution

NARCIS (Netherlands)

Blad, S.

2010-01-01

From the time that they diverged from their common ancestor, chimpanzees and humans have had a very different evolutionary path. It seems obvious that the appearance of culture and technology has increasingly alienated humans from the path of natural selection that has informed chimpanzee evolution.

Redemption in Totality

DEFF Research Database (Denmark)

Munch, Anders V.

2010-01-01

Richard Wagner is in his music dramas, philosophy and cultural critique a common ancestor of both the art forms of avant-garde and totalitarianism. Figures such as the architect Peter Behrens and the illustrator Fidus demonstrates how unpredictable the barriers ar between Wagnerian cultivators of...

Inferring the biogeographic origins of inter-continental disjunct endemics using a Bayes-DIVA approach

Institute of Scientific and Technical Information of China (English)

AJ HARRIS; Jun WEN; Qiu-Yun (Jenny) XIANG

2013-01-01

The arcto-Tertiary relictual flora is comprised of many genera that occur non-contiguously in the temperate zones of eastern Asia,Europe,eastern North America,and westem North America.Within each distributional area,species are typically endemic and may thus be widely separated from closely related species within the other areas.It is widely accepted that this common pattern of distribution resulted from of the fragmentation of a once morecontinuous arcto-Tertiary forest.The historical biogeographic events leading to the present-day disjunction have often been investigated using a phylogenetic approach.Limitations to these previous studies have included phylogenetic uncertainty and uncertainty in ancestral range reconstructions.However,the recently described Bayes-DIVA method handles both types of uncertainty.Thus,we used Bayes-DIVA analysis to reconstruct the stem lineage distributions for 185 endemic lineages from 23 disjunct genera representing 17 vascular plant families.In particular,we asked whether endemic lineages within each of the four distributional areas more often evolved from (1) widespread ancestors,(2) ancestors dispersed from other areas,or (3) endemic ancestors.We also considered which of these three biogeographic mechanisms may best explain the origins of arcto-Tertiary disjunct endemics in the neotropics.Our results show that eastern Asian endemics more often evolved from endemic ancestors compared to endemics in Europe and eastern and western North America.Present-day endemic lineages in the latter areas more often arose from widespread ancestors.Our results also provide anecdotal evidence for the importance of dispersal in the biogeographic origins of arcto-Tertiary species endemic in the neotropics.

Genome-Wide Association Study among Four Horse Breeds Identifies a Common Haplotype Associated with In Vitro CD3+ T Cell Susceptibility/Resistance to Equine Arteritis Virus Infection ▿

Science.gov (United States)

Go, Yun Young; Bailey, Ernest; Cook, Deborah G.; Coleman, Stephen J.; MacLeod, James N.; Chen, Kuey-Chu; Timoney, Peter J.; Balasuriya, Udeni B. R.

2011-01-01

Previously, we have shown that horses could be divided into susceptible and resistant groups based on an in vitro assay using dual-color flow cytometric analysis of CD3+ T cells infected with equine arteritis virus (EAV). Here, we demonstrate that the differences in in vitro susceptibility of equine CD3+ T lymphocytes to EAV infection have a genetic basis. To investigate the possible hereditary basis for this trait, we conducted a genome-wide association study (GWAS) to compare susceptible and resistant phenotypes. Testing of 267 DNA samples from four horse breeds that had a susceptible or a resistant CD3+ T lymphocyte phenotype using both Illumina Equine SNP50 BeadChip and Sequenom's MassARRAY system identified a common, genetically dominant haplotype associated with the susceptible phenotype in a region of equine chromosome 11 (ECA11), positions 49572804 to 49643932. The presence of a common haplotype indicates that the trait occurred in a common ancestor of all four breeds, suggesting that it may be segregated among other modern horse breeds. Biological pathway analysis revealed several cellular genes within this region of ECA11 encoding proteins associated with virus attachment and entry, cytoskeletal organization, and NF-κB pathways that may be associated with the trait responsible for the in vitro susceptibility/resistance of CD3+ T lymphocytes to EAV infection. The data presented in this study demonstrated a strong association of genetic markers with the trait, representing de facto proof that the trait is under genetic control. To our knowledge, this is the first GWAS of an equine infectious disease and the first GWAS of equine viral arteritis. PMID:21994447

Whakaora nga moemoea o nga tupuna--living the dreams of the ancestors. Future planning in a Kaupapa Māori CAMHS team.

Science.gov (United States)

Elder, Hinemoa; Milne, Moe; Witehira, Heemi; Mendes, Patrick; Heslin, Anneliese; Cribb-Su'a, Ainsleigh; Wilson, Riwai; Goldsmith, Arona; Kainamu, Reena; Barrett, Moana; Love, Shar; Cargo, Tania; Kalra, Vanitha

2009-08-01

The aim of this study was to identify and operationalize aspects of a future planning process for sustainable delivery of Kaupapa Māori (Specialist Māori) mental health from a team called He Kakano, within Child and Adolescent Mental Health Services in South Auckland, New Zealand. A 2-day hui (meeting) was held with members of the team and a facilitator, Whaea Moe Milne. Review of background national epidemiological data, local data, information from community, carer and tangata whaiora (consumer) stakeholders and the existing He Kakano Model of Care was undertaken. Use of tikanga (Māori protocol and practices) was evident throughout the hui. A number of aspects of tikanga were identified as essential to the positive outcomes of the future plan. This paper reports one in particular, that of whakatauakī (proverbs where the originator is known). "Whakaora nga moemoea o nga tupuna--living the dreams of the ancestors" is a whakatauakī articulated by Whaea Moe Milne, which was identified as helpful in influencing the strategic planning thinking and decision-making process for He Kakano. This whakatauakī enabled the identification of shared goals, values, beliefs, behaviours and an action plan. The existing and ongoing relationship with Whaea Moe Milne was identified as an important element in the way in which the whakatauakī was received and reflected on. Use of tikanga Māori, in this case, whakatauakī, was helpful in developing future planning for He Kakano. This suggests that use of tikanga may be beneficial in other settings where planning for sustainable Māori responsive services is undertaken. Further work in this area is likely to benefit service development, strategic planning, workforce development and have an impact on improving health outcomes for Māori.

Quantitative Analysis of Repertoire-Scale Immunoglobulin Properties in Vaccine-Induced B-Cell Responses

Science.gov (United States)

2017-05-10

share a common ancestor and have inherent parent -child 106 relationships. Fortunately, as previous studies have suggested, analysis at the clonotype...survival 609 niches. Semin Immunol, 2008. 20(1): p. 49-58. 610 5. Kuraoka, M., et al., Complex Antigens Drive Permissive Clonal Selection in Germinal

What can we infer about the origin of sex in early eukaryotes?

NARCIS (Netherlands)

Speijer, Dave

2016-01-01

Current analysis shows that the last eukaryotic common ancestor (LECA) was capable of full meiotic sex. The original eukaryotic life cycle can probably be described as clonal, interrupted by episodic sex triggered by external or internal stressors. The cycle could have started in a highly flexible

Zoology: Molluscs All Beneath the Sun, One Shell, Two Shells, More, or None.

Science.gov (United States)

Sigwart, Julia D

2017-07-24

One great remaining problem in evolutionary biology is to understand which common ancestor could have given rise to descendants as different as giant squid and microscopic pea clams. Two new papers provide important insights into molluscan body plan disparity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Runs of homozygosity implicate autozygosity as a schizophrenia risk factor

DEFF Research Database (Denmark)

Keller, Matthew C; Simonson, Matthew A; Ripke, Stephan

2012-01-01

Autozygosity occurs when two chromosomal segments that are identical from a common ancestor are inherited from each parent. This occurs at high rates in the offspring of mates who are closely related (inbreeding), but also occurs at lower levels among the offspring of distantly related mates. Her...

The evolution of fungal epiphytes

NARCIS (Netherlands)

Hongsanan, S.; Sánchez-Ramírez, S.; Crous, P.W.; Ariyawansa, H.A.; Zhao, R.L.; Hyde, K.D.

2016-01-01

Fungal epiphytes are a polyphyletic group found on the surface of plants, particularly on leaves, with a worldwide distribution. They belong in the phylum Ascomycota, which contains the largest known number of fungal genera. There has been little research dating the origins of the common ancestors

Small homologous blocks in phytophthora genomes do not point to an ancient whole-genome duplication.

Science.gov (United States)

van Hooff, Jolien J E; Snel, Berend; Seidl, Michael F

2014-05-01

Genomes of the plant-pathogenic genus Phytophthora are characterized by small duplicated blocks consisting of two consecutive genes (2HOM blocks) and by an elevated abundance of similarly aged gene duplicates. Both properties, in particular the presence of 2HOM blocks, have been attributed to a whole-genome duplication (WGD) at the last common ancestor of Phytophthora. However, large intraspecies synteny-compelling evidence for a WGD-has not been detected. Here, we revisited the WGD hypothesis by deducing the age of 2HOM blocks. Two independent timing methods reveal that the majority of 2HOM blocks arose after divergence of the Phytophthora lineages. In addition, a large proportion of the 2HOM block copies colocalize on the same scaffold. Therefore, the presence of 2HOM blocks does not support a WGD at the last common ancestor of Phytophthora. Thus, genome evolution of Phytophthora is likely driven by alternative mechanisms, such as bursts of transposon activity.

Ubiquitin Signaling: Extreme Conservation as a Source of Diversity

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Alice Zuin

2014-07-01

Full Text Available Around 2 × 103–2.5 × 103 million years ago, a unicellular organism with radically novel features, ancestor of all eukaryotes, dwelt the earth. This organism, commonly referred as the last eukaryotic common ancestor, contained in its proteome the same functionally capable ubiquitin molecule that all eukaryotic species contain today. The fact that ubiquitin protein has virtually not changed during all eukaryotic evolution contrasts with the high expansion of the ubiquitin system, constituted by hundreds of enzymes, ubiquitin-interacting proteins, protein complexes, and cofactors. Interestingly, the simplest genetic arrangement encoding a fully-equipped ubiquitin signaling system is constituted by five genes organized in an operon-like cluster, and is found in archaea. How did ubiquitin achieve the status of central element in eukaryotic physiology? We analyze here the features of the ubiquitin molecule and the network that it conforms, and propose notions to explain the complexity of the ubiquitin signaling system in eukaryotic cells.

Human cranial diversity and evidence for an ancient lineage of modern humans.

Science.gov (United States)

Schillaci, Michael A

2008-06-01

This study examines the genetic affinities of various modern human groupings using a multivariate analysis of morphometric data. Phylogenetic relationships among these groupings are also explored using neighbor-joining analysis of the metric data. Results indicate that the terminal Pleistocene/early Holocene fossils from Australasia exhibit a close genetic affinity with early modern humans from the Levant. Furthermore, recent human populations and Upper Paleolithic Europeans share a most recent common ancestor not shared with either the early Australasians or the early Levantine humans. This pattern of genetic and phylogenetic relationships suggests that the early modern humans from the Levant either contributed directly to the ancestry of an early lineage of Australasians, or that they share a recent common ancestor with them. The principal findings of the study, therefore, lend support to the notion of an early dispersal from Africa by a more ancient lineage of modern human prior to 50 ka, perhaps as early as OIS 5 times (76-100 ka).

Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum.

Science.gov (United States)

Porter, Ashleigh F; Duggan, Ana T; Poinar, Hendrik N; Holmes, Edward C

2017-09-28

The complete genome sequences of two strains of variola virus (VARV) sampled from human smallpox specimens present in the Czech National Museum, Prague, were recently determined, with one of the sequences estimated to date to the mid-19th century. Using molecular clock methods, the authors of this study go on to infer that the currently available strains of VARV share an older common ancestor, at around 1350 AD, than some recent estimates based on other archival human samples. Herein, we show that the two Czech strains exhibit anomalous branch lengths given their proposed age, and by assuming a constant rate of evolutionary change across the rest of the VARV phylogeny estimate that their true age in fact lies between 1918 and 1937. We therefore suggest that the age of the common ancestor of currently available VARV genomes most likely dates to late 16th and early 17th centuries and not ~1350 AD.

Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum

Directory of Open Access Journals (Sweden)

Ashleigh F. Porter

2017-09-01

Full Text Available The complete genome sequences of two strains of variola virus (VARV sampled from human smallpox specimens present in the Czech National Museum, Prague, were recently determined, with one of the sequences estimated to date to the mid-19th century. Using molecular clock methods, the authors of this study go on to infer that the currently available strains of VARV share an older common ancestor, at around 1350 AD, than some recent estimates based on other archival human samples. Herein, we show that the two Czech strains exhibit anomalous branch lengths given their proposed age, and by assuming a constant rate of evolutionary change across the rest of the VARV phylogeny estimate that their true age in fact lies between 1918 and 1937. We therefore suggest that the age of the common ancestor of currently available VARV genomes most likely dates to late 16th and early 17th centuries and not ~1350 AD.

Working Memory: A Cognitive Limit to Non-Human Primate Recursive Thinking Prior to Hominid Evolution

Directory of Open Access Journals (Sweden)

Dwight W. Read

2008-10-01

Full Text Available In this paper I explore the possibility that recursion is not part of the cognitive repertoire of non-human primates such as chimpanzees due to limited working memory capacity. Multiple lines of data, from nut cracking to the velocity and duration of cognitive development, imply that chimpanzees have a short-term memory size that limits working memory to dealing with two, or at most three, concepts at a time. If so, as a species they lack the cognitive capacity for recursive thinking to be integrated into systems of social organization and communication. If this limited working memory capacity is projected back to a common ancestor for Pan and Homo, it follows that early hominid ancestors would have had limited working memory capacity. Hence we should find evidence for expansion of working memory capacity during hominid evolution reflected in changes in the products of conceptually framed activities such as stone tool production. Data on the artifacts made by our hominid ancestors support this expansion hypothesis for hominid working memory, thereby leading to qualitative differences between Pan and Homo.

Population-based statistical inference for temporal sequence of somatic mutations in cancer genomes.

Science.gov (United States)

Rhee, Je-Keun; Kim, Tae-Min

2018-04-20

It is well recognized that accumulation of somatic mutations in cancer genomes plays a role in carcinogenesis; however, the temporal sequence and evolutionary relationship of somatic mutations remain largely unknown. In this study, we built a population-based statistical framework to infer the temporal sequence of acquisition of somatic mutations. Using the model, we analyzed the mutation profiles of 1954 tumor specimens across eight tumor types. As a result, we identified tumor type-specific directed networks composed of 2-15 cancer-related genes (nodes) and their mutational orders (edges). The most common ancestors identified in pairwise comparison of somatic mutations were TP53 mutations in breast, head/neck, and lung cancers. The known relationship of KRAS to TP53 mutations in colorectal cancers was identified, as well as potential ancestors of TP53 mutation such as NOTCH1, EGFR, and PTEN mutations in head/neck, lung and endometrial cancers, respectively. We also identified apoptosis-related genes enriched with ancestor mutations in lung cancers and a relationship between APC hotspot mutations and TP53 mutations in colorectal cancers. While evolutionary analysis of cancers has focused on clonal versus subclonal mutations identified in individual genomes, our analysis aims to further discriminate ancestor versus descendant mutations in population-scale mutation profiles that may help select cancer drivers with clinical relevance.

Auditory opportunity and visual constraint enabled the evolution of echolocation in bats

DEFF Research Database (Denmark)

Thiagavel, Jeneni; Cechetto, Clément; Santana, Sharlene E

2018-01-01

and flight. Here we consider anatomical constraints and opportunities that led to a sonar rather than vision-based solution. We show that bats' common ancestor had eyes too small to allow for successful aerial hawking of flying insects at night, but an auditory brain design sufficient to afford echolocation...

Virus Diseases: The Global Challenge to Health for All. Asia-Pacific Congress of Medical Virology (2nd) Held in Bangkok, Thailand on November 17-22, 1991. Abstracts

Science.gov (United States)

1992-07-01

question. This procedure allows the comparison of strains which have no more than 10% sequence divergence. Analysis using the UPGMA method revealed...unweighted pair group method using arithmetic averages ( UPGMA ) indicates that CA24v had evolved from a common ancestor which appeared in one focal place in

Investigating Tree Thinking & Ancestry with Cladograms

Science.gov (United States)

Davenport, K. D.; Milks, Kirstin Jane; Van Tassell, Rebecca

2015-01-01

Interpreting cladograms is a key skill for biological literacy. In this lesson, students interpret cladograms based on familial relationships and language relationships to build their understanding of tree thinking and to construct a definition of "common ancestor." These skills can then be applied to a true biological cladogram.

Phylogenetic networks do not need to be complex: using fewer reticulations to represent conflicting clusters

NARCIS (Netherlands)

Iersel, van L.J.J.; Kelk, S.M.; Rupp, R.; Huson, D.H.

2010-01-01

Phylogenetic trees are widely used to display estimates of how groups of species are evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees are obtained for several datasets (e.g. for different

Animal evolution: stiff or squishy notochord origins?

Science.gov (United States)

Hejnol, Andreas; Lowe, Christopher J

2014-12-01

The notochord is considered an evolutionary novelty and one of the defining characters of chordates. A new study of an annelid challenges this view and proposes an earlier evolutionary origin in the most recent common ancestor of chordates and annelids. Copyright © 2014 Elsevier Ltd. All rights reserved.

Hunter-Gatherers and the Origins of Religion.

Science.gov (United States)

Peoples, Hervey C; Duda, Pavel; Marlowe, Frank W

2016-09-01

Recent studies of the evolution of religion have revealed the cognitive underpinnings of belief in supernatural agents, the role of ritual in promoting cooperation, and the contribution of morally punishing high gods to the growth and stabilization of human society. The universality of religion across human society points to a deep evolutionary past. However, specific traits of nascent religiosity, and the sequence in which they emerged, have remained unknown. Here we reconstruct the evolution of religious beliefs and behaviors in early modern humans using a global sample of hunter-gatherers and seven traits describing hunter-gatherer religiosity: animism, belief in an afterlife, shamanism, ancestor worship, high gods, and worship of ancestors or high gods who are active in human affairs. We reconstruct ancestral character states using a time-calibrated supertree based on published phylogenetic trees and linguistic classification and then test for correlated evolution between the characters and for the direction of cultural change. Results indicate that the oldest trait of religion, present in the most recent common ancestor of present-day hunter-gatherers, was animism, in agreement with long-standing beliefs about the fundamental role of this trait. Belief in an afterlife emerged, followed by shamanism and ancestor worship. Ancestor spirits or high gods who are active in human affairs were absent in early humans, suggesting a deep history for the egalitarian nature of hunter-gatherer societies. There is a significant positive relationship between most characters investigated, but the trait "high gods" stands apart, suggesting that belief in a single creator deity can emerge in a society regardless of other aspects of its religion.

LHD1, an allele of DTH8/Ghd8, controls late heading date in common wild rice (Oryza rufipogon).

Science.gov (United States)

Dai, Xiaodong; Ding, Younian; Tan, Lubin; Fu, Yongcai; Liu, Fengxia; Zhu, Zuofeng; Sun, Xianyou; Sun, Xuewen; Gu, Ping; Cai, Hongwei; Sun, Chuanqing

2012-10-01

Flowering at suitable time is very important for plants to adapt to complicated environments and produce their seeds successfully for reproduction. In rice (Oryza rufipogon Griff.) photoperiod regulation is one of the important factors for controlling heading date. Common wild rice, the ancestor of cultivated rice, exhibits a late heading date and a more sensitive photoperiodic response than cultivated rice. Here, through map-based cloning, we identified a major quantitative trait loci (QTL) LHD1 (Late Heading Date 1), an allele of DTH8/Ghd8, which controls the late heading date of wild rice and encodes a putative HAP3/NF-YB/CBF-A subunit of the CCAAT-box-binding transcription factor. Sequence analysis revealed that several variants in the coding region of LHD1 were correlated with a late heading date, and a further complementary study successfully rescued the phenotype. These results suggest that a functional site for LHD1 could be among those variants present in the coding region. We also found that LHD1 could down-regulate the expression of several floral transition activators such as Ehd1, Hd3a and RFT1 under long-day conditions, but not under short-day conditions. This indicates that LHD1 may delay flowering by repressing the expression of Ehd1, Hd3a and RFT1 under long-day conditions. © 2012 Institute of Botany, Chinese Academy of Sciences.

Making the Common Good Common

Science.gov (United States)

Chase, Barbara

2011-01-01

How are independent schools to be useful to the wider world? Beyond their common commitment to educate their students for meaningful lives in service of the greater good, can they educate a broader constituency and, thus, share their resources and skills more broadly? Their answers to this question will be shaped by their independence. Any…

Biological chemistry as a foundation of DNA genealogy: the emergence of "molecular history".

Science.gov (United States)

Klyosov, A A

2011-05-01

This paper presents the basis of DNA genealogy, a new field of science, which is currently emerging as an unusual blend of biochemistry, history, linguistics, and chemical kinetics. The methodology of the new approach is comprised of chemical (biological) kinetics applied to a pattern of mutations in non-recombinant fragments of DNA (Y chromosome and mtDNA, the latter not being considered in this overview). The goal of the analysis is to translate DNA mutation patterns into time spans to the most recent common ancestors of a given population or tribe and to the dating of ancient migration routes. To illustrate this approach, time spans to the common ancestors are calculated for ethnic Russians, that is Eastern Slavs (R1a1 tribe), Western Slavs (I1 and I2 tribes), and Northern (or Uralic) Slavs (N1c tribe), which were found to live around 4600 years before present (R1a1), 3650 ybp (I1), 3000 and 10,500 ybp (I2, two principal DNA lineages), and 3525 ybp (N1c) (confidence intervals are given in the main text). The data were compared with the respective dates for the nearest common ancestor of the R1a1 "Indo-European" population in India, who lived 4050 years before present, whose descendants represent the majority of the upper castes in India today (up to 72%). Furthermore, it was found that the haplotypes of ethnic Russians of the R1a1 haplogroup (up to 62% of the population in the Russian Federation) and those of the R1a1 Indians (more than 100 million today) are practically identical to each other, up to 67-marker haplotypes. This essentially solves a 200-year-old mystery of who were the Aryans who arrived in India around 3500 years before the present. Haplotypes and time spans to the ancient common ancestors were also compared for the ethnic Russians of haplogroups I1 and I2, on one hand, and the respective I1 and I2 populations in Eastern and Western Europe and Scandinavia, on the other. It is suggested that the approach described in this overview lays the

Naturally occurred frame-shift mutations in the tvb receptor gene are responsible for decreased susceptibility to subgroups B, D, and E avian leukosis virus infection in chicken

Science.gov (United States)

The group of highly related avian leukosis viruses (ALVs) in chickens were thought to have evolved from a common retroviral ancestor into six subgroups, A to E and J. These ALV subgroups use diverse cellular proteins encoded by four genetic loci in chickens as receptors to gain entry into host cells...

Evolution of the 2'-5'-Oligoadenylate Synthetase family in eukaryotes and bacteria

DEFF Research Database (Denmark)

Kjær, Karina Hansen; Poulsen, Jesper Buchhave; Reitamm, Tonu

2009-01-01

in bacteria that contains the five OAS-specific motifs. This indicates a specific relationship to OAS. The wide distribution of the OAS genes has made it possible to suggest how the OAS1 gene could have evolved from a common ancestor to choanoflagellates and metazoans. Furthermore, we suggest that the OASL...

Abundant Occurrence of Basal Radial Glia in the Subventricular Zone of Embryonic Neocortex of a Lissencephalic Primate, the Common Marmoset Callithrix jacchus

Science.gov (United States)

Kelava, Iva; Reillo, Isabel; Murayama, Ayako Y.; Kalinka, Alex T.; Stenzel, Denise; Tomancak, Pavel; Matsuzaki, Fumio; Lebrand, Cécile; Sasaki, Erika; Schwamborn, Jens C.; Okano, Hideyuki; Borrell, Víctor

2012-01-01

Subventricular zone (SVZ) progenitors are a hallmark of the developing neocortex. Recent studies described a novel type of SVZ progenitor that retains a basal process at mitosis, sustains expression of radial glial markers, and is capable of self-renewal. These progenitors, referred to here as basal radial glia (bRG), occur at high relative abundance in the SVZ of gyrencephalic primates (human) and nonprimates (ferret) but not lissencephalic rodents (mouse). Here, we analyzed the occurrence of bRG cells in the embryonic neocortex of the common marmoset Callithrix jacchus, a near-lissencephalic primate. bRG cells, expressing Pax6, Sox2 (but not Tbr2), glutamate aspartate transporter, and glial fibrillary acidic protein and retaining a basal process at mitosis, occur at similar relative abundance in the marmoset SVZ as in human and ferret. The proportion of progenitors in M-phase was lower in embryonic marmoset than developing ferret neocortex, raising the possibility of a longer cell cycle. Fitting the gyrification indices of 26 anthropoid species to an evolutionary model suggested that the marmoset evolved from a gyrencephalic ancestor. Our results suggest that a high relative abundance of bRG cells may be necessary, but is not sufficient, for gyrencephaly and that the marmoset's lissencephaly evolved secondarily by changing progenitor parameters other than progenitor type. PMID:22114084

Genetic basis for spontaneous hybrid genome doubling during allopolyploid speciation of common wheat shown by natural variation analyses of the paternal species.

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Yoshihiro Matsuoka

Full Text Available The complex process of allopolyploid speciation includes various mechanisms ranging from species crosses and hybrid genome doubling to genome alterations and the establishment of new allopolyploids as persisting natural entities. Currently, little is known about the genetic mechanisms that underlie hybrid genome doubling, despite the fact that natural allopolyploid formation is highly dependent on this phenomenon. We examined the genetic basis for the spontaneous genome doubling of triploid F1 hybrids between the direct ancestors of allohexaploid common wheat (Triticum aestivum L., AABBDD genome, namely Triticumturgidum L. (AABB genome and Aegilopstauschii Coss. (DD genome. An Ae. tauschii intraspecific lineage that is closely related to the D genome of common wheat was identified by population-based analysis. Two representative accessions, one that produces a high-genome-doubling-frequency hybrid when crossed with a T. turgidum cultivar and the other that produces a low-genome-doubling-frequency hybrid with the same cultivar, were chosen from that lineage for further analyses. A series of investigations including fertility analysis, immunostaining, and quantitative trait locus (QTL analysis showed that (1 production of functional unreduced gametes through nonreductional meiosis is an early step key to successful hybrid genome doubling, (2 first division restitution is one of the cytological mechanisms that cause meiotic nonreduction during the production of functional male unreduced gametes, and (3 six QTLs in the Ae. tauschii genome, most of which likely regulate nonreductional meiosis and its subsequent gamete production processes, are involved in hybrid genome doubling. Interlineage comparisons of Ae. tauschii's ability to cause hybrid genome doubling suggested an evolutionary model for the natural variation pattern of the trait in which non-deleterious mutations in six QTLs may have important roles. The findings of this study demonstrated

Ruling the Commons. Introducing a new methodology for the analysis of historical commons

Directory of Open Access Journals (Sweden)

Tine de Moor

2016-10-01

Full Text Available Despite significant progress in recent years, the evolution of commons over the long run remains an under-explored area within commons studies. During the last years an international team of historians have worked under the umbrella of the Common Rules Project in order to design and test a new methodology aimed at advancing our knowledge on the dynamics of institutions for collective action – in particular commons. This project aims to contribute to the current debate on commons on three different fronts. Theoretically, it explicitly draws our attention to issues of change and adaptation in the commons – contrasting with more static analyses. Empirically, it highlights the value of historical records as a rich source of information for longitudinal analysis of the functioning of commons. Methodologically, it develops a systematic way of analyzing and comparing commons’ regulations across regions and time, setting a number of variables that have been defined on the basis of the “most common denominators” in commons regulation across countries and time periods. In this paper we introduce the project, describe our sources and methodology, and present the preliminary results of our analysis.

The common good

OpenAIRE

Argandoña, Antonio

2011-01-01

The concept of the common good occupied a relevant place in classical social, political and economic philosophy. After losing ground in the Modern age, it has recently reappeared, although with different and sometimes confusing meanings. This paper is the draft of a chapter of a Handbook; it explains the meaning of common good in the Aristotelian-Thomistic philosophy and in the Social Doctrine of the Catholic Church; why the common good is relevant; and how it is different from the other uses...

The Poetics of the Ancestor Songs of the Tz’utujil Maya of Guatemala

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Linda O’Brien-Rothe

2010-04-01

Full Text Available This essay attempts to define the relationship between a song tradition that survives in the Mayan highlands of Guatemala, and 16th century poetic Mayan literature. This song tradition of Santiago Atitlán, Guatemala is slowly disappearing as the socio-cultural context in which it flourished changes. By comparing the poetics of the song texts (including their rhythmic structure, versification, and use of poetic devices such as assonance, alliteration and onomatopoeia to the poetics of the Popol Vuh, a K’iché Maya text probably copied from a manuscript that predates the Spanish invasion, a continuity is discovered that places the song texts squarely within the tradition of Mayan literature and suggests common origins.

Consanguineous marriages in the genetic counseling centers of Isfahan and the ethical issues of clinical consultations

OpenAIRE

Nouri, Narges; Nouri, Nayereh; Tirgar, Samane; Soleimani, Elham; Yazdani, Vida; Zahedi, Farzaneh; Larijani, Bagher

2017-01-01

Consanguineous marriage, which is common in many regions in the world, has absorbed much attention as a causative factor in raising the incidence of genetic diseases. The adverse effects may be attributed to the expression of the genes received from common ancestors and mortality and morbidity of the offspring. Iran has a high rate of consanguineous marriages. In recent years genetic counseling has come to be considered in health care services. This cross-sectional study was conducted in orde...

Precursors to language: Social cognition and pragmatic inference in primates.

Science.gov (United States)

Seyfarth, Robert M; Cheney, Dorothy L

2017-02-01

Despite their differences, human language and the vocal communication of nonhuman primates share many features. Both constitute forms of coordinated activity, rely on many shared neural mechanisms, and involve discrete, combinatorial cognition that includes rich pragmatic inference. These common features suggest that during evolution the ancestors of all modern primates faced similar social problems and responded with similar systems of communication and cognition. When language later evolved from this common foundation, many of its distinctive features were already present.

QCI Common

Energy Technology Data Exchange (ETDEWEB)

2016-11-18

There are many common software patterns and utilities for the ORNL Quantum Computing Institute that can and should be shared across projects. Otherwise we find duplication of code which adds unwanted complexity. This is a software product seeks to alleviate this by providing common utilities such as object factories, graph data structures, parameter input mechanisms, etc., for other software products within the ORNL Quantum Computing Institute. This work enables pure basic research, has no export controlled utilities, and has no real commercial value.

The Common Good

DEFF Research Database (Denmark)

Feldt, Liv Egholm

At present voluntary and philanthropic organisations are experiencing significant public attention and academic discussions about their role in society. Central to the debate is on one side the question of how they contribute to “the common good”, and on the other the question of how they can avoid...... and concepts continuously over time have blurred the different sectors and “polluted” contemporary definitions of the “common good”. The analysis shows that “the common good” is not an autonomous concept owned or developed by specific spheres of society. The analysis stresses that historically, “the common...... good” has always been a contested concept. It is established through messy and blurred heterogeneity of knowledge, purposes and goal achievements originating from a multitude of scientific, religious, political and civil society spheres contested not only in terms of words and definitions but also...

Spatial and temporal dynamics of hepatitis B virus D genotype in Europe and the Mediterranean Basin.

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Gianguglielmo Zehender

Full Text Available Hepatitis B virus genotype D can be found in many parts of the world and is the most prevalent strain in south-eastern Europe, the Mediterranean Basin, the Middle East, and the Indian sub-continent. The epidemiological history of the D genotype and its subgenotypes is still obscure because of the scarcity of appropriate studies. We retrieved from public databases a total of 312 gene P sequences of HBV genotype D isolated in various countries throughout the world, and reconstructed the spatio-temporal evolutionary dynamics of the HBV-D epidemic using a bayesian framework.The phylogeographical analysis showed that India had the highest posterior probability of being the location of the tree root, whereas central Asia was the most probable location of the common ancestor of subgenotypes D1-D3. HBV-D5 (identified in native Indian populations diverged from the tree root earlier than D1-D3. The time of the most recent common ancestor (tMRCA of the tree root was 128 years ago, which suggests that the common ancestor of the currently circulating subgenotypes existed in the second half of the XIX century. The mean tMRCA of subgenotypes D1-D3 was between the 1940s and the 1950-60s. On the basis of our phylogeographic reconstruction, it seems that HBV-D reached the Mediterranean area in the middle of the XX century by means of at least two routes: the first pathway (mainly due to the spread of subgenotype D1 crossing the Middle East and reaching north Africa and the eastern Mediterranean, and the second pathway (closely associated with D2 that crossed the former Soviet Union and reached eastern Europe and the Mediterranean through Albania. We hypothesise that the main route of dispersion of genotype D was the unsafe use of injections and drug addiction.

Independent Evolution of Strychnine Recognition by Bitter Taste Receptor Subtypes

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Ava Yuan Xue

2018-03-01

Full Text Available The 25 human bitter taste receptors (hT2Rs recognize thousands of structurally and chemically diverse bitter substances. The binding modes of human bitter taste receptors hT2R10 and hT2R46, which are responsible for strychnine recognition, were previously established using site-directed mutagenesis, functional assays, and molecular modeling. Here we construct a phylogenetic tree and reconstruct ancestral sequences of the T2R10 and T2R46 clades. We next analyze the binding sites in view of experimental data to predict their ability to recognize strychnine. This analysis suggests that the common ancestor of hT2R10 and hT2R46 is unlikely to bind strychnine in the same mode as either of its two descendants. Estimation of relative divergence times shows that hT2R10 evolved earlier than hT2R46. Strychnine recognition was likely acquired first by the earliest common ancestor of the T2R10 clade before the separation of primates from other mammals, and was highly conserved within the clade. It was probably independently acquired by the common ancestor of T2R43-47 before the homo-ape speciation, lost in most T2Rs within this clade, but enhanced in the hT2R46 after humans diverged from the rest of primates. Our findings suggest hypothetical strychnine T2R receptors in several species, and serve as an experimental guide for further study. Improved understanding of how bitter taste receptors acquire the ability to be activated by particular ligands is valuable for the development of sensors for bitterness and for potential toxicity.

Independent Evolution of Strychnine Recognition by Bitter Taste Receptor Subtypes

Science.gov (United States)

Xue, Ava Yuan; Di Pizio, Antonella; Levit, Anat; Yarnitzky, Tali; Penn, Osnat; Pupko, Tal; Niv, Masha Y.

2018-01-01

The 25 human bitter taste receptors (hT2Rs) recognize thousands of structurally and chemically diverse bitter substances. The binding modes of human bitter taste receptors hT2R10 and hT2R46, which are responsible for strychnine recognition, were previously established using site-directed mutagenesis, functional assays, and molecular modeling. Here we construct a phylogenetic tree and reconstruct ancestral sequences of the T2R10 and T2R46 clades. We next analyze the binding sites in view of experimental data to predict their ability to recognize strychnine. This analysis suggests that the common ancestor of hT2R10 and hT2R46 is unlikely to bind strychnine in the same mode as either of its two descendants. Estimation of relative divergence times shows that hT2R10 evolved earlier than hT2R46. Strychnine recognition was likely acquired first by the earliest common ancestor of the T2R10 clade before the separation of primates from other mammals, and was highly conserved within the clade. It was probably independently acquired by the common ancestor of T2R43-47 before the homo-ape speciation, lost in most T2Rs within this clade, but enhanced in the hT2R46 after humans diverged from the rest of primates. Our findings suggest hypothetical strychnine T2R receptors in several species, and serve as an experimental guide for further study. Improved understanding of how bitter taste receptors acquire the ability to be activated by particular ligands is valuable for the development of sensors for bitterness and for potential toxicity. PMID:29552563

First steps in studying the origins of secondary woodiness in Begonia (Begoniaceae): combining anatomy, phylogenetics, and stem transcriptomics

Science.gov (United States)

Catherine Kidner; Andrew Groover; Daniel C. Thomas; Katie Emelianova; Claudia Soliz-Gamboa; Frederic Lens

2015-01-01

Since Darwin's observation that secondary woodiness is common on islands, the evolution of woody plants from herbaceous ancestors has been documented in numerous angiosperm groups. However, the evolutionary processes that give rise to this phenomenon are poorly understood. To begin addressing this we have used a range of approaches to study the anatomical and...

Enriching and understanding the wheat B genome by meiotic homoeologous recombination

Science.gov (United States)

Wheat, including common wheat (Triticum aestivum, 2n=6x=42, AABBDD) and durum wheat (T. turgidum ssp. durum, 2n=4x=28, AABB), contains three homoeologous subgenomes (A, B, and D) originated from three diploid ancestors. The wild einkorn wheat T. urartu (2n=2x=14, AA) contributed subgenome A and wild...

Some ancestors of contraction analysis

DEFF Research Database (Denmark)

Jouffroy, Jerome

2005-01-01

Contraction analysis is a recent tool for analyzing the convergence behavior of nonlinear systems in state-space form (see Lohmiller and Slotine [16] for the main reference). However, it seems that earlier results derived by mathematicians in the 1950s closely match some of the results of contrac......Contraction analysis is a recent tool for analyzing the convergence behavior of nonlinear systems in state-space form (see Lohmiller and Slotine [16] for the main reference). However, it seems that earlier results derived by mathematicians in the 1950s closely match some of the results...

Sundials: Ancestors of Our Clocks

Indian Academy of Sciences (India)

ing in mathematics and astronomy, the Greeks, the Egyptians and the Babylonians constructed ... have knowledge about some of the basic concepts and terminolo- gies in astronomy. .... Treloars College, Hamp- shire, England. Courtesy: ...

Viral ancestors of antiviral systems.

Science.gov (United States)

Villarreal, Luis P

2011-10-01

All life must survive their corresponding viruses. Thus antiviral systems are essential in all living organisms. Remnants of virus derived information are also found in all life forms but have historically been considered mostly as junk DNA. However, such virus derived information can strongly affect host susceptibility to viruses. In this review, I evaluate the role viruses have had in the origin and evolution of host antiviral systems. From Archaea through bacteria and from simple to complex eukaryotes I trace the viral components that became essential elements of antiviral immunity. I conclude with a reexamination of the 'Big Bang' theory for the emergence of the adaptive immune system in vertebrates by horizontal transfer and note how viruses could have and did provide crucial and coordinated features.

Viral Ancestors of Antiviral Systems

Directory of Open Access Journals (Sweden)

Luis P. Villarreal

2011-10-01

Full Text Available All life must survive their corresponding viruses. Thus antiviral systems are essential in all living organisms. Remnants of virus derived information are also found in all life forms but have historically been considered mostly as junk DNA. However, such virus derived information can strongly affect host susceptibility to viruses. In this review, I evaluate the role viruses have had in the origin and evolution of host antiviral systems. From Archaea through bacteria and from simple to complex eukaryotes I trace the viral components that became essential elements of antiviral immunity. I conclude with a reexamination of the ‘Big Bang’ theory for the emergence of the adaptive immune system in vertebrates by horizontal transfer and note how viruses could have and did provide crucial and coordinated features.

Science commons

CERN Multimedia

CERN. Geneva

2007-01-01

SCP: Creative Commons licensing for open access publishing, Open Access Law journal-author agreements for converting journals to open access, and the Scholar's Copyright Addendum Engine for retaining rights to self-archive in meaningful formats and locations for future re-use. More than 250 science and technology journals already publish under Creative Commons licensing while 35 law journals utilize the Open Access Law agreements. The Addendum Engine is a new tool created in partnership with SPARC and U.S. universities. View John Wilbanks's biography

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Science.gov (United States)

Green, Richard E; Braun, Edward L; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W; St John, John A; Capella-Gutiérrez, Salvador; Castoe, Todd A; Kern, Colin; Fujita, Matthew K; Opazo, Juan C; Jurka, Jerzy; Kojima, Kenji K; Caballero, Juan; Hubley, Robert M; Smit, Arian F; Platt, Roy N; Lavoie, Christine A; Ramakodi, Meganathan P; Finger, John W; Suh, Alexander; Isberg, Sally R; Miles, Lee; Chong, Amanda Y; Jaratlerdsiri, Weerachai; Gongora, Jaime; Moran, Christopher; Iriarte, Andrés; McCormack, John; Burgess, Shane C; Edwards, Scott V; Lyons, Eric; Williams, Christina; Breen, Matthew; Howard, Jason T; Gresham, Cathy R; Peterson, Daniel G; Schmitz, Jürgen; Pollock, David D; Haussler, David; Triplett, Eric W; Zhang, Guojie; Irie, Naoki; Jarvis, Erich D; Brochu, Christopher A; Schmidt, Carl J; McCarthy, Fiona M; Faircloth, Brant C; Hoffmann, Federico G; Glenn, Travis C; Gabaldón, Toni; Paten, Benedict; Ray, David A

2015-01-01

To provide context for the diversifications of archosaurs, the group that includes crocodilians, dinosaurs and birds, we generated draft genomes of three crocodilians, Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the relatively rapid evolution of bird genomes represents an autapomorphy within that clade. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these new data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs. PMID:25504731

Evolution of the YABBY gene family in seed plants.

Science.gov (United States)

Finet, Cédric; Floyd, Sandra K; Conway, Stephanie J; Zhong, Bojian; Scutt, Charles P; Bowman, John L

2016-01-01

Members of the YABBY gene family of transcription factors in angiosperms have been shown to be involved in the initiation of outgrowth of the lamina, the maintenance of polarity, and establishment of the leaf margin. Although most of the dorsal-ventral polarity genes in seed plants have homologs in non-spermatophyte lineages, the presence of YABBY genes is restricted to seed plants. To gain insight into the origin and diversification of this gene family, we reconstructed the evolutionary history of YABBY gene lineages in seed plants. Our findings suggest that either one or two YABBY genes were present in the last common ancestor of extant seed plants. We also examined the expression of YABBY genes in the gymnosperms Ephedra distachya (Gnetales), Ginkgo biloba (Ginkgoales), and Pseudotsuga menziesii (Coniferales). Our data indicate that some YABBY genes are expressed in a polar (abaxial) manner in leaves and female cones in gymnosperms. We propose that YABBY genes already acted as polarity genes in the last common ancestor of extant seed plants. © 2016 Wiley Periodicals, Inc.

Parvovirus Family Conundrum: What Makes a Killer?

Science.gov (United States)

Kailasan, Shweta; Agbandje-McKenna, Mavis; Parrish, Colin R

2015-11-01

Parvoviruses infect a wide variety of hosts, and their ancestors appear to have emerged tens to hundreds of millions of years ago and to have spread widely ever since. The diversity of parvoviruses is therefore extensive, and although they all appear to descend from a common ancestor and share common structures in their capsid and nonstructural proteins, there is often low homology at the DNA or protein level. The diversity of these viruses is also seen in the widely differing impacts they have on their hosts, which range from severe and even lethal disease to subclinical or nonpathogenic infections. In the past few years, deep sequencing of DNA samples from animals has shown just how widespread the parvoviruses are in nature, but most of the newly discovered viruses have not yet been associated with any disease. However, variants of some parvoviruses have altered their host ranges to create new epidemic or pandemic viruses. Here, we examine the properties of parvoviruses and their interactions with their hosts that are associated with these disparate pathogenic outcomes.

Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance

Directory of Open Access Journals (Sweden)

Daly Michael J

2005-10-01

Full Text Available Abstract Background Thermus thermophilus and Deinococcus radiodurans belong to a distinct bacterial clade but have remarkably different phenotypes. T. thermophilus is a thermophile, which is relatively sensitive to ionizing radiation and desiccation, whereas D. radiodurans is a mesophile, which is highly radiation- and desiccation-resistant. Here we present an in-depth comparison of the genomes of these two related but differently adapted bacteria. Results By reconstructing the evolution of Thermus and Deinococcus after the divergence from their common ancestor, we demonstrate a high level of post-divergence gene flux in both lineages. Various aspects of the adaptation to high temperature in Thermus can be attributed to horizontal gene transfer from archaea and thermophilic bacteria; many of the horizontally transferred genes are located on the single megaplasmid of Thermus. In addition, the Thermus lineage has lost a set of genes that are still present in Deinococcus and many other mesophilic bacteria but are not common among thermophiles. By contrast, Deinococcus seems to have acquired numerous genes related to stress response systems from various bacteria. A comparison of the distribution of orthologous genes among the four partitions of the Deinococcus genome and the two partitions of the Thermus genome reveals homology between the Thermus megaplasmid (pTT27 and Deinococcus megaplasmid (DR177. Conclusion After the radiation from their common ancestor, the Thermus and Deinococcus lineages have taken divergent paths toward their distinct lifestyles. In addition to extensive gene loss, Thermus seems to have acquired numerous genes from thermophiles, which likely was the decisive contribution to its thermophilic adaptation. By contrast, Deinococcus lost few genes but seems to have acquired many bacterial genes that apparently enhanced its ability to survive different kinds of environmental stresses. Notwithstanding the accumulation of

Comment on "Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage".

Science.gov (United States)

Nakagome, Shigeki; Mano, Shuhei; Hasegawa, Masami

2013-03-29

Based on nuclear and mitochondrial DNA, Hailer et al. (Reports, 20 April 2012, p. 344) suggested early divergence of polar bears from a common ancestor with brown bears and subsequent introgression. Our population genetic analysis that traces each of the genealogies in the independent nuclear loci does not support the evolutionary model proposed by the authors.

Journeys of our ancestors: Conservation science approaches to the analysis of cultural material

Science.gov (United States)

O'Grady, Caitlin Rose

The application and use of non-destructive portable x-ray fluorescence (XRF) analysis is a critical tool in the preservation and interpretation of cultural material. Portable XRF instrumentation produce elemental compositional data that is used to reconstruct current artifact composition, which can be related to materials and methods of manufacture, technological practice, as well as object condition and presence of corrosion surfaces. Portable XRF analysis is used to assess a variety of material classes utilized in artifact manufacture. The dissertation research is based on a series of three case studies that represent typical groups of material culture commonly encountered in conservation and conservation science research. Conservators and conservation scientists frequently undertake analysis and interpretation of disparate groups of materials. Often, these objects are tied together by research questions or themes directed by outside influences including preservation issues requiring action; curatorial research interests; museum exhibition programs; as well as many other cultural heritage stakeholders. To this end, both non-destructive and destructive tools that provide measurements of interest play critical roles in analysis. The case studies have been designed to answer common compositional questions relating to (a) bulk analysis of Chinese coins, (b) characterization of Southwestern ceramic colorants, and, (c) chemical examination of post-depositional manganese dioxide accretions occurring on archaeological ceramic materials. They evaluate the value of data produced using effectiveness of non-destructive portable XRF analysis for the interpretation of archaeological materials. The case studies provide a template for the development of conservation science research, predicated on object preservation, which produce meaningful data for the interpretation and conservation of the analyzed archaeological artifacts. Portable XRF provides useful data that is used to

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.

Evidence of ancient genome reduction in red algae (Rhodophyta).

Science.gov (United States)

Qiu, Huan; Price, Dana C; Yang, Eun Chan; Yoon, Hwan Su; Bhattacharya, Debashish

2015-08-01

Red algae (Rhodophyta) comprise a monophyletic eukaryotic lineage of ~6,500 species with a fossil record that extends back 1.2 billion years. A surprising aspect of red algal evolution is that sequenced genomes encode a relatively limited gene inventory (~5-10 thousand genes) when compared with other free-living algae or to other eukaryotes. This suggests that the common ancestor of red algae may have undergone extensive genome reduction, which can result from lineage specialization to a symbiotic or parasitic lifestyle or adaptation to an extreme or oligotrophic environment. We gathered genome and transcriptome data from a total of 14 red algal genera that represent the major branches of this phylum to study genome evolution in Rhodophyta. Analysis of orthologous gene gains and losses identifies two putative major phases of genome reduction: (i) in the stem lineage leading to all red algae resulting in the loss of major functions such as flagellae and basal bodies, the glycosyl-phosphatidylinositol anchor biosynthesis pathway, and the autophagy regulation pathway; and (ii) in the common ancestor of the extremophilic Cyanidiophytina. Red algal genomes are also characterized by the recruitment of hundreds of bacterial genes through horizontal gene transfer that have taken on multiple functions in shared pathways and have replaced eukaryotic gene homologs. Our results suggest that Rhodophyta may trace their origin to a gene depauperate ancestor. Unlike plants, it appears that a limited gene inventory is sufficient to support the diversification of a major eukaryote lineage that possesses sophisticated multicellular reproductive structures and an elaborate triphasic sexual cycle. © 2015 Phycological Society of America.

The Amborella vacuolar processing enzyme family

Directory of Open Access Journals (Sweden)

Valérie ePoncet

2015-08-01

Full Text Available Most vacuolar proteins are synthesized on rough endoplasmic reticulum as proprotein precursors and then transported to the vacuoles, where they are converted into their respective mature forms by vacuolar processing enzymes (VPEs. In the case of the seed storage proteins, this process is of major importance, as it conditions the establishment of vigorous seedlings. Toward the goal of identifying proteome signatures that could be associated with the origin and early diversification of angiosperms, we previously characterized the 11S-legumin-type of seed storage proteins from Amborella trichopoda, a rainforest shrub endemic to New Caledonia that is also the probable sister to all other angiosperms (Amborella Genome Project, 2013. In the present study, proteomic and genomic approaches were used to characterize the VPE family in this species. Three genes were found to encode VPEs in the Amborella’s genome. Phylogenetic analyses showed that the Amborella sequences grouped within two major clades of angiosperm VPEs, indicating that the duplication that generated the ancestors of these clades occurred before the most recent common ancestor of living angiosperms. A further important duplication within the VPE family appears to have occurred in common ancestor of the core eudicots, while many more recent duplications have also occurred in specific taxa, including both Arabidopsis thaliana and Amborella. An analysis of natural genetic variation for each of the three Amborella VPE genes revealed the absence of selective forces acting on intronic and exonic single-nucleotide polymorphisms among several natural Amborella populations of in New Caledonia.

Creative Commons

DEFF Research Database (Denmark)

Jensen, Lone

2006-01-01

En Creative Commons licens giver en forfatter mulighed for at udbyde sit værk i en alternativ licensløsning, som befinder sig på forskellige trin på en skala mellem yderpunkterne "All rights reserved" og "No rights reserved". Derved opnås licensen "Some rights reserved"......En Creative Commons licens giver en forfatter mulighed for at udbyde sit værk i en alternativ licensløsning, som befinder sig på forskellige trin på en skala mellem yderpunkterne "All rights reserved" og "No rights reserved". Derved opnås licensen "Some rights reserved"...

Shrnutí fylogenetických hypotéz nadčeledi Cobitoidea

OpenAIRE

Dvořák, Tomáš

2016-01-01

Phylogenetics is a field of systematic biology which aims to uncover the evolutionary relations betweenll species on the principle of finding their common ancestor. Phylogeny can be applied on many diferent markers, but among the most common are genetic and morphological ones. The results of the phylogenetic analyses can be applied in many other fields of research. We can use them e.g. in answering questions concerning geological events (when using fishes as model, most often in some river fl...

Giant viruses of amoebas: an update

Directory of Open Access Journals (Sweden)

Sarah eAherfi

2016-03-01

Full Text Available During the 12 past years, five new or putative virus families encompassing several members, namely Mimiviridae, Marseilleviridae, pandoraviruses, faustoviruses, and virophages were described. In addition, Pithovirus sibericum and Mollivirus sibericum represent type strains of putative new giant virus families. All these viruses were isolated using amoebal coculture methods. These giant viruses were linked by phylogenomic analyses to other large DNA viruses. They were then proposed to be classified in a new viral order, the Megavirales, on the basis of their common origin, as shown by a set of ancestral genes encoding key viral functions, a common virion architecture, and shared major biological features including replication inside cytoplasmic factories. Megavirales is increasingly demonstrated to stand in the tree of life aside Bacteria, Archaea and Eukarya, and the megavirus ancestor is suspected to be as ancient as cellular ancestors. In addition, giant amoebal viruses are visible under a light microscope and display many phenotypic and genomic features not found in other viruses, while they share other characteristics with parasitic microbes. Moreoever, these organisms appear to be common inhabitants of our biosphere, and mimiviruses and marseilleviruses were isolated from human samples and associated to diseases. In the present review, we describe the main features and recent findings on these giant amoebal viruses and virophages.

MDEP Common Position CP-DICWG-13. Common position on spurious actuation

International Nuclear Information System (INIS)

2017-01-01

Spurious actuations produced by Instrumentation and Control (I and C) systems are a safety concern if such actuations could challenge plant safety. Spurious actuations can lead to unnecessary challenges to safety equipment, challenge the ability of safety systems to provide their intended functions, or place the plant in an un-analysed state. Spurious actuation of plant equipment can be caused by factors including, but not limited to, single failures, common cause failures, human (e.g. operator) action, maintenance errors, design errors, or missing requirements. Modern I and C systems can have inter-connectivities, dependencies and commonalities that can, if the overall I and C architecture and the individual I and C systems are not adequately developed and operated, facilitate fault propagation, leading to potential spurious actuation of one or more trains of plant equipment. Sources and contributors of spurious actuations of multiple trains of plant equipment may include inadequate independence among redundant portions of I and C systems, inappropriate allocation of I and C functions, inadequate qualification or design of supporting systems (e.g. heating, ventilation and air conditioning (HVAC) system), or non-classified systems that could have been erroneously classified. Spurious actuations are a type of hazard. Generic Common Position (GCP) DICWG-10 'Common Position on Hazard Identification and Controls for Digital Instrumentation and Control Systems' provides a set of common positions pertaining to identifying and controlling hazards in an I and C system. This common position was developed to add special considerations when identifying and controlling hazards that include spurious actuations. It is expected that GCP DICWG-10 and the common positions in this document be used together for a complete analysis of hazards and their controls (e.g. prevention of spurious actuations in the design of the system/component). Spurious actuations of concern

Combined Common Person and Common Item Equating of Medical Science Examinations.

Science.gov (United States)

Kelley, Paul R.

This equating study of the National Board of Medical Examiners Examinations was a combined common persons and common items equating, using the Rasch model. The 1,000-item test was administered to about 3,000 second-year medical students in seven equal-length subtests: anatomy, physiology, biochemistry, pathology, microbiology, pharmacology, and…

Justifying group-specific common morality.

Science.gov (United States)

Strong, Carson

2008-01-01

Some defenders of the view that there is a common morality have conceived such morality as being universal, in the sense of extending across all cultures and times. Those who deny the existence of such a common morality often argue that the universality claim is implausible. Defense of common morality must take account of the distinction between descriptive and normative claims that there is a common morality. This essay considers these claims separately and identifies the nature of the arguments for each claim. It argues that the claim that there is a universal common morality in the descriptive sense has not been successfully defended to date. It maintains that the claim that there is a common morality in the normative sense need not be understood as universalist. This paper advocates the concept of group specific common morality, including country-specific versions. It suggests that both the descriptive and the normative claims that there are country-specific common moralities are plausible, and that a country-specific normative common morality could provide the basis for a country's bioethics.

The promise of common pool resource theory and the reality of commons projects

Directory of Open Access Journals (Sweden)

Fred P. Saunders

2014-08-01

Full Text Available Commons projects, such as community-based natural resource management, have widespread appeal, which has enabled them to shrug off a mixed performance in practice. This paper discusses how the theoretical assumptions of common pool resource (CPR theory may have inadvertently contributed to the unfulfilled expectations of commons projects. The paper argues that the individual ‘rational resource user’, encapsulated in the CPR design principles, struggles to provide clear direction for meaningful consideration of local norms, values and interests in commons projects. The focus of CPR theory on efficiency and functionality results in a tendency in commons projects to overlook how local conditions are forged through relations at multiple scales. Commonly politically complex and changing relations are reduced to institutional design problems based on deriving the incentives and disincentives of ‘rational resource users. The corollary is that CPR theory oversimplifies the project context that it is seeking to change because it offers little or no direction to deal with the social embeddedness of resource use or implications of different stratifications.

The evolutive aspect of the short jat substituents following the sonant r - a comparison between the Serbian literary language and the dialect of Vuk’s ancestors

Directory of Open Access Journals (Sweden)

Ostojić Vladimir B.

2015-01-01

Full Text Available The paper discusses the evolutive aspects of short “jat” following the sonant r usage during the formation of the modern Serbian literary language and its treatment in the Serbo-Croatistic and the Serbistic descriptive and normative literature. In addition to the basic issue of the distribution of the short “jat’s” substituent following the sonant r in dialects of Montenegro, particularly in the native dialect of Vuk Karadžić’s ancestors, the author also addresses the question related to the mechanisms that cause short “jat” following the sonant r in ijekavian dialects to be reduced sometimes to e, and sometimes to je. Substitution of short “jat” following the sonant r in Jezera-Šarani dialect had important evolution from the times of “classical Vukovian ijekavism”. In this dialect, forms with rje do not occur, except in the word starješina. Here, r and j remained in the same syllable, which set the stage for iotization and depalatalization. The analysis of the paper describes the situation in Jezera-Šarani dialect as well as the situation in other Montenegrian dialects of the older and newer Eastern-Herzegovian type. The author as well takes into consideration that our Pravopis has already disregarded the Vukovian tradition with omitting j that follows sonant r in the examples pogreška and greška. In order to eliminate the disunity, the author concludes that the status of the group re should not be questioned from the aspect of literary language standards.

Nicolae Milescu Spătarul - ancestor of a Nobel Laureate - Ilia I. Mecinikov. Part II. Ilia I. Mecinikov’s life and scientific work; 16th of May 2011 - 166 years since the birth of the European scholar; 15th of July 2011 - 95 years since death

Directory of Open Access Journals (Sweden)

Dan RIGA

2011-01-01

Full Text Available The work showcases the promotion of Romanian lineage - Nicolae Milescu Spătarul (1636-1708 as ancestor of scientist Ilia Ilici Mecinikov (1845-1916, Nobel Laureate (1908.A great figure in world science and bio-medicine, the scientist - creator of two new modernsciences (immunology and gerontology – is claimed and honoured by four nations: Israeli, French,Russian and Ukrainian. Despite his known Romanian descent on his paternal side – biographicallyconsecrated by his wife Olga Mecinikov – Romania has pushed him into oblivion, by not promotingthis historical truth and reality to all.In our country, Prof. Dr. doc. Ilie Th. Riga (1908-1977 publishes in 1930, in the Romanianmagazine, Natura (Nature, Originea românească a lui Metchnikoff (Metchnikoff’s Romanianorigins. In the 2007-2011 period, two of the authors of the work continuously publish, in thecountry and abroad, thus creating Dosarul ascendenţei româneşti al lui Mecinikov (Mecinikov’sfile on his Romanian lineage, for the global informational civilization. They published their worksin printed version: in scientific magazines (2007, 2011, in their own monograph Medicina antiîmbătrânireşi ştiinţele longevităţii (Anti-aging Medicine and Longevity Sciences, (2007, innewspapers Ziua USA (The Day - USA, (2008 and Clipa. Magazinul Actualităţii CulturaleRomâneşti (The Moment. The Romanian Cultural Current Affairs Magazine, (2011, inEnciclopedia medicală Românească (Encyclopaedia of Romanian Medicine, (2009 and also onSorin Riga, Dan Riga, Vasile Man - Nicolae Milescu Spătarul - ancestor of a Nobel Laureate - Ilia I. Mecinikov...250webpages (the online era: www.DacoRomanica.ro (2010, www.revista-studii-uvvg.ro (2011,www.ziuausa.com (2008, www.revistaclipa.com (2011, taken over by other internet websites.

Five Theses on the Common

Directory of Open Access Journals (Sweden)

Gigi Roggero

2011-01-01

Full Text Available I present five theses on the common within the context of the transformations of capitalist social relations as well as their contemporary global crisis. My framework involves ‘‘cognitive capitalism,’’ new processes of class composition, and the production of living knowledge and subjectivity. The commons is often discussed today in reference to the privatizationand commodification of ‘‘common goods.’’ This suggests a naturalistic and conservative image of the common, unhooked from the relations of production. I distinguish between commons and the common: the first model is related to Karl Polanyi, the second to Karl Marx. As elaborated in the postoperaista debate, the common assumes an antagonistic double status: it is boththe plane of the autonomy of living labor and it is subjected to capitalist ‘‘capture.’’ Consequently, what is at stake is not the conservation of ‘‘commons,’’ but rather the production of the common and its organization into new institutions that would take us beyond the exhausted dialectic between public and private.

MDEP Generic Common Position No DICWG-01. Common position on the treatment of common cause failure caused by software within digital safety systems

International Nuclear Information System (INIS)

2013-01-01

Common cause failures (CCF)2 have been a significant safety concern for nuclear power plant systems. The increasing dependence on software-in safety systems for nuclear power plants has increased the safety significance of CCF caused by software, when software in redundant channels or portions of safety systems has some common dependency. For example, the effect of systematic failures can lead to a loss of safety in many ways: unwanted actuations, a safety function is not provided when needed. Therefore, nuclear power plants should be systematically protected from the effects of common cause failures caused by software in DI and C safety systems. Software for nuclear power plant safety systems should be of the high quality necessary to help assure against the loss of safety (i.e. developed with high-quality engineering practices, commensurate quality assurance applied, with continuous improvement through corrective actions based on lessons learned from operating experience). However, demonstrating adequate software quality only through verification and validation activities and controls on the development process has proved to be problematic. Therefore, this common position provides guidance for the assessment of the potential for CCF for software. It is recognized that programmable logic devices do not execute software in the conventional sense; however, the application development process using these devices have many similarities with software development, and the deficiencies that may be introduced during the application development process may induce errors in the programmable logic devices that can result in common cause failures of these devices of a type similar to software common cause failure. Although deficiencies with the potential to give rise to software common cause failures can be introduced at all phases of the software life cycle, this common position will only consider the potential for software common cause failures within digital safety system

Common Law and Un-common Sense

OpenAIRE

Ballard, Roger

2000-01-01

This paper examines the practical and conceptual differences which arise when juries are invited to apply their common sense in assessing reasonable behaviour in the midst of an ethnically plural society. The author explores the conundrums which the increasing salience of ethnic pluralism has now begun to pose in legal terms, most especially with respect to organisation of system for the equitable administration and delivery of justice in the context of an increasingly heterogeneous society. ...

The tapeworm Atractolytocestus tenuicollis (Cestoda: Caryophyllidea) - a sister species or ancestor of an invasive A. huronensis?

Czech Academy of Sciences Publication Activity Database

Kraľová-Hromadová, I.; Štefka, Jan; Bazsalovicsová, E.; Bokorová, S.; Oros, M.

2013-01-01

Roč. 112, č. 10 (2013), s. 3379-3388 ISSN 0932-0113 R&D Projects: GA ČR GBP505/12/G112 Grant - others:Centre of Excellence for Parasitology(XE) 2622012011 Institutional support: RVO:60077344 Keywords : carp Cyprinus carpio * farmed common carp * Cestoda Caryophyllidea * sequence alignment * parasites * fishes Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.327, year: 2013

A Dutch Fanconi Anemia FANCC Founder Mutation in Canadian Manitoba Mennonites

Directory of Open Access Journals (Sweden)

Yne de Vries

2012-01-01

Full Text Available Fanconi anemia (FA is a recessive DNA instability disorder associated with developmental abnormalities, bone marrow failure, and a predisposition to cancer. Based on their sensitivity to DNA cross-linking agents, FA cells have been assigned to 15 complementation groups, and the associated genes have been identified. Founder mutations have been found in different FA genes in several populations. The majority of Dutch FA patients belongs to complementation group FA-C. Here, we report 15 patients of Dutch ancestry and a large Canadian Manitoba Mennonite kindred carrying the FANCC c.67delG mutation. Genealogical investigation into the ancestors of the Dutch patients shows that these ancestors lived in four distinct areas in The Netherlands. We also show that the Dutch and Manitoba Mennonite FANCC c.67delG patients share the same haplotype surrounding this mutation, indicating a common founder.

A phylogenetic view of the Out of Asia/Eurasia and Out of Africa hypotheses in the light of recent molecular and palaeontological finds.

Science.gov (United States)

Árnason, Úlfur

2017-09-05

The substantiality of the Out of Africa hypothesis was addressed in the light of recent genomic analysis of extant humans (Homo sapiens sapiens, Hss) and progress in Neanderthal palaeontology. The examination lent no support to the commonly assumed Out of Africa scenario but favoured instead a Eurasian divergence between Neanderthals and Hss (the Askur/Embla hypothesis) and an Out of Asia/Eurasia hypothesis according to which all other parts of the world were colonized by Hss migrations from Asia. The examination suggested furthermore that the ancestors of extant KhoeSan and Mbuti composed the first Hss dispersal(s) into Africa and that the ancestors of Yoruba made up a later wave into the same continent. The conclusions constitute a change in paradigm for the study of human evolution. Copyright © 2017. Published by Elsevier B.V.

Common Misconceptions about Cholesterol

Science.gov (United States)

... Venous Thromboembolism Aortic Aneurysm More Common Misconceptions about Cholesterol Updated:Jan 29,2018 How much do you ... are some common misconceptions — and the truth. High cholesterol isn’t a concern for children. High cholesterol ...

Looking for the most ``primitive'' organism(s) on Earth today: the state of the art

Science.gov (United States)

Forterre, Patrick

1995-02-01

Molecular phylogenetic studies have revealed a tripartite division of the living world into two procaryotic groups, Bacteria and Archaea, and one eucaryotic group, Eucarya. Which group is the most "primitive"? Which groups are sister? The answer to these questions would help to delineate the characters of the last common ancestor to all living beings, as a first step to reconstruct the earliest periods of biological evolution on Earth. The current "Procaryotic dogma" claims that procaryotes are primitive. Since the ancestor of Archaea was most probably a hyperthermophile, and since bacteria too might have originated from hyperthermophiles, the procaryotic dogma has been recently connected to the hot origin of life hypothesis. However, the notion that present-day hyperthermophiles are primitive has been challenged by recent findings, in these unique microorganisms, of very elaborate adaptative devices for life at high temperature. Accordingly, I discuss here alternative hypotheses that challenge the procaryotic dogma, such as the idea of a universal ancestor with molecular features in between those of eucaryotes and procaryotes, or the origin of procaryotes via thermophilic adaptation. Clearly, major evolutionary questions about early cellular evolution on Earth remain to be settled before we can speculate with confidence about which kinds of life might have appeared on other planets.

Ruang Permukiman Tradisional Jawa Berbasis Perlindungan

Directory of Open Access Journals (Sweden)

Endratno Budi Santosa

2016-03-01

Full Text Available Abstract. Traditional Javanese people and society put a lot of philosophy and symbolism in their living practices and daily life. Although in many places this custom is facing great challenges, from historical changes to material developments, there are still people who try to preserve all the traditions inherited from their ancestors. The flexible attitude of the Javanese led to a tradition that emerged as a blend of basic culture and religion (syncretism, which is manifested in a variety of shapes and forms, one of which is the formation of space and the surrounding environment. This paper aims to illustrate as well as compare examples from Javanese spatial culture. There are several basic criteria, including the physical conditions, but the most common is how the spatial organization of a settlement is an attempt or strategy to ask for protection from a higher power, one of which is finding a way to show respect for the ancestors. The study’s findings show that although the macro-concept is usually the same, the material conditions, the history of a settlement’s formation, and local cultural-religious roots led to the specific forms and spatial patterns of specific settlements. Keywords. Traditional settlements, Javanese culture, protection space, ancestor beliefs

The unique deep sea—land connection: interactive 3D visualization and molecular phylogeny of Bathyhedyle boucheti n. sp. (Bathyhedylidae n. fam.—the first panpulmonate slug from bathyal zones

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Timea P. Neusser

2016-12-01

Full Text Available The deep sea comprises vast unexplored areas and is expected to conceal significant undescribed invertebrate species diversity. Deep waters may act as a refuge for many relictual groups, including elusive and enigmatic higher taxa, but the evolutionary pathways by which colonization of the deep sea has occurred have scarcely been investigated. Sister group relationships between shallow water and deep sea taxa have been documented in several invertebrate groups, but are unknown between amphibious/terrestrial and deep-sea species. Here we describe in full and interactive 3D morphoanatomical detail the new sea slug species Bathyhedyle boucheti n. sp., dredged from the continental slope off Mozambique. Molecular and morphological analyses reveal that it represents a novel heterobranch gastropod lineage which we establish as the new family Bathyhedylidae. The family is robustly supported as sister to the recently discovered panpulmonate acochlidian family Aitengidae, which comprises amphibious species living along the sea shore as well as fully terrestrial species. This is the first marine-epibenthic representative among hedylopsacean Acochlidiida, the first record of an acochlidian from deep waters and the first documented panpulmonate deep-sea slug. Considering a marine mesopsammic ancestor, the external morphological features of Bathyhedyle n. gen. may be interpreted as independent adaptations to a benthic life style in the deep sea, including the large body size, broad foot and propodial tentacles. Alternatively, the common ancestor of Bathyhedylidae and Aitengidae may have been a macroscopic amphibious or even terrestrial species. We hypothesize that oophagy in the common ancestor of Aitengidae and Bathyhedylidae might explain the impressive ecological and evolutionary flexibility in habitat choice in the Acochlidiida.

How Common Is PTSD?

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... Center for PTSD » Public » How Common Is PTSD? PTSD: National Center for PTSD Menu Menu PTSD PTSD Home For the Public ... here Enter ZIP code here How Common Is PTSD? Public This section is for Veterans, General Public, ...

Characterization and evolutionary implications of the triad Asp-Xxx-Glu in group II phosphopantetheinyl transferases.

Science.gov (United States)

Wang, Yue-Yue; Li, Yu-Dong; Liu, Jian-Bo; Ran, Xin-Xin; Guo, Yuan-Yang; Ren, Ni-Ni; Chen, Xin; Jiang, Hui; Li, Yong-Quan

2014-01-01

Phosphopantetheinyl transferases (PPTases), which play an essential role in both primary and secondary metabolism, are magnesium binding enzymes. In this study, we characterized the magnesium binding residues of all known group II PPTases by biochemical and evolutionary analysis. Our results suggested that group II PPTases could be classified into two subgroups, two-magnesium-binding-residue-PPTases containing the triad Asp-Xxx-Glu and three-magnesium-binding-residue-PPTases containing the triad Asp-Glu-Glu. Mutations of two three-magnesium-binding-residue-PPTases and one two-magnesium-binding-residue-PPTase indicate that the first and the third residues in the triads are essential to activities; the second residues in the triads are non-essential. Although variations of the second residues in the triad Asp-Xxx-Glu exist throughout the whole phylogenetic tree, the second residues are conserved in animals, plants, algae, and most prokaryotes, respectively. Evolutionary analysis suggests that: the animal group II PPTases may originate from one common ancestor; the plant two-magnesium-binding-residue-PPTases may originate from one common ancestor; the plant three-magnesium-binding-residue-PPTases may derive from horizontal gene transfer from prokaryotes.

Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution.

Science.gov (United States)

Rogozin, Igor B; Wolf, Yuri I; Sorokin, Alexander V; Mirkin, Boris G; Koonin, Eugene V

2003-09-02

Sequencing of eukaryotic genomes allows one to address major evolutionary problems, such as the evolution of gene structure. We compared the intron positions in 684 orthologous gene sets from 8 complete genomes of animals, plants, fungi, and protists and constructed parsimonious scenarios of evolution of the exon-intron structure for the respective genes. Approximately one-third of the introns in the malaria parasite Plasmodium falciparum are shared with at least one crown group eukaryote; this number indicates that these introns have been conserved through >1.5 billion years of evolution that separate Plasmodium from the crown group. Paradoxically, humans share many more introns with the plant Arabidopsis thaliana than with the fly or nematode. The inferred evolutionary scenario holds that the common ancestor of Plasmodium and the crown group and, especially, the common ancestor of animals, plants, and fungi had numerous introns. Most of these ancestral introns, which are retained in the genomes of vertebrates and plants, have been lost in fungi, nematodes, arthropods, and probably Plasmodium. In addition, numerous introns have been inserted into vertebrate and plant genes, whereas, in other lineages, intron gain was much less prominent.

Expression of Wnt signaling skeletal development genes in the cartilaginous fish, elephant shark (Callorhinchus milii).

Science.gov (United States)

D'Souza, Damian G; Rana, Kesha; Milley, Kristi M; MacLean, Helen E; Zajac, Jeffrey D; Bell, Justin; Brenner, Sydney; Venkatesh, Byrappa; Richardson, Samantha J; Danks, Janine A

2013-11-01

Jawed vertebrates (Gnasthostomes) are broadly separated into cartilaginous fishes (Chondricthyes) and bony vertebrates (Osteichthyes). Cartilaginous fishes are divided into chimaeras (e.g. ratfish, rabbit fish and elephant shark) and elasmobranchs (e.g. sharks, rays and skates). Both cartilaginous fish and bony vertebrates are believed to have a common armoured bony ancestor (Class Placodermi), however cartilaginous fish are believed to have lost bone. This study has identified and investigated genes involved in skeletal development in vertebrates, in the cartilaginous fish, elephant shark (Callorhinchus milii). Ctnnb1 (β-catenin), Sfrp (secreted frizzled protein) and a single Sost or Sostdc1 gene (sclerostin or sclerostin domain-containing protein 1) were identified in the elephant shark genome and found to be expressed in a number of tissues, including cartilage. β-catenin was also localized in several elephant shark tissues. The expression of these genes, which belong to the Wnt/β-catenin pathway, is required for normal bone formation in mammals. These findings in the cartilaginous skeleton of elephant shark support the hypothesis that the common ancestor of cartilaginous fishes and bony vertebrates had the potential for making bone. Crown Copyright © 2013. Published by Elsevier Inc. All rights reserved.

Microbiological evidence for Fe(III) reduction on early Earth

Science.gov (United States)

Vargas, Madeline; Kashefi, Kazem; Blunt-Harris, Elizabeth L.; Lovley, Derek R.

1998-09-01

It is generally considered that sulphur reduction was one of the earliest forms of microbial respiration, because the known microorganisms that are most closely related to the last common ancestor of modern life are primarily anaerobic, sulphur-reducing hyperthermophiles. However, geochemical evidence indicates that Fe(III) is more likely than sulphur to have been the first external electron acceptor of global significance in microbial metabolism. Here we show that Archaea and Bacteria that are most closely related to the last common ancestor can reduce Fe(III) to Fe(II) and conserve energy to support growth from this respiration. Surprisingly, even Thermotoga maritima, previously considered to have only a fermentative metabolism, could grow as a respiratory organism when Fe(III) was provided as an electron acceptor. These results provide microbiological evidence that Fe(III) reduction could have been an important process on early Earth and suggest that microorganisms might contribute to Fe(III) reduction in modern hot biospheres. Furthermore, our discovery that hyperthermophiles that had previously been thought to require sulphur for cultivation can instead be grown without the production of toxic and corrosive sulphide, should aid biochemical investigations of these poorly understood organisms.

Sexual size dimorphism, canine dimorphism, and male-male competition in primates: where do humans fit in?

Science.gov (United States)

Plavcan, J Michael

2012-03-01

Sexual size dimorphism is generally associated with sexual selection via agonistic male competition in nonhuman primates. These primate models play an important role in understanding the origins and evolution of human behavior. Human size dimorphism is often hypothesized to be associated with high rates of male violence and polygyny. This raises the question of whether human dimorphism and patterns of male violence are inherited from a common ancestor with chimpanzees or are uniquely derived. Here I review patterns of, and causal models for, dimorphism in humans and other primates. While dimorphism in primates is associated with agonistic male mate competition, a variety of factors can affect male and female size, and thereby dimorphism. The causes of human sexual size dimorphism are uncertain, and could involve several non-mutually-exclusive mechanisms, such as mate competition, resource competition, intergroup violence, and female choice. A phylogenetic reconstruction of the evolution of dimorphism, including fossil hominins, indicates that the modern human condition is derived. This suggests that at least some behavioral similarities with Pan associated with dimorphism may have arisen independently, and not directly from a common ancestor.

Ancestral Sequence Reconstruction with Maximum Parsimony.

Science.gov (United States)

Herbst, Lina; Fischer, Mareike

2017-12-01

One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference and for ancestral sequence inference is Maximum Parsimony (MP). In this manuscript, we focus on this method and on ancestral state inference for fully bifurcating trees. In particular, we investigate a conjecture published by Charleston and Steel in 1995 concerning the number of species which need to have a particular state, say a, at a particular site in order for MP to unambiguously return a as an estimate for the state of the last common ancestor. We prove the conjecture for all even numbers of character states, which is the most relevant case in biology. We also show that the conjecture does not hold in general for odd numbers of character states, but also present some positive results for this case.

Invasion of Ancestral Mammals into Dim-light Environments Inferred from Adaptive Evolution of the Phototransduction Genes.

Science.gov (United States)

Wu, Yonghua; Wang, Haifeng; Hadly, Elizabeth A

2017-04-20

Nocturnality is a key evolutionary innovation of mammals that enables mammals to occupy relatively empty nocturnal niches. Invasion of ancestral mammals into nocturnality has long been inferred from the phylogenetic relationships of crown Mammalia, which is primarily nocturnal, and crown Reptilia, which is primarily diurnal, although molecular evidence for this is lacking. Here we used phylogenetic analyses of the vision genes involved in the phototransduction pathway to predict the diel activity patterns of ancestral mammals and reptiles. Our results demonstrated that the common ancestor of the extant Mammalia was dominated by positive selection for dim-light vision, supporting the predominate nocturnality of the ancestral mammals. Further analyses showed that the nocturnality of the ancestral mammals was probably derived from the predominate diurnality of the ancestral amniotes, which featured strong positive selection for bright-light vision. Like the ancestral amniotes, the common ancestor of the extant reptiles and various taxa in Squamata, one of the main competitors of the temporal niches of the ancestral mammals, were found to be predominate diurnality as well. Despite this relatively apparent temporal niche partitioning between ancestral mammals and the relevant reptiles, our results suggested partial overlap of their temporal niches during crepuscular periods.

The common ancestry of life

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Wolf Yuri I

2010-11-01

Full Text Available Abstract Background It is common belief that all cellular life forms on earth have a common origin. This view is supported by the universality of the genetic code and the universal conservation of multiple genes, particularly those that encode key components of the translation system. A remarkable recent study claims to provide a formal, homology independent test of the Universal Common Ancestry hypothesis by comparing the ability of a common-ancestry model and a multiple-ancestry model to predict sequences of universally conserved proteins. Results We devised a computational experiment on a concatenated alignment of universally conserved proteins which shows that the purported demonstration of the universal common ancestry is a trivial consequence of significant sequence similarity between the analyzed proteins. The nature and origin of this similarity are irrelevant for the prediction of "common ancestry" of by the model-comparison approach. Thus, homology (common origin of the compared proteins remains an inference from sequence similarity rather than an independent property demonstrated by the likelihood analysis. Conclusion A formal demonstration of the Universal Common Ancestry hypothesis has not been achieved and is unlikely to be feasible in principle. Nevertheless, the evidence in support of this hypothesis provided by comparative genomics is overwhelming. Reviewers this article was reviewed by William Martin, Ivan Iossifov (nominated by Andrey Rzhetsky and Arcady Mushegian. For the complete reviews, see the Reviewers' Report section.

The calmodulin-binding, short linear motif, NSCaTE is conserved in L-type channel ancestors of vertebrate Cav1.2 and Cav1.3 channels.

Directory of Open Access Journals (Sweden)

Valentina Taiakina

Full Text Available NSCaTE is a short linear motif of (xWxxx(I or Lxxxx, composed of residues with a high helix-forming propensity within a mostly disordered N-terminus that is conserved in L-type calcium channels from protostome invertebrates to humans. NSCaTE is an optional, lower affinity and calcium-sensitive binding site for calmodulin (CaM which competes for CaM binding with a more ancient, C-terminal IQ domain on L-type channels. CaM bound to N- and C- terminal tails serve as dual detectors to changing intracellular Ca(2+ concentrations, promoting calcium-dependent inactivation of L-type calcium channels. NSCaTE is absent in some arthropod species, and is also lacking in vertebrate L-type isoforms, Cav1.1 and Cav1.4 channels. The pervasiveness of a methionine just downstream from NSCaTE suggests that L-type channels could generate alternative N-termini lacking NSCaTE through the choice of translational start sites. Long N-terminus with an NSCaTE motif in L-type calcium channel homolog LCav1 from pond snail Lymnaea stagnalis has a faster calcium-dependent inactivation than a shortened N-termini lacking NSCaTE. NSCaTE effects are present in low concentrations of internal buffer (0.5 mM EGTA, but disappears in high buffer conditions (10 mM EGTA. Snail and mammalian NSCaTE have an alpha-helical propensity upon binding Ca(2+-CaM and can saturate both CaM N-terminal and C-terminal domains in the absence of a competing IQ motif. NSCaTE evolved in ancestors of the first animals with internal organs for promoting a more rapid, calcium-sensitive inactivation of L-type channels.

MDEP Common Position CP-VICWG-01. Common Position: Establishment of Common QA/QM Criteria for the Multinational Vendor Inspection CP-VICWG-01

International Nuclear Information System (INIS)

2015-01-01

This document provides a set of common positions for harmonizing inspection criteria called 'Common QA/QM Criteria' which will be used in Multinational Vendor Inspections. This document was prepared by the Vendor Inspection Co-operation Working Group (VICWG) of the Multinational Design Evaluation Program (MDEP). The 'Common QA/QM Criteria' provides the basic areas for consideration when performing Vendor Inspections. The criteria have been developed in conformity with International Codes and Standards such as IAEA, ISO, etc. that MDEP member countries have adopted

Commons problems, common ground: Earth-surface dynamics and the social-physical interdisciplinary frontier

Science.gov (United States)

Lazarus, E.

2015-12-01

In the archetypal "tragedy of the commons" narrative, local farmers pasture their cows on the town common. Soon the common becomes crowded with cows, who graze it bare, and the arrangement of open access to a shared resource ultimately fails. The "tragedy" involves social and physical processes, but the denouement depends on who is telling the story. An economist might argue that the system collapses because each farmer always has a rational incentive to graze one more cow. An ecologist might remark that the rate of grass growth is an inherent control on the common's carrying capacity. And a geomorphologist might point out that processes of soil degradation almost always outstrip processes of soil production. Interdisciplinary research into human-environmental systems still tends to favor disciplinary vantages. In the context of Anthropocene grand challenges - including fundamental insight into dynamics of landscape resilience, and what the dominance of human activities means for processes of change and evolution on the Earth's surface - two disciplines in particular have more to talk about than they might think. Here, I use three examples - (1) beach nourishment, (2) upstream/downstream fluvial asymmetry, and (3) current and historical "land grabbing" - to illustrate a range of interconnections between physical Earth-surface science and common-pool resource economics. In many systems, decision-making and social complexity exert stronger controls on landscape expression than do physical geomorphological processes. Conversely, human-environmental research keeps encountering multi-scale, emergent problems of resource use made 'common-pool' by water, nutrient and sediment transport dynamics. Just as Earth-surface research can benefit from decades of work on common-pool resource systems, quantitative Earth-surface science can make essential contributions to efforts addressing complex problems in environmental sustainability.

Twenty-First Century Diseases: Commonly Rare and Rarely Common?

Science.gov (United States)

Daunert, Sylvia; Sittampalam, Gurusingham Sitta; Goldschmidt-Clermont, Pascal J

2017-09-20

Alzheimer's drugs are failing at a rate of 99.6%, and success rate for drugs designed to help patients with this form of dementia is 47 times less than for drugs designed to help patients with cancers ( www.scientificamerican.com/article/why-alzheimer-s-drugs-keep-failing/2014 ). How can it be so difficult to produce a valuable drug for Alzheimer's disease? Each human has a unique genetic and epigenetic makeup, thus endowing individuals with a highly unique complement of genes, polymorphisms, mutations, RNAs, proteins, lipids, and complex sugars, resulting in distinct genome, proteome, metabolome, and also microbiome identity. This editorial is taking into account the uniqueness of each individual and surrounding environment, and stresses the point that a more accurate definition of a "common" disorder could be simply the amalgamation of a myriad of "rare" diseases. These rare diseases are being grouped together because they share a rather constant complement of common features and, indeed, generally respond to empirically developed treatments, leading to a positive outcome consistently. We make the case that it is highly unlikely that such treatments, despite their statistical success measured with large cohorts using standardized clinical research, will be effective on all patients until we increase the depth and fidelity of our understanding of the individual "rare" diseases that are grouped together in the "buckets" of common illnesses. Antioxid. Redox Signal. 27, 511-516.

Common sense codified

CERN Multimedia

CERN Bulletin

2010-01-01

At CERN, people of more than a hundred different nationalities and hundreds of different professions work together towards a common goal. The new Code of Conduct is a tool that has been designed to help us keep our workplace pleasant and productive through common standards of behaviour. Its basic principle is mutual respect and common sense. This is only natural, but not trivial…  The Director-General announced it in his speech at the beginning of the year, and the Bulletin wrote about it immediately afterwards. "It" is the new Code of Conduct, the document that lists our Organization's values and describes the basic standards of behaviour that we should both adopt and expect from others. "The Code of Conduct is not going to establish new rights or new obligations," explains Anne-Sylvie Catherin, Head of the Human Resources Department (HR). But what it will do is provide a framework for our existing rights and obligations." The aim of a co...

Evolution of the placenta and associated reproductive characters in bats

DEFF Research Database (Denmark)

Carter, Anthony M; Mess, Andrea

2008-01-01

Recent advances in molecular phylogenetics indicate that the order Chiroptera is monophyletic and that one of four lineages of microbats (Rhinolophoidea) shares a common origin with megabats. Against this background we undertook a comprehensive analysis of placental evolution in bats. We defined...... that characterize higher-level clades within Chiroptera, i.e. the megabats and the four lineages of microbats. The character condition occurring in the last common ancestor of Chiroptera was unequivocal for 21 of the 25 characters included in the analysis. The data did not offer support for a megabat...

The Modern Synthesis in the Light of Microbial Genomics.

Science.gov (United States)

Booth, Austin; Mariscal, Carlos; Doolittle, W Ford

2016-09-08

We review the theoretical implications of findings in genomics for evolutionary biology since the Modern Synthesis. We examine the ways in which microbial genomics has influenced our understanding of the last universal common ancestor, the tree of life, species, lineages, and evolutionary transitions. We conclude by advocating a piecemeal toolkit approach to evolutionary biology, in lieu of any grand unified theory updated to include microbial genomics.

In-frame seven amino-acid duplication in AIP arose over the last 3000 years, disrupts protein interaction & stability and is associated with gigantism.

OpenAIRE

Salvatori, R.; Radian, S.; Diekmann, Y.; Iacovazzo, D.; David, A.; Grabovska, P.; Grassi, G.; Bussell, A-M; Stals, K.; Weber, A.; Quinton, R.; Crowne, E.; Corazzini, V.; Metherell, L. A.; Kearney, T.

2017-01-01

OBJECTIVE: Mutations in the aryl hydrocarbon receptor-interacting protein (AIP) gene are associated with pituitary adenoma, acromegaly and gigantism. Identical alleles in unrelated pedigrees could be inherited from a common ancestor or result from recurrent mutation events. DESIGN & METHODS: Observational, inferential and experimental study, including: AIP mutation testing; reconstruction of 14 AIP-region (8.3 Mbp) haplotypes; coalescent-based approximate Bayesian estimation of the time to mo...

Science for common entrance physics : answers

CERN Document Server

Pickering, W R

2015-01-01

This book contains answers to all exercises featured in the accompanying textbook Science for Common Entrance: Physics , which covers every Level 1 and 2 topic in the ISEB 13+ Physics Common Entrance exam syllabus. - Clean, clear layout for easy marking. - Includes examples of high-scoring answers with diagrams and workings. - Suitable for ISEB 13+ Mathematics Common Entrance exams taken from Autumn 2017 onwards. Also available to purchase from the Galore Park website www.galorepark.co.uk :. - Science for Common Entrance: Physics. - Science for Common Entrance: Biology. - Science for Common En

The animal sialyltransferases and sialyltransferase-related genes: a phylogenetic approach.

Science.gov (United States)

Harduin-Lepers, Anne; Mollicone, Rosella; Delannoy, Philippe; Oriol, Rafael

2005-08-01

The animal sialyltransferases are Golgi type II transmembrane glycosyltransferases. Twenty distinct sialyltransferases have been identified in both human and murine genomes. These enzymes catalyze transfer of sialic acid from CMP-Neu5Ac to the glycan moiety of glycoconjugates. Despite low overall identities, they share four conserved peptide motifs [L (large), S (small), motif III, and motif VS (very small)] that are hallmarks for sialyltransferase identification. We have identified 155 new putative genes in 25 animal species, and we have exploited two lines of evidence: (1) sequence comparisons and (2) exon-intron organization of the genes. An ortholog to the ancestor present before the split of ST6Gal I and II subfamilies was detected in arthropods. An ortholog to the ancestor present before the split of ST6GalNAc III, IV, V, and VI subfamilies was detected in sea urchin. An ortholog to the ancestor present before the split of ST3Gal I and II subfamilies was detected in ciona, and an ortholog to the ancestor of all the ST8Sia was detected in amphioxus. Therefore, single examples of the four families (ST3Gal, ST6Gal, ST6GalNAc, and ST8Sia) have appeared in invertebrates, earlier than previously thought, whereas the four families were all detected in bony fishes, amphibians, birds, and mammals. As previously hypothesized, sequence similarities among sialyltransferases suggest a common genetic origin, by successive duplications of an ancestral gene, followed by divergent evolution. Finally, we propose predictions on these invertebrates sialyltransferase-related activities that have not previously been demonstrated and that will ultimately need to be substantiated by protein expression and enzymatic activity assays.

;Evolution of Photosynthesis' (1970), re-examined thirty years later.

Science.gov (United States)

Olson, J M

2001-01-01

I have re-examined my 1970 article 'Evolution of Photosynthesis' (Olson JM, Science 168: 438-446) to see whether any of my original proposals still survive. My original conviction that the evolution of photosynthesis was intimately connected with the origin of life has been replaced with the realization that photosynthesis may have been invented by the Bacteria after their divergence from the Archea. The common ancestor of all extant photosynthetic bacteria and cyanobacteria probably contained bacteriochlorophyll a, rather than chlorophyll a as originally proposed, and may have carried out CO(2) fixation instead of photoassimilation. The first electron donors were probably reduced sulfur compounds and later ferrous iron. The common ancestor of all extant reaction centers was probably similar to the homodimeric RC1 of present-day green sulfur bacteria (Chlorobiaceae) and heliobacteria. In the common ancestor of proteobacteria and cyanobacteria, the gene for the primordial RC1 was apparently duplicated and one copy split into two genes, one for RC2 and the other for a chlorophyll protein similar to CP43 and CP47 in extant cyanobacteria and chloroplasts. Homodimeric RC1 and homodimeric RC2 functioned in series as in the Z-scheme to deliver electrons from Fe(OH)(+) to NADP(+), while RC1 and/or RC2 separately drove cyclic electron flow for the production of ATP. In the line of evolution leading to proteobacteria, RC1 and the chlorophyll protein were lost, but RC2 was retained and became heterodimeric. In the line leading to cyanobacteria, both RC1 and RC2 replaced bacteriochlorophyll a with chlorophyll a and became heterodimeric. Heterodimeric RC2 further coevolved with a Mn-containing complex to utilize water as the electron donor for CO(2) fixation. The chlorophyll-protein was also retained and evolved into CP43 and CP47. Heliobacteria are the nearest photosynthetic relatives of cyanobacteria. The branching order of photosynthetic genes appears to be (1

The mitochondrial genome of Frankliniella intonsa: insights into the evolution of mitochondrial genomes at lower taxonomic levels in Thysanoptera.

Science.gov (United States)

Yan, Dankan; Tang, Yunxia; Hu, Min; Liu, Fengquan; Zhang, Dongfang; Fan, Jiaqin

2014-10-01

Thrips is an ideal group for studying the evolution of mitochondrial (mt) genomes in the genus and family due to independent rearrangements within this order. The complete sequence of the mitochondrial DNA (mtDNA) of the flower thrips Frankliniella intonsa has been completed and annotated in this study. The circular genome is 15,215bp in length with an A+T content of 75.9% and contains the typical 37 genes and it has triplicate putative control regions. Nucleotide composition is A+T biased, and the majority of the protein-coding genes present opposite CG skew which is reflected by the nucleotide composition, codon and amino acid usage. Although the known thrips have massive gene rearrangements, it showed no reversal of strand asymmetry. Gene rearrangements have been found in the lower taxonomic levels of thrips. Three tRNA genes were translocated in the genus Frankliniella and eight tRNA genes in the family Thripidae. Although the gene arrangements of mt genomes of all three thrips species differ massively from the ancestral insect, they are all very similar to each other, indicating that there was a large rearrangement somewhere before the most recent common ancestor of these three species and very little genomic evolution or rearrangements after then. The extremely similar sequences among the CRs suggest that they are ongoing concerted evolution. Analyses of the up and downstream sequence of CRs reveal that the CR2 is actually the ancestral CR. The three CRs are in the same spot in each of the three thrips mt genomes which have the identical inverted genes. These characteristics might be obtained from the most recent common ancestor of this three thrips. Above observations suggest that the mt genomes of the three thrips keep a single massive rearrangement from the common ancestor and have low evolutionary rates among them. Copyright © 2014 Elsevier Inc. All rights reserved.

Draft Genomes, Phylogenetic Reconstruction, and Comparative Genomics of Two Novel Cohabiting Bacterial Symbionts Isolated from Frankliniella occidentalis.

Science.gov (United States)

Facey, Paul D; Méric, Guillaume; Hitchings, Matthew D; Pachebat, Justin A; Hegarty, Matt J; Chen, Xiaorui; Morgan, Laura V A; Hoeppner, James E; Whitten, Miranda M A; Kirk, William D J; Dyson, Paul J; Sheppard, Sam K; Del Sol, Ricardo

2015-07-15

Obligate bacterial symbionts are widespread in many invertebrates, where they are often confined to specialized host cells and are transmitted directly from mother to progeny. Increasing numbers of these bacteria are being characterized but questions remain about their population structure and evolution. Here we take a comparative genomics approach to investigate two prominent bacterial symbionts (BFo1 and BFo2) isolated from geographically separated populations of western flower thrips, Frankliniella occidentalis. Our multifaceted approach to classifying these symbionts includes concatenated multilocus sequence analysis (MLSA) phylogenies, ribosomal multilocus sequence typing (rMLST), construction of whole-genome phylogenies, and in-depth genomic comparisons. We showed that the BFo1 genome clusters more closely to species in the genus Erwinia, and is a putative close relative to Erwinia aphidicola. BFo1 is also likely to have shared a common ancestor with Erwinia pyrifoliae/Erwinia amylovora and the nonpathogenic Erwinia tasmaniensis and genetic traits similar to Erwinia billingiae. The BFo1 genome contained virulence factors found in the genus Erwinia but represented a divergent lineage. In contrast, we showed that BFo2 belongs within the Enterobacteriales but does not group closely with any currently known bacterial species. Concatenated MLSA phylogenies indicate that it may have shared a common ancestor to the Erwinia and Pantoea genera, and based on the clustering of rMLST genes, it was most closely related to Pantoea ananatis but represented a divergent lineage. We reconstructed a core genome of a putative common ancestor of Erwinia and Pantoea and compared this with the genomes of BFo bacteria. BFo2 possessed none of the virulence determinants that were omnipresent in the Erwinia and Pantoea genera. Taken together, these data are consistent with BFo2 representing a highly novel species that maybe related to known Pantoea. © The Author(s) 2015. Published by

The rhizome of Reclinomonas americana, Homo sapiens, Pediculus humanus and Saccharomyces cerevisiae mitochondria

Directory of Open Access Journals (Sweden)

Raoult Didier

2011-10-01

Full Text Available Abstract Background Mitochondria are thought to have evolved from eubacteria-like endosymbionts; however, the origin of the mitochondrion remains a subject of debate. In this study, we investigated the phenomenon of chimerism in mitochondria to shed light on the origin of these organelles by determining which species played a role in their formation. We used the mitochondria of four distinct organisms, Reclinomonas americana, Homo sapiens, Saccharomyces cerevisiae and multichromosome Pediculus humanus, and attempted to identify the origin of each mitochondrial gene. Results Our results suggest that the origin of mitochondrial genes is not limited to the Rickettsiales and that the creation of these genes did not occur in a single event, but through multiple successive events. Some of these events are very old and were followed by events that are more recent and occurred through the addition of elements originating from current species. The points in time that the elements were added and the parental species of each gene in the mitochondrial genome are different to the individual species. These data constitute strong evidence that mitochondria do not have a single common ancestor but likely have numerous ancestors, including proto-Rickettsiales, proto-Rhizobiales and proto-Alphaproteobacteria, as well as current alphaproteobacterial species. The analysis of the multichromosome P. humanus mitochondrion supports this mechanism. Conclusions The most plausible scenario of the origin of the mitochondrion is that ancestors of Rickettsiales and Rhizobiales merged in a proto-eukaryotic cell approximately one billion years ago. The fusion of the Rickettsiales and Rhizobiales cells was followed by gene loss, genomic rearrangements and the addition of alphaproteobacterial elements through ancient and more recent recombination events. Each gene of each of the four studied mitochondria has a different origin, while in some cases, multichromosomes may allow for

Common-cause analysis using sets

International Nuclear Information System (INIS)

Worrell, R.B.; Stack, D.W.

1977-12-01

Common-cause analysis was developed at the Aerojet Nuclear Company for studying the behavior of a system that is affected by special conditions and secondary causes. Common-cause analysis is related to fault tree analysis. Common-cause candidates are minimal cut sets whose primary events are closely linked by a special condition or are susceptible to the same secondary cause. It is shown that common-cause candidates can be identified using the Set Equation Transformation System (SETS). A Boolean equation is used to establish the special conditions and secondary cause susceptibilities for each primary event in the fault tree. A transformation of variables (substituting equals for equals), executed on a minimal cut set equation, results in replacing each primary event by the right side of its special condition/secondary cause equation and leads to the identification of the common-cause candidates

Commoning in the periphery – The role of the commons for understanding rural continuities and change

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Emil Sandström

2017-03-01

Full Text Available This paper explores how commons reproduce over time and introduces the concept of commoning to discuss rural continuities and change. The point of departure is that commons are essential for local community development in that they have an important role for mediating social change and for local identity production. Through an ethnographic and historical study of a number of commons systems from the village of Ängersjö in the Midwest of Sweden, the paper argues for a more historically and socially grounded understanding of how commons evolve. The paper examines Ängersjö’s commons within two broad historical time frames – the pre-industrial (4th to 20th century and the post-industrial time periods (20th century to the present – in order to understand commons, not just as arenas for resource extraction and resource struggles, but also as important contexts for identity formation, local mobilisation and for shaping rural change. The paper reveals how the commons have co-evolved with changes in society at large and how the meanings and functions of the commons have changed throughout history – from being important economic resources – to cultural and symbolic resources that have created new avenues for collective action.

Commons - Whose Commons? - considering conceptual approaches to rural space of production

DEFF Research Database (Denmark)

Ingemann, Jan Holm

spectrum of connotations and is engaged for descriptive, prescriptive, and normative purposes. The content, character and meaning thus depend on context and dimensions in focus; the point is illustrated by means of the historical Danish commons. In a consecutive investigation of implicated concepts from...... at a lower level of abstraction. Returned to Danish farming – but now in its contemporary settings – it is concluded that the framework of commons not adequately can be copied-and-pasted into present context due to the complex interconnectivity where local agriculture have boundless prerequisites and effects....

The challenge that Confucian filial piety poses for Korean churches

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David M. Park

2014-04-01

Full Text Available Contemporary ancestor worship is currently practiced around the world in several different forms. However, the essence and practice of ancestor worship varies throughout Asia, Africa, Oceania and Latin America. The context of countries under the influence of Confucianism is very different from that of other countries. Confucianism teaches that ancestor worship is the most prized display of filial piety toward one’s dead ancestors. Amongst Asian countries under the influence of Confucianism – specifically China, Japan, Malaysia, Taiwan, Vietnam and Korea – ancestor worship has not only been accepted and propagated as a culture, but it is also considered to be filial piety. Especially the Korean people think that ancestor worship is a very important expression of filial piety, and it is a ritual which they practice regularly during their festive days. What does Confucianism teach about filial piety, and how is ancestor worship practiced? What does the Bible teach about filial piety? Are practical applications of biblical filial piety present in Korean society? Rather than allowing Confucian ancestor worship to take root in Korean society as a traditional Korean heritage, the conclusion is that Korean Christians must make an effort to teach and facilitate biblical filial piety.

Common sense and the common morality in theory and practice.

Science.gov (United States)

Daly, Patrick

2014-06-01

The unfinished nature of Beauchamp and Childress's account of the common morality after 34 years and seven editions raises questions about what is lacking, specifically in the way they carry out their project, more generally in the presuppositions of the classical liberal tradition on which they rely. Their wide-ranging review of ethical theories has not provided a method by which to move beyond a hypothetical approach to justification or, on a practical level regarding values conflict, beyond a questionable appeal to consensus. My major purpose in this paper is to introduce the thought of Bernard Lonergan as offering a way toward such a methodological breakthrough. In the first section, I consider Beauchamp and Childress's defense of their theory of the common morality. In the second, I relate a persisting vacillation in their argument regarding the relative importance of reason and experience to a similar tension in classical liberal theory. In the third, I consider aspects of Lonergan's generalized empirical method as a way to address problems that surface in the first two sections of the paper: (1) the structural relation of reason and experience in human action; and (2) the importance of theory for practice in terms of what Lonergan calls "common sense" and "general bias."

COMMON FISCAL POLICY

Directory of Open Access Journals (Sweden)

Gabriel Mursa

2014-08-01

Full Text Available The purpose of this article is to demonstrate that a common fiscal policy, designed to support the euro currency, has some significant drawbacks. The greatest danger is the possibility of leveling the tax burden in all countries. This leveling of the tax is to the disadvantage of countries in Eastern Europe, in principle, countries poorly endowed with capital, that use a lax fiscal policy (Romania, Bulgaria, etc. to attract foreign investment from rich countries of the European Union. In addition, common fiscal policy can lead to a higher degree of centralization of budgetary expenditures in the European Union.

Employing Common Limit Range Property to Prove Unified Metrical Common Fixed Point Theorems

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Mohammad Imdad

2013-01-01

Full Text Available The purpose of this paper is to emphasize the role of “common limit range property” to ascertain the existence of common fixed point in metric spaces satisfying an implicit function essentially due to the paper of Ali and Imdad (2008. As an application to our main result, we derive a fixed point theorem for four finite families of self-mappings which can be utilized to derive common fixed point theorems involving any finite number of mappings. Our results improve and extend a host of previously known results including the ones contained in the paper of Ali and Imdad (2008. We also furnish some illustrative examples to support our main results.

Efektivitas Instagram Common Grounds

OpenAIRE

Wifalin, Michelle

2016-01-01

Efektivitas Instagram Common Grounds merupakan rumusan masalah yang diambil dalam penelitian ini. Efektivitas Instagram diukur menggunakan Customer Response Index (CRI), dimana responden diukur dalam berbagai tingkatan, mulai dari awareness, comprehend, interest, intentions dan action. Tingkatan respons inilah yang digunakan untuk mengukur efektivitas Instagram Common Grounds. Teori-teori yang digunakan untuk mendukung penelitian ini yaitu teori marketing Public Relations, teori iklan, efekti...

Casuistry as common law morality.

Science.gov (United States)

Paulo, Norbert

2015-12-01

This article elaborates on the relation between ethical casuistry and common law reasoning. Despite the frequent talk of casuistry as common law morality, remarks on this issue largely remain at the purely metaphorical level. The article outlines and scrutinizes Albert Jonsen and Stephen Toulmin's version of casuistry and its basic elements. Drawing lessons for casuistry from common law reasoning, it is argued that one generally has to be faithful to ethical paradigms. There are, however, limitations for the binding force of paradigms. The most important limitations--the possibilities of overruling and distinguishing paradigm norms--are similar in common law and in casuistry, or so it is argued. These limitations explain why casuistry is not necessarily overly conservative and conventional, which is one line of criticism to which casuists can now better respond. Another line of criticism has it that the very reasoning from case to case is extremely unclear in casuistry. I suggest a certain model of analogical reasoning to address this critique. All my suggestions to understand and to enhance casuistry make use of common law reasoning whilst remaining faithful to Jonsen and Toulmin's main ideas and commitments. Further developed along these lines, casuistry can appropriately be called "common law morality."

Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey

OpenAIRE

Luo, Meizhong; Kim, HyeRan; Kudrna, Dave; Sisneros, Nicholas B; Lee, So-Jeong; Mueller, Christopher; Collura, Kristi; Zuccolo, Andrea; Buckingham, E Bryan; Grim, Suzanne M; Yanagiya, Kazuyo; Inoko, Hidetoshi; Shiina, Takashi; Flajnik, Martin F; Wing, Rod A

2006-01-01

Abstract Background Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates. Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates. Aims In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC) ...

Whole genome sequencing of Mycobacterium bovis to obtain molecular fingerprints in human and cattle isolates from Baja California, Mexico

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Sarai Estrella Sandoval-Azuara

2017-10-01

Conclusions: All isolates from humans had spoligotype patterns that matched those observed in the cattle isolates, and all human isolates shared common ancestors with cattle in Baja California based on SNP analysis. This suggests that most human tuberculosis caused by M. bovis in Baja California is derived from M. bovis circulating in Baja California cattle. These results reinforce the importance of bovine tuberculosis surveillance and control in this region.

In-frame seven amino-acid duplication in AIP arose over the last 3000 years, disrupts protein interaction and stability and is associated with gigantism

OpenAIRE

Salvatori, Roberto; Radian, Serban; Diekmann, Yoan; Iacovazzo, Donato; David, Alessia; Gabrovska, Plamena; Grassi, Giorgia; Bussell, Anna-Marie; Stals, Karen; Weber, Astrid; Quinton, Richard; Crowne, Elizabeth C; Corazzini, Valentina; Metherell, Lou; Kearney, Tara

2017-01-01

Objective Mutations in the aryl hydrocarbon receptor-interacting protein (AIP) gene are associated with pituitary adenoma, acromegaly and gigantism. Identical alleles in unrelated pedigrees could be inherited from a common ancestor or result from recurrent mutation events. Design and methods Observational, inferential and experimental study, including: AIP mutation testing; reconstruction of 14 AIP-region (8.3?Mbp) haplotypes; coalescent-based approximate Bayesian estimation of the time to mo...

The genome of the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution.

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Eva Heinz

Full Text Available The dynamics of reductive genome evolution for eukaryotes living inside other eukaryotic cells are poorly understood compared to well-studied model systems involving obligate intracellular bacteria. Here we present 8.5 Mb of sequence from the genome of the microsporidian Trachipleistophora hominis, isolated from an HIV/AIDS patient, which is an outgroup to the smaller compacted-genome species that primarily inform ideas of evolutionary mode for these enormously successful obligate intracellular parasites. Our data provide detailed information on the gene content, genome architecture and intergenic regions of a larger microsporidian genome, while comparative analyses allowed us to infer genomic features and metabolism of the common ancestor of the species investigated. Gene length reduction and massive loss of metabolic capacity in the common ancestor was accompanied by the evolution of novel microsporidian-specific protein families, whose conservation among microsporidians, against a background of reductive evolution, suggests they may have important functions in their parasitic lifestyle. The ancestor had already lost many metabolic pathways but retained glycolysis and the pentose phosphate pathway to provide cytosolic ATP and reduced coenzymes, and it had a minimal mitochondrion (mitosome making Fe-S clusters but not ATP. It possessed bacterial-like nucleotide transport proteins as a key innovation for stealing host-generated ATP, the machinery for RNAi, key elements of the early secretory pathway, canonical eukaryotic as well as microsporidian-specific regulatory elements, a diversity of repetitive and transposable elements, and relatively low average gene density. Microsporidian genome evolution thus appears to have proceeded in at least two major steps: an ancestral remodelling of the proteome upon transition to intracellular parasitism that involved reduction but also selective expansion, followed by a secondary compaction of genome

Common Ground and Delegation

DEFF Research Database (Denmark)

Dobrajska, Magdalena; Foss, Nicolai Juul; Lyngsie, Jacob

preconditions of increasing delegation. We argue that key HR practices?namely, hiring, training and job-rotation?are associated with delegation of decision-making authority. These practices assist in the creation of shared knowledge conditions between managers and employees. In turn, such a ?common ground......? influences the confidence with which managers delegate decision authority to employees, as managers improve their knowledge of the educational background, firm-specific knowledge, and perhaps even the possible actions of those to whom they delegate such authority. To test these ideas, we match a large......-scale questionnaire survey with unique population-wide employer-employee data. We find evidence of a direct and positive influence of hiring decisions (proxied by common educational background), and the training and job rotation of employees on delegation. Moreover, we find a positive interaction between common...

Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate.

Science.gov (United States)

Cutter, Asher D

2008-04-01

Accurate inference of the dates of common ancestry among species forms a central problem in understanding the evolutionary history of organisms. Molecular estimates of divergence time rely on the molecular evolutionary prediction that neutral mutations and substitutions occur at the same constant rate in genomes of related species. This underlies the notion of a molecular clock. Most implementations of this idea depend on paleontological calibration to infer dates of common ancestry, but taxa with poor fossil records must rely on external, potentially inappropriate, calibration with distantly related species. The classic biological models Caenorhabditis and Drosophila are examples of such problem taxa. Here, I illustrate internal calibration in these groups with direct estimates of the mutation rate from contemporary populations that are corrected for interfering effects of selection on the assumption of neutrality of substitutions. Divergence times are inferred among 6 species each of Caenorhabditis and Drosophila, based on thousands of orthologous groups of genes. I propose that the 2 closest known species of Caenorhabditis shared a common ancestor <24 MYA (Caenorhabditis briggsae and Caenorhabditis sp. 5) and that Caenorhabditis elegans diverged from its closest known relatives <30 MYA, assuming that these species pass through at least 6 generations per year; these estimates are much more recent than reported previously with molecular clock calibrations from non-nematode phyla. Dates inferred for the common ancestor of Drosophila melanogaster and Drosophila simulans are roughly concordant with previous studies. These revised dates have important implications for rates of genome evolution and the origin of self-fertilization in Caenorhabditis.

Are palaeoscolecids ancestral ecdysozoans?

Science.gov (United States)

Harvey, Thomas H P; Dong, Xiping; Donoghue, Philip C J

2010-01-01

The reconstruction of ancestors is a central aim of comparative anatomy and evolutionary developmental biology, not least in attempts to understand the relationship between developmental and organismal evolution. Inferences based on living taxa can and should be tested against the fossil record, which provides an independent and direct view onto historical character combinations. Here, we consider the nature of the last common ancestor of living ecdysozoans through a detailed analysis of palaeoscolecids, an early and extinct group of introvert-bearing worms that have been proposed to be ancestral ecdysozoans. In a review of palaeoscolecid anatomy, including newly resolved details of the internal and external cuticle structure, we identify specific characters shared with various living nematoid and scalidophoran worms, but not with panarthropods. Considered within a formal cladistic context, these characters provide most overall support for a stem-priapulid affinity, meaning that palaeoscolecids are far-removed from the ecdysozoan ancestor. We conclude that previous interpretations in which palaeoscolecids occupy a deeper position in the ecdysozoan tree lack particular morphological support and rely instead on a paucity of preserved characters. This bears out a more general point that fossil taxa may appear plesiomorphic merely because they preserve only plesiomorphies, rather than the mélange of primitive and derived characters anticipated of organisms properly allocated to a position deep within animal phylogeny.

Otwarty model licencjonowania Creative Commons

OpenAIRE

Tarkowski, Alek

2007-01-01

The paper presents a family of Creative Commons licenses (which form nowadays one of the basic legal tools used in the Open Access movement), as well as a genesis of the licenses – inspired by Open Software Licenses and the concept of commons. Then legal tools such as individual Creative Commons licenses are discussed as well as how to use them, with a special emphasis on practical applications in science and education. The author discusses also his research results on scientific publishers a...

Evidence for adaptive evolution of low-temperature stress response genes in a Pooideae grass ancestor

DEFF Research Database (Denmark)

Vigeland, Magnus D; Spannagl, Manuel; Asp, Torben

2013-01-01

Adaptation to temperate environments is common in the grass subfamily Pooideae, suggesting an ancestral origin of cold climate adaptation. Here, we investigated substitution rates of genes involved in low-temperature-induced (LTI) stress responses to test the hypothesis that adaptive molecular...... evolution of LTI pathway genes was important for Pooideae evolution. Substitution rates and signatures of positive selection were analyzed using 4330 gene trees including three warm climate-adapted species (maize (Zea mays), sorghum (Sorghum bicolor), and rice (Oryza sativa)) and five temperate Pooideae...... species (Brachypodium distachyon, wheat (Triticum aestivum), barley (Hordeum vulgare), Lolium perenne and Festuca pratensis). Nonsynonymous substitution rate differences between Pooideae and warm habitat-adapted species were elevated in LTI trees compared with all trees. Furthermore, signatures...

Philosophy vs the common sense

Directory of Open Access Journals (Sweden)

V. V. Chernyshov

2017-01-01

Full Text Available The paper deals with the antinomy of philosophy and the common sense. Philosophy emerges as a way of specifically human knowledge, which purposes analytics of the reality of subjective experience. The study reveals that in order to alienate philosophy from the common sense it was essential to revise the understanding of wisdom. The new, philosophical interpretation of wisdom – offered by Pythagoras – has laid the foundation of any future philosophy. Thus, philosophy emerges, alienating itself from the common sense, which refers to the common or collective experience. Moreover, the study examines the role of emotions, conformity and conventionality which they play with respect to the common sense. Next the author focuses on the role of philosophical intuition, guided with principles of rationality, nonconformity and scepticism, which the author professes the foundation stones of any sound philosophy. The common sense, described as deeply routed in the world of human emotions, aims at empathy, as the purpose of philosophy is to provide the rational means of knowledge. Therefore, philosophy uses thinking, keeping the permanent efforts to check and recheck data of its own experience. Thus, the first task of philosophical thinking appears to overcome the suggestion of the common sense, which purposes the social empathy, as philosophical intuition aims at independent thinking, the analytics of subjective experience. The study describes the fundamental principles of the common sense, on the one hand, and those of philosophy, on the other. The author arrives to conclusion that the common sense is unable to exceed the limits of sensual experience. Even there, where it apparently rises to a form of any «spiritual unity», even there it cannot avoid referring to the data of commonly shared sensual experience; though, philosophy, meanwhile, goes beyond sensuality, creating a discourse that would be able to alienate from it, and to make its rational

Component Commonality and Its Cost Implications - Increasing the Commonality of the Right Components

DEFF Research Database (Denmark)

Lyly-Yrjänäinen, Jouni; Suomala, Petri; Israelsen, Poul

Component commonality (Labro 2004, Zhou & Gruppström 2004) can be defined as the use of the same version of a component across multiple products. It is usually seen as a means to manage costs without sacrificing product variety. However, when managing costs with component commonality, the managers...... constructions was identified as the most important bottleneck for the delivery process causing many indirect costs, especially with respect to project-management-related activities. Interestingly, by eliminating the need for mechanical engineering, the context starts to approach assembly-to-order context, also...... should be able to identify rather rapidly which group of components would enable the most significant cost reductions. Unfortunately, the existing literature lacks profound discussion of how to identify the right components for increased component commonality. The objective of the paper is to discuss how...

6 Common Cancers - Skin Cancer

Science.gov (United States)

... Bar Home Current Issue Past Issues 6 Common Cancers - Skin Cancer Past Issues / Spring 2007 Table of Contents ... AP Photo/Herald-Mail, Kevin G. Gilbert Skin Cancer Skin cancer is the most common form of cancer ...

Common Sleep Problems (For Teens)

Science.gov (United States)

... Safe Videos for Educators Search English Español Common Sleep Problems KidsHealth / For Teens / Common Sleep Problems What's ... have emotional problems, like depression. What Happens During Sleep? You don't notice it, of course, but ...

Probabilistic analysis of ''common mode failures''

International Nuclear Information System (INIS)

Easterling, R.G.

1978-01-01

Common mode failure is a topic of considerable interest in reliability and safety analyses of nuclear reactors. Common mode failures are often discussed in terms of examples: two systems fail simultaneously due to an external event such as an earthquake; two components in redundant channels fail because of a common manufacturing defect; two systems fail because a component common to both fails; the failure of one system increases the stress on other systems and they fail. The common thread running through these is a dependence of some sort--statistical or physical--among multiple failure events. However, the nature of the dependence is not the same in all these examples. An attempt is made to model situations, such as the above examples, which have been termed ''common mode failures.'' In doing so, it is found that standard probability concepts and terms, such as statistically dependent and independent events, and conditional and unconditional probabilities, suffice. Thus, it is proposed that the term ''common mode failures'' be dropped, at least from technical discussions of these problems. A corollary is that the complementary term, ''random failures,'' should also be dropped. The mathematical model presented may not cover all situations which have been termed ''common mode failures,'' but provides insight into the difficulty of obtaining estimates of the probabilities of these events

The illusion of common ground

DEFF Research Database (Denmark)

Cowley, Stephen; Harvey, Matthew

2016-01-01

When people talk about “common ground”, they invoke shared experiences, convictions, and emotions. In the language sciences, however, ‘common ground’ also has a technical sense. Many taking a representational view of language and cognition seek to explain that everyday feeling in terms of how...... isolated individuals “use” language to communicate. Autonomous cognitive agents are said to use words to communicate inner thoughts and experiences; in such a framework, ‘common ground’ describes a body of information that people allegedly share, hold common, and use to reason about how intentions have......, together with concerted bodily (and vocal) activity, serve to organize, regulate and coordinate both attention and the verbal and non-verbal activity that it gives rise to. Since wordings are normative, they can be used to develop skills for making cultural sense of environments and other peoples’ doings...

Diversification of the Genus Anopheles and a Neotropical Clade from the Late Cretaceous.

Directory of Open Access Journals (Sweden)

Lucas A Freitas

Full Text Available The Anopheles genus is a member of the Culicidae family and consists of approximately 460 recognized species. The genus is composed of 7 subgenera with diverse geographical distributions. Despite its huge medical importance, a consensus has not been reached on the phylogenetic relationships among Anopheles subgenera. We assembled a comprehensive dataset comprising the COI, COII and 5.8S rRNA genes and used maximum likelihood and Bayesian inference to estimate the phylogeny and divergence times of six out of the seven Anopheles subgenera. Our analysis reveals a monophyletic group composed of the three exclusively Neotropical subgenera, Stethomyia, Kerteszia and Nyssorhynchus, which began to diversify in the Late Cretaceous, at approximately 90 Ma. The inferred age of the last common ancestor of the Anopheles genus was ca. 110 Ma. The monophyly of all Anopheles subgenera was supported, although we failed to recover a significant level of statistical support for the monophyly of the Anopheles genus. The ages of the last common ancestors of the Neotropical clade and the Anopheles and Cellia subgenera were inferred to be at the Late Cretaceous (ca. 90 Ma. Our analysis failed to statistically support the monophyly of the Anopheles genus because of an unresolved polytomy between Bironella and A. squamifemur.

Diet of Australopithecus afarensis from the Pliocene Hadar Formation, Ethiopia

Science.gov (United States)

Wynn, Jonathan G.; Sponheimer, Matt; Kimbel, William H.; Alemseged, Zeresenay; Reed, Kaye; Bedaso, Zelalem K.; Wilson, Jessica N.

2013-06-01

The enhanced dietary flexibility of early hominins to include consumption of C4/crassulacean acid metabolism (CAM) foods (i.e., foods derived from grasses, sedges, and succulents common in tropical savannas and deserts) likely represents a significant ecological and behavioral distinction from both extant great apes and the last common ancestor that we shared with great apes. Here, we use stable carbon isotopic data from 20 samples of Australopithecus afarensis from Hadar and Dikika, Ethiopia (>3.4-2.9 Ma) to show that this species consumed a diet with significant C4/CAM foods, differing from its putative ancestor Au. anamensis. Furthermore, there is no temporal trend in the amount of C4/CAM food consumption over the age of the samples analyzed, and the amount of C4/CAM food intake was highly variable, even within a single narrow stratigraphic interval. As such, Au. afarensis was a key participant in the C4/CAM dietary expansion by early australopiths of the middle Pliocene. The middle Pliocene expansion of the eastern African australopith diet to include savanna-based foods represents a shift to use of plant food resources that were already abundant in hominin environments for at least 1 million y and sets the stage for dietary differentiation and niche specialization by subsequent hominin taxa.

Host jumps shaped the diversity of extant rust fungi (Pucciniales).

Science.gov (United States)

McTaggart, Alistair R; Shivas, Roger G; van der Nest, Magriet A; Roux, Jolanda; Wingfield, Brenda D; Wingfield, Michael J

2016-02-01

The aim of this study was to determine the evolutionary time line for rust fungi and date key speciation events using a molecular clock. Evidence is provided that supports a contemporary view for a recent origin of rust fungi, with a common ancestor on a flowering plant. Divergence times for > 20 genera of rust fungi were studied with Bayesian evolutionary analyses. A relaxed molecular clock was applied to ribosomal and mitochondrial genes, calibrated against estimated divergence times for the hosts of rust fungi, such as Acacia (Fabaceae), angiosperms and the cupressophytes. Results showed that rust fungi shared a most recent common ancestor with a mean age between 113 and 115 million yr. This dates rust fungi to the Cretaceous period, which is much younger than previous estimations. Host jumps, whether taxonomically large or between host genera in the same family, most probably shaped the diversity of rust genera. Likewise, species diversified by host shifts (through coevolution) or via subsequent host jumps. This is in contrast to strict coevolution with their hosts. Puccinia psidii was recovered in Sphaerophragmiaceae, a family distinct from Raveneliaceae, which were regarded as confamilial in previous studies. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Evolutionary relationships among self-incompatibility RNases

Science.gov (United States)

Igic, Boris; Kohn, Joshua R.

2001-01-01

T2-type RNases are responsible for self-pollen recognition and rejection in three distantly related families of flowering plants—the Solanaceae, Scrophulariaceae, and Rosaceae. We used phylogenetic analyses of 67 T2-type RNases together with information on intron number and position to determine whether the use of RNases for self-incompatibility in these families is homologous or convergent. All methods of phylogenetic reconstruction as well as patterns of variation in intron structure find that all self-incompatibility RNases along with non-S genes from only two taxa form a monophyletic clade. Several lines of evidence suggest that the best interpretation of this pattern is homology of self-incompatibility RNases from the Scrophulariaceae, Solanaceae, and Rosaceae. Because the most recent common ancestor of these three families is the ancestor of ≈75% of dicot families, our results indicate that RNase-based self-incompatibility was the ancestral state in the majority of dicots. PMID:11698683

49 CFR 1185.5 - Common control.

Science.gov (United States)

2010-10-01

... 49 Transportation 8 2010-10-01 2010-10-01 false Common control. 1185.5 Section 1185.5... OF TRANSPORTATION RULES OF PRACTICE INTERLOCKING OFFICERS § 1185.5 Common control. It shall not be... carriers if such carriers are operated under common control or management either: (a) Pursuant to approval...

Facts about the Common Cold

Science.gov (United States)

... different viruses. Rhinovirus is the most common cause, accounting for 10 to 40 percent of colds. Other common cold viruses include coronavirus and ... RSS | Terms Of Use | Privacy | Sitemap Our Family Of Sites ... Introduction Risk Factors Screening Symptoms Tumor Testing Summary '; var ...

Evolutionary History of the Genus Capsella (Brassicaceae - Capsella orientalis , New for Mongolia

Directory of Open Access Journals (Sweden)

Barbara Neuffer

2014-12-01

Full Text Available To elucidate the evolutionary history of the genus Capsella , we included the hitherto poorly known species C. orientalis and C. thracica into our studies together with C. grandifl ora , C. rubella , and C. bursa-pastoris . We sequenced the ITS, and four loci of noncoding cpDNA regions (trnL – F, rps16, trnH – psbA, trnQ – rps16. In common garden fi eld experiments C. orientalis turned out as early fl owering with a specifi c leaf type. The crossing ability of the species was tested in pollen germination experiments. Capsella orientalis (self-compatible, SC; 2n = 16 forms a clade (eastern lineage with C . bursa-pastoris (SC; 2n = 32, which is a sister clade (western lineage to C. grandifl ora (self-incompatible, SI; 2n = 16 and C. rubella (SC; 2n = 16. Capsella bursa-pastoris is an autopolyploid species of multiple origin, whereas the Bulgarian endemic C. thracica (SC; 2n = 32 is allopolyploid and emerged from interspecifi c hybridisation between C. bursa-pastoris and C. grandifl ora . The common ancestor of the two lineages was diploid and SI, and its distribution ranged from eastern Europe to central Asia, predominantly confi ned to steppe like habitats. Biogeographic dynamics during the Pleistocene caused geographic and genetic subdivisions within the common ancestor giving rise to the two extant lineages. Capsella orientalis is verifi ed at several positions in western Mongolia.

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution.

Science.gov (United States)

Schwager, Evelyn E; Sharma, Prashant P; Clarke, Thomas; Leite, Daniel J; Wierschin, Torsten; Pechmann, Matthias; Akiyama-Oda, Yasuko; Esposito, Lauren; Bechsgaard, Jesper; Bilde, Trine; Buffry, Alexandra D; Chao, Hsu; Dinh, Huyen; Doddapaneni, HarshaVardhan; Dugan, Shannon; Eibner, Cornelius; Extavour, Cassandra G; Funch, Peter; Garb, Jessica; Gonzalez, Luis B; Gonzalez, Vanessa L; Griffiths-Jones, Sam; Han, Yi; Hayashi, Cheryl; Hilbrant, Maarten; Hughes, Daniel S T; Janssen, Ralf; Lee, Sandra L; Maeso, Ignacio; Murali, Shwetha C; Muzny, Donna M; Nunes da Fonseca, Rodrigo; Paese, Christian L B; Qu, Jiaxin; Ronshaugen, Matthew; Schomburg, Christoph; Schönauer, Anna; Stollewerk, Angelika; Torres-Oliva, Montserrat; Turetzek, Natascha; Vanthournout, Bram; Werren, John H; Wolff, Carsten; Worley, Kim C; Bucher, Gregor; Gibbs, Richard A; Coddington, Jonathan; Oda, Hiroki; Stanke, Mario; Ayoub, Nadia A; Prpic, Nikola-Michael; Flot, Jean-François; Posnien, Nico; Richards, Stephen; McGregor, Alistair P

2017-07-31

The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.

Governing of common cause failures

International Nuclear Information System (INIS)

Bock, H.W.

1998-01-01

Agreed strategy is to govern common cause failures by the application of diversity, to assure that the overall plant safety objectives are met even in the case that a common cause failure of a system with all redundant trains is assumed. The presented strategy aims on the application of functional diversity without the implementation of equipment diversity. In the focus are the design criteria which have to be met for the design of independent systems in such a way that the time-correlated failure of such independent systems according a common cause can be excluded deterministically. (author)

Integrative analysis of polychaete ontogeny: cell proliferation patterns and myogenesis in trochophore larvae of Sabellaria alveolata

DEFF Research Database (Denmark)

Brinkmann, Nora; Wanninger, Andreas

2010-01-01

Aspects of muscle development are still widely neglected in studies on invertebrate ontogeny, which is probably at least partly due to the inherent complexity of animal myoanatomical bodyplans. This has resulted in significant gaps in our understanding of the evolutionary and ontogenetic origin...... analysis suggests that the bodywall of the last common annelid ancestor might have been devoid of circular muscles and consisted of four separate longitudinal muscle strands that develop from anterior to posterior....

A novel endogenous betaretrovirus group characterized from polar bears (Ursus maritimus) and giant pandas (Ailuropoda melanoleuca)

OpenAIRE

Mayer, Jens; Tsangaras, Kyriakos; Heeger, Felix; Ávila-Arcos, Maria; Stenglein, Mark D.; Chen, Wei; Sun, Wei; Mazzoni, Camila; Osterrieder, Nikolaus; Greenwood, Alex D.

2013-01-01

Transcriptome analysis of polar bears (Ursus maritimus) yielded sequences with highest similarity to the human endogenous retrovirus group HERV-K(HML-2). Further analysis of the polar bear draft genome identified an endogenous betaretrovirus group comprising 26 proviral copies and 231 solo LTRs. Molecular dating indicates the group originated before the divergence of bears from a common ancestor but is not present in all carnivores. Closely related sequences were identified in the giant panda...

Ceroid-lipofuscinosis in border collie dogs.

Science.gov (United States)

Taylor, R M; Farrow, B R

1988-01-01

Five Border Collie dogs with ceroid-lipofuscinosis developed progressive neurological disease between 18 and 22 months of age. These dogs had behavioural abnormalities, gait and visual deficits and became progressively demented. All dogs examined had common ancestors. Light microscopic examination of tissues demonstrated extensive accumulation of granular, sudan black-staining autofluorescent material in the cytoplasm of neurones, retinal ganglion cells and some visceral cells. At ultrastructural examination inclusions of variable morphology were observed.

Measuring Value in the Commons-Based Ecosystem: Bridging the Gap Between the Commons and the Market

OpenAIRE

De Filippi , Primavera; Hassan , Samer

2014-01-01

International audience; Commons-based peer-production (CBPP) constitutes today an important driver for innovation and cultural development, both online and offline. This led to the establishment of an alternative, Commons-based ecosystem, based on peer-production and collaboration of peers contributing to a common good. Yet, to the extent that this operates outside of the market economy, we cannot rely on traditional market mechanisms (such as pricing) to estimate the value of CBPP. We presen...

Using variable transformations to perform common event analysis

International Nuclear Information System (INIS)

Worrell, R.B.

1977-01-01

Any analytical method for studying the effect of common events on the behavior of a system is considered as being a form of common event analysis. The particular common events that are involved often represent quite different phenomena, and this has led to the development of different kinds of common event analysis. For example, common mode failure analysis, common cause analysis, critical location analysis, etc., are all different kinds of common event analysis for which the common events involved represent different phenomena. However, the problem that must be solved for each of these different kinds of common event analysis is essentially the same: Determine the effect of common events on the behavior of a system. Thus, a technique that is useful in achieving one kind of common event analysis is often useful in achieving other kinds of common event analysis

The Tragedy of the Commons

Science.gov (United States)

Short, Daniel

2016-01-01

The tragedy of the commons is one of the principal tenets of ecology. Recent developments in experiential computer-based simulation of the tragedy of the commons are described. A virtual learning environment is developed using the popular video game "Minecraft". The virtual learning environment is used to experience first-hand depletion…

A School for the Common Good

Science.gov (United States)

Baines, Lawrence; Foster, Hal

2006-01-01

This article examines the history and the concept of the common school from the Common School Movement reformers of the 1850s to the present. These reformers envisioned schools that were to be tuition free and open to everyone, places where rich and poor met and learned together on equal terms. Central to the concept of the common school is its…

Common cause failures of reactor pressure components

International Nuclear Information System (INIS)

Mankamo, T.

1978-01-01

The common cause failure is defined as a multiple failure event due to a common cause. The existence of common failure causes may ruin the potential advantages of applying redundancy for reliability improvement. Examples relevant to large mechanical components are presented. Preventive measures against common cause failures, such as physical separation, equipment diversity, quality assurance, and feedback from experience are discussed. Despite the large number of potential interdependencies, the analysis of common cause failures can be done within the framework of conventional reliability analysis, utilizing, for example, the method of deriving minimal cut sets from a system fault tree. Tools for the description and evaluation of dependencies between components are discussed: these include the model of conditional failure causes that are common to many components, and evaluation of the reliability of redundant components subjected to a common load. (author)

20 CFR 404.1007 - Common-law employee.

Science.gov (United States)

2010-04-01

... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Common-law employee. 404.1007 Section 404... Common-law employee. (a) General. The common-law rules on employer-employee status are the basic test for.... Even though you are considered self-employed under the common-law rules, you may still be an employee...

Common Privacy Myths

Science.gov (United States)

... the common myths: Health information cannot be faxed – FALSE Your information may be shared between healthcare providers by faxing ... E-mail cannot be used to transmit health information – FALSE E-mail can be used to transmit information, ...

Common Breastfeeding Challenges

Science.gov (United States)

... or duplicated without permission of the Office on Women’s Health in the U.S. Department of Health and Human Services. Citation of the source is appreciated. Page last updated: March 02, 2018. Common breastfeeding challenges Breastfeeding can be ...

On the origin and diffusion of BRCA1 c.5266dupC (5382insC) in European populations

DEFF Research Database (Denmark)

Hamel, Nancy; Feng, Bing-Jian; Foretova, Lenka

2011-01-01

The BRCA1 mutation c.5266dupC was originally described as a founder mutation in the Ashkenazi Jewish (AJ) population. However, this mutation is also present at appreciable frequency in several European countries, which raises intriguing questions about the origins of the mutation. We genotyped 245...... carrier families from 14 different population groups (Russian, Latvian, Ukrainian, Czech, Slovak, Polish, Danish, Dutch, French, German, Italian, Greek, Brazilian and AJ) for seven microsatellite markers and confirmed that all mutation carriers share a common haplotype from a single founder individual.......5266dupC originated from a single common ancestor and was a common European mutation long before becoming an AJ founder mutation and (2) the mutation is likely present in many additional European countries where genetic screening of BRCA1 may not yet be common practice....

Parents' common pitfalls of discipline.

Science.gov (United States)

Witoonchart, Chatree; Fangsa-ard, Thitiporn; Chaoaree, Supamit; Ketumarn, Panom; Kaewpornsawan, Titawee; Phatthrayuttawat, Sucheera

2005-11-01

Problems of discipline are common among parents. These may be the results of the parents' pitfalls in disciplining their children. To find out common pitfalls of parents in disciplining their children. Parents of students with ages ranged between 60-72 months old in Bangkok-Noi district, Bangkok, were selected by random sampling. Total number of 1947 children ages between 60-72 months were recruited. Parents of these children were interviewed with a questionnaire designed to probe into problems in child rearing. There hindered and fifty questionnaires were used for data analyses. Parents had high concerns about problems in discipline their children and needed support from professional personnel. They had limited knowledge and possessed lots of wrong attitude towards discipline. Common pitfalls on the topics were problems in, 1) limit setting 2) rewarding and punishment 3) supervision on children watching TV and bedtime routines. Parents of children with ages 60-72 months old in Bangkok-Noi district, Bangkok, had several common pitfalls in disciplining their children, including attitude, knowledge and practice.

TaEDS1 genes positively regulate resistance to powdery mildew in wheat.

Science.gov (United States)

Chen, Guiping; Wei, Bo; Li, Guoliang; Gong, Caiyan; Fan, Renchun; Zhang, Xiangqi

2018-04-01

Three EDS1 genes were cloned from common wheat and were demonstrated to positively regulate resistance to powdery mildew in wheat. The EDS1 proteins play important roles in plant basal resistance and TIR-NB-LRR protein-triggered resistance in dicots. Until now, there have been very few studies on EDS1 in monocots, and none in wheat. Here, we report on three common wheat orthologous genes of EDS1 family (TaEDS1-5A, 5B and 5D) and their function in powdery mildew resistance. Comparisons of these genes with their orthologs in diploid ancestors revealed that EDS1 is a conserved gene family in Triticeae. The cDNA sequence similarity among the three TaEDS1 genes was greater than 96.5%, and they shared sequence similarities of more than 99.6% with the respective orthologs from diploid ancestors. The phylogenetic analysis revealed that the EDS1 family originated prior to the differentiation of monocots and dicots, and EDS1 members have since undergone clear structural differentiation. The transcriptional levels of TaEDS1 genes in the leaves were obviously higher than those of the other organs, and they were induced by Blumeria graminis f. sp. tritici (Bgt) infection and salicylic acid (SA) treatment. The BSMV-VIGS experiments indicated that knock-down the transcriptional levels of the TaEDS1 genes in a powdery mildew-resistant variety of common wheat compromised resistance. Contrarily, transient overexpression of TaEDS1 genes in a susceptible common wheat variety significantly reduced the haustorium index and attenuated the growth of Bgt. Furthermore, the expression of TaEDS1 genes in the Arabidopsis mutant eds1-1 complemented its susceptible phenotype to powdery mildew. The above evidences strongly suggest that TaEDS1 acts as a positive regulator and confers resistance against powdery mildew in common wheat.

Common Injuries of Collegiate Tennis Players

Directory of Open Access Journals (Sweden)

Christian Wisdom Magtajas Valleser

2017-09-01

Full Text Available The purpose of this study is to determine the common injuries of Filipino collegiate tennis players; 110 varsity tennis players with a mean of 20 years old (SD ± 1.7 with an average playing experience of 12 years participated in the study. There was a 100% occurrence of at least one injury with an average rate of 5.98 injuries per person. The authors observed that the most commonly injured anatomical region is the lower extremity; ankles were recorded as the most commonly injured part. Other commonly injured areas included the shoulders and lower back. Furthermore, the most common injury type is tendinitis, sprains, and strains. The recorded injuries were mostly associated with overuse injuries, and the findings were similar to those of most other studies on tennis injuries. A larger sample size may provide more conclusive findings on tennis injuries, particularly in different levels of competition, such as recreational or professional athletes.

Coordinated Multi-layer Multi-domain Optical Network (COMMON) for Large-Scale Science Applications (COMMON)

Energy Technology Data Exchange (ETDEWEB)

Vokkarane, Vinod [University of Massachusetts

2013-09-01

We intend to implement a Coordinated Multi-layer Multi-domain Optical Network (COMMON) Framework for Large-scale Science Applications. In the COMMON project, specific problems to be addressed include 1) anycast/multicast/manycast request provisioning, 2) deployable OSCARS enhancements, 3) multi-layer, multi-domain quality of service (QoS), and 4) multi-layer, multidomain path survivability. In what follows, we outline the progress in the above categories (Year 1, 2, and 3 deliverables).

Common envelope evolution

NARCIS (Netherlands)

Taam, Ronald E.; Ricker, Paul M.

2010-01-01

The common envelope phase of binary star evolution plays a central role in many evolutionary pathways leading to the formation of compact objects in short period systems. Using three dimensional hydrodynamical computations, we review the major features of this evolutionary phase, focusing on the

Social Justice and the Environmental Commons.

Science.gov (United States)

Flanagan, Constance A; Byington, Rachel; Gallay, Erin; Sambo, Allison

2016-01-01

In this chapter, we build on the scholarship on youth civic engagement by turning attention to the environmental commons as a space for political action. We begin with a definition of the term and arguments about ways that social justice is implied in it. Following that, we raise several psychological challenges to motivating action on behalf of the environmental commons and discuss the critical experiences and actions that can defy those challenges. Finally, drawing from Ostrom's empirical evidence opposing a tragedy of the commons, we discuss practices consistent with a social justice approach that nurture in younger generations an identification with and commitment to the environmental commons and discuss how this orientation would benefit human beings, democracies, and the earth. © 2016 Elsevier Inc. All rights reserved.

Eukaryotes first: how could that be?

Science.gov (United States)

Mariscal, Carlos; Doolittle, W Ford

2015-09-26

In the half century since the formulation of the prokaryote : eukaryote dichotomy, many authors have proposed that the former evolved from something resembling the latter, in defiance of common (and possibly common sense) views. In such 'eukaryotes first' (EF) scenarios, the last universal common ancestor is imagined to have possessed significantly many of the complex characteristics of contemporary eukaryotes, as relics of an earlier 'progenotic' period or RNA world. Bacteria and Archaea thus must have lost these complex features secondarily, through 'streamlining'. If the canonical three-domain tree in which Archaea and Eukarya are sisters is accepted, EF entails that Bacteria and Archaea are convergently prokaryotic. We ask what this means and how it might be tested. © 2015 The Author(s).

The Parody of the Commons

Directory of Open Access Journals (Sweden)

Vasilis Kostakis

2013-08-01

Full Text Available This essay builds on the idea that Commons-based peer production is a social advancement within capitalism but with various post-capitalistic aspects, in need of protection, enforcement, stimulation and connection with progressive social movements. We use theory and examples to claim that peer-to-peer economic relations can be undermined in the long run, distorted by the extra-economic means of a political context designed to maintain profit-driven relations of production into power. This subversion can arguably become a state policy, and the subsequent outcome is the full absorption of the Commons as well as of the underpinning peer-to-peer relations into the dominant mode of production. To tackle this threat, we argue in favour of a certain working agenda for Commons-based communities. Such an agenda should aim the enforcement of the circulation of the Commons. Therefore, any useful social transformation will be meaningful if the people themselves decide and apply policies for their own benefit, optimally with the support of a sovereign partner state. If peer production is to become dominant, it has to control capital accumulation with the aim to marginalise and eventually transcend capitalism.

Is there adaptation of the exocrine pancreas in wild animal? The case of the Roe Deer

OpenAIRE

Guilloteau, Paul; Vitari, Francesca; Meuth, Valérie Metzinger-Le; Le Normand, Laurence; Romé, Véronique; Savary, Gérard; Delaby, Luc; Domeneghini, Cinzia; Morisset, Jean

2012-01-01

Abstract Background Physiology of the exocrine pancreas has been well studied in domestic and in laboratory animals as well as in humans. However, it remains quite unknown in wildlife mammals. Roe deer and cattle (including calf) belong to different families but have a common ancestor. This work aimed to evaluate in the Roe deer, the adaptation to diet of the exocrine pancreatic functions and regulations related to animal evolution and domestication. Results Forty bovine were distributed into...

29 CFR 779.221 - “Common control” defined.

Science.gov (United States)

2010-07-01

... organizational units.” The meaning of “common control” is discussed comprehensively in part 776 of this chapter. ... Or Common Control § 779.221 “Common control” defined. Under the definition the “enterprise” includes all related activities performed through “common control” for a common business purpose. The word...

Towards common technical standards

International Nuclear Information System (INIS)

Rahmat, H.; Suardi, A.R.

1993-01-01

In 1989, PETRONAS launched its Total Quality Management (TQM) program. In the same year the decision was taken by the PETRONAS Management to introduce common technical standards group wide. These standards apply to the design, construction, operation and maintenance of all PETRONAS installations in the upstream, downstream and petrochemical sectors. The introduction of common company standards is seen as part of an overall technical management system, which is an integral part of Total Quality Management. The Engineering and Safety Unit in the PETRONAS Central Office in Kuala Lumpur has been charged with the task of putting in place a set of technical standards throughout PETRONAS and its operating units

[Common household traditional Chinese medicines].

Science.gov (United States)

Zhang, Shu-Yuan; Li, Mei; Fu, Dan; Liu, Yang; Wang, Hui; Tan, Wei

2016-02-01

With the enhancement in the awareness of self-diagnosis among residents, it's very common for each family to prepare common medicines for unexpected needs. Meanwhile, with the popularization of the traditional Chinese medicine knowledge, the proportion of common traditional Chinese medicines prepared at residents' families is increasingly higher than western medicines year by year. To make it clear, both pre-research and closed questionnaire research were adopted for residents in Chaoyang District, Beijing, excluding residents with a medical background. Based on the results of data, a analysis was made to define the role and influence on the quality of life of residents and give suggestions for relevant departments to improve the traditional Chinese medicine popularization and promote the traditional Chinese medicine market. Copyright© by the Chinese Pharmaceutical Association.

Governing for the Common Good.

Science.gov (United States)

Ruger, Jennifer Prah

2015-12-01

The proper object of global health governance (GHG) should be the common good, ensuring that all people have the opportunity to flourish. A well-organized global society that promotes the common good is to everyone's advantage. Enabling people to flourish includes enabling their ability to be healthy. Thus, we must assess health governance by its effectiveness in enhancing health capabilities. Current GHG fails to support human flourishing, diminishes health capabilities and thus does not serve the common good. The provincial globalism theory of health governance proposes a Global Health Constitution and an accompanying Global Institute of Health and Medicine that together propose to transform health governance. Multiple lines of empirical research suggest that these institutions would be effective, offering the most promising path to a healthier, more just world.

Recent evolutionary history of human immunodeficiency virus type 1 subtype B: Reconstruction of epidemic onset based on sequence distances to the common ancestor

NARCIS (Netherlands)

Lukashov, Vladimir V.; Goudsmit, Jaap

2002-01-01

We obtained and studied HIV-1 sequences with a known sampling year from three outbreaks of the HIV-1 epidemic: 141 env V3 (270 nt) sampled between 1984 and 1992 and 117 pol prot/RT (804 nt) sequences sampled between 1986 and 1999 from Dutch homosexual men and injecting drug users (IDUs), as well as

Sustainability of common pool resources

OpenAIRE

Timilsina, Raja Rajendra; Kotani, Koji; Kamijo, Yoshio

2017-01-01

Sustainability has become a key issue in managing natural resources together with growing concerns for capitalism, environmental and resource problems. We hypothesize that the ongoing modernization of competitive societies, which we refer to as "capitalism," affects human nature for utilizing common pool resources, thus compromising sustainability. To test this hypothesis, we design and implement a set of dynamic common pool resource games and experiments in the following two types of Nepales...

Whose commons are mobilities spaces?

DEFF Research Database (Denmark)

Freudendal-Pedersen, Malene

2015-01-01

for cyclists and cycling to be given greater consideration in broader societal understandings of the common good. I argue that this is in fact not the case. Rather the specific project identities that are nurtured by Copenhagen’s cycling community inhibit it from advocating publicly or aggressively...... for a vision of the common good that gives cyclists greater and more protected access to the city’s mobility spaces...

Common cause failure analysis methodology for complex systems

International Nuclear Information System (INIS)

Wagner, D.P.; Cate, C.L.; Fussell, J.B.

1977-01-01

Common cause failure analysis, also called common mode failure analysis, is an integral part of a complex system reliability analysis. This paper extends existing methods of computer aided common cause failure analysis by allowing analysis of the complex systems often encountered in practice. The methods presented here aid in identifying potential common cause failures and also address quantitative common cause failure analysis

Common Frame of Reference and social justice

NARCIS (Netherlands)

Hesselink, M.W.; Satyanarayana, R.

2009-01-01

The article "Common Frame of Reference and Social Justice" by Martijn W. Hesselink evaluates the Draft Common Frame of Reference (DCFR) of social justice. It discusses the important areas, namely a common frame of Reference in a broad sense, social justice and contract law, private law and

Algorithms for solving common fixed point problems

CERN Document Server

Zaslavski, Alexander J

2018-01-01

This book details approximate solutions to common fixed point problems and convex feasibility problems in the presence of perturbations. Convex feasibility problems search for a common point of a finite collection of subsets in a Hilbert space; common fixed point problems pursue a common fixed point of a finite collection of self-mappings in a Hilbert space. A variety of algorithms are considered in this book for solving both types of problems, the study of which has fueled a rapidly growing area of research. This monograph is timely and highlights the numerous applications to engineering, computed tomography, and radiation therapy planning. Totaling eight chapters, this book begins with an introduction to foundational material and moves on to examine iterative methods in metric spaces. The dynamic string-averaging methods for common fixed point problems in normed space are analyzed in Chapter 3. Dynamic string methods, for common fixed point problems in a metric space are introduced and discussed in Chapter ...

The most common friend first immunization

International Nuclear Information System (INIS)

Nian Fu-Zhong; Hu Cha-Sheng

2016-01-01

In this paper, a standard susceptible-infected-recovered-susceptible(SIRS) epidemic model based on the Watts–Strogatz (WS) small-world network model and the Barabsi–Albert (BA) scale-free network model is established, and a new immunization scheme — “the most common friend first immunization” is proposed, in which the most common friend’s node is described as being the first immune on the second layer protection of complex networks. The propagation situations of three different immunization schemes — random immunization, high-risk immunization, and the most common friend first immunization are studied. At the same time, the dynamic behaviors are also studied on the WS small-world and the BA scale-free network. Moreover, the analytic and simulated results indicate that the immune effect of the most common friend first immunization is better than random immunization, but slightly worse than high-risk immunization. However, high-risk immunization still has some limitations. For example, it is difficult to accurately define who a direct neighbor in the life is. Compared with the traditional immunization strategies having some shortcomings, the most common friend first immunization is effective, and it is nicely consistent with the actual situation. (paper)

The Messiness of Common Good

DEFF Research Database (Denmark)

Feldt, Liv Egholm

Civil society and its philanthropic and voluntary organisations are currently experiencing public and political attention and demands to safeguard society’s ‘common good’ through social cohesion and as providers of welfare services. This has raised the question by both practitioners and researchers...... that a distinction between the non-civil and the civil is more fruitful, if we want to understand the past, present and future messiness in place in defining the common good. Based on an ethnographic case analysis of a Danish corporate foundation between 1920 and 2014 the paper shows how philanthropic gift......-giving concepts, practices and operational forms throughout history have played a significant role in defining the common good and its future avenues. Through an analytical attitude based on microhistory, conceptual history and the sociology of translation it shows that civil society’s institutional logic always...

Suehiro Jurisprudence and John R. Commons

DEFF Research Database (Denmark)

Tackney, Charles T.

This is a comparative history study at the interface of industrial / employment relations and stakeholder theory. The focus concerns decades of post-World War II Japanese and U.S. path dependent national divergence from common labor legislation enactments separated by only 15 years: 1933...... or Suehiro hōgaku) document a dramatic, fascinating historical parting of two nations due to Japanese deep appreciation of the labor law and institutional economics research legacy of John R. Commons, the father of U.S. industrial relations. Understanding this common, shared source opens industrial relations...

Mathematics for common entrance three (extension) answers

CERN Document Server

Alexander, Serena

2015-01-01

This book contains answers to all exercises featured in the accompanying textbook Mathematics for Common Entrance Three (Extension) , which provides essential preparation for Level 3 of the ISEB 13+ Mathematics exam, as well as for CASE and other scholarship exams. - Clean, clear layout for easy marking. - Includes examples of high-scoring answers with diagrams and workings. Also available to purchase from the Galore Park website www.galorepark.co.uk :. - Mathematics for Common Entrance Three (Extension). - Mathematics for Common Entrance One. - Mathematics for Common Entrance One Answers. - M

Common tester platform concept.

Energy Technology Data Exchange (ETDEWEB)

Hurst, Michael James

2008-05-01

This report summarizes the results of a case study on the doctrine of a common tester platform, a concept of a standardized platform that can be applicable across the broad spectrum of testing requirements throughout the various stages of a weapons program, as well as across the various weapons programs. The common tester concept strives to define an affordable, next-generation design that will meet testing requirements with the flexibility to grow and expand; supporting the initial development stages of a weapons program through to the final production and surveillance stages. This report discusses a concept investing key leveraging technologies and operational concepts combined with prototype tester-development experiences and practical lessons learned gleaned from past weapons programs.

Genetic Variability Under the Seedbank Coalescent.

Science.gov (United States)

Blath, Jochen; González Casanova, Adrián; Eldon, Bjarki; Kurt, Noemi; Wilke-Berenguer, Maite

2015-07-01

We analyze patterns of genetic variability of populations in the presence of a large seedbank with the help of a new coalescent structure called the seedbank coalescent. This ancestral process appears naturally as a scaling limit of the genealogy of large populations that sustain seedbanks, if the seedbank size and individual dormancy times are of the same order as those of the active population. Mutations appear as Poisson processes on the active lineages and potentially at reduced rate also on the dormant lineages. The presence of "dormant" lineages leads to qualitatively altered times to the most recent common ancestor and nonclassical patterns of genetic diversity. To illustrate this we provide a Wright-Fisher model with a seedbank component and mutation, motivated from recent models of microbial dormancy, whose genealogy can be described by the seedbank coalescent. Based on our coalescent model, we derive recursions for the expectation and variance of the time to most recent common ancestor, number of segregating sites, pairwise differences, and singletons. Estimates (obtained by simulations) of the distributions of commonly employed distance statistics, in the presence and absence of a seedbank, are compared. The effect of a seedbank on the expected site-frequency spectrum is also investigated using simulations. Our results indicate that the presence of a large seedbank considerably alters the distribution of some distance statistics, as well as the site-frequency spectrum. Thus, one should be able to detect from genetic data the presence of a large seedbank in natural populations. Copyright © 2015 by the Genetics Society of America.

Three distinct modes of intron dynamics in the evolution of eukaryotes.

Science.gov (United States)

Carmel, Liran; Wolf, Yuri I; Rogozin, Igor B; Koonin, Eugene V

2007-07-01

Several contrasting scenarios have been proposed for the origin and evolution of spliceosomal introns, a hallmark of eukaryotic genes. A comprehensive probabilistic model to obtain a definitive reconstruction of intron evolution was developed and applied to 391 sets of conserved genes from 19 eukaryotic species. It is inferred that a relatively high intron density was reached early, i.e., the last common ancestor of eukaryotes contained >2.15 introns/kilobase, and the last common ancestor of multicellular life forms harbored approximately 3.4 introns/kilobase, a greater intron density than in most of the extant fungi and in some animals. The rates of intron gain and intron loss appear to have been dropping during the last approximately 1.3 billion years, with the decline in the gain rate being much steeper. Eukaryotic lineages exhibit three distinct modes of evolution of the intron-exon structure. The primary, balanced mode, apparently, operates in all lineages. In this mode, intron gain and loss are strongly and positively correlated, in contrast to previous reports on inverse correlation between these processes. The second mode involves an elevated rate of intron loss and is prevalent in several lineages, such as fungi and insects. The third mode, characterized by elevated rate of intron gain, is seen only in deep branches of the tree, indicating that bursts of intron invasion occurred at key points in eukaryotic evolution, such as the origin of animals. Intron dynamics could depend on multiple mechanisms, and in the balanced mode, gain and loss of introns might share common mechanistic features.

Biosynthesis of archaeal membrane ether lipids

Directory of Open Access Journals (Sweden)

Samta eJain

2014-11-01

Full Text Available A vital function of the cell membrane in all living organism is to maintain the membrane permeability barrier and fluidity. The composition of the phospholipid bilayer is distinct in archaea when compared to bacteria and eukarya. In archaea, isoprenoid hydrocarbon side chains are linked via an ether bond to the sn-glycerol-1-phosphate backbone. In bacteria and eukarya on the other hand, fatty acid side chains are linked via an ester bond to the sn-glycerol-3-phosphate backbone. The polar head groups are globally shared in the three domains of life. The unique membrane lipids of archaea have been implicated not only in the survival and adaptation of the organisms to extreme environments but also to form the basis of the membrane composition of the last universal common ancestor (LUCA. In nature, a diverse range of archaeal lipids is found, the most common are the diether (or archaeol and the tetraether (or caldarchaeol lipids that form a monolayer. Variations in chain length, cyclization and other modifications lead to diversification of these lipids. The biosynthesis of these lipids is not yet well understood however progress in the last decade has led to a comprehensive understanding of the biosynthesis of archaeol. This review describes the current knowledge of the biosynthetic pathway of archaeal ether lipids; insights on the stability and robustness of archaeal lipid membranes; and evolutionary aspects of the lipid divide and the last universal common ancestor LUCA. It examines recent advances made in the field of pathway reconstruction in bacteria.

Laboratories of commons: experimentation, recursivity and activism

Directory of Open Access Journals (Sweden)

Adolfo Estalella Fernández

2013-03-01

Full Text Available The urban public space, digital creations or the air, all of them are objects that have been traditionally thought within the dichotomous logic of the public and private property but in the last decade they have started to be considered as common resources. Commons is an old concept that has been recovered with intensity in the last decade; it refers to collective resources and goods that are governed collectively and whose property regime is different from the public and private. This article introduces the contributions to a monograph devoted to the topic of ‘Laboratories of commons’. Contributors discuss the diverse modalities of commons in different social domains like art, activism, the rural and the urban domain. This introduction contextualizes these contributions and identifies some of the issues that cross the different articles. In this exercise we introduce a tentative argument according to which the commons and the commons research take an exceptional configuration in Spain. Very briefly: commons are brought into existence as an epistemic object, an experimental domain quite different from the conventional conceptualizations that conceive it as a property regime or a type of good. This peculiar configuration gives a distinctive condition to commons in Spain that are different from other geographies; this is evidenced in a double shift: the emergence of new objects that are thought as commons and the location of their research in the domain of cultural and creative production.

Metabolic pathway redundancy within the apicomplexan-dinoflagellate radiation argues against an ancient chromalveolate plastid

KAUST Repository

Waller, Ross F.

2015-12-08

The chromalveolate hypothesis presents an attractively simple explanation for the presence of red algal-derived secondary plastids in 5 major eukaryotic lineages: “chromista” phyla, cryptophytes, haptophytes and ochrophytes; and alveolate phyla, dinoflagellates and apicomplexans. It posits that a single secondary endosymbiotic event occurred in a common ancestor of these diverse groups, and that this ancient plastid has since been maintained by vertical inheritance only. Substantial testing of this hypothesis by molecular phylogenies has, however, consistently failed to provide support for the predicted monophyly of the host organisms that harbour these plastids—the “chromalveolates.” This lack of support does not disprove the chromalveolate hypothesis per se, but rather drives the proposed endosymbiosis deeper into the eukaryotic tree, and requires multiple plastid losses to have occurred within intervening aplastidic lineages. An alternative perspective on plastid evolution is offered by considering the metabolic partnership between the endosymbiont and its host cell. A recent analysis of metabolic pathways in a deep-branching dinoflagellate indicates a high level of pathway redundancy in the common ancestor of apicomplexans and dinoflagellates, and differential losses of these pathways soon after radiation of the major extant lineages. This suggests that vertical inheritance of an ancient plastid in alveolates is highly unlikely as it would necessitate maintenance of redundant pathways over very long evolutionary timescales.

Multiple independent insertions of 5S rRNA genes in the spliced-leader gene family of trypanosome species.

Science.gov (United States)

Beauparlant, Marc A; Drouin, Guy

2014-02-01

Analyses of the 5S rRNA genes found in the spliced-leader (SL) gene repeat units of numerous trypanosome species suggest that such linkages were not inherited from a common ancestor, but were the result of independent 5S rRNA gene insertions. In trypanosomes, 5S rRNA genes are found either in the tandemly repeated units coding for SL genes or in independent tandemly repeated units. Given that trypanosome species where 5S rRNA genes are within the tandemly repeated units coding for SL genes are phylogenetically related, one might hypothesize that this arrangement is the result of an ancestral insertion of 5S rRNA genes into the tandemly repeated SL gene family of trypanosomes. Here, we use the types of 5S rRNA genes found associated with SL genes, the flanking regions of the inserted 5S rRNA genes and the position of these insertions to show that most of the 5S rRNA genes found within SL gene repeat units of trypanosome species were not acquired from a common ancestor but are the results of independent insertions. These multiple 5S rRNA genes insertion events in trypanosomes are likely the result of frequent founder events in different hosts and/or geographical locations in species having short generation times.

Metabolic pathway redundancy within the apicomplexan-dinoflagellate radiation argues against an ancient chromalveolate plastid

KAUST Repository

Waller, Ross F.; Gornik, Sebastian G.; Koreny, Ludek; Pain, Arnab

2015-01-01

The chromalveolate hypothesis presents an attractively simple explanation for the presence of red algal-derived secondary plastids in 5 major eukaryotic lineages: “chromista” phyla, cryptophytes, haptophytes and ochrophytes; and alveolate phyla, dinoflagellates and apicomplexans. It posits that a single secondary endosymbiotic event occurred in a common ancestor of these diverse groups, and that this ancient plastid has since been maintained by vertical inheritance only. Substantial testing of this hypothesis by molecular phylogenies has, however, consistently failed to provide support for the predicted monophyly of the host organisms that harbour these plastids—the “chromalveolates.” This lack of support does not disprove the chromalveolate hypothesis per se, but rather drives the proposed endosymbiosis deeper into the eukaryotic tree, and requires multiple plastid losses to have occurred within intervening aplastidic lineages. An alternative perspective on plastid evolution is offered by considering the metabolic partnership between the endosymbiont and its host cell. A recent analysis of metabolic pathways in a deep-branching dinoflagellate indicates a high level of pathway redundancy in the common ancestor of apicomplexans and dinoflagellates, and differential losses of these pathways soon after radiation of the major extant lineages. This suggests that vertical inheritance of an ancient plastid in alveolates is highly unlikely as it would necessitate maintenance of redundant pathways over very long evolutionary timescales.

Molecular Comparison and Evolutionary Analyses of VP1 Nucleotide Sequences of New African Human Enterovirus 71 Isolates Reveal a Wide Genetic Diversity

Science.gov (United States)

Nougairède, Antoine; Joffret, Marie-Line; Deshpande, Jagadish M.; Dubot-Pérès, Audrey; Héraud, Jean-Michel

2014-01-01

Most circulating strains of Human enterovirus 71 (EV-A71) have been classified primarily into three genogroups (A to C) on the basis of genetic divergence between the 1D gene, which encodes the VP1 capsid protein. The aim of the present study was to provide further insights into the diversity of the EV-A71 genogroups following the recent description of highly divergent isolates, in particular those from African countries, including Madagascar. We classified recent EV-A71 isolates by a large comparison of 3,346 VP1 nucleotidic sequences collected from GenBank. Analysis of genetic distances and phylogenetic investigations indicated that some recently-reported isolates did not fall into the genogroups A-C and clustered into three additional genogroups, including one Indian genogroup (genogroup D) and 2 African ones (E and F). Our Bayesian phylogenetic analysis provided consistent data showing that the genogroup D isolates share a recent common ancestor with the members of genogroup E, while the isolates of genogroup F evolved from a recent common ancestor shared with the members of the genogroup B. Our results reveal the wide diversity that exists among EV-A71 isolates and suggest that the number of circulating genogroups is probably underestimated, particularly in developing countries where EV-A71 epidemiology has been poorly studied. PMID:24598878

Multiple losses of flight and recent speciation in steamer ducks

Science.gov (United States)

Fulton, Tara L.; Letts, Brandon; Shapiro, Beth

2012-01-01

Steamer ducks (Tachyeres) comprise four species, three of which are flightless. The flightless species are believed to have diverged from a flying common ancestor during the Late Pleistocene; however, their taxonomy remains contentious. Of particular interest is the previously unstudied population of flying steamer ducks in the Falkland Islands. We present the first genetic data from this insular population, and illustrate that the flying and flightless steamer ducks on the Falkland Islands are genetically indistinguishable, in contrast to their traditional classification as separate species. The three species that reside in continental South America form a genetically distinct lineage from the Falkland Island ducks. The Falkland steamer ducks diverged from their continental relatives 2.2–0.6 million years ago, coincident with a probable land bridge connecting the Falkland Islands to the mainland. The three continental species share a common ancestor approximately 15 000 years ago, possibly owing to isolation during a recent glacial advance. The continental steamer duck species are not reciprocally monophyletic, but show some amount of genetic differentiation between them. Each lineage of Tachyeres represents a different stage between flight and flightlessness. Their phylogenetic relationships suggest multiple losses of flight and/or long-term persistence of mixed-flight capability. As such, steamer ducks may provide a model system to study the evolution of flightlessness. PMID:22319122

Adaptive evolution of mitochondrial energy metabolism genes associated with increased energy demand in flying insects.

Science.gov (United States)

Yang, Yunxia; Xu, Shixia; Xu, Junxiao; Guo, Yan; Yang, Guang

2014-01-01

Insects are unique among invertebrates for their ability to fly, which raises intriguing questions about how energy metabolism in insects evolved and changed along with flight. Although physiological studies indicated that energy consumption differs between flying and non-flying insects, the evolution of molecular energy metabolism mechanisms in insects remains largely unexplored. Considering that about 95% of adenosine triphosphate (ATP) is supplied by mitochondria via oxidative phosphorylation, we examined 13 mitochondrial protein-encoding genes to test whether adaptive evolution of energy metabolism-related genes occurred in insects. The analyses demonstrated that mitochondrial DNA protein-encoding genes are subject to positive selection from the last common ancestor of Pterygota, which evolved primitive flight ability. Positive selection was also found in insects with flight ability, whereas no significant sign of selection was found in flightless insects where the wings had degenerated. In addition, significant positive selection was also identified in the last common ancestor of Neoptera, which changed its flight mode from direct to indirect. Interestingly, detection of more positively selected genes in indirect flight rather than direct flight insects suggested a stronger selective pressure in insects having higher energy consumption. In conclusion, mitochondrial protein-encoding genes involved in energy metabolism were targets of adaptive evolution in response to increased energy demands that arose during the evolution of flight ability in insects.

Comparative functional analyses of ultrabithorax reveal multiple steps and paths to diversification of legs in the adaptive radiation of semi-aquatic insects.

Science.gov (United States)

Khila, Abderrahman; Abouheif, Ehab; Rowe, Locke

2014-08-01

Invasion of new ecological habitats is often associated with lineage diversification, yet the genetic changes underlying invasions and radiations are poorly understood. Over 200 million years ago, the semi-aquatic insects invaded water surface from a common terrestrial ancestor and diversified to exploit a wide array of niches. Here, we uncover the changes in regulation and function of the gene Ultrabithorax associated with both the invasion of water surface and the subsequent diversification of the group. In the common ancestor of the semi-aquatic insects, a novel deployment of Ubx protein in the mid-legs increased their length, thereby enhancing their role in water surface walking. In derived lineages that specialize in rowing on the open water, additional changes in the timing of Ubx expression further elongated the mid-legs thereby facilitating their function as oars. In addition, Ubx protein function was selectively reversed to shorten specific rear-leg segments, thereby enabling their function as rudders. These changes in Ubx have generated distinct niche-specialized morphologies that account for the remarkable diversification of the semi-aquatic insects. Therefore, changes in the regulation and function of a key developmental gene may facilitate both the morphological change necessary to transition to novel habitats and fuel subsequent morphological diversification. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Death and resurrection of the human IRGM gene.

Directory of Open Access Journals (Sweden)

Cemalettin Bekpen

2009-03-01

Full Text Available Immunity-related GTPases (IRG play an important role in defense against intracellular pathogens. One member of this gene family in humans, IRGM, has been recently implicated as a risk factor for Crohn's disease. We analyzed the detailed structure of this gene family among primates and showed that most of the IRG gene cluster was deleted early in primate evolution, after the divergence of the anthropoids from prosimians ( about 50 million years ago. Comparative sequence analysis of New World and Old World monkey species shows that the single-copy IRGM gene became pseudogenized as a result of an Alu retrotransposition event in the anthropoid common ancestor that disrupted the open reading frame (ORF. We find that the ORF was reestablished as a part of a polymorphic stop codon in the common ancestor of humans and great apes. Expression analysis suggests that this change occurred in conjunction with the insertion of an endogenous retrovirus, which altered the transcription initiation, splicing, and expression profile of IRGM. These data argue that the gene became pseudogenized and was then resurrected through a series of complex structural events and suggest remarkable functional plasticity where alleles experience diverse evolutionary pressures over time. Such dynamism in structure and evolution may be critical for a gene family locked in an arms race with an ever-changing repertoire of intracellular parasites.

gious role of ancestors in Nyakyusa belief

African Journals Online (AJOL)

the Nyakyusa religion on Malawi's northern border with Tanzania challenges John. Mbiti's reductionist ... Divinitiy or divinities? .... al rather than in dogma, but dogma is rather implicit than explicit. ... Any attitude to or in connection with the ...

Apparatus Named after Our Academic Ancestors--I

Science.gov (United States)

Greenslade, Thomas B., Jr.

2010-01-01

Let us now praise famous physicists, and the apparatus named after them, with apologies to the writer of Ecclesiastes. I once compiled a list of about 300 pieces of apparatus known to us as X's Apparatus. Some of the values of X are familiar, like Wheatstone and Kelvin and Faraday, but have you heard of Pickering or Rhumkorff or Barlow? In an…

Common Ground with "A Common Faith": Dewey's Idea of the "Religious"

Science.gov (United States)

Baurain, Bradley

2011-01-01

In "A Common Faith", Dewey rejects organized religion and belief in the supernatural, instead arguing for an authentically "religious" attitude which this interpretive essay analyzes in terms of four propositions: (1) Knowledge is unified. (2) Knowledge is democratic. (3) The pursuit of moral ideals requires moral faith. (4) The authority for…

Common Vestibular Disorders

Directory of Open Access Journals (Sweden)

Dimitrios G. Balatsouras

2017-01-01

Full Text Available The three most common vestibular diseases, benign paroxysmal positional vertigo (BPPV, Meniere's disease (MD and vestibular neuritis (VN, are presented in this paper. BPPV, which is the most common peripheral vestibular disorder, can be defined as transient vertigo induced by a rapid head position change, associated with a characteristic paroxysmal positional nystagmus. Canalolithiasis of the posterior semicircular canal is considered the most convincing theory of its pathogenesis and the development of appropriate therapeutic maneuvers resulted in its effective treatment. However, involvement of the horizontal or the anterior canal has been found in a significant rate and the recognition and treatment of these variants completed the clinical picture of the disease. MD is a chronic condition characterized by episodic attacks of vertigo, fluctuating hearing loss, tinnitus, aural pressure and a progressive loss of audiovestibular functions. Presence of endolymphatic hydrops on postmortem examination is its pathologic correlate. MD continues to be a diagnostic and therapeutic challenge. Patients with the disease range from minimally symptomatic, highly functional individuals to severely affected, disabled patients. Current management strategies are designed to control the acute and recurrent vestibulopathy but offer minimal remedy for the progressive cochlear dysfunction. VN is the most common cause of acute spontaneous vertigo, attributed to acute unilateral loss of vestibular function. Key signs and symptoms are an acute onset of spinning vertigo, postural imbalance and nausea as well as a horizontal rotatory nystagmus beating towards the non-affected side, a pathological headimpulse test and no evidence for central vestibular or ocular motor dysfunction. Vestibular neuritis preferentially involves the superior vestibular labyrinth and its afferents. Symptomatic medication is indicated only during the acute phase to relieve the vertigo and nausea

Common Core: Teaching Optimum Topic Exploration (TOTE)

Science.gov (United States)

Karge, Belinda Dunnick; Moore, Roxane Kushner

2015-01-01

The Common Core has become a household term and yet many educators do not understand what it means. This article explains the historical perspectives of the Common Core and gives guidance to teachers in application of Teaching Optimum Topic Exploration (TOTE) necessary for full implementation of the Common Core State Standards. An effective…

Characteristics of common infections in Nicaragua

NARCIS (Netherlands)

Matute Moreno, A.J.

2006-01-01

The main purpose of the studies outlined in this thesis was to gain empirical epidemiological and therapeutic knowledge of some common infectious diseases in Nicaragua. So far, relatively little was known about the incidence, etiology, management and antibiotic resistance patterns of common

Institutional property rights structure, common pool resource (CPR), tragedy of the urban commons: A Review

Science.gov (United States)

Ling, G.; Ho, C. S.; Ali, H. M.

2014-02-01

There have been a plethora of researches on the significance of public open space (POS) in contributing to societies' sustainability. However, by virtue of identified maladaptive policy-based-property rights structure, such a shared good becomes vulnerable to tragedy of the urban commons (overexploitation) that subsequently leads to burgeoning number of mismanaged POS e.g., degraded and unkempt urban public spaces. By scrutinising the literatures within property rights domain and commons resources, an objective is highlighted in this paper which is to insightfully discourse institutional property rights structure pertaining to the mechanism, roles and interrelationship between property-rights regimes, bundle of property rights and resource domains; types of goods on how they act upon and tie in the POS with the social quandary. In summary, urban POS tragedy can potentially be triggered by the institutional structure especially if the ownership is left under open-access resource regime and ill-defined property rights which both successively constitute the natures of Common Pool Resource (CPR) within the commons, POS. Therefore, this paper sparks an idea to policy makers that property rights structure is a determinant in sustainably governing the POS in which adaptive assignment of property regimes and property rights are impelled.

Institutional property rights structure, common pool resource (CPR), tragedy of the urban commons: A Review

International Nuclear Information System (INIS)

Ling, G; Ho, C S; Ali, H M

2014-01-01

There have been a plethora of researches on the significance of public open space (POS) in contributing to societies' sustainability. However, by virtue of identified maladaptive policy-based-property rights structure, such a shared good becomes vulnerable to tragedy of the urban commons (overexploitation) that subsequently leads to burgeoning number of mismanaged POS e.g., degraded and unkempt urban public spaces. By scrutinising the literatures within property rights domain and commons resources, an objective is highlighted in this paper which is to insightfully discourse institutional property rights structure pertaining to the mechanism, roles and interrelationship between property-rights regimes, bundle of property rights and resource domains; types of goods on how they act upon and tie in the POS with the social quandary. In summary, urban POS tragedy can potentially be triggered by the institutional structure especially if the ownership is left under open-access resource regime and ill-defined property rights which both successively constitute the natures of Common Pool Resource (CPR) within the commons, POS. Therefore, this paper sparks an idea to policy makers that property rights structure is a determinant in sustainably governing the POS in which adaptive assignment of property regimes and property rights are impelled

Philosophy vs the common sense

OpenAIRE

V. V. Chernyshov

2017-01-01

The paper deals with the antinomy of philosophy and the common sense. Philosophy emerges as a way of specifically human knowledge, which purposes analytics of the reality of subjective experience. The study reveals that in order to alienate philosophy from the common sense it was essential to revise the understanding of wisdom. The new, philosophical interpretation of wisdom – offered by Pythagoras – has laid the foundation of any future philosophy. Thus, philosophy emerges, alienating itself...

Attachments to the common-place

DEFF Research Database (Denmark)

Blok, Anders

2015-01-01

This article builds on ethnographic work concerning on-going collective efforts in the Japanese city of Kyoto aiming to reposition a vernacular style of wooden housing, known as kyō-machiya, into a hybrid eco-design widely considered an appropriate local response to the global challenges of climate...... change. To understand the dynamic interplay of architecture and community-building in this case, the article stages a theoretical debate on the politics of shared attachments between three proponents of French pragmatic sociology: Bruno Latour, Antoine Hennion, and Laurent Thévenot. Drawing in particular...... on Thévenot's notion of ‘commonality in the plural’, the article shows how a range of personal affinities to the architectural form of the kyō-machiya, positioned as an urban ‘common-place’, serves to coordinate across otherwise divergent interests. By taking seriously the role of attachments to common...

Simplifying the ELA Common Core; Demystifying Curriculum

Science.gov (United States)

Schmoker, Mike; Jago, Carol

2013-01-01

The English Language Arts (ELA) Common Core State Standards ([CCSS], 2010) could have a transformational effect on American education. Though the process seems daunting, one can begin immediately integrating the essence of the ELA Common Core in every subject area. This article shows how one could implement the Common Core and create coherent,…

Common Fixed Point Theorems in Fuzzy Metric Spaces Satisfying -Contractive Condition with Common Limit Range Property

Directory of Open Access Journals (Sweden)

Sunny Chauhan

2013-01-01

Full Text Available The objective of this paper is to emphasize the role of “common limit range property” to ascertain the existence of common fixed point in fuzzy metric spaces. Some illustrative examples are furnished which demonstrate the validity of the hypotheses and degree of utility of our results. We derive a fixed point theorem for four finite families of self-mappings which can be utilized to derive common fixed point theorems involving any finite number of mappings. As an application to our main result, we prove an integral-type fixed point theorem in fuzzy metric space. Our results improve and extend a host of previously known results including the ones contained in Imdad et al. (2012.

The gastro-oesophageal common cavity revisited

NARCIS (Netherlands)

Aanen, M. C.; Bredenoord, A. J.; Samsom, M.; Smout, A. J. P. M.

2006-01-01

The manometric common cavity phenomenon has been used as indicator of gastro-oesophageal reflux of liquid or gaseous substances. Using combined pH and impedance recording as reference standard the value of a common cavity as indicator of gastro-oesophageal reflux was tested. Ten healthy male

Common Frame of Reference & social justice

NARCIS (Netherlands)

Hesselink, M.

2008-01-01

This paper evaluates the draft Common Frame of Reference (DCFR) in terms of social justice. It concludes the DCFR has all the characteristics of a typical European compromise. Ideological and esthetical purists will certainly be disappointed. In this respect, it has much in common with the

Recipe of the project Common Translation

Directory of Open Access Journals (Sweden)

Florencio Cabello Fernández-Delgado

2013-03-01

Full Text Available The recipe presented in this paper aims at synthetising metaphorically the methodology deployed in the project Commons Translation, an effort of distributed cooperative translation of books related to free culture and the commons carried out by university lecturers and students, as well as external collaborators. This recipe of what we call “commons-based peer translation” is inspired in the ideas of lots of cooks, and some of those ideas are extracted from the same works we translate. In this sense, two cookery books have been especially helpful: the first one is Yochai Benkler's The Wealth of Networks, a crucial recipe book about the art of commons-based peer production; the second one is Chris Kelty's Two Bits, where the anthropologist analyses thoroughly (and exquisitely the condiment characteristic of the best cooking of free software: recursion. Both works are an inspiration for our translation efforts and at the same time constituye the objects of such translation: the cooking of new communities and knowledges.

Common cycles and common trends in the stock and oil markets: Evidence from more than 150 years of data

International Nuclear Information System (INIS)

Balcilar, Mehmet; Gupta, Rangan; Wohar, Mark E.

2017-01-01

This paper investigates the role of permanent and transitory shocks, within the framework of common cycles and common trends, in explaining stock and oil prices. We perform a multivariate variance decomposition analysis of monthly data on the West Texas Intermediate (WTI) oil price and the S&P 500. The dataset used in the study spans a long period of 150 years and therefore contains a rich history to examine both the short- and long-run comovement properties of oil and stock prices. Given that the oil and stock markets might comove both in the short- and long-run, it is of interest to see the relative impacts of transitory and permanent shocks on both variables. We find that (log) oil price and (log) S&P 500 share a common stochastic trend for our full sample of September 1859 to July 2015, but a common cycle only exists during the post-WW II period. Full and post-WW II samples have quite different common feature estimates in terms of the impact of permanent and transitory shocks as measured by the impulse responses and forecast error variance decompositions. We also find that in the short-run oil is driven mostly by cycles (transitory shocks) and stock market is mostly driven by permanent shocks. But, permanent shocks dominate in the long-run. - Highlights: • Role of permanent and transitory shocks analyzed for oil and stock markets • The framework of common cycles and common trends used over 1859 to 2015 • Common stochastic trend for full-sample and common cycle post-World War II • Stock market driven by permanent shock in short- and long-runs • Oil market driven by temporary (permanent) shocks in short-run (long-run)

Cell wall degrading enzymes in Trichoderma asperellum grown on wheat bran

DEFF Research Database (Denmark)

Bech, Lasse; Busk, Peter Kamp; Lange, Lene

2015-01-01

. asperellum was grown on wheat bran, the greatest range of enzymes activity was detected and a total of 175 glycoside hydrolases from 48 glycoside hydrolase families were identified in the transcriptome. The glycoside hydrolases were identified on a functional level using the bioinformatical tool Peptide...... the theory that the glycoside hydrolases have evolved from a common ancestor, followed by a specialization in which saprotrophic fungi such as T. reesei and T. longibrachiatum lost a significant number of genes including several glycoside hydrolases....

Evolutionary analysis of a large mtDNA translocation (numt) into the nuclear genome of the Panthera genus species

OpenAIRE

Kim, Jae-Heup; Antunes, Agostinho; Luo, Shu-Jin; Menninger, Joan; Nash, William G.; O’Brien, Stephen J.; Johnson, Warren E.

2005-01-01

Translocation of cymtDNA into the nuclear genome, also referred to as numt, has been reported in many species, including several closely related to the domestic cat (Felis catus). We describe the recent transposition of 12,536 bp of the 17 kb mitochondrial genome into the nucleus of the common ancestor of the five Panthera genus species: tiger, P. tigris; snow leopard, P. uncia; jaguar, P. onca; leopard, P. pardus; and lion, P. leo. This nuclear integration, representing 74% of the mitochondr...

Multiple Endocrine Neoplasia Type 1 (MEN1) and Pituitary Adenoma Predisposition (PAP) in Northern Finland

OpenAIRE

Vierimaa, O. (Outi)

2008-01-01

Abstract Multiple endocrine neoplasia type 1 (MEN1) is an inherited syndrome characterized by parathyroid, gastroenteropancreatic and pituitary neuroendocrine tumours. In Northern Finland, two founder mutations of the MEN1 gene (1466del12, 1657insC) accounting for the majority of the MEN1 cases, have common ancestors born in the 18th and 19th centuries, respectively. Three small clusters of familial pituitary adenoma have also been detected, two of which could be linked by genealogy to a ...

The cytochrome p450 homepage.

Science.gov (United States)

Nelson, David R

2009-10-01

The Cytochrome P450 Homepage is a universal resource for nomenclature and sequence information on cytochrome P450 ( CYP ) genes. The site has been in continuous operation since February 1995. Currently, naming information for 11,512 CYPs are available on the web pages. The P450 sequences are manually curated by David Nelson, and the nomenclature system conforms to an evolutionary scheme such that members of CYP families and subfamilies share common ancestors. The organisation and content of the Homepage are described.

The Salmon Smai Family of Short Interspersed Repetitive Elements (Sines): Interspecific and Intraspecific Variation of the Insertion of Sines in the Genomes of Chum and Pink Salmon

OpenAIRE

Takasaki, N.; Yamaki, T.; Hamada, M.; Park, L.; Okada, N.

1997-01-01

The genomes of chum salmon and pink salmon contain a family of short interspersed repetitive elements (SINEs), designated the salmon SmaI family. It is restricted to these two species, a distribution that suggests that this SINE family might have been generated in their common ancestor. When insertions of the SmaI SINEs at 10 orthologous loci of these species were analyzed, however, it was found that there were no shared insertion sites between chum and pink salmon. Furthermore, at six loci w...

Evolutionary origin and function of NOX4-art, an arthropod specific NADPH oxidase

OpenAIRE

Gandara, Ana Caroline Paiva; Torres, Andr?; Bahia, Ana Cristina; Oliveira, Pedro L.; Schama, Renata

2017-01-01

Background NADPH oxidases (NOX) are ROS producing enzymes that perform essential roles in cell physiology, including cell signaling and antimicrobial defense. This gene family is present in most eukaryotes, suggesting a common ancestor. To date, only a limited number of phylogenetic studies of metazoan NOXes have been performed, with few arthropod genes. In arthropods, only NOX5 and DUOX genes have been found and a gene called NOXm was found in mosquitoes but its origin and function has not b...

Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum

OpenAIRE

Porter, Ashleigh F.; Duggan, Ana T.; Poinar, Hendrik N.; Holmes, Edward C.

2017-01-01

The complete genome sequences of two strains of variola virus (VARV) sampled from human smallpox specimens present in the Czech National Museum, Prague, were recently determined, with one of the sequences estimated to date to the mid-19th century. Using molecular clock methods, the authors of this study go on to infer that the currently available strains of VARV share an older common ancestor, at around 1350 AD, than some recent estimates based on other archival human samples. Herein, we show...

[Genome similarity of Baikal omul and sig].

Science.gov (United States)

Bychenko, O S; Sukhanova, L V; Ukolova, S S; Skvortsov, T A; Potapov, V K; Azhikina, T L; Sverdlov, E D

2009-01-01

Two members of the Baikal sig family, a lake sig (Coregonus lavaretus baicalensis Dybovsky) and omul (C. autumnalis migratorius Georgi), are close relatives that diverged from the same ancestor 10-20 thousand years ago. In this work, we studied genomic polymorphism of these two fish species. The method of subtraction hybridization (SH) did not reveal the presence of extended sequences in the sig genome and their absence in the omul genome. All the fragments found by SH corresponded to polymorphous noncoding genome regions varying in mononucleotide substitutions and short deletions. Many of them are mapped close to genes of the immune system and have regions identical to the Tc-1-like transposons abundant among fish, whose transcription activity may affect the expression of adjacent genes. Thus, we showed for the first time that genetic differences between Baikal sig family members are extremely small and cannot be revealed by the SH method. This is another endorsement of the hypothesis on the close relationship between Baikal sig and omul and their evolutionarily recent divergence from a common ancestor.

The common polymorphism of apolipoprotein E

DEFF Research Database (Denmark)

Gerdes, Ulrik

2003-01-01

from only 10-15% in southern Europe to 40-50% in the north. The gradient may be a trace of the demic expansion of agriculture that began about 10,000 years ago, but it may also reflect the possibility that APOE*4 carriers are less likely to develop vitamin D deficiency. The common APOE polymorphism......Apolipoprotein E (apoE) has important functions in systemic and local lipid transport, but also has other functions. The gene (APOE) shows a common polymorphism with three alleles--APOE*2, APOE*3, and APOE*4. Their frequencies vary substantially around the world, but APOE*3 is the most common...

Common Core in the Real World

Science.gov (United States)

Hess, Frederick M.; McShane, Michael Q.

2013-01-01

There are at least four key places where the Common Core intersects with current efforts to improve education in the United States--testing, professional development, expectations, and accountability. Understanding them can help educators, parents, and policymakers maximize the chance that the Common Core is helpful to these efforts and, perhaps…

[Asymmetric effect of in-group social values on identity with common-identity and common-bond in-groups].

Science.gov (United States)

Nakashima, Ken'ichiro; Isobe, Chikae; Toshihiko, Souma; Ura, Mitsuhiro

2013-06-01

Moderating effects of group type on the relationship between in-group social values and group identity were investigated. Previous research has indicated that values attached to the in-group, such as its status, privileges, and power, lead to increased group identity. However, these studies have not investigated the role of the type of in-groups on this effect. We conducted an experiment that manipulated the in-group type. In the common-identity type of in-group condition, formation of in- and out-groups on the basis of social categorization was established. In the common-bond type of in-group condition, interactions between the group members were conducted. Results indicated that in the former condition, the degree of in-group social values affected group identity; however, this effect was not found in the latter condition. These results suggest that social values of the in-group have an asymmetric effect on group identity, depending upon the in-group type as a common-identity or common-bond group.

Common symptoms during pregnancy

Science.gov (United States)

... keep your gums healthy Swelling, Varicose Veins, and Hemorrhoids Swelling in your legs is common. You may ... In your rectum, veins that swell are called hemorrhoids. To reduce swelling: Raise your legs and rest ...

A case of fascioliasis in common bile duct

Energy Technology Data Exchange (ETDEWEB)

Ham, Soo Youn; Park, Cheol Min; Chung, Kyu Byung; Lee, Chang Hong; Park, Seung Chul; Choi, Sang Yong; Lim, Han Jong [Korea University College of Medicine, Seoul (Korea, Republic of)

1989-10-15

A case of Fascioliasis of common bile duct is confirmed by visualization of adult fluke. Fascioliasis caused by Fasciola hepatica, is common parasitic disease in cattle and sheep. Human is an accidental host. ERCP demonstrated irregular linear conglomerated filling defects in common bile duct. Through surgical intervention, we found adult flukes of F. hepatica and adenomatous hyperplasia of common bile duct.

A case of fascioliasis in common bile duct

International Nuclear Information System (INIS)

Ham, Soo Youn; Park, Cheol Min; Chung, Kyu Byung; Lee, Chang Hong; Park, Seung Chul; Choi, Sang Yong; Lim, Han Jong

1989-01-01

A case of Fascioliasis of common bile duct is confirmed by visualization of adult fluke. Fascioliasis caused by Fasciola hepatica, is common parasitic disease in cattle and sheep. Human is an accidental host. ERCP demonstrated irregular linear conglomerated filling defects in common bile duct. Through surgical intervention, we found adult flukes of F. hepatica and adenomatous hyperplasia of common bile duct

Workshop on transport for a common ion driver

International Nuclear Information System (INIS)

Olson, C.C.; Lee, E.; Langdon, B.

1994-01-01

This report contains research in the following areas related to beam transport for a common ion driver: multi-gap acceleration; neutralization with electrons; gas neutralization; self-pinched transport; HIF and LIF transport, and relevance to common ion driver; LIF and HIF reactor concepts and relevance to common ion driver; atomic physics for common ion driver; code capabilities and needed improvement

The central nervous system of sea cucumbers (Echinodermata: Holothuroidea shows positive immunostaining for a chordate glial secretion

Directory of Open Access Journals (Sweden)

Grondona Jesus M

2009-06-01

Full Text Available Abstract Background Echinoderms and chordates belong to the same monophyletic taxon, the Deuterostomia. In spite of significant differences in body plan organization, the two phyla may share more common traits than was thought previously. Of particular interest are the common features in the organization of the central nervous system. The present study employs two polyclonal antisera raised against bovine Reissner's substance (RS, a secretory product produced by glial cells of the subcomissural organ, to study RS-like immunoreactivity in the central nervous system of sea cucumbers. Results In the ectoneural division of the nervous system, both antisera recognize the content of secretory vacuoles in the apical cytoplasm of the radial glia-like cells of the neuroepithelium and in the flattened glial cells of the non-neural epineural roof epithelium. The secreted immunopositive material seems to form a thin layer covering the cell apices. There is no accumulation of the immunoreactive material on the apical surface of the hyponeural neuroepithelium or the hyponeural roof epithelium. Besides labelling the supporting cells and flattened glial cells of the epineural roof epithelium, both anti-RS antisera reveal a previously unknown putative glial cell type within the neural parenchyma of the holothurian nervous system. Conclusion Our results show that: a the glial cells of the holothurian tubular nervous system produce a material similar to Reissner's substance known to be synthesized by secretory glial cells in all chordates studied so far; b the nervous system of sea cucumbers shows a previously unrealized complexity of glial organization. Our findings also provide significant clues for interpretation of the evolution of the nervous system in the Deuterostomia. It is suggested that echinoderms and chordates might have inherited the RS-producing radial glial cell type from the central nervous system of their common ancestor, i.e., the last common

Common Childhood Orthopedic Conditions

Science.gov (United States)

... Parents Parents site Sitio para padres General Health Growth & Development Infections Diseases & Conditions Pregnancy & Baby Nutrition & Fitness Emotions & ... pain. Toe Walking Toe walking is common among toddlers as they learn to walk, especially during the ...

A General Solution Framework for Component-Commonality Problems

Directory of Open Access Journals (Sweden)

Nils Boysen

2009-05-01

Full Text Available Component commonality - the use of the same version of a component across multiple products - is being increasingly considered as a promising way to offer high external variety while retaining low internal variety in operations. However, increasing commonality has both positive and negative cost effects, so that optimization approaches are required to identify an optimal commonality level. As components influence to a greater or lesser extent nearly every process step along the supply chain, it is not surprising that a multitude of diverging commonality problems is being investigated in literature, each of which are developing a specific algorithm designed for the respective commonality problem being considered. The paper on hand aims at a general framework which is flexible and efficient enough to be applied to a wide range of commonality problems. Such a procedure based on a two-stage graph approach is presented and tested. Finally, flexibility of the procedure is shown by customizing the framework to account for different types of commonality problems.

Commons, Piracy and the Crisis of Property

Directory of Open Access Journals (Sweden)

James Arvanitakis

2016-02-01

Full Text Available This article takes the politicisation of copyright and file sharing as a starting point to discuss the concept of the commons and the construction of property. Empirically, the article draws on a series of interviews with Pirate Party members in Sweden, Australia, Germany, the UK and USA; placed in the theoretical framework of the commons. We argue that piracy, as an act and an ideology, interrogates common understandings of property as something self-evident, natural and uncontestable. Such constructions found liberal market ideology. The article has two broad aims: to outline the different phases of enclosure, from the physical commons, to the institutional and finally the cultural commons; and to discuss the way that piracy highlights the emergent crisis in private property rights, brought to the fore by the global financial crisis and ongoing privatization of public resources. We conclude by questioning what new modes of enclosure are emerging in a digital economy driven by excessive data mining and centralized streaming services.

UMTS Common Channel Sensitivity Analysis

DEFF Research Database (Denmark)

Pratas, Nuno; Rodrigues, António; Santos, Frederico

2006-01-01

and as such it is necessary that both channels be available across the cell radius. This requirement makes the choice of the transmission parameters a fundamental one. This paper presents a sensitivity analysis regarding the transmission parameters of two UMTS common channels: RACH and FACH. Optimization of these channels...... is performed and values for the key transmission parameters in both common channels are obtained. On RACH these parameters are the message to preamble offset, the initial SIR target and the preamble power step while on FACH it is the transmission power offset....

Five Common Glaucoma Tests

Science.gov (United States)

... About Us Donate In This Section Five Common Glaucoma Tests en Español email Send this article to ... year or two after age 35. A Comprehensive Glaucoma Exam To be safe and accurate, five factors ...

Common Mental Health Issues

Science.gov (United States)

Stock, Susan R.; Levine, Heidi

2016-01-01

This chapter provides an overview of common student mental health issues and approaches for student affairs practitioners who are working with students with mental illness, and ways to support the overall mental health of students on campus.

By-product mutualism with evolving common enemies.

Science.gov (United States)

De Jaegher, Kris

2017-05-07

The common-enemy hypothesis of by-product mutualism states that organisms cooperate when it is in their individual interests to do so, with benefits for other organisms arising as a by-product; in particular, such cooperation is hypothesized to arise when organisms face the common enemy of a sufficiently adverse environment. In an evolutionary game where two defenders can cooperate to defend a common resource, this paper analyzes the common-enemy hypothesis when adversity is endogenous, in that an attacker sets the number of attacks. As a benchmark, we first consider exogenous adversity, where adversity is not subject to evolution. In this case, the common-enemy hypothesis is predicted when the degree of complementarity between defenders' defensive efforts is sufficiently low. When the degree of complementarity is high, the hypothesis is predicted only when cooperation costs are high; when cooperation costs are instead low, a competing hypothesis is predicted, where adversity discourages cooperation. Second, we consider the case of endogenous adversity. In this case, we continue to predict the competing hypothesis for a high degree of complementarity and low cooperation costs. The common-enemy hypothesis, however, only continues to be predicted for the lowest degrees of complementarity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Auditory verbal hallucinations in schizophrenia and post-traumatic stress disorder: common phenomenology, common cause, common interventions?

Science.gov (United States)

McCarthy-Jones, Simon; Longden, Eleanor

2015-01-01

Auditory verbal hallucinations (AVH: 'hearing voices') are found in both schizophrenia and post-traumatic stress disorder (PTSD). In this paper we first demonstrate that AVH in these two diagnoses share a qualitatively similar phenomenology. We then show that the presence of AVH in schizophrenia is often associated with earlier exposure to traumatic/emotionally overwhelming events, as it is by definition in PTSD. We next argue that the content of AVH relates to earlier traumatic events in a similar way in both PTSD and schizophrenia, most commonly having direct or indirect thematic links to emotionally overwhelming events, rather than being direct re-experiencing. We then propose, following cognitive models of PTSD, that the reconstructive nature of memory may be able to account for the nature of these associations between trauma and AVH content, as may threat-hypervigilance and the individual's personal goals. We conclude that a notable subset of people diagnosed with schizophrenia with AVH are having phenomenologically and aetiologically identical experiences to PTSD patients who hear voices. As such we propose that the iron curtain between AVH in PTSD (often termed 'dissociative AVH') and AVH in schizophrenia (so-called 'psychotic AVH') needs to be torn down, as these are often the same experience. One implication of this is that these trauma-related AVH require a common trans-diagnostic treatment strategy. Whilst antipsychotics are already increasingly being used to treat AVH in PTSD, we argue for the centrality of trauma-based interventions for trauma-based AVH in both PTSD and in people diagnosed with schizophrenia.

Auditory verbal hallucinations in schizophrenia and post-traumatic stress disorder: common phenomenology, common cause, common interventions?

Directory of Open Access Journals (Sweden)

Simon eMccarthy-Jones

2015-07-01

Full Text Available Auditory verbal hallucinations (AVH: ‘hearing voices’ are found in both schizophrenia and post-traumatic stress disorder (PTSD. In this paper we first demonstrate that AVH in these two diagnoses share a qualitatively similar phenomenology. We then show that the presence of AVH in schizophrenia is often associated with earlier exposure to traumatic/emotionally overwhelming events, as it is by definition in PTSD. We next argue that the content of AVH relates to earlier traumatic events in a similar way in both PTSD and schizophrenia, most commonly having direct or indirect thematic links to emotionally overwhelming events, rather than being direct re-experiencing. We then propose, following cognitive models of PTSD, that the reconstructive nature of memory may be able to account for the nature of these associations between trauma and AVH content, as may threat-hypervigilance and the individual’s personal goals. We conclude that a notable subset of people diagnosed with schizophrenia with AVH are having phenomenologically and aetiologically identical experiences to PTSD patients who hear voices. As such we propose that the iron curtain between AVH in PTSD (often termed ‘dissociative AVH’ and AVH in schizophrenia (so-called ‘psychotic AVH’ needs to be torn down, as these are often the same experience. One implication of this is that these trauma-related AVH require a common trans-diagnostic treatment strategy. Whilst antipsychotics are already increasingly being used to treat AVH in PTSD, we argue for the centrality of trauma-based interventions for trauma-based AVH in both PTSD and in people diagnosed with schizophrenia.

Genomic Data Commons launches

Science.gov (United States)

The Genomic Data Commons (GDC), a unified data system that promotes sharing of genomic and clinical data between researchers, launched today with a visit from Vice President Joe Biden to the operations center at the University of Chicago.

Childhood Obesity: Common Misconceptions

Science.gov (United States)

... Issues Listen Español Text Size Email Print Share Childhood Obesity: Common Misconceptions Page Content Article Body Everyone, it ... for less than 1% of the cases of childhood obesity. Yes, hypothyroidism (a deficit in thyroid secretion) and ...

George Combe and common sense.

Science.gov (United States)

Dyde, Sean

2015-06-01

This article examines the history of two fields of enquiry in late eighteenth- and early nineteenth-century Scotland: the rise and fall of the common sense school of philosophy and phrenology as presented in the works of George Combe. Although many previous historians have construed these histories as separate, indeed sometimes incommensurate, I propose that their paths were intertwined to a greater extent than has previously been given credit. The philosophy of common sense was a response to problems raised by Enlightenment thinkers, particularly David Hume, and spurred a theory of the mind and its mode of study. In order to succeed, or even to be considered a rival of these established understandings, phrenologists adapted their arguments for the sake of engaging in philosophical dispute. I argue that this debate contributed to the relative success of these groups: phrenology as a well-known historical subject, common sense now largely forgotten. Moreover, this history seeks to question the place of phrenology within the sciences of mind in nineteenth-century Britain.

Gestalt grouping and common onset masking.

Science.gov (United States)

Kahan, Todd A; Mathis, Katherine M

2002-11-01

A four-dot mask that surrounds and is presented simultaneously with a briefly presented target will reduce a person's ability to identity that target if the mask persists beyond target offset and attention is divided (Enns & Di Lollo, 1997, 2000). This masking effect, referred to as common onset masking, reflects reentrant processing in the visual system and can best be explained with a theory of object substitution (Di Lollo, Enns, & Rensink, 2000). In the present experiments, we investigated whether Gestalt grouping variables would influence the strength of common onset masking. The results indicated that (1) masking was impervious to grouping by form, similarity of color, position, luminance polarity, and common region and (2) masking increased with the number of elements in the masking display.

Organising pneumonia in common variable immunodeficiency.

Science.gov (United States)

Boujaoude, Ziad; Arya, Rohan; Rafferty, William; Dammert, Pedro

2013-06-07

Common variable immunodeficiency (CVID) is the most common of the primary immunodeficiency disorders. Pulmonary manifestations are characterised by recurrent rhinosinusitis, respiratory tract infections and bronchiectasis. Less commonly the lung may be affected by lymphoid disorders and sarcoid-like granulomas. Organising pneumonia (OP) is a rare pulmonary manifestation. We report the case of a 32-year-old woman with CVID who presented with fever, dyspnoea and persistent lung infiltrates despite antibiotic therapy. CT of the chest showed bilateral patchy alveolar infiltrates. Pulmonary function tests revealed moderate restriction and reduction in diffusion capacity. Initial bronchoscopy with transbronchial biopsies did not yield a diagnosis but surgical lung biopsies identified OP. Significant clinical, radiographic and physiological improvement was achieved after institution of corticosteroid therapy.

Structures for common-cause failure analysis

International Nuclear Information System (INIS)

Vaurio, J.K.

1981-01-01

Common-cause failure methodology and terminology have been reviewed and structured to provide a systematical basis for addressing and developing models and methods for quantification. The structure is based on (1) a specific set of definitions, (2) categories based on the way faults are attributable to a common cause, and (3) classes based on the time of entry and the time of elimination of the faults. The failure events are then characterized by their likelihood or frequency and the average residence time. The structure provides a basis for selecting computational models, collecting and evaluating data and assessing the importance of various failure types, and for developing effective defences against common-cause failure. The relationships of this and several other structures are described

The origin and evolution of Homo sapiens

OpenAIRE

Stringer, Chris

2016-01-01

If we restrict the use of Homo sapiens in the fossil record to specimens which share a significant number of derived features in the skeleton with extant H. sapiens, the origin of our species would be placed in the African late middle Pleistocene, based on fossils such as Omo Kibish 1, Herto 1 and 2, and the Levantine material from Skhul and Qafzeh. However, genetic data suggest that we and our sister species Homo neanderthalensis shared a last common ancestor in the middle Pleistocene approx...

The evolution of chemical defenses in passion vine butterflies

DEFF Research Database (Denmark)

Pinheiro de Castro, Érika Cristina

heliconiine subfamily. Despite sequestration of these compounds being an older adaptation than expected, biosynthesis of aliphatic CNglcs is hypothesized to be even more ancient, arising in lepidopterans before butterflies and moths diverged from a common ancestor. In addition, this study shows...... degrade into cyanide.. During its life cycle, Heliconius melpomene is most cyanogenic when it is a mature adult, due to intense biosynthesis of aliphatic CNglcs. Males of this species transfer linamarin and lotaustralin during copula to females, confirming earlier suggestions that CNglcs are used...

Nervous and muscle system development in Phascolion strombus (Sipuncula)

DEFF Research Database (Denmark)

Wanninger, Andreas; Koop, Demian; Bromham, Lindell

2005-01-01

possible cryptic segmentation patterns. In this paper, we present the first immunocytochemical data on the ontogeny of the nervous system and the musculature in the sipunculan Phascolion strombus. Myogenesis of the first anlagen of the body wall ring muscles occurs synchronously and not subsequently from......Recent interpretations of developmental gene expression patterns propose that the last common metazoan ancestor was segmented, although most animal phyla show no obvious signs of segmentation. Developmental studies of non-model system trochozoan taxa may shed light on this hypothesis by assessing...

Ancestral sequence reconstruction with Maximum Parsimony

OpenAIRE

Herbst, Lina; Fischer, Mareike

2017-01-01

One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference as well as for ancestral sequence inference is Maximum Parsimony (...

Collaborating with Staff: Sharing a Common Philosophy, Working To Achieve Common Goals.

Science.gov (United States)

Salzman, Jeff

1999-01-01

A well-understood camp philosophy motivates the entire staff to work toward a common purpose, which is more meaningful than money. Camp administrators can ensure that staff members implement the camp philosophy by interviewing prospective staff members with the mission in mind, teaching staff the camp's vision, praising staff with specifics,…

The tomato wilt fungus Fusarium oxysporum f. sp. lycopersici shares common ancestors with nonpathogenic F. oxysporum isolated from wild tomatoes in the Peruvian Andes.

Science.gov (United States)

Inami, Keigo; Kashiwa, Takeshi; Kawabe, Masato; Onokubo-Okabe, Akiko; Ishikawa, Nobuko; Pérez, Enrique Rodríguez; Hozumi, Takuo; Caballero, Liliana Aragón; de Baldarrago, Fatima Cáceres; Roco, Mauricio Jiménez; Madadi, Khalid A; Peever, Tobin L; Teraoka, Tohru; Kodama, Motoichiro; Arie, Tsutomu

2014-01-01

Fusarium oxysporum is an ascomycetous fungus that is well-known as a soilborne plant pathogen. In addition, a large population of nonpathogenic F. oxysporum (NPF) inhabits various environmental niches, including the phytosphere. To obtain an insight into the origin of plant pathogenic F. oxysporum, we focused on the tomato (Solanum lycopersicum) and its pathogenic F. oxysporum f. sp. lycopersici (FOL). We collected F. oxysporum from wild and transition Solanum spp. and modern cultivars of tomato in Chile, Ecuador, Peru, Mexico, Afghanistan, Italy, and Japan, evaluated the fungal isolates for pathogenicity, VCG, mating type, and distribution of SIX genes related to the pathogenicity of FOL, and constructed phylogenies based on ribosomal DNA intergenic spacer sequences. All F. oxysporum isolates sampled were genetically more diverse than FOL. They were not pathogenic to the tomato and did not carry SIX genes. Certain NPF isolates including those from wild Solanum spp. in Peru were grouped in FOL clades, whereas most of the NPF isolates were not. Our results suggested that the population of NPF isolates in FOL clades gave rise to FOL by gaining pathogenicity.

Common morality and moral reform.

Science.gov (United States)

Wallace, K A

2009-01-01

The idea of moral reform requires that morality be more than a description of what people do value, for there has to be some measure against which to assess progress. Otherwise, any change is not reform, but simply difference. Therefore, I discuss moral reform in relation to two prescriptive approaches to common morality, which I distinguish as the foundational and the pragmatic. A foundational approach to common morality (e.g., Bernard Gert's) suggests that there is no reform of morality, but of beliefs, values, customs, and practices so as to conform with an unchanging, foundational morality. If, however, there were revision in its foundation (e.g., in rationality), then reform in morality itself would be possible. On a pragmatic view, on the other hand, common morality is relative to human flourishing, and its justification consists in its effectiveness in promoting flourishing. Morality is dependent on what in fact does promote human flourishing and therefore, could be reformed. However, a pragmatic approach, which appears more open to the possibility of moral reform, would need a more robust account of norms by which reform is measured.

Development of a Common Nordic Balance Settlement

Energy Technology Data Exchange (ETDEWEB)

NONE

2006-02-15

NordREG finds it essential for the customers that a common integrated end-user electricity market is developed and that all end-users are able to take part in the Nordic market. A common Nordic balance settlement is one important part of such a change. However, attention has to be paid to the comments that a badly designed common system is worse than well-designed national systems. It is thus important that the change to a common balance settlement is so thoroughly investigated that the common system gives a basis for a well-functioning market. An important basis for such a change is an agreed vision for the process: The present different systems for balance settlement shall by the year 2010 be replaced by a common Nordic balance settlement. This means that: It will be possible for a supplier to sell to the whole Nordic market from one legal entity and using only one system for customer management and reporting. The common Nordic balance settlement will be designed in such a way that it contributes to a well functioning market. This means for example that it will be attractive even for small suppliers and some end-users to be balance responsible parties. It is feasible that the first phase is focused on those present differences that are most decisive for fulfilment of the vision. NordREG recommends that the following issues shall be discussed and agreed in co-operation between NordREG, Nordel and relevant stakeholders in the first phase: The definition shall include how the common Nordic balance settlement shall interact with the balance control and the balance regulation of the interconnected power system and the balance settlement between countries performed by the TSOs. The definition should include the cost-base for common Nordic balance settlement in relation to other system responsibility costs. The core activities of system responsibility have also been analyzed by NordREG. It is important to find a balance between inter alia the need for simplicity and the

Development of a Common Nordic Balance Settlement

International Nuclear Information System (INIS)

2006-02-01

NordREG finds it essential for the customers that a common integrated end-user electricity market is developed and that all end-users are able to take part in the Nordic market. A common Nordic balance settlement is one important part of such a change. However, attention has to be paid to the comments that a badly designed common system is worse than well-designed national systems. It is thus important that the change to a common balance settlement is so thoroughly investigated that the common system gives a basis for a well-functioning market. An important basis for such a change is an agreed vision for the process: The present different systems for balance settlement shall by the year 2010 be replaced by a common Nordic balance settlement. This means that: It will be possible for a supplier to sell to the whole Nordic market from one legal entity and using only one system for customer management and reporting. The common Nordic balance settlement will be designed in such a way that it contributes to a well functioning market. This means for example that it will be attractive even for small suppliers and some end-users to be balance responsible parties. It is feasible that the first phase is focused on those present differences that are most decisive for fulfilment of the vision. NordREG recommends that the following issues shall be discussed and agreed in co-operation between NordREG, Nordel and relevant stakeholders in the first phase: The definition shall include how the common Nordic balance settlement shall interact with the balance control and the balance regulation of the interconnected power system and the balance settlement between countries performed by the TSOs. The definition should include the cost-base for common Nordic balance settlement in relation to other system responsibility costs. The core activities of system responsibility have also been analyzed by NordREG. It is important to find a balance between inter alia the need for simplicity and the

The brown adipocyte differentiation pathway in birds: An evolutionary road not taken

Science.gov (United States)

Mezentseva, Nadejda V; Kumaratilake, Jaliya S; Newman, Stuart A

2008-01-01

Background Thermogenic brown adipose tissue has never been described in birds or other non-mammalian vertebrates. Brown adipocytes in mammals are distinguished from the more common white fat adipocytes by having numerous small lipid droplets rather than a single large one, elevated numbers of mitochondria, and mitochondrial expression of the nuclear gene UCP1, the uncoupler of oxidative phosphorylation responsible for non-shivering thermogenesis. Results We have identified in vitro inductive conditions in which mesenchymal cells isolated from the embryonic chicken limb bud differentiate into avian brown adipocyte-like cells (ABALCs) with the morphological and many of the biochemical properties of terminally differentiated brown adipocytes. Avian, and as we show here, lizard species lack the gene for UCP1, although it is present in amphibian and fish species. While ABALCs are therefore not functional brown adipocytes, they are generated by a developmental pathway virtually identical to brown fat differentiation in mammals: both the common adipogenic transcription factor peroxisome proliferator-activated receptor-γ (PPARγ), and a coactivator of that factor specific to brown fat differentiation in mammals, PGC1α, are elevated in expression, as are mitochondrial volume and DNA. Furthermore, ABALCs induction resulted in strong transcription from a transfected mouse UCP1 promoter. Conclusion These findings strongly suggest that the brown fat differentiation pathway evolved in a common ancestor of birds and mammals and its thermogenicity was lost in the avian lineage, with the degradation of UCP1, after it separated from the mammalian lineage. Since this event occurred no later than the saurian ancestor of birds and lizards, an implication of this is that dinosaurs had neither UCP1 nor canonically thermogenic brown fat. PMID:18426587

Common morality: comment on Beauchamp and Childress.

Science.gov (United States)

Rauprich, Oliver

2008-01-01

The notion of common morality plays a prominent role in some of the most influential theories of biomedical ethics. Here, I focus on Beauchamp and Childress's models in the fourth and fifth edition of Principles of Biomedical Ethics as well as on a revision that Beauchamp proposed in a recent article. Although there are significant differences in these works that require separate analysis, all include a role for common morality as starting point and normative framework for theory construction in combination with a coherence theory of moral justification. I defend to some extent the existence and empirical significance of common morality, as delineated by Beauchamp and Childress in different versions, but criticize its normative role. It is neither convincing as a moral foundation nor well compatible with a standard coherentist justification. I suggest that the authors should give up the foundational account for a more modest account of common morality as resource of well-established moral insights and experiences, which have proved generally valid but neither sufficient nor infallible. Beauchamp's latest proposal appears as a step in this direction; indeed, it may be the beginning of the end of his common-morality theory.

Common congenital malformations of the brain

International Nuclear Information System (INIS)

Naidich, T.P.; Zimmerman, R.A.

1987-01-01

In nearly all cases, congenital malformations are characterized most easily by their anatomic features and are best images with T1-weighted short TR/short TE pulse sequences. T2-weighted, long TR/long TE images are used primarily for the phakomatoses that are commonly associated with brain tumors. This chapter reviews the features of the most common congenital malformations and illustrates their typical magnetic resonance imaging (MRI) appearance

Common Metrics for Human-Robot Interaction

Science.gov (United States)

Steinfeld, Aaron; Lewis, Michael; Fong, Terrence; Scholtz, Jean; Schultz, Alan; Kaber, David; Goodrich, Michael

2006-01-01

This paper describes an effort to identify common metrics for task-oriented human-robot interaction (HRI). We begin by discussing the need for a toolkit of HRI metrics. We then describe the framework of our work and identify important biasing factors that must be taken into consideration. Finally, we present suggested common metrics for standardization and a case study. Preparation of a larger, more detailed toolkit is in progress.

The Politics of the Commons: Reform or Revolt?

Directory of Open Access Journals (Sweden)

Vangelis Papadimitropoulos

2017-06-01

Full Text Available In this paper I present a critical overview of the contemporary political theories of the Commons, classified in three main categories: 1 the liberal 2 the reformist and 3 the anti-capitalist. Advocates of the liberal theory of the Commons take a stand in favour of the coexistence of the Commons with the state and the market. The reformists argue for the gradual adjustment of capitalism to the Commons with the aid of a partner state, while the anti-capitalists contrast both the liberals and the reformists by supporting the development of the commons against and beyond capitalism. I make the case that both the liberal and the anti-capitalist theorists miss the likelihood of technology rendering redundant large-scale production in the future, and forcing thus capitalism to adjust to the Commons in the long run. The prospect, therefore, of an open cooperativism introduced by the reformist theory holds significant potential with respect to the future development of the Commons. For the Commons however to expand and flourish, a global institutional reform, followed by a set of inter-local and international principles, is sine qua non. Hence, transparency of information, distribution of value, solidarity and bottom-up self-management are the core variables of individual and collective autonomy inasmuch as they permit a community or group to formulate its values in relation to the needs and skills of its members.

Accounting and marketing: searching a common denominator

Directory of Open Access Journals (Sweden)

David S. Murphy

2012-06-01

Full Text Available Accounting and marketing are very different disciplines. The analysis of customer profitability is one concept that can unite accounting and marketing as a common denominator. In this article I search for common ground between accounting and marketing in the analysis of customer profitability to determine if a common denominator really exists between the two. This analysis focuses on accounting profitability, customer lifetime value, and customer equity. The article ends with a summary of what accountants can do to move the analysis of customer value forward, as an analytical tool, within companies.

Logical Normativity and Common Sense Reasoning

Directory of Open Access Journals (Sweden)

Evandro Agazzi

2011-04-01

Full Text Available Logic, considered as a technical discipline inaugurated by Aristotle and typically represented by the variety of the modern logical calculi, constitutes a clarification and refinement of a conviction and practice present in common sense, that is, the fact that humans believe that truth can be acquired not only by immediate evidence, but also by means of arguments. As a first step logic can be seen as a “descriptive” record of the main forms of the arguments present in common sense, but the fact that some of these patterns can actually allow for the derivation of false consequences from true premises imposes the task of making explicit what patterns correspond to a “correct reasoning” and what not. At this point logic (that contains the presentation of such patterns appears endowed with a “normative” characteristic. This amounts to saying that logical calculi are intended to adequately mirror the intuitive notion of “logical consequence” and in this sense they cannot be totally arbitrary or conventional, but must satisfy certain basic requirements such as the conditions of soundness and (as far as possible of semantic completeness. In such a way they are “judged” according to the fundamental requirements present at the level of common sense and appear as “idealizations” of the kinds of reasoning practiced in common sense. For this reason also several kinds of logical calculi are fully justified since they make explicit in an idealized form the concrete ways of reasoning that are imposed by the particular domain of reference of the discipline in which they are used and which are basically recognized in common sense.

Evolutionary history of the alpha2,8-sialyltransferase (ST8Sia) gene family: tandem duplications in early deuterostomes explain most of the diversity found in the vertebrate ST8Sia genes.

Science.gov (United States)

Harduin-Lepers, Anne; Petit, Daniel; Mollicone, Rosella; Delannoy, Philippe; Petit, Jean-Michel; Oriol, Rafael

2008-09-23

The animal sialyltransferases, which catalyze the transfer of sialic acid to the glycan moiety of glycoconjugates, are subdivided into four families: ST3Gal, ST6Gal, ST6GalNAc and ST8Sia, based on acceptor sugar specificity and glycosidic linkage formed. Despite low overall sequence identity between each sialyltransferase family, all sialyltransferases share four conserved peptide motifs (L, S, III and VS) that serve as hallmarks for the identification of the sialyltransferases. Currently, twenty subfamilies have been described in mammals and birds. Examples of the four sialyltransferase families have also been found in invertebrates. Focusing on the ST8Sia family, we investigated the origin of the three groups of alpha2,8-sialyltransferases demonstrated in vertebrates to carry out poly-, oligo- and mono-alpha2,8-sialylation. We identified in the genome of invertebrate deuterostomes, orthologs to the common ancestor for each of the three vertebrate ST8Sia groups and a set of novel genes named ST8Sia EX, not found in vertebrates. All these ST8Sia sequences share a new conserved family-motif, named "C-term" that is involved in protein folding, via an intramolecular disulfide bridge. Interestingly, sequences from Branchiostoma floridae orthologous to the common ancestor of polysialyltransferases possess a polysialyltransferase domain (PSTD) and those orthologous to the common ancestor of oligosialyltransferases possess a new ST8Sia III-specific motif similar to the PSTD. In osteichthyans, we have identified two new subfamilies. In addition, we describe the expression profile of ST8Sia genes in Danio rerio. Polysialylation appeared early in the deuterostome lineage. The recent release of several deuterostome genome databases and paralogons combined with synteny analysis allowed us to obtain insight into events at the gene level that led to the diversification of the ST8Sia genes, with their corresponding enzymatic activities, in both invertebrates and vertebrates. The

Evolutionary history of the alpha2,8-sialyltransferase (ST8Sia gene family: Tandem duplications in early deuterostomes explain most of the diversity found in the vertebrate ST8Sia genes

Directory of Open Access Journals (Sweden)

Petit Jean-Michel

2008-09-01

Full Text Available Abstract Background The animal sialyltransferases, which catalyze the transfer of sialic acid to the glycan moiety of glycoconjugates, are subdivided into four families: ST3Gal, ST6Gal, ST6GalNAc and ST8Sia, based on acceptor sugar specificity and glycosidic linkage formed. Despite low overall sequence identity between each sialyltransferase family, all sialyltransferases share four conserved peptide motifs (L, S, III and VS that serve as hallmarks for the identification of the sialyltransferases. Currently, twenty subfamilies have been described in mammals and birds. Examples of the four sialyltransferase families have also been found in invertebrates. Focusing on the ST8Sia family, we investigated the origin of the three groups of α2,8-sialyltransferases demonstrated in vertebrates to carry out poly-, oligo- and mono-α2,8-sialylation. Results We identified in the genome of invertebrate deuterostomes, orthologs to the common ancestor for each of the three vertebrate ST8Sia groups and a set of novel genes named ST8Sia EX, not found in vertebrates. All these ST8Sia sequences share a new conserved family-motif, named "C-term" that is involved in protein folding, via an intramolecular disulfide bridge. Interestingly, sequences from Branchiostoma floridae orthologous to the common ancestor of polysialyltransferases possess a polysialyltransferase domain (PSTD and those orthologous to the common ancestor of oligosialyltransferases possess a new ST8Sia III-specific motif similar to the PSTD. In osteichthyans, we have identified two new subfamilies. In addition, we describe the expression profile of ST8Sia genes in Danio rerio. Conclusion Polysialylation appeared early in the deuterostome lineage. The recent release of several deuterostome genome databases and paralogons combined with synteny analysis allowed us to obtain insight into events at the gene level that led to the diversification of the ST8Sia genes, with their corresponding enzymatic

The lipoxygenase gene family: a genomic fossil of shared polyploidy between Glycine max and Medicago truncatula

Directory of Open Access Journals (Sweden)

Choi Beom-Soon

2008-12-01

Full Text Available Abstract Background Soybean lipoxygenases (Lxs play important roles in plant resistance and in conferring the distinct bean flavor. Lxs comprise a multi-gene family that includes GmLx1, GmLx2 and GmLx3, and many of these genes have been characterized. We were interested in investigating the relationship between the soybean lipoxygenase isozymes from an evolutionary perspective, since soybean has undergone two rounds of polyploidy. Here we report the tetrad genome structure of soybean Lx regions produced by ancient and recent polyploidy. Also, comparative genomics with Medicago truncatula was performed to estimate Lxs in the common ancestor of soybean and Medicago. Results Two Lx regions in Medicago truncatula showing synteny with soybean were analyzed. Differential evolutionary rates between soybean and Medicago were observed and the median Ks values of Mt-Mt, Gm-Mt, and Gm-Gm paralogs were determined to be 0.75, 0.62, and 0.46, respectively. Thus the comparison of Gm-Mt paralogs (Ks = 0.62 and Gm-Mt orthologs (Ks = 0.45 supports the ancient duplication of Lx regions in the common ancestor prior to the Medicago-Glycine split. After speciation, no Lx regions generated by another polyploidy were identified in Medicago. Instead tandem duplication of Lx genes was observed. On the other hand, a lineage-specific duplication occurred in soybean resulting in two pairs of Lx regions. Each pair of soybean regions was co-orthologous to one Lx region in Medicago. A total of 34 Lx genes (15 MtLxs and 19 GmLxs were divided into two groups by phylogenetic analysis. Our study shows that the Lx gene family evolved from two distinct Lx genes in the most recent common ancestor. Conclusion This study analyzed two pairs of Lx regions generated by two rounds of polyploidy in soybean. Each pair of soybean homeologous regions is co-orthologous to one region of Medicago, demonstrating the quartet structure of the soybean genome. Differential evolutionary rates between

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

Directory of Open Access Journals (Sweden)

Wolf Yuri I

2007-11-01

Full Text Available Abstract Background An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs. Rapid accumulation of genome sequences creates opportunities for refining COGs but also represents a challenge because of error amplification. One of the practical strategies involves construction of refined COGs for phylogenetically compact subsets of genomes. Results New Archaeal Clusters of Orthologous Genes (arCOGs were constructed for 41 archaeal genomes (13 Crenarchaeota, 27 Euryarchaeota and one Nanoarchaeon using an improved procedure that employs a similarity tree between smaller, group-specific clusters, semi-automatically partitions orthology domains in multidomain proteins, and uses profile searches for identification of remote orthologs. The annotation of arCOGs is a consensus between three assignments based on the COGs, the CDD database, and the annotations of homologs in the NR database. The 7538 arCOGs, on average, cover ~88% of the genes in a genome compared to a ~76% coverage in COGs. The finer granularity of ortholog identification in the arCOGs is apparent from the fact that 4538 arCOGs correspond to 2362 COGs; ~40% of the arCOGs are new. The archaeal gene core (protein-coding genes found in all 41 genome consists of 166 arCOGs. The arCOGs were used to reconstruct gene loss and gene gain events during archaeal evolution and gene sets of ancestral forms. The Last Archaeal Common Ancestor (LACA is conservatively estimated to possess 996 genes compared to 1245 and 1335 genes for the last common ancestors of Crenarchaeota and Euryarchaeota, respectively. It is inferred that LACA was a chemoautotrophic hyperthermophile

The challenge that Confucian filial piety poses for Korean churches ...

African Journals Online (AJOL)

Journal Home > Vol 70, No 2 (2014) > ... Contemporary ancestor worship is currently practiced around the world in several different forms. However, the essence and practice of ancestor worship varies throughout Asia, Africa, Oceania and ...

Economic Analysis of Social Common Capital

Science.gov (United States)

Uzawa, Hirofumi

2005-06-01

Social common capital provides members of society with those services and institutional arrangements that are crucial in maintaining human and cultural life. The term æsocial common capital' is comprised of three categories: natural capital, social infrastructure, and institutional capital. Natural capital consists of all natural environment and natural resources including the earth's atmosphere. Social infrastructure consists of roads, bridges, public transportation systems, electricity, and other public utilities. Institutional capital includes hospitals, educational institutions, judicial and police systems, public administrative services, financial and monetary institutions, and cultural capital. This book attempts to modify and extend the theoretical premises of orthodox economic theory to make them broad enough to analyze the economic implications of social common capital. It further aims to find the institutional arrangements and policy measures that will bring about the optimal state of affairs.

The Common and its potential creativity

DEFF Research Database (Denmark)

Agustin, Oscar Garcia

2015-01-01

of capital in exploiting it but it can also contribute to shaping other scenarios. In the first case, creative capitalism moves towards a mode of production based on clustering, mostly in the cities, to produce untraded externalities or interdependencies. In the second case, the interconnected and potential...... creativity of the common allows for the production of other forms of life. This article explores an alternative model of creative capitalism, whereby the common is expropriated through its marketization and individualization. This model is based on three pillars: the city as the place of creation of new...... social bonds, the production of general intellect and the transformation of public spaces; the precarious multitude as a new class composition opposed to the entrepreneurial conception of creative class; and the cultural commons as an exit strategy from the dichotomy between private and public leading...

An engineering approach to common mode failure analysis

International Nuclear Information System (INIS)

Gangloff, W.C.; Franke, T.H.

1975-01-01

Safety systems for nuclear reactors can be designed using standard reliability engineering techniques such that system failure due to random component faults is extremely unlikely. However, the common-mode failure where several components fail together from a common cause is not susceptible to prevention by the usual tactics. In systems where a high degree of redundancy has been employed, the actual reliability of the system in service may be limited by common-mode failures. A methodical and thorough procedure for evaluation of system vulnerability to common-mode failures is presented. This procedure was developed for use in nuclear reactor safety systems and has been applied specifically to reactor protection. The method offers a qualitative assessment of a system whereby weak points can be identified and the resistance to common-mode failure can be judged. It takes into account all factors influencing system performance including design, manufacturing, installation, operation, testing, and maintenance. It is not a guarantee or sure solution, but rather a practical tool which can provide good assurance that the probability of common-mode protection failure has been made acceptably low. (author)

Common mistakes of investors

Directory of Open Access Journals (Sweden)

Yuen Wai Pong Raymond

2012-09-01

Full Text Available Behavioral finance is an actively discussed topic in the academic and investment circle. The main reason is because behavioral finance challenges the validity of a cornerstone of the modern financial theory: rationality of investors. In this paper, the common irrational behaviors of investors are discussed

Haplotype analysis suggest that the MLH1 c.2059C > T mutation is a Swedish founder mutation.

Science.gov (United States)

von Salomé, Jenny; Liu, Tao; Keihäs, Markku; Morak, Moni; Holinski-Feder, Elke; Berry, Ian R; Moilanen, Jukka S; Baert-Desurmont, Stéphanie; Lindblom, Annika; Lagerstedt-Robinson, Kristina

2017-12-29

Lynch syndrome (LS) predisposes to a spectrum of cancers and increases the lifetime risk of developing colorectal- or endometrial cancer to over 50%. Lynch syndrome is dominantly inherited and is caused by defects in DNA mismatch-repair genes MLH1, MSH2, MSH6 or PMS2, with the vast majority detected in MLH1 and MSH2. Recurrent LS-associated variants observed in apparently unrelated individuals, have either arisen de novo in different families due to mutation hotspots, or are inherited from a founder (a common ancestor) that lived several generations back. There are variants that recur in some populations while also acting as founders in other ethnic groups. Testing for founder mutations can facilitate molecular diagnosis of Lynch Syndrome more efficiently and more cost effective than screening for all possible mutations. Here we report a study of the missense mutation MLH1 c.2059C > T (p.Arg687Trp), a potential founder mutation identified in eight Swedish families and one Finnish family with Swedish ancestors. Haplotype analysis confirmed that the Finnish and Swedish families shared a haplotype of between 0.9 and 2.8 Mb. While MLH1 c.2059C > T exists worldwide, the Swedish haplotype was not found among mutation carriers from Germany or France, which indicates a common founder in the Swedish population. The geographic distribution of MLH1 c.2059C > T in Sweden suggests a single, ancient mutational event in the northern part of Sweden.

Neurospora crassa ASM-1 complements the conidiation defect in a stuA mutant of Aspergillus nidulans.

Science.gov (United States)

Chung, Dawoon; Upadhyay, Srijana; Bomer, Brigitte; Wilkinson, Heather H; Ebbole, Daniel J; Shaw, Brian D

2015-01-01

Aspergillus nidulans StuA and Neurospora crassa ASM-1 are orthologous APSES (ASM-1, PHD1, SOK2, Efg1, StuA) transcription factors conserved across a diverse group of fungi. StuA and ASM-1 have roles in asexual (conidiation) and sexual (ascospore formation) development in both organisms. To address the hypothesis that the last common ancestor of these diverse fungi regulated conidiation with similar genes, asm-1 was introduced into the stuA1 mutant of A. nidulans. Expression of asm-1 complemented defective conidiophore morphology and restored conidia production to wild type levels in stuA1. Expression of asm-1 in the stuA1 strain did not rescue the defect in sexual development. When the conidiation regulator AbaA was tagged at its C-terminus with GFP in A. nidulans, it localized to nuclei in phialides. When expressed in the stuA1 mutant, AbaA::GFP localized to nuclei in conidiophores but no longer was confined to phialides, suggesting that expression of AbaA in specific cell types of the conidiophore was conditioned by StuA. Our data suggest that the function in conidiation of StuA and ASM-1 is conserved and support the view that, despite the great morphological and ontogenic diversity of their condiphores, the last common ancestor of A. nidulans and N. crassa produced an ortholog of StuA that was involved in conidiophore development. © 2015 by The Mycological Society of America.

Disproportionate Cochlear Length in Genus Homo Shows a High Phylogenetic Signal during Apes’ Hearing Evolution

Science.gov (United States)

Braga, J.; Loubes, J-M.; Descouens, D.; Dumoncel, J.; Thackeray, J. F.; Kahn, J-L.; de Beer, F.; Riberon, A.; Hoffman, K.; Balaresque, P.; Gilissen, E.

2015-01-01

Changes in lifestyles and body weight affected mammal life-history evolution but little is known about how they shaped species’ sensory systems. Since auditory sensitivity impacts communication tasks and environmental acoustic awareness, it may have represented a deciding factor during mammal evolution, including apes. Here, we statistically measure the influence of phylogeny and allometry on the variation of five cochlear morphological features associated with hearing capacities across 22 living and 5 fossil catarrhine species. We find high phylogenetic signals for absolute and relative cochlear length only. Comparisons between fossil cochleae and reconstructed ape ancestral morphotypes show that Australopithecus absolute and relative cochlear lengths are explicable by phylogeny and concordant with the hypothetized ((Pan,Homo),Gorilla) and (Pan,Homo) most recent common ancestors. Conversely, deviations of the Paranthropus oval window area from these most recent common ancestors are not explicable by phylogeny and body weight alone, but suggest instead rapid evolutionary changes (directional selection) of its hearing organ. Premodern (Homo erectus) and modern human cochleae set apart from living non-human catarrhines and australopiths. They show cochlear relative lengths and oval window areas larger than expected for their body mass, two features corresponding to increased low-frequency sensitivity more recent than 2 million years ago. The uniqueness of the “hypertrophied” cochlea in the genus Homo (as opposed to the australopiths) and the significantly high phylogenetic signal of this organ among apes indicate its usefulness to identify homologies and monophyletic groups in the hominid fossil record. PMID:26083484

The phenotype of polycythemia due to Croatian homozygous VHL (571C>G:H191D) mutation is different from that of Chuvash polycythemia (VHL 598C>T:R200W).

Science.gov (United States)

Tomasic, Nikica Ljubas; Piterkova, Lucie; Huff, Chad; Bilic, Ernest; Yoon, Donghoon; Miasnikova, Galina Y; Sergueeva, Adelina I; Niu, Xiaomei; Nekhai, Sergei; Gordeuk, Victor; Prchal, Josef T

2013-04-01

Mutations of VHL (a negative regulator of hypoxia-inducible factors) have position-dependent distinct cancer phenotypes. Only two known inherited homozygous VHL mutations exist and they cause polycythemia: Chuvash R200W and Croatian H191D. We report a second polycythemic Croatian H191D homozygote distantly related to the first propositus. Three generations of both families were genotyped for analysis of shared ancestry. Biochemical and molecular tests were performed to better define their phenotypes, with an emphasis on a comparison with Chuvash polycythemia. The VHL H191D mutation did not segregate in the family defined by the known common ancestors of the two subjects, suggesting a high prevalence in Croatians, but haplotype analysis indicated an undocumented common ancestor ∼six generations ago as the founder of this mutation. We show that erythropoietin levels in homozygous VHL H191D individuals are higher than in VHL R200W patients of similar ages, and their native erythroid progenitors, unlike Chuvash R200W, are not hypersensitive to erythropoietin. This observation contrasts with a report suggesting that polycythemia in VHL R200W and H191D homozygotes is due to the loss of JAK2 regulation from VHL R200W and H191D binding to SOCS1. In conclusion, our studies further define the hematologic phenotype of VHL H191D and provide additional evidence for phenotypic heterogeneity associated with the positional effects of VHL mutations.

Towards a Computational Comparative Neuroprimatology: Framing the language-ready brain

Science.gov (United States)

Arbib, Michael A.

2016-03-01

We make the case for developing a Computational Comparative Neuroprimatology to inform the analysis of the function and evolution of the human brain. First, we update the mirror system hypothesis on the evolution of the language-ready brain by (i) modeling action and action recognition and opportunistic scheduling of macaque brains to hypothesize the nature of the last common ancestor of macaque and human (LCA-m); and then we (ii) introduce dynamic brain modeling to show how apes could acquire gesture through ontogenetic ritualization, hypothesizing the nature of evolution from LCA-m to the last common ancestor of chimpanzee and human (LCA-c). We then (iii) hypothesize the role of imitation, pantomime, protosign and protospeech in biological and cultural evolution from LCA-c to Homo sapiens with a language-ready brain. Second, we suggest how cultural evolution in Homo sapiens led from protolanguages to full languages with grammar and compositional semantics. Third, we assess the similarities and differences between the dorsal and ventral streams in audition and vision as the basis for presenting and comparing two models of language processing in the human brain: A model of (i) the auditory dorsal and ventral streams in sentence comprehension; and (ii) the visual dorsal and ventral streams in defining ;what language is about; in both production and perception of utterances related to visual scenes provide the basis for (iii) a first step towards a synthesis and a look at challenges for further research.

Genome evolution during progression to breast cancer

KAUST Repository

Newburger, D. E.; Kashef-Haghighi, D.; Weng, Z.; Salari, R.; Sweeney, R. T.; Brunner, A. L.; Zhu, S. X.; Guo, X.; Varma, S.; Troxell, M. L.; West, R. B.; Batzoglou, S.; Sidow, A.

2013-01-01

Cancer evolution involves cycles of genomic damage, epigenetic deregulation, and increased cellular proliferation that eventually culminate in the carcinoma phenotype. Early neoplasias, which are often found concurrently with carcinomas and are histologically distinguishable from normal breast tissue, are less advanced in phenotype than carcinomas and are thought to represent precursor stages. To elucidate their role in cancer evolution we performed comparative whole-genome sequencing of early neoplasias, matched normal tissue, and carcinomas from six patients, for a total of 31 samples. By using somatic mutations as lineage markers we built trees that relate the tissue samples within each patient. On the basis of these lineage trees we inferred the order, timing, and rates of genomic events. In four out of six cases, an early neoplasia and the carcinoma share a mutated common ancestor with recurring aneuploidies, and in all six cases evolution accelerated in the carcinoma lineage. Transition spectra of somatic mutations are stable and consistent across cases, suggesting that accumulation of somatic mutations is a result of increased ancestral cell division rather than specific mutational mechanisms. In contrast to highly advanced tumors that are the focus of much of the current cancer genome sequencing, neither the early neoplasia genomes nor the carcinomas are enriched with potentially functional somatic point mutations. Aneuploidies that occur in common ancestors of neoplastic and tumor cells are the earliest events that affect a large number of genes and may predispose breast tissue to eventual development of invasive carcinoma.

Genome evolution during progression to breast cancer

KAUST Repository

Newburger, D. E.

2013-04-08

Cancer evolution involves cycles of genomic damage, epigenetic deregulation, and increased cellular proliferation that eventually culminate in the carcinoma phenotype. Early neoplasias, which are often found concurrently with carcinomas and are histologically distinguishable from normal breast tissue, are less advanced in phenotype than carcinomas and are thought to represent precursor stages. To elucidate their role in cancer evolution we performed comparative whole-genome sequencing of early neoplasias, matched normal tissue, and carcinomas from six patients, for a total of 31 samples. By using somatic mutations as lineage markers we built trees that relate the tissue samples within each patient. On the basis of these lineage trees we inferred the order, timing, and rates of genomic events. In four out of six cases, an early neoplasia and the carcinoma share a mutated common ancestor with recurring aneuploidies, and in all six cases evolution accelerated in the carcinoma lineage. Transition spectra of somatic mutations are stable and consistent across cases, suggesting that accumulation of somatic mutations is a result of increased ancestral cell division rather than specific mutational mechanisms. In contrast to highly advanced tumors that are the focus of much of the current cancer genome sequencing, neither the early neoplasia genomes nor the carcinomas are enriched with potentially functional somatic point mutations. Aneuploidies that occur in common ancestors of neoplastic and tumor cells are the earliest events that affect a large number of genes and may predispose breast tissue to eventual development of invasive carcinoma.

Parallel Epidemics of Community-Associated Methicillin-Resistant Staphylococcus aureus USA300 Infection in North and South America.

Science.gov (United States)

Planet, Paul J; Diaz, Lorena; Kolokotronis, Sergios-Orestis; Narechania, Apurva; Reyes, Jinnethe; Xing, Galen; Rincon, Sandra; Smith, Hannah; Panesso, Diana; Ryan, Chanelle; Smith, Dylan P; Guzman, Manuel; Zurita, Jeannete; Sebra, Robert; Deikus, Gintaras; Nolan, Rathel L; Tenover, Fred C; Weinstock, George M; Robinson, D Ashley; Arias, Cesar A

2015-12-15

The community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) epidemic in the United States is attributed to the spread of the USA300 clone. An epidemic of CA-MRSA closely related to USA300 has occurred in northern South America (USA300 Latin-American variant, USA300-LV). Using phylogenomic analysis, we aimed to understand the relationships between these 2 epidemics. We sequenced the genomes of 51 MRSA clinical isolates collected between 1999 and 2012 from the United States, Colombia, Venezuela, and Ecuador. Phylogenetic analysis was used to infer the relationships and times since the divergence of the major clades. Phylogenetic analyses revealed 2 dominant clades that segregated by geographical region, had a putative common ancestor in 1975, and originated in 1989, in North America, and in 1985, in South America. Emergence of these parallel epidemics coincides with the independent acquisition of the arginine catabolic mobile element (ACME) in North American isolates and a novel copper and mercury resistance (COMER) mobile element in South American isolates. Our results reveal the existence of 2 parallel USA300 epidemics that shared a recent common ancestor. The simultaneous rapid dissemination of these 2 epidemic clades suggests the presence of shared, potentially convergent adaptations that enhance fitness and ability to spread. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Basic concept of common reactor physics code systems. Final report of working party on common reactor physics code systems (CCS)

International Nuclear Information System (INIS)

2004-03-01

A working party was organized for two years (2001-2002) on common reactor physics code systems under the Research Committee on Reactor Physics of JAERI. This final report is compilation of activity of the working party on common reactor physics code systems during two years. Objectives of the working party is to clarify basic concept of common reactor physics code systems to improve convenience of reactor physics code systems for reactor physics researchers in Japan on their various field of research and development activities. We have held four meetings during 2 years, investigated status of reactor physics code systems and innovative software technologies, and discussed basic concept of common reactor physics code systems. (author)

Cycles and Common Cycles in Property and Related Sectors

OpenAIRE

Peijie Wang

2003-01-01

This paper examines cycles and common cycles in the property market and the economy. While focusing on common cycles, the study also incorporates common trends in the meantime, so it covers the whole spectrum of dynamic analysis. It has been found that property shares common cycles, particularly with those sectors that are the user markets of property. The mechanisms of common cycles and the relative magnitudes of cycles of the sectors related to property are discussed to shed light on proper...

Common micronutrient deficiencies among food aid beneficiaries ...

African Journals Online (AJOL)

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Abstract. Background: Ethiopia is amongst the African countries that have received significant food aid. Nonetheless, the common micronutrient deficiencies among food aid beneficiaries are not well documented. Objective: To find out the common micronutrient deficiencies among food aid beneficiaries in the country based ...

common problems affecting supranational attempts in africa

African Journals Online (AJOL)

user

Politico-legal Framework for Integration in Africa: Exploring the Attainability of a ... laws, the common international trade policy, the common fisheries policy and the .... among the member states according to the annual imports, production and ...... Fredland R (eds) Integration and Disintegration in East Africa (University.

Common Influence Join

DEFF Research Database (Denmark)

Yiu, Man Lung; Mamoulis, Nikos; Karras, Panagiotis

2008-01-01

We identify and formalize a novel join operator for two spatial pointsets P and Q. The common influence join (CIJ) returns the pairs of points (p,q),p isin P,q isin Q, such that there exists a location in space, being closer to p than to any other point in P and at the same time closer to q than ......-demand, is very efficient in practice, incurring only slightly higher I/O cost than the theoretical lower bound cost for the problem....

Common anorectal disorders.

Science.gov (United States)

Foxx-Orenstein, Amy E; Umar, Sarah B; Crowell, Michael D

2014-05-01

Anorectal disorders result in many visits to healthcare specialists. These disorders include benign conditions such as hemorrhoids to more serious conditions such as malignancy; thus, it is important for the clinician to be familiar with these disorders as well as know how to conduct an appropriate history and physical examination. This article reviews the most common anorectal disorders, including hemorrhoids, anal fissures, fecal incontinence, proctalgia fugax, excessive perineal descent, and pruritus ani, and provides guidelines on comprehensive evaluation and management.

Management of common head and neck masses.

Science.gov (United States)

Tracy, Thomas F; Muratore, Christopher S

2007-02-01

Head and neck masses are a common clinical concern in infants, children, and adolescents. The differential diagnosis for a head or neck mass includes congenital, inflammatory, and neoplastic lesions. An orderly and thorough examination of the head and neck with an appropriate directed workup will facilitate the diagnosis. The most common entities occur repeatedly within the various age groups and can be differentiated with a clear understanding of embryology and anatomy of the region, and an understanding of the natural history of a specific lesion. Congenital lesions most commonly found in the pediatric population include the thyroglossal duct cyst and the branchial cleft and arch anomalies. The inflammatory masses are secondary to local or systemic infections. The most common etiology for cervical adenopathy in children is reactive lymphadenopathy following a viral or bacterial illness. Persistent adenopathy raises more concerns, especially enlarged lymph nodes within the posterior triangle or supraclavicular space, nodes that are painless, firm, and not mobile, or a single dominant node that persists for more than 6 weeks should all heighten concern for malignancy. In this review, we discuss the current principles of surgical management of the most common head and neck masses that present to pediatricians and pediatric surgeons.

Characterization of a Common-Gate Amplifier Using Ferroelectric Transistors

Science.gov (United States)

Hunt, Mitchell; Sayyah, Rana; MacLeod, Todd C.; Ho, Fat D.

2011-01-01

In this paper, the empirical data collected through experiments performed using a FeFET in the common-gate amplifier circuit is presented. The FeFET common-gate amplifier was characterized by varying all parameters in the circuit, such as load resistance, biasing of the transistor, and input voltages. Due to the polarization of the ferroelectric layer, the particular behavior of the FeFET common-gate amplifier presents interesting results. Furthermore, the differences between a FeFET common-gate amplifier and a MOSFET common-gate amplifier are examined.

Sustainability of common pool resources.

Science.gov (United States)

Timilsina, Raja Rajendra; Kotani, Koji; Kamijo, Yoshio

2017-01-01

Sustainability has become a key issue in managing natural resources together with growing concerns for capitalism, environmental and resource problems. We hypothesize that the ongoing modernization of competitive societies, which we refer to as "capitalism," affects human nature for utilizing common pool resources, thus compromising sustainability. To test this hypothesis, we design and implement a set of dynamic common pool resource games and experiments in the following two types of Nepalese areas: (i) rural (non-capitalistic) and (ii) urban (capitalistic) areas. We find that a proportion of prosocial individuals in urban areas is lower than that in rural areas, and urban residents deplete resources more quickly than rural residents. The composition of proself and prosocial individuals in a group and the degree of capitalism are crucial in that an increase in prosocial members in a group and the rural dummy positively affect resource sustainability by 65% and 63%, respectively. Overall, this paper shows that when societies move toward more capitalistic environments, the sustainability of common pool resources tends to decrease with the changes in individual preferences, social norms, customs and views to others through human interactions. This result implies that individuals may be losing their coordination abilities for social dilemmas of resource sustainability in capitalistic societies.

Importance analysis for the systems with common cause failures

International Nuclear Information System (INIS)

Pan Zhijie; Nonaka, Yasuo

1995-01-01

This paper extends the importance analysis technique to the research field of common cause failures to evaluate the structure importance, probability importance, and β-importance for the systems with common cause failures. These importance measures would help reliability analysts to limit the common cause failure analysis framework and find efficient defence strategies against common cause failures

Childhood Obesity & Dental Disease: Common Causes, Common Solutions. Oral Health & Obesity Policy Brief

Science.gov (United States)

Children Now, 2011

2011-01-01

Too many California children suffer from high rates of preventable chronic conditions associated with childhood obesity and dental disease. The state is experiencing a crisis in both areas. Fortunately, common factors that contribute to both conditions--including the rates of breastfeeding, access to healthy food and the consumption of…

Phenotyping common beans for adaptation to drought

Science.gov (United States)

Beebe, Stephen E.; Rao, Idupulapati M.; Blair, Matthew W.; Acosta-Gallegos, Jorge A.

2013-01-01

Common beans (Phaseolus vulgaris L.) originated in the New World and are the grain legume of greatest production for direct human consumption. Common bean production is subject to frequent droughts in highland Mexico, in the Pacific coast of Central America, in northeast Brazil, and in eastern and southern Africa from Ethiopia to South Africa. This article reviews efforts to improve common bean for drought tolerance, referring to genetic diversity for drought response, the physiology of drought tolerance mechanisms, and breeding strategies. Different races of common bean respond differently to drought, with race Durango of highland Mexico being a major source of genes. Sister species of P. vulgaris likewise have unique traits, especially P. acutifolius which is well adapted to dryland conditions. Diverse sources of tolerance may have different mechanisms of plant response, implying the need for different methods of phenotyping to recognize the relevant traits. Practical considerations of field management are discussed including: trial planning; water management; and field preparation. PMID:23507928

Common Systems Integration Lab (CSIL)

Data.gov (United States)

Federal Laboratory Consortium — The Common Systems Integration Lab (CSIL)supports the PMA-209 Air Combat Electronics Program Office. CSIL also supports development, test, integration and life cycle...

Common Technologies for Environmental Research Infrastructures in ENVRIplus

Science.gov (United States)

Paris, Jean-Daniel

2016-04-01

Environmental and geoscientific research infrastructures (RIs) are dedicated to distinct aspects of the ocean, atmosphere, ecosystems, or solid Earth research, yet there is significant commonality in the way they conceive, develop, operate and upgrade their observation systems and platforms. Many environmental Ris are distributed network of observatories (be it drifting buoys, geophysical observatories, ocean-bottom stations, atmospheric measurements sites) with needs for remote operations. Most RIs have to deal with calibration and standardization issues. RIs use a variety of measurements technologies, but this variety is based on a small, common set of physical principles. All RIs have set their own research and development priorities, and developed their solution to their problems - however many problems are common across RIs. Finally, RIs may overlap in terms of scientific perimeter. In ENVRIplus we aim, for the first time, to identify common opportunities for innovation, to support common research and development across RIs on promising issues, and more generally to create a forum to spread state of the art techniques among participants. ENVRIplus activities include 1) measurement technologies: where are the common types of measurement for which we can share expertise or common development? 2) Metrology : how do we tackle together the diversified challenge of quality assurance and standardization? 3) Remote operations: can we address collectively the need for autonomy, robustness and distributed data handling? And 4) joint operations for research: are we able to demonstrate that together, RIs are able to provide relevant information to support excellent research. In this process we need to nurture an ecosystem of key players. Can we involve all the key technologists of the European RIs for a greater mutual benefit? Can we pave the way to a growing common market for innovative European SMEs, with a common programmatic approach conducive to targeted R&D? Can we

A study of common-mode failures

International Nuclear Information System (INIS)

Edwards, G.T.; Watson, I.A.

1979-07-01

The purpose of the report is to investigate problems of the identification of the common failure mode (CFM) the reliability models used and the data required for their solution, particularly with regard to automatic protection systems for nuclear reactors. The available literature which was surveyed during the study is quoted and used as a basis for the main work of the study. The type of redundancy system under consideration is initially described and the types of CFM to which these systems are prone are identified before a general definition of the term 'common mode failure' is proposed. The definition and proposed classification system for CMF are based on the common cause of failure, so identifying the primary events. Defences against CFM are included and proposals for an overall strategy and detailed recommendations for design and operation are made. Common mode failures in US nuclear reactor systems, aircraft systems, and other sources including chemical plant systems are surveyed. The data indicates the importance of the human error problem in the causes of CMF in design, maintenance and operation. From a study of the collected data a redundancy sub-system model for CMF is developed which identifies three main categories of failure, non-recurrent engineering design errors, maintenance and test errors, and random interest events. The model proposed allows for the improvement in sub-system reliability where appropriate defences are applied. (author)

By-product mutualism with evolving common enemies

NARCIS (Netherlands)

De Jaegher, K.J.M.

2017-01-01

The common-enemy hypothesis of by-product mutualism states that organisms cooperate when it is in their individual interests to do so, with benefits for other organisms arising as a by-product; in particular, such cooperation is hypothesized to arise when organisms face the common enemy of a

Clinical chemistry of common apolipoprotein E isoforms

NARCIS (Netherlands)

Brouwer, DAJ; vanDoormaal, JJ; Muskiet, FAJ

1996-01-01

Apolipoprotein E plays a central role in clearance of lipoprotein remnants by serving as a ligand for low-density lipoprotein and apolipoprotein E receptors. Three common alleles (apolipoprotein E(2), E(3) and E(4)) give rise to six phenotypes. Apolipoprotein E(3) is the ancestral form. Common

Evolution of Streptococcus pneumoniae and its close commensal relatives

DEFF Research Database (Denmark)

Kilian, Mogens; Poulsen, Knud; Blomqvist, Trinelise

2008-01-01

Streptococcus pneumoniae is a member of the Mitis group of streptococci which, according to 16S rRNA-sequence based phylogenetic reconstruction, includes 12 species. While other species of this group are considered prototypes of commensal bacteria, S. pneumoniae is among the most frequent microbial...... of unique genes and their origin support the model that the entire cluster of S. pneumoniae, S. pseudopneumoniae, and S. mitis lineages evolved from pneumococcus-like bacteria presumably pathogenic to the common immediate ancestor of hominoids. During their adaptation to a commensal life style, most...

Chromosomal phylogeny of Lagothrix, Brachyteles, and Cacajao.

Science.gov (United States)

Viegas Péquignot, E; Koiffmann, C P; Dutrillaux, B

1985-01-01

Based on a comparison of the karyotypes of two Plathyrrhini species, Cacajao melanocephalus (Pitheciinae) and Brachyteles arachnoides (Atelinae), with those of two previously studied species, Lagothrix lagothrica (Atelinae) and C calvus rubicundus (Pitheciinae), it appears that the two Cacajao species have undergone the same number of chromosome rearrangements since they diverged from their common ancestor and that the karyotype of Brachyteles is ancestral to that of Lagothrix. The chromosomal phylogeny of these four species is proposed. A Y-autosome translocation is present in the karyotypes of the two Cacajao species.

New Insights about Enzyme Evolution from Large Scale Studies of Sequence and Structure Relationships*

Science.gov (United States)

Brown, Shoshana D.; Babbitt, Patricia C.

2014-01-01

Understanding how enzymes have evolved offers clues about their structure-function relationships and mechanisms. Here, we describe evolution of functionally diverse enzyme superfamilies, each representing a large set of sequences that evolved from a common ancestor and that retain conserved features of their structures and active sites. Using several examples, we describe the different structural strategies nature has used to evolve new reaction and substrate specificities in each unique superfamily. The results provide insight about enzyme evolution that is not easily obtained from studies of one or only a few enzymes. PMID:25210038

Authenticating Performances

DEFF Research Database (Denmark)

Rudolph, Michael

2015-01-01

by government bodies which have sought to demonstrate their nativist or multiculturalist orientations, aboriginal elites not only publicly worshipped ancestor gods and enacted animal sacrifices in so called ‘revitalized’ public rituals, but also used these occasions to point to the primordial power...... of aborigines vis-à-vis their former colonizers, the Han Chinese. In many cases, however, the ‘revitalized’ rituals described here conflicted with the interests of common people in aboriginal society, who wished public ritual to be compatible with their newly adopted Christian traditions. Taking a closer look...

The infinite sites model of genome evolution.

Science.gov (United States)

Ma, Jian; Ratan, Aakrosh; Raney, Brian J; Suh, Bernard B; Miller, Webb; Haussler, David

2008-09-23

We formalize the problem of recovering the evolutionary history of a set of genomes that are related to an unseen common ancestor genome by operations of speciation, deletion, insertion, duplication, and rearrangement of segments of bases. The problem is examined in the limit as the number of bases in each genome goes to infinity. In this limit, the chromosomes are represented by continuous circles or line segments. For such an infinite-sites model, we present a polynomial-time algorithm to find the most parsimonious evolutionary history of any set of related present-day genomes.

Talaromyces atroroseus

DEFF Research Database (Denmark)

Rasmussen, Kasper Bøwig

2015-01-01

Monascus pigments have been used for food colouring in Asia for centuries. However, industrially produced Monascus pigments are not approved for use in foods in neither Europe nor the United States. This is partly due to potential risk of co-production of the mycotoxin citrinin by the Monascus...... the Monascus pigment and the mitorubrin gene cluster in Talaromyces and Monascus give strong evidence that the two clusters originate from a deep segmental duplication of an ancestral azaphilone gene cluster in a common ancestor to Talaromyces, Monascus and Aspergillus lineages. The mitorubrin cluster has...

Learning commons evolution and collaborative essentials

CERN Document Server

Schader, Barbara

2008-01-01

This book examines successfully planned and implemented learning commons at several different academic institutions around the world. These case studies provide a methodology for effective planning, implementation and assessment. Practical information is provided on how to collaborate with campus stakeholders, estimate budgeting and staffing and determine the equipment, hardware and software needs. Also provided are memoranda of understandings (MOUs), planning checklists and assessment tools. This book reflects a unifying focus on both the evolution of learning commons to learning spaces and t

Ecology and the Tragedy of the Commons

Directory of Open Access Journals (Sweden)

Peter Roopnarine

2013-02-01

Full Text Available This paper develops mathematical models of the tragedy of the commons analogous to ecological models of resource consumption. Tragedies differ fundamentally from predator–prey relationships in nature because human consumers of a resource are rarely controlled solely by that resource. Tragedies do occur, however, at the level of the ecosystem, where multiple species interactions are involved. Human resource systems are converging rapidly toward ecosystem-type systems as the number of exploited resources increase, raising the probability of system-wide tragedies in the human world. Nevertheless, common interests exclusive of exploited commons provide feasible options for avoiding tragedy in a converged world.

Ten years of common-rail injection systems for passenger cars; Gemeine Drucksache. Zehn Jahre Common-Rail-Einspritzsystem fuer Pkw

Energy Technology Data Exchange (ETDEWEB)

Hohenthal, M.Y. von

2007-07-15

The future of the diesel engine started in 1997 with the Bosch common rail injection system which provided higher power, higher rotary momentum, lower consumption, lower noise and lower pollutant emissions. Since then, high-pressure common-rail injection systems have become state of the art. (orig.)

Common mode and coupled failure

International Nuclear Information System (INIS)

Taylor, J.R.

1975-10-01

Based on examples and data from Abnormal Occurence Reports for nuclear reactors, a classification of common mode or coupled failures is given, and some simple statistical models are investigated. (author)

Defense against common-mode failures in protection system design

International Nuclear Information System (INIS)

Wyman, R.H.; Johnson, G.L.

1998-01-01

The introduction of digital instrumentation and control into reactor safety systems creates a heightened concern about common-mode failure. This paper discusses the concern and methods of cope with the concern. Common-mode failures have been a 'fact-of-life' in existing systems. The informal introduction of defense-in-depth and diversity (D-in-D and D) - coupled with the fact that hardware common-mode failures are often distributed in time - has allowed systems to deal with past common-mode failures. However, identical software operating in identical redundant systems presents the potential for simultaneous failure. Consequently, the use of digital systems raises the concern about common-mode failure to a new level. A more methodical approach to mitigating common-mode failure is needed to address these concerns. Purposeful introduction of D-in-D and D has been used as a defense against common-mode failure in reactor protection systems. At least two diverse systems are provided to mitigate any potential initiating event. Additionally, diverse displays and controls are provided to allow the operator to monitor plant status and manually initiate engineered safety features. A special form of common-mode failure analysis called 'defense-in-depth and diversity analysis' has been developed to identify possible common-mode failure vulnerabilities in digital systems. An overview of this analysis technique is provided. (author)

Common carotid artery disease in Takayasu's arteritis

International Nuclear Information System (INIS)

Hamdan, Nabil; Calderon, Luis I; Castro, Pablo and others

2004-01-01

Takayasu's arteritis is a disease of unknown etiology with main involvement of the common carotid 5 artery and its branches. we report the case of a 69 years old female patient with Tokays arteritis with 2 bilateral involvements of the common carotid arteries, treated with percutaneous angioplasty and Stent implantation

Simulated population responses of common carp to commercial exploitation

Energy Technology Data Exchange (ETDEWEB)

Weber, Michael J.; Hennen, Matthew J.; Brown, Michael L.

2011-12-01

Common carp Cyprinus carpio is a widespread invasive species that can become highly abundant and impose deleterious ecosystem effects. Thus, aquatic resource managers are interested in controlling common carp populations. Control of invasive common carp populations is difficult, due in part to the inherent uncertainty of how populations respond to exploitation. To understand how common carp populations respond to exploitation, we evaluated common carp population dynamics (recruitment, growth, and mortality) in three natural lakes in eastern South Dakota. Common carp exhibited similar population dynamics across these three systems that were characterized by consistent recruitment (ages 3 to 15 years present), fast growth (K = 0.37 to 0.59), and low mortality (A = 1 to 7%). We then modeled the effects of commercial exploitation on size structure, abundance, and egg production to determine its utility as a management tool to control populations. All three populations responded similarly to exploitation simulations with a 575-mm length restriction, representing commercial gear selectivity. Simulated common carp size structure modestly declined (9 to 37%) in all simulations. Abundance of common carp declined dramatically (28 to 56%) at low levels of exploitation (0 to 20%) but exploitation >40% had little additive effect and populations were only reduced by 49 to 79% despite high exploitation (>90%). Maximum lifetime egg production was reduced from 77 to 89% at a moderate level of exploitation (40%), indicating the potential for recruitment overfishing. Exploitation further reduced common carp size structure, abundance, and egg production when simulations were not size selective. Our results provide insights to how common carp populations may respond to exploitation. Although commercial exploitation may be able to partially control populations, an integrated removal approach that removes all sizes of common carp has a greater chance of controlling population abundance

MDEP Design-Specific Common Position CP-APR1400WG-01. Common position addressing Fukushima Daiichi nuclear power plant accident

International Nuclear Information System (INIS)

2016-05-01

The MDEP APR1400 Working Group (APR1400WG) members consist of members from Republic of Korea, United Arab Emirates, and the United States. A main objectives of MDEP is to encourage convergence of code, standard and safety goals with exploring the opportunities for harmonization of regulatory practice and cooperation on safety review of APR-1400 specific designs. This common position addressing is aimed at sharing knowledge, information and experience on safety improvement related to lessons learned from the Fukushima Daiichi NPP Accident or Fukushima Daiichi NPP Accident-related issues amongst APR-1400 WG member states to achieve the MEDP goal. Because not all of these Regulators have completed the regulatory review of their APR1400 applications yet, this paper identifies common preliminary approaches to address potential safety improvements for APR1400 plants, as well as common general expectations for new nuclear power plants, as related to lessons learned from the Fukushima Daiichi NPP Accident or Fukushima Daiichi NPP Accident-related issues. While some asymmetry exists among those of three Regulators in terms of design, regulatory practice and licensing milestone sharing information and common understanding on post-Fukushima Daiichi NPP Accident enhancement would be promote resilient design for countering beyond design extreme external event like Fukushima Daiichi NPP nuclear disaster. This common position paper aims at identifying characteristics of post-Fukushima Daiichi NPP Accident enhancements putting in place by each country and setting common position to achieve balanced and harmonized APR-1400 design. After the safety reviews of the APR1400 design applications that are currently in review are completed, the regulators will update this paper to reflect their safety conclusions regarding the APR1400 design and how the design could be enhanced to address Fukushima Daiichi NPP Accident-related issues. The common preliminary approaches are organised into

On 'Common time' in the four-dimensional symmetry framework

International Nuclear Information System (INIS)

Gulati, Shobha

1980-01-01

Recently Hsu has advanced a 'Four-Dimensional Symmetry Theory' with a 'Common time' for all inertial frames. He believes that such a 'Common time' is physically possible. However, as a consequence of 'Common time', Hsu asserts that the speed of light in some inertial frames is not necessarily invariant and isotropic - a result, quite contrary to Einstein's Principle of the constancy of the velocity of light. In the present paper, taking Hsu's 'Common time' at its face value, the author has demonstrated that his formulation itself leads to physically absurd results. A 'Common time' for all inertial frames is just not possible. (author)

Phylogenomics and evolution of floral traits in the Neotropical tribe Malmeeae (Annonaceae)

NARCIS (Netherlands)

Lopes, J.C.; Chatrou, L.W.; Mello-Silva, de R.; Rudall, P.J.; Sajo, M.G.

2017-01-01

Androdioecy is the rarest sexual system among plants. The majority of androdioecious species are herbaceous plants that have evolved from dioecious ancestors. Nevertheless, some woody and androdioecious plants have hermaphrodite ancestors, as in the Annonaceae, where androdioecious genera have

Strategi Mengatasi Common Measures Bias dalam Balanced Scorecard

Directory of Open Access Journals (Sweden)

Sekar Akrom Faradiza

2016-06-01

Balanced Scorecard (BSC is a comprehensive performance measurement. BSC is not only used financial indicators but also non financial indicators there are customer, internal process business and learning and growth perspective. By using BSC, evaluators have common and unique measures. When evaluate manager performance, evaluator tends to only use common measures and ignore unique measures. This is called common measures bias. This study aims to investigate whether dissaggregated and aggregated BSC and management communication can overcome common measures bias and intent to BSC approach. This study also will evaluate whether these approach will affect evaluator decision when allocated compensation. We conduct 2x2x2 experiment of undergraduate accounting students. Participant act as a senior manager and evaluate the performance of two divisions and then allocated the bonus. ANOVA repeated measurement are used to conduct hypothesis test. The results showed that dissaggregated BSC and management communication could not overcome common measures bias but effected  management decision when allocated compensation.

Litigation-proof patents: avoiding the most common patent mistakes

National Research Council Canada - National Science Library

Goldstein, Larry M

2014-01-01

"Litigation-Proof Patents: Avoiding the Most Common Patent Mistakes explains the principles of excellent patents, presents the ten most common errors in patents, and details a step-by-step method for avoiding these common errors...

Dynamic Ising model: reconstruction of evolutionary trees

International Nuclear Information System (INIS)

De Oliveira, P M C

2013-01-01

An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. ‘Species’ here is a general denomination for biological species, spoken languages or any other entity which evolves through heredity. From the N currently alive species within a clade, distances are measured through pairwise comparisons made by geneticists, linguists, etc. The larger is such a distance that, for a pair of species, the older is their last common ancestor. The aim is to reconstruct the previously unknown bifurcations, i.e. the whole clade, from knowledge of the N(N − 1)/2 quoted distances, which are taken for granted. A mechanical method is presented and its applicability is discussed. (paper)

Strengthening the Ubuntu social canopy after the Afrophobic attacks

Directory of Open Access Journals (Sweden)

Zorodzai Dube

2016-03-01

Full Text Available In view of the aftermath of the Afrophobic attacks in South Africa, this study regards Paul�s emphasis concerning common humanity and morality as a possible lacuna towards strengthening Ubuntu. Paul taught that both the Jews and the Gentiles have their common ancestor � Adam, and that good morality is a better identity marker than ethnicity. In view of the aftermath of the Afrophobic attacks in South Africa, this study suggests that similar arguments can be used to amend the Ubuntu social canopy.Intradisciplinary and/or interdisciplinary implications: This study is interdisciplinary in nature in that it uses perspectives from social sciences to seek solutions towards a more inclusive communityKeywords: Afrophobia; Xenophobia; Ubuntu; Social Canopy; Christ-like Anthropology

Acquisition through common slave (servus communis)

OpenAIRE

Bogunović Mirjana B.

2016-01-01

Common slave (servus communis) is a slave who belongs to two masters. Both masters may entirely dispose with the slave because their joint ownership allows it. However, acquisitions through common slave (servus communis) is not that clear. Does a slave evenly oblige co-masters or only the master on whose behalf he has acted? Is it possible for a slave to work in the interest of one master and oblige another? Who does the unconscientious slave correspond to, the third party or a betrayed maste...

Common Ground Between Three Cultures

Directory of Open Access Journals (Sweden)

Gloria Dunnivan

2009-12-01

Full Text Available The Triwizard program with Israel brought together students from three different communities: an Israeli Arab school, an Israeli Jewish school, and an American public school with few Jews and even fewer Muslims. The two Israeli groups met in Israel to find common ground and overcome their differences through dialogue and understanding. They communicated with the American school via technology such as video-conferencing, Skype, and emails. The program culminated with a visit to the U.S. The goal of the program was to embark upon a process that would bring about intercultural awareness and acceptance at the subjective level, guiding all involved to develop empathy and an insider's view of the other's culture. It was an attempt to have a group of Israeli high school students and a group of Arab Israeli students who had a fearful, distrustful perception of each other find common ground and become friends. TriWizard was designed to have participants begin a dialogue about issues, beliefs, and emotions based on the premise that cross-cultural training strategies that are effective in changing knowledge are those that engage the emotions, and actively develop empathy and an insider's views of another culture focused on what they have in common. Participants learned that they could become friends despite their cultural differences.

Fish based diets cause archaeological dating problems

DEFF Research Database (Denmark)

Philippsen, Bente; Rørbæk, Rasmus

2013-01-01

Every time our ancestors cooked freshwater fish in ceramic vessels, they unwittingly set a Carbon-14 trap for future archaeologists......Every time our ancestors cooked freshwater fish in ceramic vessels, they unwittingly set a Carbon-14 trap for future archaeologists...

The Common Framework for Earth Observation Data

Science.gov (United States)

Gallo, J.; Stryker, T. S.; Sherman, R.

2016-12-01

Each year, the Federal government records petabytes of data about our home planet. That massive amount of data in turn provides enormous benefits to society through weather reports, agricultural forecasts, air and water quality warnings, and countless other applications. To maximize the ease of transforming the data into useful information for research and for public services, the U.S. Group on Earth Observations released the first Common Framework for Earth Observation Data in March 2016. The Common Framework recommends practices for Federal agencies to adopt in order to improve the ability of all users to discover, access, and use Federal Earth observations data. The U.S. Government is committed to making data from civil Earth observation assets freely available to all users. Building on the Administration's commitment to promoting open data, open science, and open government, the Common Framework goes beyond removing financial barriers to data access, and attempts to minimize the technical impediments that limit data utility. While Earth observation systems typically collect data for a specific purpose, these data are often also useful in applications unforeseen during development of the systems. Managing and preserving these data with a common approach makes it easier for a wide range of users to find, evaluate, understand, and utilize the data, which in turn leads to the development of a wide range of innovative applications. The Common Framework provides Federal agencies with a recommended set of standards and practices to follow in order to achieve this goal. Federal agencies can follow these best practices as they develop new observing systems or modernize their existing collections of data. This presentation will give a brief on the context and content of the Common Framework, along with future directions for implementation and keeping its recommendations up-to-date with developing technology.

Tragedy of the commons in Melipona bees

OpenAIRE

Wenseleers, Tom; Ratnieks, Francis L.W.

2004-01-01

In human society selfish use of common resources can lead to disaster, a situation known as the 'tragedy of the commons' (TOC). Although a TOC is usually prevented by coercion, theory predicts that close kinship ties can also favour reduced exploitation. We test this prediction using data on a TOC occurring in Melipona bee societies.

Might "Unique" Factors Be "Common"? On the Possibility of Indeterminate Common-Unique Covariances

Science.gov (United States)

Grayson, Dave

2006-01-01

The present paper shows that the usual factor analytic structured data dispersion matrix lambda psi lambda' + delta can readily arise from a set of scores y = lambda eta + epsilon, shere the "common" (eta) and "unique" (epsilon) factors have nonzero covariance: gamma = Cov epsilon,eta) is not equal to 0. Implications of this finding are discussed…

NIH Common Data Elements Repository

Data.gov (United States)

U.S. Department of Health & Human Services — The NIH Common Data Elements (CDE) Repository has been designed to provide access to structured human and machine-readable definitions of data elements that have...

Genetic divergence of common bean cultivars.

Science.gov (United States)

Veloso, J S; Silva, W; Pinheiro, L R; Dos Santos, J B; Fonseca, N S; Euzebio, M P

2015-09-22

The aim of this study was to evaluate genetic divergence in the 'Carioca' (beige with brown stripes) common bean cultivar used by different institutions and in 16 other common bean cultivars used in the Rede Cooperativa de Pesquisa de Feijão (Cooperative Network of Common Bean Research), by using simple sequence repeats associated with agronomic traits that are highly distributed in the common bean genome. We evaluated 22 polymorphic loci using bulks containing DNA from 30 plants. There was genetic divergence among the Carioca cultivar provided by the institutions. Nevertheless, there was lower divergence among them than among the other cultivars. The cultivar used by Instituto Agronômico do Paraná was the most divergent in relation to the Carioca samples. The least divergence was observed among the samples used by Universidade Federal de Lavras and by Embrapa Arroz e Feijão. Of all the cultivars, 'CNFP 10104' and 'BRSMG Realce' showed the greatest dissimilarity. The cultivars were separated in two groups of greatest similarity using the Structure software. Genetic variation among cultivars was greater than the variation within or between the groups formed. This fact, together with the high estimate of heterozygosity observed and the genetic divergence of the samples of the Carioca cultivar in relation to the original provided by Instituto Agronômico de Campinas, indicates a mixture of cultivars. The high divergence among cultivars provides potential for the utilization of this genetic variability in plant breeding.

The most common types of injuries in judo

OpenAIRE

Ječmínek, Jan

2014-01-01

Title: The most common types of injuries in judo Objectives: The aim of this study was to determine the most common injuries that occur during training and judo competitions. Identify treatment options, prevention and identify most common causes of injury. Methods: The chosen method was theoretical and empirical, ie collecting data and information from other publications and conduct its own research. Selecting what is relevant for judo injuries and comparsion whith author's experience and res...

Genealogy and gene trees.

Science.gov (United States)

Rasmuson, Marianne

2008-02-01

Heredity can be followed in persons or in genes. Persons can be identified only a few generations back, but simplified models indicate that universal ancestors to all now living persons have occurred in the past. Genetic variability can be characterized as variants of DNA sequences. Data are available only from living persons, but from the pattern of variation gene trees can be inferred by means of coalescence models. The merging of lines backwards in time leads to a MRCA (most recent common ancestor). The time and place of living for this inferred person can give insights in human evolutionary history. Demographic processes are incorporated in the model, but since culture and customs are known to influence demography the models used ought to be tested against available genealogy. The Icelandic data base offers a possibility to do so and points to some discrepancies. Mitochondrial DNA and Y chromosome patterns give a rather consistent view of human evolutionary history during the latest 100 000 years but the earlier epochs of human evolution demand gene trees with longer branches. The results of such studies reveal as yet unsolved problems about the sources of our genome.

Molecular phylogeography of canine distemper virus: Geographic origin and global spreading.

Science.gov (United States)

Panzera, Yanina; Sarute, Nicolás; Iraola, Gregorio; Hernández, Martín; Pérez, Ruben

2015-11-01

Canine distemper virus (CDV) (Paramyxoviridae-Morbillivirus) is a worldwide spread virus causing a fatal systemic disease in a broad range of carnivore hosts. In this study we performed Bayesian inferences using 208 full-length hemagglutinin gene nucleotide sequences isolated in 16 countries during 37 years (1975-2011). The estimated time to the most recent common ancestor suggested that current CDV strains emerged in the United States in the 1880s. This ancestor diversified through time into two ancestral clades, the current America 1 lineage that recently spread to Asia, and other ancestral clade that diversified and spread worldwide to originate the remaining eight lineages characterized to date. The spreading of CDV was characterized by several migratory events with posterior local differentiation, and expansion of the virus host range. A significant genetic flow between domestic and wildlife hosts is displayed; being domestic hosts the main viral reservoirs worldwide. This study is an extensive and integrative description of spatio/temporal population dynamics of CDV lineages that provides a novel evolutionary paradigm about the origin and dissemination of the current strains of the virus. Copyright © 2015 Elsevier Inc. All rights reserved.

Expression of Fox genes in the cephalochordate Branchiostoma lanceolatum

Directory of Open Access Journals (Sweden)

Daniel eAldea

2015-07-01

Full Text Available Forkhead box (Fox genes code for transcription factors that play important roles in different biological processes. They are found in a wide variety of organisms and appeared in unicellular eukaryotes. In metazoans, the gene family includes many members that can be subdivided into 24 classes. Cephalochordates are key organisms to understand the functional evolution of gene families in the chordate lineage due to their phylogenetic position as an early divergent chordate, their simple anatomy and genome structure. In the genome of the cephalochordate amphioxus Branchiostoma floridae, 32 Fox genes were identified, with at least one member for each of the classes that were present in the ancestor of bilaterians. In this work we describe the expression pattern of 13 of these genes during the embryonic development of the Mediterranean amphioxus, Branchiostoma lanceolatum. We found that FoxK and FoxM genes present an ubiquitous expression while all the others show specific expression patterns restricted to diverse embryonic territories. Many of these expression patterns are conserved with vertebrates, suggesting that the main functions of Fox genes in chordates were present in their common ancestor.

Tragedy of the commons in Melipona bees.

Science.gov (United States)

Wenseleers, Tom; Ratnieks, Francis L W

2004-01-01

In human society selfish use of common resources can lead to disaster, a situation known as the 'tragedy of the commons' (TOC). Although a TOC is usually prevented by coercion, theory predicts that close kinship ties can also favour reduced exploitation. We test this prediction using data on a TOC occurring in Melipona bee societies. PMID:15504003

Young Children's Understanding of Cultural Common Ground

Science.gov (United States)

Liebal, Kristin; Carpenter, Malinda; Tomasello, Michael

2013-01-01

Human social interaction depends on individuals identifying the common ground they have with others, based both on personally shared experiences and on cultural common ground that all members of the group share. We introduced 3- and 5-year-old children to a culturally well-known object and a novel object. An experimenter then entered and asked,…

Finding common ground in implementation: towards a theory of gradual commonality.

Science.gov (United States)

Ter Haar, Marian; Aarts, Noelle; Verhoeven, Piet

2016-03-01

This article reports on an empirical study that aimed to design a practice-based theory about collaboration on the local implementation of a nationally developed health-promoting intervention. The study's objective is to better understand the dynamic process of complex collaboration. The research is based on a Delphi study among some 100 individuals in local and regional networks, in which various professionals work together to implement the BeweegKuur, which translates as 'course of exercise'. The BeweegKuur is a combined lifestyle intervention aimed at promoting sufficient physical exercise and a healthy diet among people in the Netherlands who are overweight and at risk of diabetes. The Delphi study in three rounds systematically and interactively constructs a common perspective on implementation, reflecting stakeholders' ideas about the collaboration and providing an insight into how these ideas are influenced by the context of the implementation. The statistical and qualitative analyses of the responses to the feedback in the Delphi study form the basis for this practice-based theory on complex collaboration, called the theory of gradual commonality. During interaction, consensus gradually emerges about co-creation as a collaboration strategy. Co-creation leaves room for various ways of achieving the ambitions of the BeweegKuur. This article discusses the importance of this practice-based theory and the value of the Delphi research strategy for promoting health. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Common Readout System in ALICE

CERN Document Server

Jubin, Mitra

2016-01-01

The ALICE experiment at the CERN Large Hadron Collider is going for a major physics upgrade in 2018. This upgrade is necessary for getting high statistics and high precision measurement for probing into rare physics channels needed to understand the dynamics of the condensed phase of QCD. The high interaction rate and the large event size in the upgraded detectors will result in an experimental data flow traffic of about 1 TB/s from the detectors to the on-line computing system. A dedicated Common Readout Unit (CRU) is proposed for data concentration, multiplexing, and trigger distribution. CRU, as common interface unit, handles timing, data and control signals between on-detector systems and online-offline computing system. An overview of the CRU architecture is presented in this manuscript.

Common Readout System in ALICE

CERN Document Server

Jubin, Mitra

2017-01-01

The ALICE experiment at the CERN Large Hadron Collider is going for a major physics upgrade in 2018. This upgrade is necessary for getting high statistics and high precision measurement for probing into rare physics channels needed to understand the dynamics of the condensed phase of QCD. The high interaction rate and the large event size in the upgraded detectors will result in an experimental data flow traffic of about 1 TB/s from the detectors to the on-line computing system. A dedicated Common Readout Unit (CRU) is proposed for data concentration, multiplexing, and trigger distribution. CRU, as common interface unit, handles timing, data and control signals between on-detector systems and online-offline computing system. An overview of the CRU architecture is presented in this manuscript.

Autism spectrum disorders and drug addiction: Common pathways, common molecules, distinct disorders?

Directory of Open Access Journals (Sweden)

Patrick E. Rothwell

2016-02-01

Full Text Available Autism spectrum disorders (ASDs and drug addiction do not share substantial comorbidity or obvious similarities in etiology or symptomatology. It is thus surprising that a number of recent studies implicate overlapping neural circuits and molecular signaling pathways in both disorders. The purpose of this review is to highlight this emerging intersection and consider implications for understanding the pathophysiology of these seemingly distinct disorders. One area of overlap involves neural circuits and neuromodulatory systems in the striatum and basal ganglia, which play an established role in addiction and reward but are increasingly implicated in clinical and preclinical studies of ASDs. A second area of overlap relates to molecules like Fragile X mental retardation protein (FMRP and methyl CpG-binding protein-2 (MECP2, which are best known for their contribution to the pathogenesis of syndromic ASDs, but have recently been shown to regulate behavioral and neurobiological responses to addictive drug exposure. These shared pathways and molecules point to common dimensions of behavioral dysfunction, including the repetition of behavioral patterns and aberrant reward processing. The synthesis of knowledge gained through parallel investigations of ASDs and addiction may inspire the design of new therapeutic interventions to correct common elements of striatal dysfunction.

Autism Spectrum Disorders and Drug Addiction: Common Pathways, Common Molecules, Distinct Disorders?

Science.gov (United States)

Rothwell, Patrick E

2016-01-01

Autism spectrum disorders (ASDs) and drug addiction do not share substantial comorbidity or obvious similarities in etiology or symptomatology. It is thus surprising that a number of recent studies implicate overlapping neural circuits and molecular signaling pathways in both disorders. The purpose of this review is to highlight this emerging intersection and consider implications for understanding the pathophysiology of these seemingly distinct disorders. One area of overlap involves neural circuits and neuromodulatory systems in the striatum and basal ganglia, which play an established role in addiction and reward but are increasingly implicated in clinical and preclinical studies of ASDs. A second area of overlap relates to molecules like Fragile X mental retardation protein (FMRP) and methyl CpG-binding protein-2 (MECP2), which are best known for their contribution to the pathogenesis of syndromic ASDs, but have recently been shown to regulate behavioral and neurobiological responses to addictive drug exposure. These shared pathways and molecules point to common dimensions of behavioral dysfunction, including the repetition of behavioral patterns and aberrant reward processing. The synthesis of knowledge gained through parallel investigations of ASDs and addiction may inspire the design of new therapeutic interventions to correct common elements of striatal dysfunction.

Sleep-related problems in common medical conditions.

Science.gov (United States)

Parish, James M

2009-02-01

Common medical problems are often associated with abnormalities of sleep. Patients with chronic medical disorders often have fewer hours of sleep and less restorative sleep compared to healthy individuals, and this poor sleep may worsen the subjective symptoms of the disorder. Individuals with lung disease often have disturbed sleep related to oxygen desaturations, coughing, or dyspnea. Both obstructive lung disease and restrictive lung diseases are associated with poor quality sleep. Awakenings from sleep are common in untreated or undertreated asthma, and cause sleep disruption. Gastroesophageal reflux is a major cause of disrupted sleep due to awakenings from heartburn, dyspepsia, acid brash, coughing, or choking. Patients with chronic renal disease commonly have sleep complaints often due to insomnia, insufficient sleep, sleep apnea, or restless legs syndrome. Complaints related to sleep are very common in patients with fibromyalgia and other causes of chronic pain. Sleep disruption increases the sensation of pain and decreases quality of life. Patients with infectious diseases, including acute viral illnesses, HIV-related disease, and Lyme disease, may have significant problems with insomnia and hypersomnolence. Women with menopause have from insomnia, sleep-disordered breathing, restless legs syndrome, or fibromyalgia. Patients with cancer or receiving cancer therapy are often bothered by insomnia or other sleep disturbances that affect quality of life and daytime energy. The objective of this article is to review frequently encountered medical conditions and examine their impact on sleep, and to review frequent sleep-related problems associated with these common medical conditions.

Communication, timing, and common learning

Czech Academy of Sciences Publication Activity Database

Steiner, Jakub; Stewart, C.

2011-01-01

Roč. 146, č. 1 (2011), s. 230-247 ISSN 0022-0531 Institutional research plan: CEZ:AV0Z70850503 Keywords : common knowledge * learning * communication Subject RIV: AH - Economics Impact factor: 1.235, year: 2011

Common diagnoses and treatments in professional voice users.

Science.gov (United States)

Franco, Ramon A; Andrus, Jennifer G

2007-10-01

Common problems among all patients seen by the laryngologist are also common among professional voice users. These include laryngopharyngeal reflux, muscle tension dysphonia, fibrovascular vocal fold lesions (eg, nodules and polyps), cysts, vocal fold scarring, changes in vocal fold mobility, and age-related changes. Microvascular lesions and their associated sequelae of vocal fold hemorrhage and laryngitis due to voice overuse are more common among professional voice users. Much more common among professional voice users is the negative impact that voice problems have on their ability to work, on their overall sense of well-being, and sometimes on their very sense of self. This article reviews the diagnosis and treatment options for these and other problems among professional voice users, describing the relevant roles of medical treatment, voice therapy, and surgery. The common scenario of multiple concomitant entities contributing to a symptom complex is underscored. Emphasis is placed on gaining insight into the "whole" patient so that individualized management plans can be developed. Videos of select diagnoses accompany this content online.

Evolution of king crabs from hermit crab ancestors

Science.gov (United States)

Cunningham, C. W.; Blackstone, N. W.; Buss, L. W.

1992-02-01

KING crabs (Family Lithodidae) are among the world's largest arthropods, having a crab-like morphology and a strongly calcified exoskeleton1-6. The hermit crabs, by contrast, have depended on gastropod shells for protection for over 150 million years5,7. Shell-living has constrained the morphological evolution of hermit crabs by requiring a decalcified asymmetrical abdomen capable of coiling into gastropod shells and by preventing crabs from growing past the size of the largest available shells1-6. Whereas reduction in shell-living and acquisition of a crab-like morphology (carcinization) has taken place independently in several hermit crab lineages, and most dramatically in king crabs1-6, the rate at which this process has occurred was entirely unknown2,7. We present molecular evidence that king crabs are not only descended from hermit crabs, but are nested within the hermit crab genus Pagurus. We estimate that loss of the shell-living habit and the complete carcinization of king crabs has taken between 13 and 25 million years.

6 Common Cancers - Colorectal Cancer

Science.gov (United States)

... Home Current Issue Past Issues 6 Common Cancers - Colorectal Cancer Past Issues / Spring 2007 Table of Contents For ... of colon cancer. Photo: AP Photo/Ron Edmonds Colorectal Cancer Cancer of the colon (large intestine) or rectum ( ...

6 Common Cancers - Breast Cancer

Science.gov (United States)

... Home Current Issue Past Issues 6 Common Cancers - Breast Cancer Past Issues / Spring 2007 Table of Contents For ... slow her down. Photo: AP Photo/Brett Flashnick Breast Cancer Breast cancer is a malignant (cancerous) growth that ...

Common carotid artery thrombosis; Clinical and radiological evaluation

Energy Technology Data Exchange (ETDEWEB)

Ito, Yasuhiro; Yasuda, Takeshi; Hakusui, Shigetaka; Yanagi, Tsutomu (Nagoya Daini Red Cross Hospital (Japan)); Ito, Eiichi

1994-02-01

Common carotid artery thrombosis (CCAT) is not common. We studied 4 patients with CCAT to clarify the clinical and radiological features of this disorder. Case 1 had only episodes of TIA. Case 2 was diagnosed by chance as having CCAT at the time of admission due to cerebellar infarction. On the contrary, Cases 3 and 4 were admitted because of disturbance of consciousness and hemiparesis. Case 4 died soon after his stroke because of complications. We evaluated cases 1, 2 and 3 using head CT, head MRI, neck MRI, MR angiography, SPECT and cerebral angiography. Case 4, who was evaluated with head CT and cerebral angiography, was autopsied to confirm the occlusion of the common carotid artery. The clinical severity of CCAT varies from asymptomatic to severe, because each case differs in the time taken for complete occlusion of the common carotid artery; the development of collateral circulation; and hemodynamics of the brain. As for the collaterals their contribution is variable; for example, the thyrocervical and other arteries function as the bypass. We can diagnose CCAT easily and noninvasively using MR angiography and neck MRI based on disappearance of the flow void in the common carotid artery or internal carotid artery. On physical examination, it is important to detect faded pulsation of the superficial temporal artery that is ipsilateral to the occluded common carotid artery. (author).

Data needs for common cause failure analysis

International Nuclear Information System (INIS)

Parry, G.W.; Paula, H.M.; Rasmuson, D.; Whitehead, D.

1990-01-01

The procedures guide for common cause failure analysis published jointly by USNRC and EPRI requires a detailed historical event analysis. Recent work on the further development of the cause-defense picture of common cause failures introduced in that guide identified the information that is necessary to perform the detailed analysis in an objective manner. This paper summarizes these information needs

The agricultural policy of Serbia and common agricultural policy

Directory of Open Access Journals (Sweden)

Stanković Milica

2012-01-01

Full Text Available The agricultural sector has a relatively high importance in the economic structure of Serbia. The Common Agricultural Policy (CAP, Common Agricultural Policy is one of the main policies of the European Union. It is very important to point out the fundamental principles and objectives of the Common Agricultural Policy. Harmonization of the national agricultural policy of Serbia with the Common Agricultural Policy and acceptance of its mechanisms is crucial for the development of the agricultural sector as a whole.

Typicality of Incest in Common-law Marriages

Directory of Open Access Journals (Sweden)

Yor Alexander Casas Villamizar

2015-04-01

Full Text Available This article shows the way Law 54 of 1990 defined common-law marriage in Colombia. Legally, common-law marriage is a way to constitute a family through natural ties. This family is expressed in the Superior Statute, which establishes this union as the essential core of the society, acquiring integral quality within the social state of law and forcing the State and the society to protect it as a legal right by means of the Criminal Law. Incest –understood as carnal knowledge or other sexual act with a predecessor, descendant, adoptive parent, or sibling– destabilizes and imperils the family institution. Common-law marriages composed by incestuous relatives are a punishable behavior and not a marital estate.

6 Common Cancers - Lung Cancer

Science.gov (United States)

... Bar Home Current Issue Past Issues 6 Common Cancers - Lung Cancer Past Issues / Spring 2007 Table of Contents ... Desperate Housewives. (Photo ©2005 Kathy Hutchins / Hutchins) Lung Cancer Lung cancer causes more deaths than the next three ...

True and common balsams

Directory of Open Access Journals (Sweden)

Dayana L. Custódio

2012-08-01

Full Text Available Balsams have been used since ancient times, due to their therapeutic and healing properties; in the perfume industry, they are used as fixatives, and in the cosmetics industry and in cookery, they are used as preservatives and aromatizers. They are generally defined as vegetable material with highly aromatic properties that supposedly have the ability to heal diseases, not only of the body, but also of the soul. When viewed according to this concept, many substances can be considered balsams. A more modern concept is based on its chemical composition and origin: a secretion or exudate of plants that contain cinnamic and benzoic acids, and their derivatives, in their composition. The most common naturally-occurring balsams (i.e. true balsams are the Benzoins, Liquid Storaque and the Balsams of Tolu and Peru. Many other aromatic exudates, such as Copaiba Oil and Canada Balsam, are wrongly called balsam. These usually belong to other classes of natural products, such as essential oils, resins and oleoresins. Despite the understanding of some plants, many plants are still called balsams. This article presents a chemical and pharmacological review of the most common balsams.

From Common Struggles to Common Dreams: Neoliberalism and Multicultural Education in a Globalized Environment

Science.gov (United States)

Lee, Pei-Lun

2012-01-01

Major troubling contours of neoliberalism and high-stakes education have common features. Consequently, the author discusses how multicultural education can serve as praxis for collective empowerment in a globalized context. The author asserts that equitable representation and localized multicultural knowledge production are the foundation of a…

Building the common

DEFF Research Database (Denmark)

Agustin, Oscar Garcia

document, A Common Immigration Policy for Europe: Principles, actions and tools (2008) as a part of Hague Programme (2004) on actions against terrorism, organised crime and migration and asylum management and influenced by the renewed Lisbon Strategy (2005-2010) for growth and jobs. My aim is to explore...... policy in the European Union is constructed and the categories and themes that are discussed. I will look also at the discourse strategies to show the linguistic representations of the social actors, who are excluded from or include in such representations. I will analysis a European Commission’s policy...

Common Errors in Ecological Data Sharing

Directory of Open Access Journals (Sweden)

Robert B. Cook

2013-04-01

Full Text Available Objectives: (1 to identify common errors in data organization and metadata completeness that would preclude a “reader” from being able to interpret and re-use the data for a new purpose; and (2 to develop a set of best practices derived from these common errors that would guide researchers in creating more usable data products that could be readily shared, interpreted, and used.Methods: We used directed qualitative content analysis to assess and categorize data and metadata errors identified by peer reviewers of data papers published in the Ecological Society of America’s (ESA Ecological Archives. Descriptive statistics provided the relative frequency of the errors identified during the peer review process.Results: There were seven overarching error categories: Collection & Organization, Assure, Description, Preserve, Discover, Integrate, and Analyze/Visualize. These categories represent errors researchers regularly make at each stage of the Data Life Cycle. Collection & Organization and Description errors were some of the most common errors, both of which occurred in over 90% of the papers.Conclusions: Publishing data for sharing and reuse is error prone, and each stage of the Data Life Cycle presents opportunities for mistakes. The most common errors occurred when the researcher did not provide adequate metadata to enable others to interpret and potentially re-use the data. Fortunately, there are ways to minimize these mistakes through carefully recording all details about study context, data collection, QA/ QC, and analytical procedures from the beginning of a research project and then including this descriptive information in the metadata.

Common High Blood Pressure Myths

Science.gov (United States)

... Disease Venous Thromboembolism Aortic Aneurysm More Common High Blood Pressure Myths Updated:May 4,2018 Knowing the facts ... This content was last reviewed October 2016. High Blood Pressure • Home • Get the Facts About HBP Introduction What ...

Multiple groups of endogenous epsilon-like retroviruses conserved across primates.

Science.gov (United States)

Brown, Katherine; Emes, Richard D; Tarlinton, Rachael E

2014-11-01

Several types of cancer in fish are caused by retroviruses, including those responsible for major outbreaks of disease, such as walleye dermal sarcoma virus and salmon swim bladder sarcoma virus. These viruses form a phylogenetic group often described as the epsilonretrovirus genus. Epsilon-like retroviruses have become endogenous retroviruses (ERVs) on several occasions, integrating into germ line cells to become part of the host genome, and sections of fish and amphibian genomes are derived from epsilon-like retroviruses. However, epsilon-like ERVs have been identified in very few mammals. We have developed a pipeline to screen full genomes for ERVs, and using this pipeline, we have located over 800 endogenous epsilon-like ERV fragments in primate genomes. Genomes from 32 species of mammals and birds were screened, and epsilon-like ERV fragments were found in all primate and tree shrew genomes but no others. These viruses appear to have entered the genome of a common ancestor of Old and New World monkeys between 42 million and 65 million years ago. Based on these results, there is an ancient evolutionary relationship between epsilon-like retroviruses and primates. Clearly, these viruses had the potential to infect the ancestors of primates and were at some point a common pathogen in these hosts. Therefore, this result raises questions about the potential of epsilonretroviruses to infect humans and other primates and about the evolutionary history of these retroviruses. Epsilonretroviruses are a group of retroviruses that cause several important diseases in fish. Retroviruses have the ability to become a permanent part of the DNA of their host by entering the germ line as endogenous retroviruses (ERVs), where they lose their infectivity over time but can be recognized as retroviruses for millions of years. Very few mammals are known to have epsilon-like ERVs; however, we have identified over 800 fragments of endogenous epsilon-like ERVs in the genomes of all major

Tuning chaos in network sharing common nonlinearity

Science.gov (United States)

Paul Asir, M.; Jeevarekha, A.; Philominathan, P.

2016-06-01

In this paper, a novel type of network called network sharing common nonlinearity comprising both autonomous and non-autonomous oscillators have been investigated. We propose that these networks are robust for operating at desired modes i.e., chaotic or periodic by altering the v-i characteristics of common nonlinear element alone. The dynamics of these networks were examined through numerical, analytical, experimental and Multisim simulations.

The E180splice mutation in the GHR gene causing Laron syndrome: witness of a Sephardic Jewish exodus from the Iberian Peninsula to the New World?

Science.gov (United States)

Gonçalves, Fernanda T; Fridman, Cintia; Pinto, Emília M; Guevara-Aguirre, Jaime; Shevah, Orit; Rosembloom, Arlan L; Hwa, Vivian; Cassorla, Fernando; Rosenfeld, Ron G; Lins, Theresa S S; Damiani, Durval; Arnhold, Ivo J P; Laron, Zvi; Jorge, Alexander A L

2014-05-01

Laron syndrome (LS) is a genetic disorder caused by mutations in the growth hormone receptor (GHR) gene. The most frequent GHR mutation is E180splice (rs121909360), which was initially found in an inbred population of Spanish descent in Ecuador and subsequently in Israel, Brazil, Chile, and the United States. The aim of the present study is to determine if the E180splice mutation arose from a common origin. We studied 22 patients with LS from Ecuador, Israel (of Moroccan origin), Brazil, Chile, and the United States (of Mexican origin) who were homozygous for the E180splice mutation and compared them to control individuals for markers surrounding the GHR, intragenic polymorphisms, and Y-chromosome STR. An identical haplotype was found in all but one of the subjects carrying the E180splice mutation: D5S665: 150/150; D5S2082: 192/192; D5S2087: 246/246; rs6179 G/G; and rs6180 C/C. One patient differed from the others only at D5S2082 (168/192). This haplotype is rare (~1%) in control individuals and confirmed that the E180splice-associated haplotype was not derived from independent origins but represented recombination from a common ancestor. The analysis of paternal lineage markers showed that 50% belong to haplogroup R1b (found in Portugal and Spain) and 40% to haplogroups J and E (typical in the Middle East and in Eastern European Jews). The germline E180Splice mutation appears to have originated from a single common ancestor. The presence of Y-chromosome markers associated with Sephardic populations in persons harboring the E180splice mutation provides genetic evidence in support of the historical tracking of the exodus of this specific population. © 2014 Wiley Periodicals, Inc.

Reconstructing the muscular ground pattern of phylactolaemate bryozoans: first data from gelatinous representatives.

Science.gov (United States)

Gawin, Natalie; Wanninger, Andreas; Schwaha, Thomas

2017-11-07

Phylactolaemata is commonly regarded the earliest branch within Bryozoa and thus the sister group to the other bryozoan taxa, Cyclostomata and Gymnolaemata. Therefore, the taxon is important for the reconstruction of the bryozoan morphological ground pattern. In this study the myoanatomy of Pectinatella magnifica, Cristatella mucedo and Hyalinella punctata was analysed by means of histology, f-actin staining and confocal laser-scanning microscopy in order to fill gaps in knowledge concerning the myoanatomy of Phylactolaemata. The retractor muscles and muscles of the aperture, gut, body wall, tentacle sheath, lophophore constitute the most prominent muscular subsets in these species. The lophophore shows longitudinal muscle bands in the tentacles, lophophoral arm muscles, epistome musculature and hitherto undescribed muscles of the ring canal. In general the muscular system of the three species is very similar with differences mainly in the body wall, tentacle sheath and epistome. The body wall contains an orthogonal grid of musculature. The epistome exhibits either a muscular meshwork in the epistomal wall or muscle fibers traversing the epistomal cavity. The whole tentacle sheath possesses a regular mesh of muscles in Pectinatella and Cristatella, whereas circular muscles are limited to the tentacle sheath base in Hyalinella. This study is the first to describe muscles of the ring canal and contributes to reconstructing muscular features for the last common ancestor of all bryozoans. The data available suggest that two longitudinal muscle bands in the tentacles, as well as retractor muscles and longitudinal and circular muscles in the tentacle sheath, were present in the last common bryozoan ancestor. Comparisons among bryozoans shows that several apomorphies are present in the myoanatomy of each class- level taxon such as the epistomal musculature and musculature of the lophophoral arms in phylactolaemates, annular muscles in cyclostomes and parietal muscles in

Prolonged Adaptive Evolution of a Defensive Gene in the Solanaceae.

Science.gov (United States)

Rausher, Mark D; Huang, Jie

2016-01-01

Although plants and their natural enemies may coevolve for prolonged periods, little is known about how long individual plant defensive genes are involved in the coevolutionary process. We address this issue by examining patterns of selection on the defensive gene threonine deaminase (TD). Tomato (Solanum lycopersicum) has two copies of this gene. One performs the canonical housekeeping function in amino acid metabolism of catalyzing the first reaction in the conversion of threonine to isoleucine. The second copy functions as an antinutritive defense against lepidopteran herbivores by depleting threonine in the insect gut. Wild tobacco (Nicotiana attenuata) also contains a defensive copy. We show that a single copy of TD underwent two or three duplications near the base of the Solanaceae. One copy retains the housekeeping function, whereas a second copy evolved defensive functions. Positive selection occurred on the branch of the TD2 gene tree subtending the common ancestor of the Nicotianoideae and Solanoideae. It also occurred within the Solanoideae clade but not within the Nicotianoideae clade. Finally, it occurred on most branches leading from the common ancestor to S. lycopersicum. Based on recent calibrations of the Solanaceae phylogeny, TD2 experienced adaptive substitutions for a period of 30-50 My. We suggest that the most likely explanation for this result is fluctuating herbivore abundances: When herbivores are rare, relaxed selection increases the likelihood that slightly disadvantageous mutations will be fixed by drift; when herbivores are common, increased selection causes the evolution of compensatory adaptive mutations. Alternative explanations are also discussed. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Successful Endovascular Treatment of a Left Common Carotid Artery Aneurysm Following Failed Surgery of a Right Common Carotid Artery Aneurysm

International Nuclear Information System (INIS)

Cil, Barbaros E.; Ucar, Ibrahim; Ozsoy, Fatma; Arat, Anil; Yorgancioglu, Cem; Boeke, Erkmen

2005-01-01

Aneurysm of the common carotid artery is a rare and serious disease requiring prompt treatment in order to avoid neurologic complications. A 39-year-old man presented with voice impairment and a pulsatile mass at the right side of his neck and was found by color Doppler examination to have bilateral common carotid artery aneurysms of unknown origin. The right-sided large aneurysm was treated with placement of an 8 mm interposition Gore-Tex graft between the right common and internal carotid arteries. The surgical graft thrombosed 7 days after the surgery but the left-sided aneurysm was successfully treated by a Jostent peripheral stent-graft. Color Doppler examination showed a patent stent and no filling of the aneurysm on his first and sixth-month follow-up. Bilateral common carotid artery aneurysm is an exceptionally unusual condition and endovascular treatment of carotid artery aneurysms with covered stents may become an effective treatment alternative for these lesions

Radiation-induced bilateral common carotid artery stenosis

International Nuclear Information System (INIS)

Kobayashi, Nobuaki; Nakagawa, Yoku; Tashiro, Kunio; Abe, Hiroshi

1986-01-01

A case of radiation-induced bilateral common carotid artery stenosis is reported. This 60 years old housewife was hospitalized in 1982 because of sudden onset of mild left hemiparesis. Twenty-five years ago, she underwent radiation therapy of approximately 5,000 rads to the anterior cervical region because of thyroid cancer. Angiograms in 1982 revealed bilateral common carotid artery stenosis, especially in the right common carotid artery, the legion of which were included within the field of radiation performed in 1952. Right thromboendarterectomy was performed in 1983. At operation, slight periarterial fibrosis with calcified arteriosclerotic change was found, and dissection between the thickened intima and the media was not so difficult. Histological change of resected thromboendarterium was similar to the one observed in the pure arteriosclerotic disease. (author)

Topical vitamin A treatment of recalcitrant common warts

Directory of Open Access Journals (Sweden)

Gaston Anca

2012-01-01

Full Text Available Abstract Background Common warts (verruca vulgaris are benign epithelial proliferations associated with human papillomavirus (HPV infection. Salicylic acid and cryotherapy are the most frequent treatments for common warts, but can be painful and cause scarring, and have high failure and recrudescence rates. Topical vitamin A has been shown to be a successful treatment of common warts in prior informal studies. Case The subject is a healthy, physically-active 30 old female with a 9 year history of common warts on the back of the right hand. The warts resisted treatment with salicylic acid, apple cider vinegar and an over-the-counter blend of essential oils marketed for the treatment of warts. Daily topical application of natural vitamin A derived from fish liver oil (25,000 IU led to replacement of all the warts with normal skin. Most of the smaller warts had been replaced by 70 days. A large wart on the middle knuckle required 6 months of vitamin A treatment to resolve completely. Conclusion Retinoids should be further investigated in controlled studies to determine their effectiveness in treating common warts and the broad range of other benign and cancerous lesions induced by HPVs.

49 CFR 1150.22 - Exemptions and common carrier status.

Science.gov (United States)

2010-10-01

... the line itself, it will be considered a common carrier. However, when a State acquires a rail line... 49 Transportation 8 2010-10-01 2010-10-01 false Exemptions and common carrier status. 1150.22... common carrier status. The acquisition by a State of a fully abandoned line is not subject to the...

20 CFR 404.726 - Evidence of common-law marriage.

Science.gov (United States)

2010-04-01

... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Evidence of common-law marriage. 404.726... DISABILITY INSURANCE (1950- ) Evidence Evidence of Age, Marriage, and Death § 404.726 Evidence of common-law marriage. (a) General. A common-law marriage is one considered valid under certain State laws even though...

Simultaneously Discovering and Localizing Common Objects in Wild Images.

Science.gov (United States)

Wang, Zhenzhen; Yuan, Junsong

2018-09-01

Motivated by the recent success of supervised and weakly supervised common object discovery, in this paper, we move forward one step further to tackle common object discovery in a fully unsupervised way. Generally, object co-localization aims at simultaneously localizing objects of the same class across a group of images. Traditional object localization/detection usually trains specific object detectors which require bounding box annotations of object instances, or at least image-level labels to indicate the presence/absence of objects in an image. Given a collection of images without any annotations, our proposed fully unsupervised method is to simultaneously discover images that contain common objects and also localize common objects in corresponding images. Without requiring to know the total number of common objects, we formulate this unsupervised object discovery as a sub-graph mining problem from a weighted graph of object proposals, where nodes correspond to object proposals, and edges represent the similarities between neighbouring proposals. The positive images and common objects are jointly discovered by finding sub-graphs of strongly connected nodes, with each sub-graph capturing one object pattern. The optimization problem can be efficiently solved by our proposed maximal-flow-based algorithm. Instead of assuming that each image contains only one common object, our proposed solution can better address wild images where each image may contain multiple common objects or even no common object. Moreover, our proposed method can be easily tailored to the task of image retrieval in which the nodes correspond to the similarity between query and reference images. Extensive experiments on PASCAL VOC 2007 and Object Discovery data sets demonstrate that even without any supervision, our approach can discover/localize common objects of various classes in the presence of scale, view point, appearance variation, and partial occlusions. We also conduct broad

Common rail technology for future low emission diesel vehicles; Common Rail Technologie fuer zukuenftige Diesel Fahrzeuge mit niedrigen Emissionswerten

Energy Technology Data Exchange (ETDEWEB)

Schoeppe, D.; Bercher, P.; Guerrassi, N.; Spadafora, P.

2004-07-01

The diesel fuel injection equipment will remain a key element for diesel engine technology evolution. Achieving emission targets at competitive prices has been and will continue to be a major technical challenge to the engine manufacturer. Delphi is continuously developing its common rail system and its components to fulfill future stricter emission legislation while simultaneously improving performance on noise, fuel consumption and power output. This paper will describe the latest developments that delphi introduced into the market in their common rail system to comply with future legislative emission targets. Further, a novel common rail injector will be presented, that uses a revolutionary, direct acting operating principle, where the nozzle is directly operated by a piezo actuator, without the use of a servo-hydraulic flow circuit. The superior performance of this injector concept will be shown, especially in minimum quantity capability as well as multiple injection performance. The direct acting operating principle allows rapid opening and closing of the injector, without compromising pilot quantity capability. The emission benefit obtained by such opening and closing behavior will be shown. Finally, based on the findings discussed, the paper will conclude on key features of future common rail systems. (orig.)

Common dental and periodontal diseases: evaluation and management.

Science.gov (United States)

Laudenbach, Joel M; Simon, Ziv

2014-11-01

Physicians may encounter patients with dental and periodontal diseases in the context of outpatient medical practice. It is important for physicians to be aware of common dental and periodontal conditions and be able to assess for the presence and severity of these diseases. This article reviews common dental and periodontal conditions, their cardinal signs and symptoms, outpatient-setting assessment techniques, as well as common methods of treatment. Physicians detecting gross abnormalities on clinical examination should refer the patient to a dentist for further evaluation and management. Copyright © 2014 Elsevier Inc. All rights reserved.

Common sunflower (Helianthus annuus) interference in soybean (Glycine max)

International Nuclear Information System (INIS)

Geier, P.W.; Maddux, L.D.; Moshier, L.J.; Stahlman, P.W.

1996-01-01

Multiple weed species in the field combine to cause yield losses and can be described using one of several empirical models. Field studies were conducted to compare observed corn yield loss caused by common sunflower and shattercane populations with predicted yield losses modeled using a multiple species rectangular hyperbola model, an additive model, or the yield loss model in the decision support system, WeedSOFT, and to derive competitive indices for common sunflower and shattercane. Common sunflower and shattercane emerged with corn and selected densities established in field experiments at Scandia and Rossville, KS, between 2000 and 2002. The multiple species rectangular hyperbola model fit pooled data from three of five location–years with a predicted maximum corn yield loss of 60%. Initial slope parameter estimate for common sunflower was 49.2 and 4.2% for shattercane. A ratio of these estimates indicated that common sunflower was 11 times more competitive than shattercane. When common sunflower was assigned a competitive index (CI) value of 10, shattercane CI was 0.9. Predicted yield losses modeled for separate common sunflower or shattercane populations were additive when compared with observed yield losses caused by low-density mixed populations of common sunflower (0 to 0.5 plants m −2 ) and shattercane (0 to 4 plants m −2 ). However, a ratio of estimates of these models indicated that common sunflower was only four times as competitive as shattercane, with a CI of 2.5 for shattercane. The yield loss model in WeedSOFT underpredicted the same corn losses by 7.5%. Clearly, both the CI for shattercane and the yield loss model in WeedSOFT need to be reevaluated, and the multiple species rectangular hyperbola model is proposed. (author)

Secondary Syphilis: Uncommon Manifestations a Common Disease

OpenAIRE

McPhee, Stephen J.

1984-01-01

Reports of cases of primary and secondary syphilis are increasing in the United States, particularly in urban areas and among homosexual men. While primary syphilis poses little diagnostic difficulty, many physicians are unfamiliar with the multisystem nature of secondary lues. Patients who have secondary syphilis commonly present with systemic signs, skin rash, mucous membrane lesions and generalized adenopathy. Less commonly, secondary syphilis may occur as acute meningitis, sensorineural h...

Common Superficial Bursitis.

Science.gov (United States)

Khodaee, Morteza

2017-02-15

Superficial bursitis most often occurs in the olecranon and prepatellar bursae. Less common locations are the superficial infrapatellar and subcutaneous (superficial) calcaneal bursae. Chronic microtrauma (e.g., kneeling on the prepatellar bursa) is the most common cause of superficial bursitis. Other causes include acute trauma/hemorrhage, inflammatory disorders such as gout or rheumatoid arthritis, and infection (septic bursitis). Diagnosis is usually based on clinical presentation, with a particular focus on signs of septic bursitis. Ultrasonography can help distinguish bursitis from cellulitis. Blood testing (white blood cell count, inflammatory markers) and magnetic resonance imaging can help distinguish infectious from noninfectious causes. If infection is suspected, bursal aspiration should be performed and fluid examined using Gram stain, crystal analysis, glucose measurement, blood cell count, and culture. Management depends on the type of bursitis. Acute traumatic/hemorrhagic bursitis is treated conservatively with ice, elevation, rest, and analgesics; aspiration may shorten the duration of symptoms. Chronic microtraumatic bursitis should be treated conservatively, and the underlying cause addressed. Bursal aspiration of microtraumatic bursitis is generally not recommended because of the risk of iatrogenic septic bursitis. Although intrabursal corticosteroid injections are sometimes used to treat microtraumatic bursitis, high-quality evidence demonstrating any benefit is unavailable. Chronic inflammatory bursitis (e.g., gout, rheumatoid arthritis) is treated by addressing the underlying condition, and intrabursal corticosteroid injections are often used. For septic bursitis, antibiotics effective against Staphylococcus aureus are generally the initial treatment, with surgery reserved for bursitis not responsive to antibiotics or for recurrent cases. Outpatient antibiotics may be considered in those who are not acutely ill; patients who are acutely ill

MDEP Generic Common Position No DICWG-03. Common position on verification and validation throughout the life cycle of digital safety systems

International Nuclear Information System (INIS)

2013-01-01

Verification and validation (V and V) is essential throughout the life cycle of nuclear power plant safety systems. This common position applies to V and V activities for digital safety systems throughout their life cycles. This encompasses both the software and hardware of such systems. The Digital Instrumentation and Controls Working Group (DICWG) has agreed that a common position on this topic is warranted given the use of Digital I and C in new reactor designs, its safety implications, and the need to develop a common understanding from the perspectives of regulatory authorities. This action follows the DICWG examination of the regulatory requirements of the participating members and of relevant industry standards and IAEA documents. The DICWG proposes a common position based on its recent experience with the new reactor application reviews and operating plant issues

Acquisition through common slave (servus communis

Directory of Open Access Journals (Sweden)

Bogunović Mirjana B.

2016-01-01

Full Text Available Common slave (servus communis is a slave who belongs to two masters. Both masters may entirely dispose with the slave because their joint ownership allows it. However, acquisitions through common slave (servus communis is not that clear. Does a slave evenly oblige co-masters or only the master on whose behalf he has acted? Is it possible for a slave to work in the interest of one master and oblige another? Who does the unconscientious slave correspond to, the third party or a betrayed master? This paper will analyze the opinions of two Roman iurists, which will partly solve doubts that this institute causes.

Common anorectal disorders: diagnosis and treatment.

Science.gov (United States)

Lacy, Brian E; Weiser, Kirsten

2009-10-01

Anorectal disorders affect men and women of all ages. Their management is not limited to the evaluation and treatment of hemorrhoids. Rather, a spectrum of anorectal disorders ranges from benign and irritating (pruritus ani) to potentially life-threatening (anorectal cancer). Symptoms are nonspecific, which can make the evaluation of patients difficult. In addition, treatment can be frustrating because clinicians are hamstrung by a lack of well-designed, prospective, clinical trials. Some of the most common anorectal disorders include fecal incontinence, pelvic floor dyssynergia, anal fissures, pruritus ani, proctalgia fugax, and solitary rectal ulcer syndrome. This article provides an update on the evaluation and treatment of common anorectal disorders.

Design principles for global commons: Natural resources and emerging technologies

Directory of Open Access Journals (Sweden)

Paul C. Stern

2011-09-01

Full Text Available Ostrom’s design principles for managing common pool resources were developed largely by examining local commons involving natural resources. This paper enumerates several key characteristics that distinguish such commons from more complex commons involving global resources and the risks of emerging technologies. It considers the degree to which the design principles transfer to those commons and concludes that although they have considerable external validity, the list needs some modification and elaboration to apply to global resources and risk commons. A list of design principles is offered for global resource commons and the risks of emerging technologies. Applying Ostrom’s approach to global resources and emerging technologies can improve understanding and expand the solution set for these problems from international treaties, top-down national regulation, and interventions in market pricing systems to include non-governmental institutions that embody principles of self-governance.

Common mental disorders and intimate partner violence in pregnancy

Directory of Open Access Journals (Sweden)

Ana Bernarda Ludermir

2014-02-01

Full Text Available OBJECTIVE : To investigate the association between common mental disorders and intimate partner violence during pregnancy. METHODS : A cross sectional study was carried out with 1,120 pregnant women aged 18-49 years old, who were registered in the Family Health Program in the city of Recife, Northeastern Brazil, between 2005 and 2006. Common mental disorders were assessed using the Self-Reporting Questionnaire (SRQ-20. Intimate partner violence was defined as psychologically, physically and sexually abusive acts committed against women by their partners. Crude and adjusted odds ratios were estimated for the association studied utilizing logistic regression analysis. RESULTS : The most common form of partner violence was psychological. The prevalence of common mental disorders was 71.0% among women who reported all form of violence in pregnancy and 33.8% among those who did not report intimate partner violence. Common mental disorders were associated with psychological violence (OR 2.49, 95%CI 1.8;3.5, even without physical or sexual violence. When psychological violence was combined with physical or sexual violence, the risk of common mental disorders was even higher (OR 3.45; 95%CI 2.3;5.2. CONCLUSIONS : Being assaulted by someone with whom you are emotionally involved can trigger feelings of helplessness, low self-esteem and depression. The pregnancy probably increased women`s vulnerability to common mental disorders

Defense against common-mode failures in protection system design

International Nuclear Information System (INIS)

Wyman, R.H.; Johnson, G.L.

1997-01-01

The introduction of digital instrumentation and control into reactor safety systems creates a heightened concern about common-mode failure. This paper discusses the concern and methods to cope with the concern. Common-mode failures have been a ''fact-of-life'' in existing systems. The informal introduction of defense-in-depth and diversity (D-in-D ampersand D)-coupled with the fact that hardware common-mode failures are often distributed in time-has allowed systems to deal with past common-mode failures. However, identical software operating in identical redundant systems presents the potential for simultaneous failure. Consequently, the use of digital systems raises the concern about common-mode failure to a new level. A more methodical approach to mitigating common-mode failure is needed to address these concerns. Purposeful introduction of D-in-D ampersand D has been used as a defense against common-mode failure in reactor protection systems. At least two diverse systems are provided to mitigate any potential initiating event. Additionally, diverse displays and controls are provided to allow the operator to monitor plant status and manually initiate engineered safety features. A special form of conimon-mode failure analysis called ''defense-in-depth and diversity analysis'' has been developed to identify possible conimon-mode failure vulnerabilities in digital systems. An overview of this analysis technique is provided

The Evolution of the Scavenger Receptor Cysteine-Rich Domain of the Class A Scavenger Receptors

Directory of Open Access Journals (Sweden)

Nicholas eYap

2015-07-01

Full Text Available The class A Scavenger Receptor (cA-SR family is a group of five evolutionarily related innate immune receptors. The cA-SRs are known for their promiscuous ligand binding; as they have been shown to bind bacteria such as Streptococcus pneumoniae, and Escherichia coli, as well as different modified forms of low-density lipoprotein. Three of the five family members possess a Scavenger Receptor Cysteine Rich (SRCR domain while the remaining two receptors lack the domain. Previous work has suggested that the Macrophage Associated Receptor with COllagenous structure (MARCO shares a recent common ancestor with the non-SRCR-containing receptors; however the origin of the SRCR domain within the cA-SRs remains unknown. We hypothesize that the SRCR domains of the cA-SRs have a common origin that predates teleost fish. Using the newly available sequence data from sea lamprey and ghost shark genome projects, we have shown that MARCO shares a common ancestor with the SRCR-containing proteins. In addition, we explored the evolutionary relationships within the SRCR domain by reconstructing the ancestral SRCR domains of the cA-SRs. We identified a motif that is highly conserved between the cA-SR SRCR domains and the ancestral SRCR domain that consist of WGTVCDD. We also show that the GRAEVYY motif, a functionally important motif within MARCO, is poorly conserved in the other cA-SRs and in the reconstructed ancestral domain. Further, we identified three sites within MARCO’s SRCR domain which are under positive selection. Two of these sites lie adjacent to the conserved WGTVCDD motif, and may indicate a potential biological function for these sites. Together these findings indicate a common origin of the SRCR domain within the cA-SRs; however different selective pressures between the proteins may have caused MARCOs SRCR domain to evolve to contain different functional motifs when compared to the other SRCR-containing cA-SRs.

Genome-Wide Association Study Identifies NBS-LRR-Encoding Genes Related with Anthracnose and Common Bacterial Blight in the Common Bean.

Science.gov (United States)

Wu, Jing; Zhu, Jifeng; Wang, Lanfen; Wang, Shumin

2017-01-01

Nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes represent the largest and most important disease resistance genes in plants. The genome sequence of the common bean ( Phaseolus vulgaris L.) provides valuable data for determining the genomic organization of NBS-LRR genes. However, data on the NBS-LRR genes in the common bean are limited. In total, 178 NBS-LRR-type genes and 145 partial genes (with or without a NBS) located on 11 common bean chromosomes were identified from genome sequences database. Furthermore, 30 NBS-LRR genes were classified into Toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) types, and 148 NBS-LRR genes were classified into coiled-coil (CC)-NBS-LRR (CNL) types. Moreover, the phylogenetic tree supported the division of these PvNBS genes into two obvious groups, TNL types and CNL types. We also built expression profiles of NBS genes in response to anthracnose and common bacterial blight using qRT-PCR. Finally, we detected nine disease resistance loci for anthracnose (ANT) and seven for common bacterial blight (CBB) using the developed NBS-SSR markers. Among these loci, NSSR24, NSSR73, and NSSR265 may be located at new regions for ANT resistance, while NSSR65 and NSSR260 may be located at new regions for CBB resistance. Furthermore, we validated NSSR24, NSSR65, NSSR73, NSSR260, and NSSR265 using a new natural population. Our results provide useful information regarding the function of the NBS-LRR proteins and will accelerate the functional genomics and evolutionary studies of NBS-LRR genes in food legumes. NBS-SSR markers represent a wide-reaching resource for molecular breeding in the common bean and other food legumes. Collectively, our results should be of broad interest to bean scientists and breeders.

Are common names becoming less common? The rise in uniqueness and individualism in Japan.

Science.gov (United States)

Ogihara, Yuji; Fujita, Hiroyo; Tominaga, Hitoshi; Ishigaki, Sho; Kashimoto, Takuya; Takahashi, Ayano; Toyohara, Kyoko; Uchida, Yukiko

2015-01-01

We examined whether Japanese culture has become more individualistic by investigating how the practice of naming babies has changed over time. Cultural psychology has revealed substantial cultural variation in human psychology and behavior, emphasizing the mutual construction of socio-cultural environment and mind. However, much of the past research did not account for the fact that culture is changing. Indeed, archival data on behavior (e.g., divorce rates) suggest a rise in individualism in the U.S. and Japan. In addition to archival data, cultural products (which express an individual's psyche and behavior outside the head; e.g., advertising) can also reveal cultural change. However, little research has investigated the changes in individualism in East Asia using cultural products. To reveal the dynamic aspects of culture, it is important to present temporal data across cultures. In this study, we examined baby names as a cultural product. If Japanese culture has become more individualistic, parents would be expected to give their children unique names. Using two databases, we calculated the rate of popular baby names between 2004 and 2013. Both databases released the rankings of popular names and their rates within the sample. As Japanese names are generally comprised of both written Chinese characters and their pronunciations, we analyzed these two separately. We found that the rate of popular Chinese characters increased, whereas the rate of popular pronunciations decreased. However, only the rate of popular pronunciations was associated with a previously validated collectivism index. Moreover, we examined the pronunciation variation of common combinations of Chinese characters and the written form variation of common pronunciations. We found that the variation of written forms decreased, whereas the variation of pronunciations increased over time. Taken together, these results showed that parents are giving their children unique names by pairing common