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Many first-year university courses are large and content-driven, which can contribute to low student engagement and difficulty involving students in the dynamic, cross-disciplinary nature of inquiry. Learning communities can address these goals, but their implementation often poses logistical challenges, especially in large courses. Here, we apply learning communities using a linked-course model to enhance student engagement and inquiry across three large, first-year biology courses. These three courses (Discovering Biodiversity, Molecular and Cell Biology, and Biological Concepts of Health) offer different contexts for biological inquiry, introduce key biological concepts, and are connected through jointly mapped learning outcomes, shared online skill workshops, and integrative learning communities composed of students from each course. Diverse modes of student learning are used across the three courses, and contemporary problems are explored within classes and small group seminars, which promote the development of skills necessary for inquiry. This course structure requires the coordinated scheduling of seminars and interdisciplinary projects but allows flexibility in the use of lecture periods and online content while offering increased resource efficiency. Collectively, these courses provide opportunities for integration, skill development, and problem solving. In contrast to many other forms of learning communities, this particular model promotes both a disciplinary foundation and cross-disciplinary applications for large numbers of students.

BackgroundThe barber's pole worm, Haemonchus contortus, is one of the most economically important parasites of small ruminants worldwide. Although this parasite can be controlled using anthelmintic drugs, resistance against most drugs in common use has become a widespread problem. We provide a draft of the genome and the transcriptomes of all key developmental stages of H. contortus to support biological and biotechnological research areas of this and related parasites.ResultsThe draft genome of H. contortus is 320 Mb in size and encodes 23,610 protein-coding genes. On a fundamental level, we elucidate transcriptional alterations taking place throughout the life cycle, characterize the parasite's gene silencing machinery, and explore molecules involved in development, reproduction, host-parasite interactions, immunity, and disease. The secretome of H. contortus is particularly rich in peptidases linked to blood-feeding activity and interactions with host tissues, and a diverse array of molecules is involved in complex immune responses. On an applied level, we predict drug targets and identify vaccine molecules.ConclusionsThe draft genome and developmental transcriptome of H. contortus provide a major resource to the scientific community for a wide range of genomic, genetic, proteomic, metabolomic, evolutionary, biological, ecological, and epidemiological investigations, and a solid foundation for biotechnological outcomes, including new anthelmintics, vaccines and diagnostic tests. This first draft genome of any strongylid nematode paves the way for a rapid acceleration in our understanding of a wide range of socioeconomically important parasites of one of the largest nematode orders.

Birds exhibit small, constrained genome sizes relative to many other vertebrates. This has often been attributed to the metabolic constraints of powered flight, which requires small cells for efficient gas exchange. Small cells, in turn, are achieved in part by limiting nucleus size and thus DNA content. However, metabolism is not the only organismal trait that correlates with genome size in birds; relationships have also been reported with body size (positive) and relative brain size (inverse). In this study, a recent data set on cell numbers in the brains of birds was combined with available data on genome sizes to demonstrate a relationship between genome size and density of cells per gram of brain tissue. This suggests that small genomes are relevant not only in the evolution of avian flight but may also be associated with the extraordinary behavioural complexity shown by birds. Key words: brain complexity, cell size, C value, DNA content, neurons, parrots, songbirds. Les genomes des oiseaux sont relativement petits et limites par rapport a ceux de nombreux autres vertebres. Ce phenomene a souvent ete attribue aux contraintes metaboliques qu'impose le vol propulse, qui necessite des cellules de petite taille pour un echange gazeux efficace. Les petites cellules sont quant a elles obtenues en limitant la taille du noyau et, donc, le contenu en ADN. Le metabolisme n'est toutefois pas le seul caractere des organismes correle a la taille du genome chez les oiseaux; des relations ont egalement ete notees avec la taille du corps (positive) et avec la taille relative du cerveau (negative). Un ensemble de donnees recent sur le nombre de cellules dans les cerveaux d'oiseaux est combine aux donnees disponibles sur la taille des genomes pour demontrer l'existence d'une relation entre la taille du genome et la densite de cellules par gramme de tissu cerebral. Ce lien indiquerait que, en plus d'importants pour l'evolution du vol des oiseaux, les petits genomes pourraient egalement etre associes a l'extraordinaire complexite comportementale dont font preuve les oiseaux. [Traduit par la Redaction] Mots-cles: complexite du cerveau, taille des cellules, valeur C, contenu en ADN, neurones, perroquets, oiseaux chanteurs., Introduction The amount of DNA in the genome varies more than 300-fold among vertebrates, from less than 400 Mb (megabase) in puffer-fish to more than 130 000 Mb in African [...]

In this paper, the utility of a partial sequence of the COI gene, the DNA barcoding region, for the identification of species of black flies in the austral region was [...]

Lake Baikal in Russia is a large, ancient lake that has been the site of a major radiation of amphipod crustaceans. Nearly 400 named species are known in this single [...]

The genus Plethodon is the most species-rich salamander genus in North America, and nearly half of its species face an uncertain future. It is also one of the most diverse [...]

Although crustaceans vary extensively in genome size, little is known about how genome size may affect the ecology and evolution of species in this diverse group, in part due to [...]

Ribbon worms (phylum Nemertea) are among several animal groups that have been overlooked in past studies of genome-size diversity. Here, we report genome-size estimates for eight species of nemerteans, including representatives of the major lineages in the phylum. Genome sizes in these species ranged more than fivefold, and there was some indication of a positive relationship with body size. Somatic endopolyploidy also appears to be common in these animals. Importantly, this study demonstrates that both of the most common methods of genome-size estimation (flow cytometry and Feulgen image analysis densitometry) can be used to assess genome size in ribbon worms, thereby facilitating additional efforts to investigate patterns of variability in nuclear DNA content in this phylum. Key words: Nemertea, genetics, evolution, saltwater, DNA, polyploidy. Les vers rubanes (phylum des nemertes) figurent parmi plusieurs groupes d'animaux que les etudes passees sur la diversite de la taille des genomes ont negliges. Nous faisons etat d'estimations de la taille des genomes pour huit especes de nemertiens, dont des representants des principales lignees du phylum. Les variations de la taille des genomes chez ces especes varient du simple au quintuple et plus, et il semble y avoir une relation positive avec la taille du corps. L'endopolyploidie somatique semble egalement repandue chez ces animaux. Fait a noter, l'etude demontre que les deux methodes les plus repandues d'estimation de la taille des genomes (la cytometrie de flux et la densitometrie a l'aide de la coloration de Feulgen) peuvent etre utilisees pour evaluer la taille des genomes chez les vers rubanes, facilitant ainsi les efforts futurs visant l'etude des motifs de variabilite du contenu de l'ADN nucleaire dans ce phylum. [Traduit par la Redaction] Mots-cles: nemertes, genetique, evolution, eau salee, ADN, polyploidie., Introduction The first estimates of genome size (haploid nuclear DNA content) were made more than six decades ago (Vendrely and Vendrely 1948; Mirsky and Ris 1951), and since that time [...]

Introduction The biology of transposable elements Transposable elements (TEs) are mobile segments of DNA capable of being cut or copied from one location in the genome and reinserted into another. [...], Transposable elements (TEs) are among the most abundant components of many eukaryotic genomes. Efforts to explain TE abundance, as well as TE diversity among genomes, have led some researchers to draw an analogy between genomic and ecological processes. Adopting this perspective, we conducted an analysis of the cow (Bos taurus) genome using techniques developed by community ecologists to determine whether environmental factors influence community composition. Specifically, each chromosome within the Bos taurus genome was treated as a 'linear transect', and a multivariate redundancy analysis (RDA) was used to identify large-scale spatial patterns in TE communities associated with 10 TE families. The position of each TE community on the chromosome accounted for ~50% of the variation along the chromosome 'transect'. Multivariate analysis further revealed an effect of gene density on TE communities that is influenced by several other factors in the (genomic) environment, including chromosome length and TE density. The results of this analysis demonstrate that ecological methods can be applied successfully to help answer genomic questions. Key words: genome ecology, transposon ecology, transposable elements, spatial patterns, gene density, chromosome length. Les elements transposables (TE) sont parmi les composantes les plus abondantes au sein de plusieurs genomes eucaryotes. Les efforts visant a expliquer cette abondance et diversite des TE au sein des genomes ont amene certains chercheurs a voir une analogie entre les processus genomiques et evolutifs. C'est dans cette perspective que les auteurs ont realise une analyse du genome de la vache (Bos taurus) en employant des techniques developpees par les ecologistes des communautes pour determiner si des facteurs environnementaux influencent la composition d'une communaute. Specifiquement, chaque chromosome au sein du genome du Bos taurus a ete traite comme un <> et une analyse de redondance (RDA) multivariee a ete realisee pour identifier les grandes lignes de la repartition de communautes de TE appartenant a 10 familles de TE. La position de chaque communaute de TE au sein du chromosome expliquait ~50 % de la variation le long d'un'transect' chromosomique. Une analyse multivariee a ensuite revele un effet de la densite genique sur les communautes de TE qui est influence par plusieurs autres composantes de l'environnement (genomique), dont la longueur du chromosome et la densite en TE. Les resultats de cette analyse montrent que les methodes de l'ecologie peuvent servir a repondre a des questions genomiques. [Traduit par la Redaction] Mots-cles : ecologie du genome, ecologie des transposons, elements transposables, distribution spatiale, densite genique, longueur du chromosome.

Introduction To date, genome size estimates have been carried out for more than 13 000 species of animals and plants (Bennett and Leitch 2012; Gregory 2013). These data are important [...], A study was undertaken to evaluate both a pre-existing method and a newly proposed approach for the estimation of nuclear genome sizes in arthropods. First, concerns regarding the reliability of the well-established method of flow cytometry relating to impacts of rearing conditions on genome size estimates were examined. Contrary to previous reports, a more carefully controlled test found negligible environmental effects on genome size estimates in the fly Drosophila melanogaster. Second, a more recently touted method based on quantitative real-time PCR (qPCR) was examined in terms of ease of use, efficiency, and (most importantly) accuracy using four test species: the flies Drosophila melanogaster and Musca domestica and the beetles Tribolium castaneum and Dendroctonus ponderosa. The results of this analysis demonstrated that qPCR has the tendency to produce substantially different genome size estimates from other established techniques while also being far less efficient than existing methods. Key words: Arthropoda, genome size, flow cytometry, real-time PCR, polymerase chain reaction. Cette etude a ete initiee afin de comparer une methode existante et une nouvelle approche pour l&apos;estimation de la taille du genome nucleaire chez les arthropodes. Tout d&apos;abord, les auteurs ont examine l&apos;impact des conditions d&apos;elevage sur la mesure de la taille des genomes par cytometrie en flux, une methode bien etablie mais dont la fiabilite suscitait des inquietudes. Contrairement a ce qui a ete rapporte dans d&apos;autres travaux, des analyses realisees en apportant un grand soin pour controler ces conditions n&apos;ont pas revele d&apos;effets environnementaux significatifs sur les estimes de la taille du genome chez le Drosophila melanogaster. Deuxiemement, la facilite d&apos;utilisation, l&apos;efficience et, primordialement, l&apos;exactitude d&apos;une methode recente basee sur la PCR quantitative en temps reel (qPCR) ont ete examinees chez quatre especes: les mouches Drosophila melanogaster et Musca domestica ainsi que les coleopteres Tribolium castaneum et Dendroctonus ponderosa. Les resultats de cette analyse ont montre que la qPCR tendait a produire des estimes qui differaient de maniere substantielle des resultats obtenus au moyen de methodes etablies tout en etant beaucoup moins efficientes que celles-ci. [Traduit par la Redaction] Mots-cles: Arthropoda, taille du genome, cytometrie en flux, PCR en temps reel, reaction de polymerisation en chame.

Introduction The order Chiroptera is the second largest in mammals after rodents, and with >1100 species in 18 families it represents more than one-fifth of all mammalian diversity (Wilson and [...], Despite being a group of particular interest in considering relationships between genome size and metabolic parameters, bats have not been well studied from this perspective. This study presents new estimates for 121 'microbat' species from 12 families and complements a previous study on members of the family Pteropodidae ('megabats'). The results confirm that diversity in genome size in bats is very limited even compared with other mammals, varying approximately 2-fold from 1.63 pg in Lophostoma carrikeri to 3.17 pg in Rhinopoma hardwickii and averaging only 2.35 pg ± 0.02 SE (versus 3.5 pg overall for mammals). However, contrary to some other vertebrate groups, and perhaps owing to the narrow range observed, genome size correlations were not apparent with any chromosomal, physiological, flight-related, developmental, or ecological characteristics within the order Chiroptera. Genome size is positively correlated with measures of body size in bats, though the strength of the relationships differs between pteropodids ('megabats') and nonpteropodids ('microbats'). Key words: Chiroptera, genome size, C-value, flight, metabolism. Bien qu'elles constituent un groupe presentant un interet particulier pour l'etude des relations entre la taille du genome et les parametres metaboliques, les chauves-souris n'ont pas ete bien etudiees sous cet angle. Dans ce travail, les auteurs presentent des estimes pour 121 especes de 'microchiropteres' appartenant a 12 familles et ceci vient completer une etude anterieure sur des membres de la famille des Pteropodidae ('megachiropteres'). Les resultats confirment que la diversite de la taille des genomes chez les chauves-souris est limitee par rapport a d'autres mammiferes, variant environ du simple au double entre 1,63 pg chez le Lophostoma carrikeri a 3,17 pg chez le Rhinopoma hardwickii pour une moyenne de 2,35 pg ± 0,02 (contre 3,5 pg globalement chez les mammiferes). Cependant, contrairement a ce qui est observe chez d'autres vertebres, peut-etre en raison de la faible variation observee, la taille du genome ne semblait pas correlee avec des caracteristiques chromosomiques, physiologiques, liees au vol, developpementales ou ecologiques chez les chiropteres. La taille du genome etait cependant positivement correlee avec divers parametres de la taille du corps chez les chauves-souris, bien que le degre de correlation differait chez les pteropodides ('megachiropteres') et les non-pteropodides ('microchiropteres'). [Traduit par la Redaction] Mots-cles: Chiroptera, taille du genome, valeur C, vol, metabolisme.

Introduction The various animal phyla commonly described as early branching have become the subject of increasing interest from a genomic and evolutionary perspective in recent years. This includes the Cnidaria [...], The phyla known as early-branching lineages of animals have become the subject of increasing interest from the perspectives of genomics and evolutionary biology. Unfortunately, data on even the most fundamental properties of their genomes, such as genome size, remain very scarce. In this study, genome size estimates are reported for 75 species of sponges (phylum Porifera) representing 33 families and 12 orders, marking the first large survey of genome size diversity for an early-branching phylum. Sponge genome sizes averaged around 0.2 pg but exhibited a 17-fold range overall (0.04-0.63 pg). In addition, the results of comparisons of two methods of genome size quantification (flow cytometry and Feulgen image analysis densitometry) are presented, thereby facilitating future work on these animals. Some particularly promising avenues for future investigation are highlighted. Key words: C-value, Demospongiae, DNA content, flow cytometry, Feulgen image analysis densitometry, Porifera. Les embranchements comprenant les branches dites primitives au sein des animaux suscitent un interet croissant en genomique et en biologie de revolution. Malheureusement, les donnees sur les proprietes meme les plus elementaires de leurs genomes, comme la taille du genome, demeurent limitees. Dans ce travail, les auteurs rapportent la taille estimee des genomes pour 75 especes d'eponges (Porifera) representant 33 familles et 12 ordres, ce qui en fait la plus grande etude de la diversite de la taille des genomes chez une branche primitive. Les genomes des eponges font en moyenne 0,2 pg mais varient grandement (de 0,04 a 0,63 pg); ainsi, les plus petits sont 17 fois plus petits que les plus grands. De plus, les resultats de deux methodes d'evaluation de la taille des genomes (cytometrie en flux et densitometrie Feulgen) sont comparees, ce qui facilitera de futurs travaux chez ces animaux. Certaines avenues de recherche particulierement prometteuses sont soulignees. [Traduit par la Redaction] Mots-cles: valeur C, Demospongiae, contenu en ADN, cytometrie en flux, densitometrie Feulgen, Porifera.

Genome size (haploid nuclear DNA content) has been found to correlate positively with cell size and negatively with cell division rate in a variety of taxa. These cytological relationships manifest in various ways at the organism level, for example, in terms of body size, metabolic rate, or developmental rate, depending on the biology of the organisms. In birds, it has been suggested that high metabolic rate and strong flight ability are linked to small genome size. However, it was also hypothesized that the exceptional cognitive abilities of birds may impose additional constraints on genome size through effects on neuron size and differentiation, as has been observed in amphibians. To test this hypothesis, a comparative analysis was made between genome size, cell (erythrocyte) size, and brain size in 54 species of parrots and cockatoos (order Psittaciformes, family Psittacidae). Relative brain volume, which is taken as an indicator of investment in brain tissue and is widely correlated with behavioural and ecological traits, was found to correlate inversely with genome size. Several possible and mutually compatible explanations for this relationship are described. Key words: cell size, C-value, neuron, Psittacidae, relative brain volume. Il a ete observe que la taille du genome (contenu en ADN d'un noyau haploide) etait correlee positivement avec la taille des cellules et negativement avec le taux de division cellulaire chez nombre de taxons. Ces relations cytologiques se manifestent de diverses facons au niveau de l'organisme; cela peut se traduire en termes de la taille de l'organisme, de son taux metabolique ou de developpement selon la biologie de l'organisme. Chez les oiseaux, il a ete suggere qu'un taux metabolique eleve et une forte aptitude pour le vol seraient lies a un petit genome. Cependant, il a egalement ete postule que les capacites cognitives exceptionnelles des oiseaux imposeraient des contraintes additionnelles sur la taille des genomes via des effets sur la taille et la differenciation des neurones comme cela a ete observe chez les amphibiens. Pour tester cette hypothese, une analyse a ete faite de la taille du genome, de la taille des cellules (des erythrocytes) et de la taille du cerveau chez 54 especes de perroquets et de cacatoes (ordre Psittaciformes, famille Psittacidae). Le volume relatif du cerveau, lequel constitue un indicateur de l'investissement en tissus cerebraux et montre une grande correlation avec des caracteres comportementaux et ecologiques, s'est avere inversement correle avec la taille du genome. Plusieurs explications possibles, sans etre mutuellement exclusives, sont proposees pour cette relation. Mots-cles : taille des cellules, valeur C, neurone, Psittacidae, volume cerebral relatif. [Traduit par la Redaction], Introduction Recent research has revealed that the cognitive abilities of birds far exceed traditional expectations (e.g., Lefebvre et al. 2004; Sol and Price 2008). It has been shown, for instance, [...]

Abstract: The several thousand-fold range in genome size among animals has remained a subject of active research and debate for more than half a century, but no satisfactory explanation has [...]

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2007.09.055 Byline: Willow N. Gabriel (a), Robert McNuff (b), Sapna K. Patel (a), T. Ryan Gregory (c), William R. Jeck (a), Corbin D. Jones (a), Bob Goldstein (a) Keywords: Development; Evolution; Ecdysozoa; Tardigrade; Lineage; Model system Abstract: Studying development in diverse taxa can address a central issue in evolutionary biology: how morphological diversity arises through the evolution of developmental mechanisms. Two of the best-studied developmental model organisms, the arthropod Drosophila and the nematode Caenorhabditis elegans, have been found to belong to a single protostome superclade, the Ecdysozoa. This finding suggests that a closely related ecdysozoan phylum could serve as a valuable model for studying how developmental mechanisms evolve in ways that can produce diverse body plans. Tardigrades, also called water bears, make up a phylum of microscopic ecdysozoan animals. Tardigrades share many characteristics with C. elegans and Drosophila that could make them useful laboratory models, but long-term culturing of tardigrades historically has been a challenge, and there have been few studies of tardigrade development. Here, we show that the tardigrade Hypsibius dujardini can be cultured continuously for decades and can be cryopreserved. We report that H. dujardini has a compact genome, a little smaller than that of C. elegans or Drosophila, and that sequence evolution has occurred at a typical rate. H. dujardini has a short generation time, 13-14 days at room temperature. We have found that the embryos of H. dujardini have a stereotyped cleavage pattern with asymmetric cell divisions, nuclear migrations, and cell migrations occurring in reproducible patterns. We present a cell lineage of the early embryo and an embryonic staging series. We expect that these data can serve as a platform for using H. dujardini as a model for studying the evolution of developmental mechanisms. Author Affiliation: (a) Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA (b) Sciento, 61 Bury Old Road, Whitefield, Manchester, M45 6TB, England, UK (c) Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 Article History: Received 3 July 2007; Revised 12 September 2007; Accepted 28 September 2007