Accelerated evolution and Muller's rachet in endosymbiotic bacteria.

Many bacteria live only within animal cells and infect hosts through cytoplasmic inheritance. These endosymbiotic lineages show distinctive population structure, with small population size and effectively no recombination. As a result, endosymbionts are expected to accumulate mildly deleterious mutations. If these constitute a substantial proportion of new mutations, endosymbionts will show (i) faster sequence evolution and (ii) a possible shift in base composition reflecting mutational bias. Analyses of 16S rDNA of five independently derived endosymbiont clades show, in every case, faster evolution in endosymbionts than in free-living relatives. For aphid endosymbionts (genus Buchnera), coding genes exhibit accelerated evolution and unusually low ratios of synonymous to nonsynonymous substitutions compared to ratios for the same genes for enterics. This concentration of the rate increase in nonsynonymous substitutions is expected under the hypothesis of increased fixation of deleterious mutations. Polypeptides for all Buchnera genes analyzed have accumulated amino acids with codon families rich in A+T, supporting the hypothesis that substitutions are deleterious in terms of polypeptide function. These observations are best explained as the result of Muller's ratchet within small asexual populations, combined with mutational bias. In light of this explanation, two observations reported earlier for Buchnera, the apparent loss of a repair gene and the overproduction of a chaperonin, may reflect compensatory evolution. An alternative hypothesis, involving selection on genomic base composition, is contradicted by the observation that the speedup is concentrated at nonsynonymous sites.

Accelerated evolution in the protein-coding regions is universal in crotalinae snake venom gland phospholipase A2 isozyme genes.

The nucleotide sequences of four genes encoding Trimeresurus gramineus (green habu snake, crotalinae) venom gland phospholipase A2 (PLA2; phosphatidylcholine 2-acylhydrolase, EC 3.1.1.4) isozymes were compared internally and externally with those of six genes encoding Trimeresurus flavoviridis (habu snake, crotalinae) venom gland PLA2 isozymes. The numbers of nucleotide substitutions per site (KN) for the noncoding regions including introns were one-third to one-eighth of the numbers of nucleotide substitutions per synonymous site (KS) for the protein-coding regions of exons, indicating that the noncoding regions are much more conserved than the protein-coding regions. The KN values for the introns were found to be nearly equivalent to those of introns of T. gramineus and T. flavoviridis TATA box-binding protein genes, which are assumed to be a general (nonvenomous) gene. Thus, it is evident that the introns of venom gland PLA2 isozyme genes have evolved at a similar rate to those of nonvenomous genes. The numbers of nucleotide substitutions per nonsynonymous site (KA) were close to or larger than the KS values for the protein-coding regions in venom gland PLA2 isozyme genes. All of the data combined reveal that Darwinian-type accelerated evolution has universally occurred only in the protein-coding regions of crotalinae snake venom PLA2 isozyme genes.

Análise exômica em pacientes portadores de cardiomiopatia hipertrófica

A cardiomiopatia hipertrófica (CMH) é uma doença geneticamente determinada, caracterizada por hipertrofia ventricular primária, com prevalência estimada de 0.2% na população geral. Qualquer portador tem 50% de chance de transmitir esta doença para seus filhos, o que torna cada vez mais relevante a importância do estudo genético dos indivíduos acometidos e de seus familiares. Já foram descritas diversas mutações genéticas causadoras de CMH, a maioria em genes que codificam proteínas do sarcômero, e algumas mutações mais raras em genes não sarcoméricos. O objetivo desse estudo é sequenciar as regiões exônicas de genes candidatos, incluindo os principais envolvidos na hipertrofia miocárdica, utilizando o sequenciamento de nova geração (Generation Sequencing); testar a aplicabilidade e viabilidade deste sistema para identificar mutações já confirmadas e propor as prováveis novas mutações causadoras de CMH. Métodos e resultados: 66 pacientes não aparentados portadores de CMH foram estudados e submetidos à coleta de sangue para obtenção do DNA para analisar as regiões exômicas de 82 genes candidatos, utilizando a plataforma MiSeq (Illumina). Identificou-se 99 mutações provavelmente patogênicas em 54 pacientes incluídos no estudo (81,8%) relacionadas ou não a CMH, e distribuídas em 42 genes diferentes. Destas mutações 27 já haviam sido publicadas, sendo que 17 delas descritas como causadoras de CMH. Em 28 pacientes (42,4%) identificou-se mutação nos três principais genes sarcoméricos relacionados à CMH (MYH7, MYBPC3, TNNT2). Encontrou-se também um grande número de variantes não sonôminas de efeito clínico incerto e algumas mutações relacionadas a outras enfermidades. Conclusão: a análise da sequencia dos exônos de genes candidatos, demonstrou ser uma técnica promissora para o diagnóstico genético de CMH de forma mais rápida e sensível. A quantidade de dados gerados é o um fator limitante até o momento, principalmente em doenças geneticamente complexas com envolvimento de diversos genes e com sistema de bioinformática limitado.

Restrictive and Expansive Views of Equality: A Grounded Theory Study that Explores the Influence of Racial Consciousness on the Behaviors of White Faculty in the Classroom

Attempts to address the ever increasing achievement gap among students have failed to explain how and why educational traditions and teaching practices perpetuate the devaluing of some and the overvaluing of others. This predicament, which plagues our educational system, has been of increased concern, given the growing racial diversity among college students and the saturation of White faculty in the academy. White faculty make up the majority, 79%, of all faculty in the academy. White faculty, whether consciously or unconsciously, are less likely to interrogate how race and racism both privilege them within the academy and influence their faculty behaviors. The result of this cyclical, highly cemented process suggests that there is a relationship between racial consciousness and White faculty members' ability to employ behaviors in their classroom that promote equitable educational outcomes for racially minoritized students. An investigation of the literature revealed that racial consciousness and the behaviors of White faculty in the classroom appeared to be inextricably linked. A conceptual framework, Racial Consciousness and Its Influence on the Behaviors of White Faculty in the Classroom was developed by the author and tested in this study. Constructivist grounded theory was used to explore the role White faculty believe they play in the dismantling of the white supremacy embedded in their classrooms through their faculty behaviors. A substantive theory subsequently emerged. Findings indicate that White faculty with a higher level of racial consciousness employ behaviors in their classroom reflective of a more expansive view of equality in their pursuit of social justice, which they consider synonymous with excellence in teaching. This research bears great significance to higher education research and practice, as it is the first of its kind to utilize critical legal scholar Kimberlé Crenshaw's (1988) restrictive and expansive views of equality framework to empirically measure and describe excellence in college teaching. Implications for faculty preparation and continued education are also discussed.

Disipation Functions of Flow Equations in Models of Complex Systems

In an open system, each disequilibrium causes a force. Each force causes a flow process, these being represented by a flow variable formally written as an equation called flow equation, and if each flow tends to equilibrate the system, these equations mathematically represent the tendency to that equilibrium. In this paper, the authors, based on the concepts of forces and conjugated fluxes and dissipation function developed by Onsager and Prigogine, they expose the following hypothesis: Is replaced in Prigogine’s Theorem the flow by its equation or by a flow orbital considering conjugate force as a gradient. This allows to obtain a dissipation function for each flow equation and a function of orbital dissipation.

Fado - diferentes sonoridades, uma tradição

No presente artigo, apresenta-se um registo sobre o atual universo do Fado, reflexo da sua adaptação à contemporaneidade e, como tal, enquadrando multiplicidade e fusão de géneros musicais. Tal como qualquer outro género musical, o Fado foi tocado pelo tempo, marcado por diferentes conjunturas sociais, culturais e estéticas, mantendo, contudo, uma forte ligação à sua genuinidade (o fado tradicional), no imaginário coletivo de públicos e intérpretes. Reflete-se, a partir da diversidade estética que o Fado nos oferece, sobre o seu percurso evolutivo num passado próximo. De igual modo se reflete sobre a grande diversidade deste universo muito próprio e destaca-se a capacidade de partilhar os mesmos tempos, os mesmos espaços e os mesmos públicos, sinónimo de vitalidade, dinâmica e atualidade.

Turkey's economy: a story of success with an uncertain future. OSW Commentary No. 120, 2013-11-05

In the decade since the Justice and Development Party (AKP) came to power, Turkey’s economy has become synonymous with success and well-implemented reforms. Economic development has been the basis of both socio-political stability inside the country and of an ambitious foreign policy agenda pursued by the AKP. However, the risks associated with a series of unresolved issues are becoming increasingly apparent. These include the country’s current account deficit, its over-reliance on short-term external financing, and unfinished reforms, for example of the education sector. This leaves Turkey exposed to over-dependence on investors, especially from the West. Consequently, Ankara has become a hostage of its own image as an economically successful state with a stable socio-political system. Any changes to this image would cause capital flight, as exemplified by the outflow of portfolio investment1 and an increase in the cost of external debt2 that followed the nationwide protests over the proposed closure of Gezi Park last summer. In addition, Turkey remains vulnerable to potential changes in investor sentiment towards emerging markets.

Service Science

Service Science is an emerging interdisciplinary field to systematically improve the design and innovation of service. Although many of the concepts used in service science have been around for some decades, this term is usually associated with an initiative called Service Science, Management, and Engineering (SSME), led by IBM in the first half of the 2000s to advance service research and education (in this entry, Service Science and SSME are considered synonymous, but the shorter term will be used here). Service Science is receiving growing attention due to the rising importance of service industries in world economies. The relevance of this topic is also justified because it helps organizations improve service performance, including service quality. This entry describes the key drivers, analyzes the evolution, examines the theoretical underpinnings, and defines Service Science. It concludes with a brief discussion of the challenges facing Service Science.

Genetic variability of the equine casein genes.

The casein genes are known to be highly variable in typical dairy species, such as cattle and goat, but the knowledge about equine casein genes is limited. Nevertheless, mare milk production and consumption is gaining importance because of its high nutritive value, use in naturopathy, and hypoallergenic properties with respect to cow milk protein allergies. In the current study, the open reading frames of the 4 casein genes CSN1S1 (αS1-casein), CSN2 (β-casein), CSN1S2 (αS2-casein), and CSN3 (κ-casein) were resequenced in 253 horses of 14 breeds. The analysis revealed 21 nonsynonymous nucleotide exchanges, as well as 11 synonymous nucleotide exchanges, leading to a total of 31 putative protein isoforms predicted at the DNA level, 26 of which considered novel. Although the majority of the alleles need to be confirmed at the transcript and protein level, a preliminary nomenclature was established for the equine casein alleles.

Pentecôte et langues de feu : analyse structurelle et interprétation d’Actes des Apôtres 2,3

Le récit de la Pentecôte (Actes des Apôtres 2) présente au lecteur un élément particulier qui se retrouve rarement dans le canon biblique : les « langues comme de feu ». Seuls les passages d’Isaïe 5,24 et Actes 2,3 utilisent cette expression; pourtant, leurs contextes diffèrent largement. Nous trouvons certains commentaires rabbiniques et fragments de rouleaux de la Mer Morte qui emploient cette même expression, et la littérature gréco-romaine utilise une image similaire où un feu divin se pose sur la tête de certains personnages. Puisque la fonction de cet élément diffère d’un ouvrage littéraire à un autre, comment devons-nous interpréter les langues de feu dans le récit de la Pentecôte? Les commentaires bibliques qui examinent cet élément proposent différentes hypothèses sur la symbolique des langues de feu. Afin de répondre à cette problématique, nous commencerons notre étude avec une présentation sur l’état de la question et des approches synchroniques utilisées. Nous présenterons ensuite l’analyse structurelle du récit de la Pentecôte afin de percevoir la place que notre expression occupe dans cette péricope. Au chapitre trois, nous ferons une analyse grammaticale de notre segment afin de voir la fonction grammaticale de l’expression, et présenter une recension des ouvrages hébraïques et gréco-romains qui utilisent cette expression ou une image similaire. Enfin, l’analyse philologique des termes γλῶσσα et πῦρ sera élaborée et comparée à l’utilisation retrouvée dans le livre des Actes des Apôtres. Subséquemment, nous serons en mesure de porter un regard critique sur quelques interprétations proposées afin de percevoir que la mise en réseau structurel du membre γλῶσσαι ὡσεὶ πυρός, avec les termes répétitifs et synonymiques du récit, nous orientent à percevoir l’accomplissement de la promesse du Saint-Esprit, qui à son tour habilite le croyant à réaliser la mission donnée : la proclamation du message christologique à toutes les ethnies.

Bicycle Touring Infrastructure: An Architectural Proposal for Sustainable Bicycle Tourism

Thesis (Master's)--University of Washington, 2016-06

Modulation of Translation Efficiency in S. cerevisiae by Codon Pairs and mRNA Structure

Thesis (Ph.D.)--University of Washington, 2016-06

Evolution of the regular zone of histone H1 in Fabaceae plants

An analysis of the historic H1 subtype, H1-1, in eight legumes belonging to four genera of the tribe Vicieae (Pisum, Lathyrus, Lens, and Vicia), revealed an extended region consisting of the tandemly repeated AKPAAK motifs. We named this region the Regular zone (RZ). The AKPAAK motifs are organized into two blocks separated by a short (two or six amino acids) intervening sequence (IS). The distal block contains six AKPAAK motifs, while the number of repeats in the proximal block varies from six in V. faba to seven in the other species. In V. hirsuta, the first two repeated units of the proximal block are octapeptides AKAKPAAK. The apparent rate of synonymous substitutions in the blocks of RZ is much higher than in the rest of the gene. This can be explained by repeat shuffling within each block. In the C-domain of the orthologous H1 subtype froth Medicago truncatula (tribe Trifolieae), a region corresponding to the RZ of Vicieae species was found. It also consists of two blocks of AKPAAK motifs (four and three repeats in the proximal and distal blocks, respectively). These blocks are separated by a 20-amino acid IS. The first 20 amino acids of the Medicago RZ are not part of AKPAAK repeats. We hypothesise that the RZ has most probably evolved as a result of an expansion of AKPAAK repeats from two separate sites in the C-domain. This process started tens of millions of years ago and was most likely directed by positive selection.

The abundance of short proteins in the mammalian proteome

Short proteins play key roles in cell signalling and other processes, but their abundance in the mammalian proteome is unknown. Current catalogues of mammalian proteins exhibit an artefactual discontinuity at a length of 100 aa, so that protein abundance peaks just above this length and falls off sharply below it. To clarify the abundance of short proteins, we identify proteins in the FANTOM collection of mouse cDNAs by analysing synonymous and nonsynonymous substitutions with the computer program CRITICA. This analysis confirms that there is no real discontinuity at length 100. Roughly 10% of mouse proteins are shorter than 100 aa, although the majority of these are variants of proteins longer than 100 aa. We identify many novel short proteins, including a dark matter'' subset containing ones that lack detectable homology to other known proteins. Translation assays confirm that some of these novel proteins can be translated and localised to the secretory pathway.

Genorne sequence of the thermostable Newcastle disease virus (strain I-2) reveals a possible phenotypic locus

The complete genome sequence of the Australian 1-2 heat-tolerant Newcastle disease virus (NDV) vaccine (master seed stocks) was determined and compared to the sequence of the parent virus from which it had been derived after exposure of the parent stock at 56 degrees C for 30 min. Nucleotide changes were observed at a number of positions with synonymous mutations being greater than those observed for non-synonymous mutations. Sequence data for the HN gene of a parental culture of V4 and two heat-tolerant variants of V4 were obtained. These were compared with the data for the 1-2 viruses and with published sequences for parental V4 and for a number of ND vaccine strains. Sequence analyses did not reveal the ARG 303 deletion in the HN protein, previously claimed to be responsible for the thermostable phenotype. No consistent changes were detected that would indicate involvement of the HN protein in heat resistance. The majority of alterations were observed in the L protein of the virus and it is proposed that these alterations were responsible for the heat-tolerant phenotype of the 1-2 NDV vaccine. (c) 2005 Elsevier B.V. All rights reserved.