Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome

Pseudogenes are non-functioning copies of genes in genomic DNA, which may either result from reverse transcription from an mRNA transcript (processed pseudogenes) or from gene duplication and subsequent disablement (non-processed pseudogenes). As pseudogenes are apparently ‘dead’, they usually have a variety of obvious disablements (e.g., insertions, deletions, frameshifts and truncations) relative to their functioning homologs. We have derived an initial estimate of the size, distribution and characteristics of the pseudogene population in the Caenorhabditis elegans genome, performing a survey in ‘molecular archaeology’. Corresponding to the 18 576 annotated proteins in the worm (i.e., in Wormpep18), we have found an estimated total of 2168 pseudogenes, about one for every eight genes. Few of these appear to be processed. Details of our pseudogene assignments are available from http://bioinfo.mbb.yale.edu/genome/worm/pseudogene. The population of pseudogenes differs significantly from that of genes in a number of respects: (i) pseudogenes are distributed unevenly across the genome relative to genes, with a disproportionate number on chromosome IV; (ii) the density of pseudogenes is higher on the arms of the chromosomes; (iii) the amino acid composition of pseudogenes is midway between that of genes and (translations of) random intergenic DNA, with enrichment of Phe, Ile, Leu and Lys, and depletion of Asp, Ala, Glu and Gly relative to the worm proteome; and (iv) the most common protein folds and families differ somewhat between genes and pseudogenes—whereas the most common fold found in the worm proteome is the immunoglobulin fold and the most common ‘pseudofold’ is the C-type lectin. In addition, the size of a gene family bears little overall relationship to the size of its corresponding pseudogene complement, indicating a highly dynamic genome. There are in fact a number of families associated with large populations of pseudogenes. For example, one family of seven-transmembrane receptors (represented by gene B0334.7) has one pseudogene for every four genes, and another uncharacterized family (represented by gene B0403.1) is approximately two-thirds pseudogenic. Furthermore, over a hundred apparent pseudogenic fragments do not have any obvious homologs in the worm.

CEG after a morning of cave digging

Loay, Bohol, Philippines

Morphological and physiological specialization for digging in amphisbaenians, an ancient lineage of fossorial vertebrates

Amphisbaenians are legless reptiles that differ significantly from other vertebrate lineages. Most species dig underground galleries of similar diameter to that of the animal. We studied the muscle physiology and morphological attributes of digging effort in the Brazilian amphisbaenid Leposternon microcephalum (Squamata; Amphisbaenia), which burrows by compressing soil against the upper wall of the tunnel by means of upward strokes of the head. The individuals tested (

Digging Deeper than Platinum: South Africa's Participation in an Emergent Fuel Cell Industry

South’s Africa’s position as global platinum supplier provides a unique opportunity for an emergent fuel cell industry. The innovative technology’s reliance on platinum has sparked interest in the mining sector, promoting the clean energy-producing devices in their own operations. This research focuses upon contemporary structures of racial oppression within the industry, to analyse how these dynamics influence the development and implementation of innovative technology. It also challenges the sustainability discourse associated with fuel cell technology in South Africa. The study follows a qualitative research approach, incorporating a political ecology focus to highlight the politicized nature of these interactions. The methodology incorporates a literature review, key informant interviews, fieldwork observations and document analysis. Findings indicate that the implementation of fuel cell technology in South Africa’s platinum mines will disproportionately burden historically disadvantaged South Africans, with the lack in technical knowledge-base considered a major challenge. Additionally, it was found that sustainability claims surrounding fuel cell technology are largely based on environmental characteristics. This has resulted in an oversimplification and a depoliticised account of the impacts of the technology. This study looked critically at the convergence of history and innovation, placing emphasis on context, power relations and knowledge to provide a more holistic account of the research problem. Opportunities exist for making a meaningful and viable contribution towards development and sustainability by means of investing in a South African fuel cell industry. The challenge will be in deliberately seeking pathways which address the more complex components of sustainability, benefitting all stakeholders and paying particular attention to the historical, political and social contexts from which the technology emerges. It is this particular context which allows for a questioning and perhaps even a re-evaluation of the sustainability narratives broadly applied to fuel cell technology.

Digging up the frequency of phrasal verbs in English for the Police: the case of "up"

The present study focuses on the frequency of phrasal verbs with the particle up in the context of crime and police investigative work. This research emerges from the need to enlarge McCarthy and O’Dell’s (2004) scope from purely criminal behavior to police investigative actions. To do so, we relied on a corpus of 504,124 running words made up of spoken dialogues extracted from the script of the American TV series Castle shown on ABC since 2009. Based on Rudzka-Ostyn’s (2003) cognitive motivations for the particle up, we have identified five different meaning extensions for our phrasal verbs. Drawing from these findings, we have designed pedagogical activities for those L2 learners that study English at the Police Academy.

Natural recovery of the benthic nematode assemblages associated to Zostera noltii seagrass beds after physical disturbance caused by digging harvest activity

Seagrass beds are productive ecosystems that maintain high levels of biodiversity, making them susceptible to anthropogenic pressures such as bivalve harvesting. Nematodes are considered great ecological indicators as changes in their density, diversity and structure may represent changes in the environment. This experimental fieldwork aimed to assess the impact of the bivalve harvesting on the nematodes assemblage of a seagrass bed in the Mira estuary by simulating the digging activity. Two plots were subjected to the digging (D1 and D19) and two plots were control (C11 and C18). The sampling took place in five occasions: T0 – before digging; T1 – 14 days; T2 – 45 days; T3 – 75 days; and T4 – 165 days after digging. The results showed no significant difference in the nematode assemblages’ density, diversity and trophic composition between treatments and sampling times, evidencing their high tolerance for naturally stressed environments and to the level of digging they were exposed; Recuperação natural das comunidades de nematodes bentónicos associados aos povoamentos de Zostera noltii após atividade de marisqueio Resumo: As pradarias marinhas são ecossistemas produtivos que suportam elevados níveis de biodiversidade, pelo que estão sujeitos a pressões antropogénicas. Os nematodes são bons indicadores ecológicos pois respondem rapidamente a qualquer perturbação por alterações na densidade, diversidade e estrutura. Este trabalho experimental teve como finalidade o estudo da recuperação natural das comunidades de nematodes associados aos povoamentos de Zostera noltii pela simulação da atividade de marisqueio. Dois plots foram sujeitos a revolvimento (D1 e D19) e dois plots serviram como controlo (C11 e C18) e foram efetuadas amostragens em cinco ocasiões: T0 – antes do revolvimento; T1 – 14 dias; T2 – 45 dias; T3 – 75 dias; e T4 – 165 dias após revolvimento. Os resultados obtidos não mostraram diferenças significativas na diversidade, densidade e composição trófica das comunidades de nematodes entre tratamentos e tempos de amostragem, evidenciando a sua elevada tolerância a ambientes naturalmente dinâmicos e ao nível de revolvimento a que foram expostas.

Digging Deeper than Platinum: South Africa's Participation in an Emergent Fuel Cell Industry

Thesis (Master, Environmental Studies) -- Queen's University, 2016-09-09 11:52:31.446

Enzymatic activity on sediments and nematode assemblage responses during seagrass beds habitat recovery following the disturbance of the traditional digging activity of bivalves harvesting.

Sediment digging is an anthropogenic activity connected to the exploitation of living resources in estuarine and marine environments. The knowledge on the functional responses of the benthic assemblages to the physical disturbance is an important baseline to understand the ecological processes of the habitat recovery and restoration and to develop tools for the management of the harvesting activities. To investigate the effects of the digging activity of the bivalves on Zostera noltii seagrass beds a manipulative field experiment was conducted that included the enzymatic activity of sediments and the associated nematode assemblages. Four plots (two undisturbed serving as control and two dug to collect bivalves - treatment) with 18 subplots were randomly located at seagrass beds in the Mira estuary at the SW coast of Portugal. Samples were randomly and unrepeatably collected from three subplots of each plot in five different occasions, before sediment digging (T0) up to six months after disturbance (T5). Microbial activity in sediments was assess by determining the extracelular enzymatic activity of six hydrolytic enzymes (sulfatase, phosphatase, b -N-acetilglucosaminidase, b-glucosidase, urease, protease) and two oxidoreductases (phenol oxidase and peroxidase). The microbial community status was also assessed through the measurement of dehydrogenase, which reflects microbial respiration. The nematode assemblages composition, biodiversity and trophic composition at different sampling occasions were also analyzed. The fluorometric and biochemical parameters analysed of the Z. noltii plants during the experimental period showed a recovery of the seagrass beds, and it was detected an increase of the enzymatic activity of the sediments after disturbance. The nematodes assemblages were similar in all sampling occasions. The seagrass beds and the nematodes assemblages associated showed a high resilience to the stress caused by the traditional bivalves digging activity. The obtained results allow the development of a management programme for the commercial fishing activity to maintain the good environmental status and minimized the secondary environmental effects on marine and estuarine habitats through the establishment of a baseline for the regulation of the harvesting frequency.

A study of the interaction between operator style and machine capability for a hydraulic mining excavator

This paper presents a case study that explores how operator digging style juxtaposes with mechanical capability for a class of hydraulic mining excavators. The relationships between actuator and digging forces are developed and these are used to identify the excavator's capability to apply forces in various directions. Two distinct modes of operation are examined to see how they relate to the mechanical capabilities of the linkage and to establish if one has merit over the other. It is found that one of these styles results in lower loading of the machine.

Drogas, sujeito e proibicionismo: uma discussão sobre os modelos de atenção aos usuários de drogas

Pós-graduação em Psicologia - FCLAS

Instrumentação e monitorização na avaliação do comportamento de maciços e estruturas envolventes: caso de poços em meio urbano

Atualmente, a escavação de poços em locais densamente ocupados requer medidas severas para reduzir riscos e possíveis influências quer na própria obra quer em estruturas próximas. Neste campo, a instrumentação geotécnica e a sua monitorização tem um papel determinante na execução de obras geotécnicas, sendo que neste trabalho é dado um especial realce à instrumentação utilizada, às atividades de observação geotécnica, bem como à análise e interpretação das leituras para o controlo de movimentos induzidos no terreno pelas escavações. Este acompanhamento é baseado num plano de instrumentação, sendo descrito de uma forma transversal a importância do projeto e em particular das fases do processo de investigação geotécnica. O acompanhamento da execução dos poços para a futura Estação da Reboleira, permitiu validar as soluções de projeto para um determinado método construtivo, determinadas através de métodos numéricos e semi-empíricos, e abordados neste trabalho. A monitorização sistemática desde o início das escavações até ao revestimento secundário, permitiu tecer apreciações sobre os valores obtidos, apresentando-se alguns registos. Todas estas ações visam controlar e antecipar riscos de acidentes provocados pela execução de escavações, pelo que nesta tese é também realçada a importância da segurança e higiene no trabalho na prevenção dos riscos profissionais, independentemente da sua origem.

Ocorrência de nematódeos do gênero Ditylenchus em tubérculos de batatinha no Est. de São Paulo

Irish potato tubers imported from Holland and Germany were planted at the Instituto Agronômico Experiment Station, Campinas, in April, 1955. At digging time, in July, 1955, the tubers were found to be injured by nematodes belonging to the genus Ditylenchus. No visible symptoms were found on the plants during the growing season, since the nematodes did not attack the stems. However, prevailing weather conditions from April to July were not favorable for nema activities, with low temperature and rain precipitation. Therefore, it does not seem safe to assume that, as a rule, the nemas do not attack buds and stems, for further observations may reveal such an occurrence, as it has been reported in the literature. The injury was characterized by spots consisting of decaying brown tissue, the nematodes being found mainly between this and the uninjured tissue. Larvae and adults occurred simultaneously. Fourteen different potato varieties were attacked by the nematodes, the percentage of disfigured tubers ranging from 6 (vars. Irene, Barima and Tedria) to 38 (var. Stamm 456). Studies en the morphology cf the parasites disclosed that two different Ditylenchus forms were present, with Apheten-chus sp. and Aphelenchoides sp. associated with them. The writers have not yet drawn a final conclusion about the identification of the Ditylenchi. However, it was clearly seen that no form can be identified either with D. dipsaci or with D. destructor. Both forms have lateral fields made up of 6 incisures, what separates them from D. dipsaci. On the other hand, measurements as well as some details in the organization of the oesophagus make the identification with D. destructor quite impossible. As far as the origin of the parasites is concerned, the fact that they could not be determined either as D. dipsaci or as D. destructor emphasizes the possibility of being two native species, not introduced with the tubers imported.