bluuebunny/crossref_metadata_2025 huggingface dataset:
Educação Ambiental: uma prática interdisciplinar
Authors: KNECHTEL Maria do Rosário
Published: July 2014

Este texto traz primeiramente, algumas premissas teóricas e fundamentos que possibilitem construir uma prática interdisciplinar em Educação Ambiental, a partir de ações integradas entre a pesquisa e o ensino. Em um segundo momento, apresenta a prática interdisciplinar implementada no Curso de Doutorado em Meio Ambiente e Desenvolvimento, da Universidade Federal do Paraná (UFPR), Brasil, na disciplina Educação Ambiental; trata-se de uma proposta de atividade para a construção e reconstrução do conhecimento, a qual desencadeia uma interação de disciplinas das áreas de Ciências Sociais e Naturais, em uma prática de ensino e pesquisa coletiva. As idéias e a prática desenvolvidas têm como base experiências com a metodologia da Problematização, realizadas por Maguerez (BORDENAVE; PEREIRA, 1982); Berbel (1994) e Knechtel (1998). A fundamentação se apoia em Leff (1995); Piaget (1970); Vygotski (1988); Floriani (1998-99); Medina (1997); Fazenda (1995-97); Vásquez (1977); Fourez (1995), entre outros. Environmental education: limits and possibilities to an interdisciplinary pratice Abstract This text aims first at presenting some theoretical premises and fundaments that allow for the construction of an interdisciplinary practice in Environmental Education by means of integrated actions between teaching and research. Secondly, the interdisciplinary practice implemented in the Doctorate in Environment and Development from the Federal University of Paraná, Brazil, is presented in the Course of Environment Education. The proposed activity concerns the construction and reconstruction of knowledge and brings up an interaction between de Courses in the fields of Social and Natural Sciences, allowing for a joint practice of teaching and research. The ideas and practices developed are based on experiences with problematics methodology conducted by Maguerez (BORDENAVE; PEREIRA, 1982); Berbel (1994) and Knechtel (1998). The fundamental is supported by Leff (1995); Piaget (1970); Vygotski (1988); Floriani (1998-99); Medina (1997); Fazenda (1995-97); Vásquez (1977); Fourez (1995), among others.
Olhares sobre a tradição
Authors: CUNHA Lúcia Helena De Oliveira
Published: July 2014

Este artigo reflete a respeito dos diferentes olhares que a modernidade projeta sobre as sociedades da tradição, vendo-as ora do ponto de vista negativo, em suas desordens, ora do ponto de vista positivo, a partir de suas ordens imanentes. Pierre Clastres é um dos antropólogos contemporâneos que focaliza o modo através do qual as sociedades ditas primitivas são freqüentemente percebidas pela ausência, no prisma da civilização ocidental: pela falta de trabalho, de Estado e de ordem. George Balandier coloca em questão esse imaginário ocidental sobre as sociedades tradicionais, mesmo quando tais sociedades aparecem como expressão do positivo, do equilíbrio. Entendendo que ordem e desordem são categorias reguladoras da vida humana, para o autor, é preciso repensar o conceito de tradição dotado de movimento. Assim, os povos da tradição não podem ser vistos como estagnados, parados no tempo, mas imersos em outros ritmos temporais, mesmo no encontro (confronto) com a modernidade. Observing tradition Abstract This article pretend procedure to the reflection of different view that the modernity project over societies of tradition, look at them sometimes from the negative point of view in its disorder, sometimes from the positive point of view, from its order immanent. Pierre Clastres is one of our present anthropologist that focus the manner through the societies supposed primitive are often perceive by absence in the prism of occidental civilization: because of absence of job, state and order. George Balandier puts in question this occidental imaginary about traditional societies, even when those societies appears like expression of positive and of the balance. For Balandier order and disorder are regulator category of human life; this author thinks that we need rethink the conceit of tradition endowed of movement. Thus, the people of tradition, can not be viewed like stagnated, standing up still, but immersed in others temporary rhythm, with own dynamics, even in the meeting (confront) with the modernity.
Uma abordagem sistêmica da atual crise ambiental
Authors: KRÜGER Eduardo L.
Published: July 2014

Neste artigo, é traçado inicialmente um quadro histórico acerca do surgimento da sociedade tecnológica. Em seguida, aponta-se para alguns problemas criados por essa sociedade, à luz do conflito existente entre os avanços tecnológicos e os prejuízos causados ao meio ambiente. As seções seguintes discutem o enfoque ambientalista e a abordagem sistêmica para essa questão, para que se possa, por fim, esboçar algumas estratégias no sentido de propor melhorias para o sistema global. A systemic approach of present environmental crises Abstract In this article, we first present a brief historical picture from the beginnings of the technological society. Then, we point out some problems created by this society in the light of the existing conflict between technological progress and the damages brought to the environment. The following sections discuss the environmentalist vision and the systemic approach to this issue, in order to outline some strategies to improve the global system.
A ética no montanhismo
Authors: STRUMINSKI Edson
Published: July 2014

Imagens sobre montanhas e sobre suas ascensões têm tradicionalmente um forte impacto na sociedade, de tal forma que é praticamente impossível ficar indiferente a estas imagens ou às histórias relacionadas a este assunto. Como se explica isto? Neste trabalho serão apresentadas algumas considerações a respeito da relação que os seres humanos mantém com as montanhas. Para entender esta relação utilizarei o conceito de biofilia. A visão que os humanos tem das montanhas variam bastante conforme a cultura e o período histórico em que vivem, gerando diferentes tipologias biofílicas. Esta visão pode modificar-se também individualmente conforme varie o envolvimento da pessoa com a montanha, de modo que transite de uma tipologia para outra. Para exemplificar este caso, apresentarei as trajetórias de envolvimento de alguns montanhistas com as montanhas. Finalmente, comentarei como estas tipologias biofílicas modificam aspectos éticos presentes no próprio montanhismo para atender a demandas presentes na sociedade circundante. Mountaineering ethics Abstract This paper presents some considerations about the relationship between human being and mountains. It will use the concept of biophilia. The human beings vision about the mountains is associated to the culture and to the historic period. According to the involvement of people with the mountains, the vision modifies itself. It concludes that biophilical typologies modify ethical aspects within mountains practices to fulfill social demands.
A cidade e os sentidos: sentir a cidade
Authors: KANASHIRO Milena
Published: July 2014

Este artigo trata da questão de como o espaço urbano é sentido através da percepção sensorial dos seres humanos, procurando abordar, de maneira sucinta, as contribuições dos sentidos na apreensão das qualidades espaciais dos ambientes construídos. The city and the senses: to feel the city Abstract This article deals with the subject of the human sensorial perception related to the urban spaces. This is an attempt to contribute to the discussion of the senses and the perception of space qualities of built environments.
Multiespacialidades metropolitanas e construção social do lugar  rumos para a sustentabilidade
Authors: LIMA Cristina De Araújo
Published: July 2014

A Região Metropolitana de Curitiba  RMC2  é constituída de espacialidades diferenciadas e, ao mesmo tempo em que sedia atualmente o terceiro maior pólo industrial automobilístico do país, é a única região metropolitana brasileira em que houve crescimento demográfico tanto do pólo, Curitiba, quanto da periferia imediata superiores à taxa de crescimento da população brasileira. Entre 1970 e 2000, Curitiba apresentou a maior taxa geométrica de crescimento anual, 2,13% no pólo e 4,86% a.a. na periferia. (IBGE, 2000). Contudo, na periferia metropolitana, onde se concentra 90% da população da RMC, as condições sociais e de infra-estrutura urbana são precárias. 12,46% dos domicílios têm chefes de família com renda de até 1 salário mínimo, ou aproximadamente US$ 80,00 por mês, o que justifica a existência de locais com favelas e sub-habitações na cidade. No entanto, essa proporção sobe para 50% ou mais nos municípios vizinhos. Enquanto em Curitiba o montante populacional triplicou em apenas 20 anos, no restante da região metropolitana o incremento populacional foi muito reduzido. No debate acerca dos rumos de uma sustentabilidade metropolitana, busca-se compreender a dimensão ambiental como o todo de inter-relações socioambientais, analisando-se as condições da população do primeiro patamar de adensamento urbano no qual se entende que um reforço ao sentido de lugar seria pressuposto para uma maior sustentabilidade. Metropolitan multispecialities and social constrution − sustainability ways Abstract The metropolitan region of Curitiba  MRC  contains several spatial configurations and, besides having the third automobile industry of the country; it is currently the only metropolitan region with a population growth rate higher than the national average. Between 1970 and 2000, it had the highest geometric growth rate among metropolitan regions in Brazil: it grew 2.13% in its core and 4.18% in the suburbs (IBGE, 2000). However, last places are where 90% of the population live. There, social and urban structures are underdeveloped and the population number has risen three times in the last twenty years. Whereas in Curitiba 12.46% of the houses have an income around US $80 per month, in the suburbs this proportion rises to 50% or more. Discussing sustainability, it is necessary to understand the environmental dimension as a social and natural whole. In this paper analyze some aspects of the population conditions in the nearest neighborhood of Curitiba, where an improvement of the locus sense of place could contribute to a metropolitan and urban sustainability.
Pensando a sustentabilidade: um olhar sobre a Agenda 21
Authors: BASSANI Paulo , De CARVALHO Maria Aparecida Vivan
Published: July 2014

Trata-se neste ensaio de uma reflexão que permite subsidiar práticas politicamente avançadas que delineiem ações emancipadas. Nas últimas décadas, a degradação ambiental tem aumentado em níveis insuportáveis, caracterizada por diferentes estágios de desenvolvimento econômico e de ação humana, levando- nos a acreditar que medidas concretas e efetivas precisam ser tomadas no sentido de articular o crescimento das condições socioeconômicas com a sustentabilidade. Um dos caminhos teórico-práticos diz respeito à implantação da Agenda 21, contemplando normas e diretrizes para implementar ações locais e regionais. Thinking over sustainability: a reflection over Agenda 21 Abstract This paper is about a reflection that allows us to subsidise policie advanced which sketch emancipated actions. In the last decades, the environmental degradation has increased to intolerable levels, characterized by different stages of economic development and human action, leading us to believe that real and effective measures have to be taken to articulate the growth of the social economic conditions with sustainabillity. One of the theoretical practical ways concerns the introduction of Agenda 21 which contemplates rules and principles to implement local and regional actions.
Analysis and glycosyl composition of the exopolysaccharide isolated from submerged fermentation of Ganoderma lucidum CG144
Authors: Rubel Rosália , Dos Santos Leandro Freire , Stutz Dalla Santa Herta , Porto de Souza Vandenberghe Luciana , Lorenci Woiciechowski Adenise , Cesar de Carvalho Júlio , Habu Sascha , Menino Destéfanis Vítola Francisco , Augur Christopher , Ricardo Soccol Carlos
Published: July 2014

The evaluation of glycosyl composition is an essential step to guide future research designs applied in bioactivity. In the same way, the unexplored potential bioactivity of exopolysaccharide from Ganoderma lucidum is huge. Therefore, this study investigated the glycosyl composition of the exopolysaccharide isolated from submerged fermentation of G. lucidum to serve as guide for future studies on bioactivity. Glycosyl content and composition were evaluated by combined GC/MS of the TMS derivatives of the monosaccharide methyl glycosides produced from the sample by acidic methanolysis. Glycosyl composition analysis showed that the dominant carbohydrate component in all samples of exopolysaccharide isolated from submerged fermentation of G. lucidum CG 144 was glucose (58.1%), mannose (26.6%) and galactose (12.5%) which can be referred to as heteroglycan. These results suggest that this Ganoderma exopolysaccharide may be a new immunomodulatory agent.
Proposition pour l’induction en analyse du discours
Authors: Normand Ariane
Published: July 2014

L’analyse du discours intéresse des chercheurs d’horizons divers. Comme les nombreuses influences disciplinaires de l’analyse du discours s’entrelacent de plus en plus, les choix méthodologiques se multiplient. Comprendre les choix méthodologiques possibles, sélectionner le plus adapté et trouver des références devient ainsi parfois ardu.

Cet article constitue une réflexion sur les choix méthodologiques qui s’offrent aux analystes du discours et propose une méthodologie qui pourrait convenir à ceux dont les travaux sont de nature inductive. Nous montrons ainsi que l’approche de la MTE constitue une avenue intéressante car elle s’enracine dans les données, ce qui permet au chercheur de mettre le discours au centre de sa démarche. Le retour réflexif que nous faisons sur un projet de recherche terminé permet également de réfléchir de manière plus concrète aux problèmes que peuvent rencontrer les chercheurs durant leurs travaux de recherche.
Donner priorité aux données : adopter l’induction au cours d’une recherche sur les relations publiques et le journalisme
Authors: Boulay Sophie , Francoeur Chantal
Published: July 2014

Cet article expose le parcours d’une équipe dont le projet de recherche s’est développé d’une manière inattendue. Amorcé dans une épistémologie positiviste et dans un paradigme hypothéticodéductif, le projet a dû être redéployé. Le design de recherche et les méthodes de collecte de données suscitaient plus de questions qu’ils n’apportaient de réponses. Posant un regard critique sur le processus, nous réalisons que les décisions jalonnant la démarche s’inscrivent dans une démarche inductive. L’article décrit l’évolution intuitive d’une recherche où les préconceptions de ce qu’est une excellente méthodologie sont chamboulées pour finalement reconnaître la valeur et le rôle des données en tant que guides pour l’exploration d’objets de recherche.
« Chantez au Seigneur un chant nouveau… » (Ps.95.1) : le portrait de la musique rock chrétienne
Authors: Falardeau Marie-Chantal , Perreault Stéphane
Published: July 2014

Le but de cet article est de présenter les raisons du choix d’une approche inductive, plutôt qu’une approche déductive, afin d’étudier la musique rock chrétienne. Cette étude dresse un portrait des chansons les plus populaires de la musique rock chrétienne tout en décrivant quantitativement les éléments structurels de ces dernières. Afin de réaliser ce projet, nous avons répertorié tous les numéros un du palmarès américainChristian Songsdepuis sa création en 2003 jusqu’à la fin de l’année 2011, soit 65 chansons. Le portrait de la musique rock chrétienne se décline en onze catégories dont les plus récurrentes sont la dévotion, la présence de Dieu et l’espoir. Cette musique est aussi chantée majoritairement par des hommes et se caractérise par un rythme lent.
Diagnosis of Lysosomal Storage Disorders: Gaucher Disease
Authors: Johnson Britt A. , Dajnoki Angela , Bodamer Olaf
Published: July 2014

Gaucher Disease (GD) is a progressive lysosomal storage disorder caused by deficiency of glucocerebrosidase (GBA). The clinical phenotype follows a spectrum ranging from severe early‐onset to milder late‐onset disease. The absence of neurological involvement defines GD type I, whereas neuronopathic features define GD type II and III. Early diagnosis may be important for timely initiation of enzyme replacement therapy to prevent disease complications, although the enzyme does not cross the blood brain barrier. Diagnosis of GD can be readily achieved by analysis of GBA in leukocytes, fibroblasts, and/or dried blood spots using fluorometric, microfluidic or mass spectrometry‐based assays. Low GBA activities are typically confirmed through molecular analysis of the GBA gene. GBA analysis in dried blood spots may be attractive for high‐throughput screening of at‐risk individuals and/or newborn infants. The method detailed in this unit is based on GBA analysis by tandem mass spectrometry following incubation of dried blood spots with the GBA‐specific substrate D‐glucosyl‐β1‐1′‐N‐dodecanoyl‐D‐erythro‐sphingosine [C12‐glucocerebroside (C36H69NO8)] and internal standard N‐myristoyl‐D‐erythro‐sphingosine [C14‐ceramide (C32H63NO3)]. GBA activities in more than 2,000 newborn infants showed a mean of 22.0 ± 13.8 μmol/hr/liter (median: 19.9 μmol/hr/liter; 95% CI: 21.41‐22.59 μmol/hr/liter). GBA activities in an adult population (n >1,200) showed generally lower enzyme activities than newborns, with a mean of 9.87 ± 9.35 μmol/hr/liter (median: 8.06 μmol/hr/liter). GBA activities in ten adult patients with confirmed GD were less than 4.2 μmol/hr/liter and in seven infants and children with GD less than 1.24 μmol/hr/liter. This method is robust, sensitive, and suitable for high‐throughput analysis of hundreds of samples. Curr. Protoc. Hum. Genet. 82:17.15.1‐17.15.6. © 2014 by John Wiley & Sons, Inc.
On the seawater temperature dependence of the sea spray aerosol generated by a continuous plunging jet
Authors: Salter M. E. , Nilsson E. D. , Butcher A. , Bilde M.
Published: July 2014

Breaking waves on the ocean surface produce bubbles which, upon bursting, deliver seawater constituents into the atmosphere as sea spray aerosol particles. One way of investigating this process in the laboratory is to generate a bubble plume by a continuous plunging jet. We performed a series of laboratory experiments to elucidate the role of seawater temperature on aerosol production from artificial seawater free from organic contamination using a plunging jet. The seawater temperature was varied from −1.3°C to 30.1°C, while the volume of air entrained by the jet, surface bubble size distributions, and size distribution of the aerosol particles produced was monitored. We observed that the volume of air entrained decreased as the seawater temperature was increased. The number of surface bubbles with film radius smaller than 2 mm decreased nonlinearly with seawater temperature. This decrease was coincident with a substantial reduction in particle production. The number concentrations of particles with dry diameter less than ∼1 μm decreased substantially as the seawater temperature was increased from −1.3°C to ∼9°C. With further increase in seawater temperature (up to 30°C), a small increase in the number concentration of larger particles (dry diameter >∼0.3 μm) was observed. Based on these observations, we infer that as seawater temperature increases, the process of bubble fragmentation changes, resulting in decreased air entrainment by the plunging jet, as well as the number of bubbles with film radius smaller than 2 mm. This again results in decreased particle production with increasing seawater temperature.
Constraining the carbon tetrachloride (CCl4) budget using its global trend and inter‐hemispheric gradient
Authors: Liang Qing , Newman Paul A. , Daniel John S. , Reimann Stefan , Hall Bradley D. , Dutton Geoff , Kuijpers Lambert J. M.
Published: July 2014

Carbon tetrachloride (CCl4) is a major anthropogenic ozone‐depleting substance and greenhouse gas and has been regulated under the Montreal Protocol. However, the near‐zero 2007–2012 emissions estimate based on the UNEP reported production and feedstock usage cannot be reconciled with the observed slow decline of atmospheric concentrations and the inter‐hemispheric gradient (IHG) for CCl4. Our 3‐D model simulations suggest that the observed IHG (1.5 ± 0.2 ppt for 2000–2012) is primarily caused by ongoing current emissions, while ocean and soil losses and stratosphere‐troposphere exchange together contribute a small negative gradient (~0 – −0.3 ppt). Using the observed CCl4 global trend and IHG, we deduce that the mean global emissions for the 2000–2012 period are  Gg/yr (~30% of the peak 1980s emissions) and a corresponding total lifetime of  years.
The “footloose” mechanism: Iceberg decay from hydrostatic stresses
Authors: Wagner Till J. W. , Wadhams Peter , Bates Richard , Elosegui Pedro , Stern Alon , Vella Dominic , Abrahamsen E. Povl , Crawford Anna , Nicholls Keith W.
Published: July 2014

We study a mechanism of iceberg breakup that may act together with the recognized melt and wave‐induced decay processes. Our proposal is based on observations from a recent field experiment on a large ice island in Baffin Bay, East Canada. We observed that successive collapses of the overburden from above an unsupported wavecut at the iceberg waterline created a submerged foot fringing the berg. The buoyancy stresses induced by such a foot may be sufficient to cause moderate‐sized bergs to break off from the main berg. A mathematical model is developed to test the feasibility of this mechanism. The results suggest that once the foot reaches a critical length, the induced stresses are sufficient to cause calving. The theoretically predicted maximum stable foot length compares well to the data collected in situ. Further, the model provides analytical expressions for the previously observed “rampart‐moat” iceberg surface profiles.
Experimental study of sealing performance: Effects of particle size and particle‐packing state on threshold pressure of sintered compacts
Authors: Sorai Masao , Fujii Takashi , Kano Yuki , Uehara Shinichi , Honda Katsuya
Published: July 2014

Threshold pressure Pcth (kPa), a parameter controlling rock's sealing performance in cases of CO2 geological sequestration, was studied in a supercritical CO2‐water system under conditions of 1000 m depth (10 MPa and 40°C). With respect to correlation between Pcth and another important parameter of permeability, k (mdarcy), the closest‐packing structure of spherical particles is defined theoretically as a line having slope of −0.5 on a double logarithmic plot. This study found this line by measuring Pcth of a capillary plate with known throat diameter as Pcth = 188.8 k– 0.5. This function is directly applicable to different depth and salinity conditions, although it requires minor correction at some temperature conditions. As a first step in determining the range of variation of rocks' Pcth and k from internal particle structures, we used sintered compacts of uniform spherical silica particles with diameters of 0.1–10 µm. Results show that measured values of sintered compacts were scattered around the closest‐packing line, with the difference of packing state depending on different sintered additives and sintering temperatures. The change of packing state, occurring independently of resultant changes of porosity, varied sensitively according to Pcth. Therefore, Pcth is inferred to depend strongly on the local structure within rocks. The Knudsen number estimated for supercritical CO2 at 1000 m depth indicated that CO2 transmuted into a noncontinuum at k < 0.1 µdarcy in the closest‐packing structure. Future studies should consider whether the concept of Pcth is applicable in this situation.
Modeling immersion freezing with aerosol‐dependent prognostic ice nuclei in Arctic mixed‐phase clouds
Authors: Paukert M. , Hoose C.
Published: July 2014

While recent laboratory experiments have thoroughly quantified the ice nucleation efficiency of different aerosol species, the resulting ice nucleation parameterizations have not yet been extensively evaluated in models on different scales. Here the implementation of an immersion freezing parameterization based on laboratory measurements of the ice nucleation active surface site density of mineral dust and ice nucleation active bacteria, accounting for nucleation scavenging of ice nuclei, into a cloud‐resolving model with two‐moment cloud microphysics is presented. We simulated an Arctic mixed‐phase stratocumulus cloud observed during Flight 31 of the Indirect and Semi‐Direct Aerosol Campaign near Barrow, Alaska. Through different feedback cycles, the persistence of the cloud strongly depends on the ice number concentration. It is attempted to bring the observed cloud properties, assumptions on aerosol concentration, and composition and ice formation parameterized as a function of these aerosol properties into agreement. Depending on the aerosol concentration and on the ice crystal properties, the simulated clouds are classified as growing, dissipating, and quasi‐stable. In comparison to the default ice nucleation scheme, the new scheme requires higher aerosol concentrations to maintain a quasi‐stable cloud. The simulations suggest that in the temperature range of this specific case, mineral dust can only contribute to a minor part of the ice formation. The importance of ice nucleation active bacteria and possibly other ice formation modes than immersion freezing remains poorly constrained in the considered case, since knowledge on local variations in the emissions of ice nucleation active organic aerosols in the Arctic is scarce.
Large‐scale vapor transport of remotely evaporated seawater by a Rossby wave response to typhoon forcing during the Baiu/Meiyu season as revealed by the JRA‐55 reanalysis
Authors: Kudo Tadasuke , Kawamura Ryuichi , Hirata Hidetaka , Ichiyanagi Kimpei , Tanoue Masahiro , Yoshimura Kei
Published: July 2014

The modulation of large‐scale moisture transport from the tropics into East Asia in response to typhoon‐induced heating during the mature stage of the Baiu/Meiyu season is investigated using the Japanese 55‐year reanalysis (JRA‐55), aided by a Rayleigh‐type global isotope circulation model (ICM). We highlighted the typhoons that migrate northward along the western periphery of the North Pacific subtropical high and approach the vicinity of Japan. Anomalous anticyclonic circulations to the northeast and southeast of typhoons and cyclonic circulation to their west become evident as they migrate toward Japan, which could be interpreted as a Rossby wave response to typhoon heating. These resultant anomalous circulation patterns form moisture conveyor belt (MCB) stretching from the South Asian monsoon region to East Asia via the confluence region between the monsoon westerlies and central Pacific easterlies. The ICM results confirm that the well‐defined nature of the MCB leads to penetration of the Indian Ocean, South China Sea, Philippine Sea, and Pacific Ocean water vapors into western Japan. The typhoons have the potential to accumulate large amounts of moisture from distant tropical oceans through the interaction of their Rossby wave response with the background flow. In the case of a typical typhoon, the total precipitable water around the typhoon center as it approaches Japan is maintained by the moisture supply from distant oceans rather than from the underlying ocean, which indirectly leads to the occurrence of heavy rainfall over western Japan.
Spirochaetes
Authors: Houston Simon , Taylor John S , Cameron Caroline E
Published: July 2014

Species in the phylum Spirochaetes (order: Spirochaetales) are thin, spiral‐shaped or wave‐like, highly motile bacteria that are best visualised by darkfield microscopy. Spirochaetes are Gram‐negative‐like, in that they possess inner and outer membranes separated by a peptidoglycan‐containing periplasmic space. Beyond these ultrastructural similarities, few parallels exist with conventional Gram‐negative bacteria. There have been more than 90 spirochaete species identified, including the well‐known pathogenic, disease‐causing species

Treponema pallidum

(syphilis),
Leptospira
sp. (leptospirosis) and

Borrelia burgdorferi

(Lyme disease). The phylogenetic relationship among spirochaetes is evident at the level of gross phenotypic characteristics, which include a distinctive morphology derived from the presence of periplasmic flagella. In this article, the authors describe the genomic, physiologic, structural and functional features that make Spirochaetes unique among the prokaryotes.

Key Concepts:

Spirochaetes are a genetically and morphologically distinct group of bacteria.

Spirochaetes are thin spiral‐shaped or wave‐like bacteria that are highly motile.

Endoflagella/periplasmic flagella provide spirochaetes with their characteristic corkscrew‐like motility.

Spirochaetes differ from typical Gram‐negative bacteria at the ultrastructural level.

Spirochaetes are chemo‐organotrophic, grow in diverse conditions and are comprised of both pathogenic and nonpathogenic members.

Complete genome sequencing has allowed for the characterisation and differentiation of spirochaetes at the genetic level.

Medically important spirochaetes belong to the three genera
Borrelia
,
Leptospira
and
Treponema
.
DNA
Double‐Strand Breaks and Their Consequences in Bacterial Genomes
Authors: Kobayashi Ichizo , Handa Naofumi , Kusano Kohji
Published: July 2014

Deoxyribonucleic acid (DNA)
double‐strand breaks, which are caused by many factors such as chemical treatments, radiations and, often, biological factors, are lethal events in organisms carrying DNA as their genome, which include bacteria. There are various mechanisms that work in the processing of these breaks, sometimes in collaboration or competition with each other. These include exonucleolytic degradation, end joining and recombination repair. These may bring about death, restoration or recombinational/mutational changes in the genome. Intragenomic collaboration and conflict between various pathways can be a force in their genome evolution. Recent analyses suggest that DNA double‐strand breaks switch on the programme of cell death in bacteria. DNA double‐strand breakage and its consequences in bacteria may provide a good model system to analyse the dynamic relationship between life, death and evolution. Understanding these processes in bacteria is important in medicine, environmental studies and industrial application.

Key Concepts:

DNA double‐strand breakage and its consequences in bacteria may provide a model system to analyse the relationship between life, death and evolution.

DNA double‐strand breakage may switch on programmes of cell death in bacteria.

Repair of DNA double‐strand breakage provides accurate products and innacurate products for host genome.

Small and large genome alterations are important in bacterial genome evolution.

The concept of intragenomic conflict may lead to meanings of the generation, processing and consequences of double‐strand breaks.
Peptidases
Authors: Rawlings Neil D , Barrett Alan J
Published: July 2014

Peptidases are catalytically active proteins (enzymes) that cleave peptide bonds in proteins and peptides by hydrolysis. Not only do peptidases break down proteins and peptides so that the amino acids can be recycled and used during growth and remodelling, but they are also important for modifying proteins. These processing events ensure proteins are sent to the correct cellular or extracellular locations, are activated or inactivated when required, and that biologically important peptides are excised. There are six catalytic types (serine, cysteine, threonine, aspartic, glutamic and metallo). Peptidases can be classified by sequence similarities into approximately 250 families, and these in turn can be arranged into approximately 60 clans by comparing tertiary structures.

Key Concepts:

A peptidase is a catalytically active protein that cleaves one or more peptide bonds in a protein or peptide by hydrolysis.

There are six different catalytic types of peptidases.

Comparison of the amino acid sequences of peptidases allows them to be classified into about 250 families.

Comparison of the structural folds of peptidases allows them to be classified into about 60 clans.

A peptidase that acts only within three residues of the amino or carboxyl termini of a substrate protein is known as an exopeptidase.

A peptidase that cleaves any bond in a substrate protein that is more than three residues from the amino or carboxyl termini is known as an endopeptidase.

A peptidase has an active site containing amino acids that are important for catalysis and which are usually conserved in all active members of a family.

The active site of a peptidase is flanked by substrate binding pockets, each of which accommodates one residue from the substrate.

Some peptidases have additional substrate binding sites remote from the active site that are known as exosites.
Establishment of Left–Right Asymmetry in Chick and Mouse Embryos
Authors: Komatsu Yoshihiro , Mishina Yuji
Published: July 2014

All vertebrates have consistent left–right structural asymmetry, and deviations from the typical asymmetry in humans are clinically important. Studies elucidating the mechanisms that establish left–right asymmetry have lead to some of the most elegant advances in the field of embryology. In the past several decades, while we have gained an extensive understanding of the development of left–right asymmetry during embryogenesis, many questions remain to be addressed to fully appreciate the molecular mechanisms underlying its establishment. In this review article, the authors summarise the gene regulatory network that controls left–right patterning. They also focus on our current understanding of how left–right symmetry is broken.

Key Concepts:

Primary cilia rotating in a clockwise direction generate a unidirectional leftward fluid flow at a structure called the node, resulting in left–right symmetry breakage in mouse embryos. Similar leftward flow is observed in many vertebrate embryos.

Planar cell polarity (PCP) signalling, initially identified in the fruitfly, controls the uniform orientation of hairs and bristles on the body.

A primary cilium is a microtubule‐based antenna‐like structure lacking the central pairs of microtubules. This ‘9+0’ microtubular structure and lack of dynein arms render them immotile, whereas motile cilia have a ‘9+2’ microtubular structure with dynein arms.

BMP signalling negatively regulates cell cycle at the ventral surface of the node.

The posterior tilt of nodal cilia regulated by planar cell polarity is critical to generate a unilateral leftward flow from the rotation of the nodal cilia.

The ventral surface of the node is quiescent that allows formation of cilia.
Immunological Tolerance: Mechanisms
Authors: Zouali Moncef
Published: July 2014

Immunological tolerance refers to a reduction or complete inhibition of the ability of an individual to mount a specific immune response upon immunisation. Several mechanisms are involved in induction and maintenance of tolerance, including clonal deletion, clonal anergy, receptor editing, receptor down‐modulation and lymphocyte sequestration. The number of antigen presenting cells, the number and activity of regulatory T cells and regulatory B cells, the nature and amount of antigenic peptides generated and the presence of co‐stimulatory signals in a particular tissue are also important. Depending on the site and the level of antigen expression, different states of peripheral B‐cell and T‐cell tolerance can be reached. In certain situations, they could act in an additive manner. In humans, induction of immunological tolerance is an important issue in both transplantation biology and autoimmune diseases, and present research aims at designing novel strategies to induce specific tolerance.

Key Concepts:

Tolerance induction is easier in animals with an immature immune system or with a mature immune system that has been compromised by irradiation, drugs or thoracic drug drainage.

In general, when a given antigen is used over a wide range of concentrations, intermediate doses induce immunity, and low and high doses induce tolerance.

The introduction route is a key variable in tolerance induction, particularly in adult animals, presumably by determining the accessibility of the antigen to professional antigen presenting cells.

The tolerant state is not absolute and tolerance is rarely complete. With time, it gradually wanes and eventually disappears, but it can be deliberately terminated by several means.

Persistence of the tolerogen in the periphery and its accessibility to the immune system are generally required to maintain tolerance, which continuously inactivates newly emerging T and B cells that develop in lymphoid organs.

T lymphocytes specific for self‐peptides bound to major histocompatibility complex peptides are eliminated by clonal deletion, a process known as negative selection. Similarly, self‐reactive B cells are purged from the functional repertoire during the transition from the pre‐B to mature B‐cell stage in the bone marrow.

Anergy is a functionally silent state induced in B cells and T cells, allowing them to persist functionally inactivated in tolerant animals.

Receptor editing is a form of receptor processing that markedly alters the variable region genes expressed by B cells and, consequently, changes the specificity of the surface immunoglobulin and maintains B‐cell tolerance to self.

Two functional lymphocyte subsets, called regulatory T cells and regulatory B cells, have recently been found to contribute to the maintenance of the fine equilibrium required for immune tolerance.

In humans, induction of immunological tolerance in the adult is an important issue in both transplantation biology and autoimmune diseases, and present research aims at designing novel strategies to induce specific tolerance.
Meiosis
Authors: Cha Rita S , Hartsuiker Edgar
Published: July 2014

Meiosis is a differentiation programme used by sexually reproducing organisms for generating reproductive cells. Its purpose is to reduce the genetic complement by half to ensure restoration of the correct number of chromosomes upon union of two sex cells. The halving of the genome is achieved by a single round of genome duplication followed by two successive rounds of genome division. During the period between completion of genome duplication and the first division, homologous maternal and paternal chromosomes pair with one another and exchange genetic material, culminating in formation of crossovers, which physically link the homologous chromosomes until they are separated at anaphase I. During the second genome division, the duplicated sister chromatids, which remain connected during meiosis I, are separated. Following the second division, four separated haploid genomes undergo a series of developmental steps, which give rise to reproductive cells capable of forming a diploid organism upon fertilisation.

Key Concepts:

Meiosis is a specialized cell division programme for generating reproductive cells.

The aim of meiosis is to generate haploid reproductive cells from a diploid precursor.

Reduction of the genome content by half is achieved by a single round of genome duplication followed by two successive rounds of genome divisions.

During the first meiotic genome division (meiosis I), homologous maternal and paternal chromosomes separate; during the second genome division (meiosis II), the newly duplicated sister chromatids separate.

Physical connection between homologous maternal and paternal chromatids or a crossover is essential for homologue separation during meiosis I.

Crossover formation depends on meiosis‐specific pairing of the homologues and genetic recombination between the homologues.

Meiotic recombination is initiated by developmentally programmed formation of DNA double‐strand breaks.

Meiotic recombination leads to exchange of genetic information between homologous maternal and paternal DNA and contributes to genome variation and evolution.

Meiotic homologue pairing and recombination are evolutionarily conserved from yeast to humans.

Defects in meiotic homologue pairing and recombination contribute to infertility, birth defects and aneuploidy (e.g. Downs syndrome) in humans.
Thrombin
Authors: Thiagarajan P , Narayanan AS
Published: July 2014

Thrombin (factor IIa) is a serine protease that converts fibrinogen into fibrin in blood coagulation. The precursor of thrombin, prothrombin (inactive zymogen), is one of the several coagulation proteins containing γ‐carboxyglutamic acid. Prothrombin is synthesised in the liver and secreted into blood circulation, and is activated by vascular injury by limited proteolysis following upstream activation of the coagulation cascade. Thrombin activity is regulated by serum inhibitors and by its own action. With its procoagulant and anticoagulant functions, it plays a central role in thrombosis and haemostasis. It is an agonist for a number of cellular responses during inflammation and wound repair. Many diseases including stroke and myocardial infarction involve thrombosis; therefore, thrombin is a preferred target of antithrombotic drugs. Drugs available to block thrombin action include heparins, hirudins (lepirudin and bivalirudin), vitamin K antagonists and a new generation of direct thrombin inhibitors such as dabigatran and argatroban.

Key Concepts:

Thrombin is a serine protease that converts fibrinogen into fibrin and plays a crucial role in haemostasis and thrombosis.

During coagulation, factor Xa/Va complex formed on phospholipid or platelet membrane converts prothrombin to thrombin in the presence of Ca
2+
.

Thrombin also activates platelets and factors V, VIII and XI to enhance haemostasis.

In addition to haemostasis, thrombin plays a major role in inflammation and wound healing, and it is a potent mitogenic factor.

Thrombin has anticoagulant effects by activating the protein C pathway and by releasing plasminogen activators from endothelial cells, which promote fibrinolytic cascade.

Consequences of thrombosis include vascular diseases such as stroke, myocardial infarction and deep‐vein thrombosis and pulmonary embolism.

Both direct and indirect inhibitors are used clinically to treat thrombotic disorders.
Bioluminescence
Authors: De Abhijit
Published: July 2014

Bioluminescence is the active luminescence light producing event encountered among diverse group of living organisms in nature, more commonly in deep sea organisms. The event is a result of high‐quantum yield enzyme–substrate catalysis reaction resulting in the production of light devoid of any heat. The chemical reactions behind bioluminescence light emission can be broadly categorised as
adenosine triphosphate (ATP)
‐dependent and ATP‐independent mechanisms. Bioluminescence identified from firefly beetle is an example of ATP‐dependent photo‐production, whereas in jellyfish and
Renilla
sp. bioluminescence is an ATP‐independent process. In recent years several new biotechnology applications have used bioluminescence demonstrating their utility as highly sensitive assays for measuring cellular functions
in vivo
. Often genetic modifications in the luciferase structure or chemical modifications of their substrate have added new functionalities making these assays even more robust. Finally, noninvasive bioluminescence imaging has also evolved as an attractive tool for interrogating human cellular biology in rodent models.

Key Concepts:

Bioluminescence is light producing event caused by luciferase enzyme mediated substrate catalysis.

Bioluminescence can be co‐factor (e.g. ATP and Ca
2+
) dependent or independent process.

Evolutionary relationship among the structure of various luciferase proteins or their organic chemical substrates are hard to establish, with little or no commonality.

Luciferase proteins obtained from diverse organisms are used as bioluminescent reporters because they enable monitoring of intracellular events with high sensitivity, and without destroying the cells or tissues.

In biotechnology, mutations can be performed on luciferase gene sequence obtained from nature to make it suitable for use in higher order organisms and/or attribute better characters such as brightness, change spectral properties or protein stability.

Bioluminescence is extensively used in basic laboratory experiments for biotechnology and biomedical research, particularly in the format of various assays such as BRET and other diagnostic methods.

Noninvasive small animal imaging using luciferase reporter is gaining ground to provide simultaneous qualitative and quantitative measurements of disease interrogation
in vivo
.
Mimicry
Authors: Speed Mike
Published: July 2014

In its most general form mimicry refers to phenotypes of an organism that are adaptively modified to resemble living or nonliving components of its environments. Phenotype mimicry can be used in a number of different ways, most notably, to protect individuals against predators and other enemies. Such protective mimicry includes masquerade (copying an inanimate object in the environment), Batesian mimicry (an edible prey copies a defended prey) and Müllerian mimicry (shared warning signals between defended prey species). Phenotype mimicry may also be used aggressively, where for example, a predaceous mimic uses mimicry to hide from or to lure victims. In sexual mimicry (e.g. females look like males or vice versa), phenotype mimicry may be used to remove costs of sexual selection. In song mimicry, mimicry may be used to attract mates, to deter predation or facilitate grouping. Although mimicry is used in very diverse ways in nature, there may be similarities in the evolutionary ecology of mimetic phenotypes. A key point is that if the fitness of individual mimics increases with the number of mimics in a habitat then we may expect monomorphisms in the phenotypes; but if fitness declines as abundance increases we may anticipate the opposite.

Key Concepts:

Mimicry refers to phenotypes of an organism that are adaptively modified to resemble living or nonliving components of their environments.

The most extensively studied forms of mimicry are those used to protect prey from predators (especially mimetic resemblance of the colour patterns of a warningly coloured animal: Batesian and Müllerian mimicries).

In masquerade edible prey mimics inanimate objects in their environment (twigs and stones) to prevent predators noticing and attacking them.

Nature has found many different uses for phenotype mimicry in addition to avoidance of predation (e.g. aggressive use by predators to enable predation; by nectarless flowers to attract pollinators and by sexual mimicry and vocal mimicry).

Though mimicry is used in various ways there may be some common evolutionary issues; for example, how phenotype mimicry can evolve when the intermediate forms are less fit than both the original ancestral and the perfectly mimetic trait.

The benefits to a mimic are likely to change with the local abundance of the mimetic phenotype in a locality. Sometimes mimics benefit when there are many present (and we expect monomorphism in mimicry).

Often mimics lose benefits as the mimetic phenotype increases in abundance (in which case diversification of mimetic phenotypes may be expected).

When mimicry harms another organism we may expect counteractive measures in the form of adaptive change within an organism's lifetime (by learning) or by adaptive change across generations (coevolution).