A molecular perspective of the Laurencia complex (Ceramiales, Rhodophyta) in Macaronesia region

IV Congress of Marine Sciences. Las Palmas de Gran Canaria, June 11th to 13th 2014.

Biblioteca de referência de DNA barcodes de bivalves (Mollusca: Bivalvia) e gastrópodes (Mollusca: Gastropoda) da costa Portuguesa

Dissertação de mestrado em Ecologia

DNA barcodes de peixes marinhos da Europa: compilação de uma biblioteca de referência validada e investigação de padrões de divergência genética

Dissertação de mestrado em Ecologia

Barcoding human physical activity to assess chronic pain conditions.

BACKGROUND: Modern theories define chronic pain as a multidimensional experience - the result of complex interplay between physiological and psychological factors with significant impact on patients' physical, emotional and social functioning. The development of reliable assessment tools capable of capturing the multidimensional impact of chronic pain has challenged the medical community for decades. A number of validated tools are currently used in clinical practice however they all rely on self-reporting and are therefore inherently subjective. In this study we show that a comprehensive analysis of physical activity (PA) under real life conditions may capture behavioral aspects that may reflect physical and emotional functioning.¦METHODOLOGY: PA was monitored during five consecutive days in 60 chronic pain patients and 15 pain-free healthy subjects. To analyze the various aspects of pain-related activity behaviors we defined the concept of PA 'barcoding'. The main idea was to combine different features of PA (type, intensity, duration) to define various PA states. The temporal sequence of different states was visualized as a 'barcode' which indicated that significant information about daily activity can be contained in the amount and variety of PA states, and in the temporal structure of sequence. This information was quantified using complementary measures such as structural complexity metrics (information and sample entropy, Lempel-Ziv complexity), time spent in PA states, and two composite scores, which integrate all measures. The reliability of these measures to characterize chronic pain conditions was assessed by comparing groups of subjects with clinically different pain intensity.¦CONCLUSION: The defined measures of PA showed good discriminative features. The results suggest that significant information about pain-related functional limitations is captured by the structural complexity of PA barcodes, which decreases when the intensity of pain increases. We conclude that a comprehensive analysis of daily-life PA can provide an objective appraisal of the intensity of pain.

Molecular comparison of topotypic specimens confirms Anopheles (Nyssorhynchus) dunhami Causey (Diptera: Culicidae) in the Colombian Amazon

The presence of Anopheles (Nyssorhynchus) dunhami Causey in Colombia (Department of Amazonas) is confirmed for the first time through direct comparison of mtDNA cytochrome c oxidase I (COI) barcodes and nuclear rDNA second internal transcribed spacer (ITS2) sequences with topotypic specimens of An. dunhami from Tefé, Brazil. An. dunhami was identified through retrospective correlation of DNA sequences following misidentification as Anopheles nuneztovari s.l. using available morphological keys for Colombian mosquitoes. That An. dunhami occurs in Colombia and also possibly throughout the Amazon Basin, is of importance to vector control programs, as this non-vector species is morphologically similar to known malaria vectors including An. nuneztovari, Anopheles oswaldoi and Anopheles trinkae. Species identification of An. dunhami and differentiation from these closely related species are highly robust using either DNA ITS2 sequences or COI DNA barcode. DNA methods are advocated for future differentiation of these often sympatric taxa in South America.

Prey identification in nests of the potter wasp Hypodynerus andeus (Packard) (Hymenoptera, Vespidae, Eumeninae) using DNA barcodes

Prey identification in nests of the potter wasp Hypodynerus andeus (Packard) (Hymenoptera, Vespidae, Eumeninae) using DNA barcodes. Geometrid larvae are the only prey known for larvae of the Neotropical potter wasp Hypodynerus andeus (Packard, 1869) (Hymenoptera, Vespidae, Eumeninae) in the coastal valleys of the northern Chilean Atacama Desert. A fragment of the mitochondrial gene cytochrome oxidase c subunit 1 was amplified from geometrid larvae collected from cells of H. andeus in the Azapa Valley, Arica Province, and used to provide taxonomic identifications. Two species, Iridopsis hausmanni Vargas, 2007 and Macaria mirthae Vargas, Parra & Hausmann, 2005 were identified, while three others could be identified only at higher taxonomic levels, because the barcode reference library of geometrid moths is still incomplete for northern Chile.

Anopheles goeldii Rozeboom & Gabaldón (Diptera, Culicidae): a species of the Nuneztovari Complex of Anopheles Meigen

Anopheles (Nyssorhynchus) goeldiiRozeboom & Gabaldón, 1941, a species of the Nuneztovari Complex, was described based on morphological characteristics of the male, female, larva, pupa, and eggs. The type locality is Boa Vista (= Fordlândia), a district in the vicinity of Rio Tapajós, in the municipality of Aveiro, in the state of Pará, Brazil. Anopheles goeldii is redescribed based on morphological traits of the fourth instar larva, pupa, egg, and male and female. DNA sequences from the cytochrome oxidase subunit I (COI barcode region) of the mitochondrial genome were utilized for species characterization. Specimens of An. goeldii from the Pará, Amapá, and Amazonas states were employed to redescribe the species and to compare with morphologically similar taxa.

Sistemes logístics de codificació i identificació, i perspectives de futur

Comptar amb sistemes sofisticats de gestió o programes ERP (Enterprise Resource Planning) no és suficient per a les organitzacions. Per a què aquests recursos donin resultats adequats i actualitzats, la informació d’entrada ha de llegir-se de forma automàtica, per aconseguir estalviar en recursos, eliminació d’errors i assegurar el compliment de la qualitat. Per aquest motiu és important comptar amb eines i serveis d’identificació automàtica i col•lecció de dades. Els principals objectius a assolir (a partir de la introducció al lector de la importància dels sistemes logístics d’identificació en un entorn global d’alta competitivitat), són conèixer i comprendre el funcionament de les tres principals tecnologies existents al mercat (codis de barres lineals, codis de barres bidimensionals i sistemes RFID), veure en quin estat d’implantació es troba cadascuna i les seves principals aplicacions. Un cop realitzat aquest primer estudi es pretén comparar les tres tecnologies per o poder obtenir perspectives de futur en l’àmbit de l’autoidentificació. A partir de la situació actual i de les necessitats de les empreses, juntament amb el meravellós món que sembla obrir la tecnologia RFID (Radio Frequency Identification), la principal conclusió a la que s’arribarà és que malgrat les limitacions tècniques dels codis de barres lineals, aquests es troben completament integrats a tota la cadena logística gràcies a l’estandarització i la utilització d’un llenguatge comú, sota el nom de simbologies GTIN (Global Trade Item Number), durant tota la cadena de subministres que garanteixen total traçabilitat dels productes gràcies en part a la gestió de les bases de dades i del flux d’informació. La tecnologia RFUD amb l’EPC (Electronic Product Code) supera aquestes limitacions, convertint-se en el màxim candidat per a substituir els limitats codis de barres. Tot i això, RFID, amb l’EPC, no serà un adequat identificador logístic fins que es superin importants barreres, com són la falta d’estandarització i l’elevat cost d’implantació.

DNA barcodes for soil animal taxonomy

The biodiversity of soil communities remains very poorly known and understood. Soil biological sciences are strongly affected by the taxonomic crisis, and most groups of animals in that biota suffer from a strong taxonomic impediment. The objective of this work was to investigate how DNA barcoding - a novel method using a microgenomic tag for species identification and discrimination - permits better evaluation of the taxonomy of soil biota. A total of 1,152 barcode sequences were analyzed for two major groups of animals, collembolans and earthworms, which presented broad taxonomic and geographic sampling. Besides strongly reflecting the taxonomic impediment for both groups, with a large number of species-level divergent lineages remaining unnamed so far, the results also highlight a high level (15%) of cryptic diversity within known species of both earthworms and collembolans. These results are supportive of recent local studies using a similar approach. Within an impeded taxonomic system for soil animals, DNA-assisted identification tools can facilitate and improve biodiversity exploration and description. DNA-barcoding campaigns are rapidly developing in soil animals and the community of soil biologists is urged to embrace these methods.

Land plants and DNA barcodes: short-term and long-term goals.

Land plants have had the reputation of being problematic for DNA barcoding for two general reasons: (i) the standard DNA regions used in algae, animals and fungi have exceedingly low levels of variability and (ii) the typically used land plant plastid phylogenetic markers (e.g. rbcL, trnL-F, etc.) appear to have too little variation. However, no one has assessed how well current phylogenetic resources might work in the context of identification (versus phylogeny reconstruction). In this paper, we make such an assessment, particularly with two of the markers commonly sequenced in land plant phylogenetic studies, plastid rbcL and internal transcribed spacers of the large subunits of nuclear ribosomal DNA (ITS), and find that both of these DNA regions perform well even though the data currently available in GenBank/EBI were not produced to be used as barcodes and BLAST searches are not an ideal tool for this purpose. These results bode well for the use of even more variable regions of plastid DNA (such as, for example, psbA-trnH) as barcodes, once they have been widely sequenced. In the short term, efforts to bring land plant barcoding up to the standards being used now in other organisms should make swift progress. There are two categories of DNA barcode users, scientists in fields other than taxonomy and taxonomists. For the former, the use of mitochondrial and plastid DNA, the two most easily assessed genomes, is at least in the short term a useful tool that permits them to get on with their studies, which depend on knowing roughly which species or species groups they are dealing with, but these same DNA regions have important drawbacks for use in taxonomic studies (i.e. studies designed to elucidate species limits). For these purposes, DNA markers from uniparentally (usually maternally) inherited genomes can only provide half of the story required to improve taxonomic standards being used in DNA barcoding. In the long term, we will need to develop more sophisticated barcoding tools, which would be multiple, low-copy nuclear markers with sufficient genetic variability and PCR-reliability; these would permit the detection of hybrids and permit researchers to identify the 'genetic gaps' that are useful in assessing species limits.

IngredientApp

Aquest document descriu una aplicació per a dispositius Android. L'aplicació IngredientApp és un intent d'autocontrolar el que comprem, fem servir o mengem. Es tracta d'una aplicació a la qual s'hi defineixen unes preferències sobre els ingredients dels productes i, fent servir un smartphone, sense haver de mirar la llista d'ingredients, l'aplicatiu li advertirà si el producte compleix els seus criteris.

DNA barcoding of Corsican mayflies (Ephemeroptera) with implications on biogeography, systematics and biodiversity

Mayflies (Ephemeroptera) are known to generally present a high degree of insular endemism: half of the 28 species known from Corsica and Sardinia are considered as endemic. We sequenced the DNA barcode (a fragment of the mitochondrial COI gene) of 349 specimens from 50 localities in Corsica, Sardinia, continental Europe and North Africa. We reconstructed gene trees of eight genera or species groups representing the main mayfly families. Alternative topologies were built to test if our reconstructions suggested a single or multiple Corsican/Sardinian colonization event(s) in each genus or species group. A molecular clock calibrated with different evolution rates was used to try to link speciation processes with geological events. Our results confirm the high degree of endemism of Corsican and Sardinian mayflies and the close relationship between these two faunas. Moreover, we have evidence that the mayfly diversity of the two islands is highly underestimated as at least six new putative species occur on the two islands. We demonstrated that the Corsican and Sardinian mayfly fauna reveals a complex history mainly related to geological events. The Messinian Salinity Crisis, which is thought to have reduced marine barriers, thus facilitating gene flow between insular and continental populations, was detected as the most important event in the speciation of most lineages. Vicariance processes related to the split and rotation of the Corso-Sardinian microplate had a minor impact as they involved only two genera with limited dispersal and ecological range. Colonization events posterior to the Messinian Salinity Crisis had only marginal effects as we had indication of recent gene flow only in two clades. With very limited recent gene flow and a high degree of endemism, mayflies from Corsica and Sardinia present all the criteria for conservation prioritization.

Viivakoodin lukeminen matkapuhelimella

Purpose of this work was to study different types of barcodes and possibilities of reading them with mobile phones camera. Another goal was to transfer product information from a server to a mobile phone according to a barcode. There is existing software to read barcodes with mobile phones camera. They also open a www – page to mobile phones browser according to a URL address interpreted from a barcode. I simulated a use-case scenario, in which product delivery related information was controlled by a mobile phone. The information was located in a MySQL database and it was controlled with www – pages through mobile phones browser. I also made tests about how possible difficulties effect on successful interpretation of a barcode.

Sistemes logístics de codificació i identificació, i perspectives de futur

Comptar amb sistemes sofisticats de gestió o programes ERP (Enterprise Resource Planning) no és suficient per a les organitzacions. Per a què aquests recursos donin resultats adequats i actualitzats, la informació d’entrada ha de llegir-se de forma automàtica, per aconseguir estalviar en recursos, eliminació d’errors i assegurar el compliment de la qualitat. Per aquest motiu és important comptar amb eines i serveis d’identificació automàtica i col•lecció de dades. Els principals objectius a assolir (a partir de la introducció al lector de la importància dels sistemes logístics d’identificació en un entorn global d’alta competitivitat), són conèixer i comprendre el funcionament de les tres principals tecnologies existents al mercat (codis de barres lineals, codis de barres bidimensionals i sistemes RFID), veure en quin estat d’implantació es troba cadascuna i les seves principals aplicacions. Un cop realitzat aquest primer estudi es pretén comparar les tres tecnologies per o poder obtenir perspectives de futur en l’àmbit de l’autoidentificació. A partir de la situació actual i de les necessitats de les empreses, juntament amb el meravellós món que sembla obrir la tecnologia RFID (Radio Frequency Identification), la principal conclusió a la que s’arribarà és que malgrat les limitacions tècniques dels codis de barres lineals, aquests es troben completament integrats a tota la cadena logística gràcies a l’estandarització i la utilització d’un llenguatge comú, sota el nom de simbologies GTIN (Global Trade Item Number), durant tota la cadena de subministres que garanteixen total traçabilitat dels productes gràcies en part a la gestió de les bases de dades i del flux d’informació. La tecnologia RFUD amb l’EPC (Electronic Product Code) supera aquestes limitacions, convertint-se en el màxim candidat per a substituir els limitats codis de barres. Tot i això, RFID, amb l’EPC, no serà un adequat identificador logístic fins que es superin importants barreres, com són la falta d’estandarització i l’elevat cost d’implantació.

Varastoinnin kehittäminen eräässä huolintaliikkeessä

Tässä työssä kuvataan Saimaa Linesin varastointiin ja työturvallisuuteen liittyviä ongelmia sekä esitetään ehdotuksia niin varastoinnin tehostamiseksi kuin työturvallisuuden parantamiseksi. Saimaa Lines on lappeenrantalainen huolintaliike, jonka asiakkaat sijaitsevat pääasiassa entisen Neuvostoliiton alueella. Varastolla on lastausongelmia ja työturvallisuus on puutteellisesti hoidettu. Aluksi työssä tutkitaan ja vertaillaan viivakoodi- sekä RFID-järjestelmiä. Vertailujen pohjalta valitaan järjestelmistä toinen ja selvitetään, kuinka järjestelmä parantaisi varastointia Saimaa Linesilla sekä selvitetään käyttöönottokustannukset. Omana osionaan tarkastellaan työturvallisuutta ensin teoreettiselta pohjalta ja sen jälkeen esitellään tulokset Saimaa Linesille tehdystä Turvallisuuskympistä. Osion lopussa esitetään ehdotuksia turvallisuuden parantamiseksi.