Distribution, diversity and evolution of endogenous retroviruses in perissodactyl genomes

The evolution of mammalian genomes has been shaped by interactions with endogenous retroviruses (ERVs). In this study, we investigated the distribution and diversity of ERVs in the mammalian order Perissodactyla, with a view to understanding their impact on the evolution of modern equids (family Equidae). We characterize the major ERV lineages in the horse genome in terms of their genomic distribution, ancestral genome organization and time of activity. Our results show that subsequent to their ancestral divergence from rhinos and tapirs, equids acquired four novel ERV lineages. We show that two of these proliferated extensively in the lineage leading to modern horses, and one contains loci that are actively transcribed in specific tissues. In addition, we show that the white rhinoceros has resisted germline colonisation by retroviruses for over 54 million years - longer than any other extant mammalian species. The map of equine ERVs that we provide here will be of great utility to future studies aiming to investigate the potential functional roles of equine ERVs, and their impact on equine evolution

Inhibition of the mitochondrial pyruvate carrier protects from excitotoxic neuronal death.

Glutamate is the dominant excitatory neurotransmitter in the brain, but under conditions of metabolic stress it can accumulate to excitotoxic levels. Although pharmacologic modulation of excitatory amino acid receptors is well studied, minimal consideration has been given to targeting mitochondrial glutamate metabolism to control neurotransmitter levels. Here we demonstrate that chemical inhibition of the mitochondrial pyruvate carrier (MPC) protects primary cortical neurons from excitotoxic death. Reductions in mitochondrial pyruvate uptake do not compromise cellular energy metabolism, suggesting neuronal metabolic flexibility. Rather, MPC inhibition rewires mitochondrial substrate metabolism to preferentially increase reliance on glutamate to fuel energetics and anaplerosis. Mobilizing the neuronal glutamate pool for oxidation decreases the quantity of glutamate released upon depolarization and, in turn, limits the positive-feedback cascade of excitotoxic neuronal injury. The finding links mitochondrial pyruvate metabolism to glutamatergic neurotransmission and establishes the MPC as a therapeutic target to treat neurodegenerative diseases characterized by excitotoxicity

Facilitating Private Forestland Management: Relating Landowners’ Experience of their Forestland and their Conceptualization of Forest Management to their Management Behavior

Privately owned forestland accounts for the majority of forested land in the US and provides numerous ecological, economic and social benefits to its owners and society at large. However, numerous issues ranging from fragmentation and parcelization, to pressure from the forest products industry, to increasing land values for development and real estate interests threaten to “unravel” the forest landscape. Active management of forestland is seen as one way to combat such threats. Active management of private forestland has been linked to numerous factors such as private forest landowners’ (PFLs’) general education level and familiarity with forest management, their goals, interests, objectives, attitudes, values, beliefs, and socio-cultural identity and the size and tenure of their ownership, among others. However, despite numerous efforts to understand private forest landowners (PFLs) and their interests, goals and objectives in owning private forestland, and to educate them about, and provide assistance for, private forest management, most privately owned forestland is not managed and most landowners remain unaware of the assistance and information available to them. In addition, the primarily quantitative studies investigating how these factors relate to private forestland management have been criticized for producing diminishing returns and insufficiently updating survey instruments. Using a mixed methods study design, including both quantitative and qualitative approaches, this study, conducted in the Emory-Obed watershed of East Tennessee, examined how the meaning of PFLs’ experience of their forestland and their conceptualization of forest management, two variables previously unaddressed in the literature, relate to PFL management behavior. Based on their experiences with their land, PFLs were found to form strong personal attachments to their land. Both the strength and the nature of these attachments varied relative to the degree to which PFLs actively engaged in forest management practices. The experience of those who actively engage in forest management activities is focused on the land and its condition, while the experience of those who do not actively engage in forest management activities is focused on themselves and how the experience makes them feel. Private forestland was also experienced as place. When these ways of experiencing forestland were quantified, a set of five components characteristic of the experience of forestland were identified: emotional connection to forestland, connection to nature via forestland, connection to family via forestland, forestland provision of PFL personal and financial gain, and forestland provision of financial investment. The more actively engaged with private forest land management PFLs were, the more strongly they agreed that each of these components was both meaningful and important to them. Landowners also varied in the ways in which they understood the forest management concept. Landowners simultaneously conceptualized forest management as property maintenance, as creating and enhancing forest habitat and as making money. As with the meaning of PFLs experience of their forestland, the more actively engaged in forest management activities PFLs were, the more strongly they agreed each of these components defined forest management. Lastly, the vast majority of PFLs participating in this study stated they believe they manage their forestland. This is in stark contrast to conclusions reported in the literature concerning the percentage of PFLs actually managing their forestland and is attributed in part to lack of standardization in the operationalization of forest management participation measures reported in the literature. Several implications of the findings for professional forestry practice, research, outreach and education are made based on recognizing the importance of the meaning of landowners’ experience of their forestland and their conceptualization of forest management to their interest in and engagement in forest management activities. For example, as the findings indicate PFLs may not see a relationship between the ways their forestland is meaningful to them and their understanding of what it means to manage their forestland, forest landowner educational opportunities and events capitalizing on the strong personal attachments PFLs feel to their land and utilizing language similar to their own ways of speaking about these attachments such as, “Getting to Know Your Woods”, “The Woods in Your Backyard: What’s There and Why You Should Care” and “Having Your Cake and Eating It Too: Enjoying and Profiting From Your Forestland” may prove more effective than traditional programs

Identifying noncoding risk variants using disease-relevant gene regulatory networks.

Identifying noncoding risk variants remains a challenging task. Because noncoding variants exert their effects in the context of a gene regulatory network (GRN), we hypothesize that explicit use of disease-relevant GRNs can significantly improve the inference accuracy of noncoding risk variants. We describe Annotation of Regulatory Variants using Integrated Networks (ARVIN), a general computational framework for predicting causal noncoding variants. It employs a set of novel regulatory network-based features, combined with sequence-based features to infer noncoding risk variants. Using known causal variants in gene promoters and enhancers in a number of diseases, we show ARVIN outperforms state-of-the-art methods that use sequence-based features alone. Additional experimental validation using reporter assay further demonstrates the accuracy of ARVIN. Application of ARVIN to seven autoimmune diseases provides a holistic view of the gene subnetwork perturbed by the combinatorial action of the entire set of risk noncoding mutations. Nat Commun 2018 Feb 16; 9(1):702

Latitude does not influence cavity entrance orientation of South American avian excavators

In the Northern Hemisphere, several avian cavity excavators (e.g., woodpeckers) orient their cavities increasingly toward the equator as latitude increases (i.e., farther north), and it is proposed that they do so to take advantage of incident solar radiation at their nests. If latitude is a key driver of cavity orientations globally, this pattern should extend to the Southern Hemisphere. Here, we test the prediction that cavities are oriented increasingly northward at higher (i.e., colder) latitudes in the Southern Hemisphere and describe the preferred entrance direction(s) of 1501 cavities excavated by 25 avian species (n = 22 Picidae, 2 Trogonidae, 1 Furnariidae) across 12 terrestrial ecoregions (15°S ? 55°S) in South America. We used Bayesian projected normal mixed-effects models for circular data to examine the influence of latitude, and potential confounding factors, on cavity orientation. Also, a probability model selection procedure was used to simultaneously examine multiple orientation hypotheses in each ecoregion, to explore underlying cavity-orientation patterns. Contrary to predictions, and patterns from the Northern Hemisphere, birds did not orient their cavities more toward the equator with increasing latitude, suggesting that latitude may not be an important underlying selective force shaping excavation behavior in South America. Moreover, unimodal cavity-entrance orientations were not frequent among the ecoregions analyzed (infour ecoregions), whereas bimodal (in five ecoregions) or uniform (in three ecoregions) werealso common, although many of these patterns were not very sharp. Our results highlight the need to include data from under-studied biotas and regions to improve inferences at macroecology scales. Furthermore, we suggest a re-analysis of Northern Hemisphere cavity orientation patterns using a multimodel approach, and a more comprehensive assessment of the role of environmental factors as drivers of cavity orientation at different spatial scales in both hemispheres.Fil: Ojeda, Valeria Susana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; ArgentinaFil: Schaaf, Alejandro Alberto. Universidad Nacional de Jujuy. Instituto de Ecorregiones Andinas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Ecorregiones Andinas; ArgentinaFil: Altamirano, Tatiana Edith. University of British Columbia; CanadáFil: Bonaparte, Eugenia Bianca. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; ArgentinaFil: Bragagnolo, Laura Araceli. Universidad Nacional de La Pampa. Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Chazarreta, L.. Secretaría de Ambiente y Desarrallo Sustentable de la Nación; ArgentinaFil: Cockle, Kristina Louise. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; ArgentinaFil: Dias, R.. Universidade do Brasília; BrasilFil: Di Sallo, Facundo Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; ArgentinaFil: Ibarra, T.. Pontificia Universidad Católica de Chile; ChileFil: Ippi, Silvina Graciela. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Jauregui, Adrian. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Área Zoología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Jimenez, Jaime E.. Universidad de Magallanes; ChileFil: Lammertink, J. Martjan. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; ArgentinaFil: Lopez, F.. Universidad Nacional de La Pampa; ArgentinaFil: Nuñez Montellano, Maria Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Ciencias de la Tierra y Ambientales de La Pampa. Universidad Nacional de La Pampa. Facultad de Ciencias Exactas y Naturales. Instituto de Ciencias de la Tierra y Ambientales de La Pampa; ArgentinaFil: de la Peña, Martín. No especifíca;Fil: Rivera, Luis Osvaldo. Universidad Nacional de Jujuy. Instituto de Ecorregiones Andinas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Ecorregiones Andinas; ArgentinaFil: Vivanco, Constanza Guadalupe. Universidad Nacional de Jujuy. Instituto de Ecorregiones Andinas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Ecorregiones Andinas; ArgentinaFil: Santillán, Miguel. Museo de Historia Natural de La Pampa; ArgentinaFil: Soto, G.. Cornell University; Estados UnidosFil: Vergara, P.. Universidad de Santiago de Chile; ChileFil: Politi, Natalia. University of North Texas; Estados Unido

PRODUCTION SEQUENCING AND STABILITY ANALYSIS OF A JUST-IN-TIME SYSTEM WITH SEQUENCE DEPENDENT SETUPS

Just-In-Time (JIT) production systems is a popular area for researchers but real-world issues such as sequence dependent setups are often overlooked. This research investigates an approach for determining stability and an approach for mixed product sequencing in production systems with sequence dependent setups and buffer thresholds which signal replenishment of a given buffer. Production systems in this research operate under JIT pull production principles by producing only when demand exists and idle when no demand exists. In the first approach, an iterative method is presented to determine stability for a multi-product production system that operates with replenishment signals and may have sequence dependent setups. In this method, a network of nodes representing machine states and arcs representing the buffer inventory levels is used to find a stable trajectory for the production system via an iterative procedure. The method determines suitable buffer levels for the production system that ensure that a trajectory originating from any point within a buffer region will always map to a point contained on another buffer region for all future mappings. This iterative method for determining the stability of a production system was implemented using an algorithm to calculate the buffer inventory regions for all arcs in a given arc-node network. The algorithm showed favorable results for two and three product systems in which sequence dependent setups may exist. In the second approach, a product sequencing algorithm determines a product sequence for a production system based on system parameters – setup times, buffer levels, usage rates, production rates, etc. The algorithm selects a product by evaluating the goodness of each product that has reached the replenishment threshold at the current time. The algorithm also incorporates a lookahead function that calculates the goodness for some time interval into the future. The lookahead function considers all branches of the tree of potential sequences to prevent the sequence from travelling down a dead-end branch in which the system will be unable to avoid a depleted buffer. The sequencing algorithm allows the user to weight the five terms of the goodness equations (current and lookahead) to control the behavior of the sequence

On the origin of Acochlidia and other enigmatic euthyneuran gastropods, with implications for the systematics of Heterobranchia

<p>Abstract</p> <p>Background</p> <p>A robust phylogenetic hypothesis of euthyneuran gastropods, as a basis to reconstructing their evolutionary history, is still hindered by several groups of aberrant, more or less worm-like slugs with unclear phylogenetic relationships. As a traditional "order" in the Opisthobranchia, the Acochlidia have a long history of controversial placements, among others influenced by convergent adaptation to the mainly meiofaunal habitats. The present study includes six out of seven acochlidian families in a comprehensive euthyneuran taxon sampling with special focus on minute, aberrant slugs. Since there is no fossil record of tiny, shell-less gastropods, a molecular clock was used to estimate divergence times within Euthyneura.</p> <p>Results</p> <p>Our multi-locus molecular study confirms Acochlidia in a pulmonate relationship, as sister to Eupulmonata. Previous hypotheses of opisthobranch relations, or of a common origin with other meiofaunal Euthyneura, are clearly rejected. The enigmatic amphibious and insectivorous Aitengidae <it>incerta sedis </it>clusters within Acochlidia, as sister to meiofaunal and brackish Pseudunelidae and limnic Acochlidiidae. Euthyneura, Opisthobranchia and Pulmonata as traditionally defined are non-monophyletic. A relaxed molecular clock approach indicates a late Palaeozoic diversification of Euthyneura and a Mesozoic origin of the major euthyneuran diversity, including Acochlidia.</p> <p>Conclusions</p> <p>The present study shows that the inclusion of small, enigmatic groups is necessary to solve deep-level phylogenetic relationships, and underlines that "pulmonate" and "opisthobranch" phylogeny, respectively, cannot be solved independently from each other. Our phylogenetic hypothesis requires reinvestigation of the traditional classification of Euthyneura: morphological synapomorphies of the traditionally defined Pulmonata and Opisthobranchia are evaluated in light of the presented phylogeny, and a redefinition of major groups is proposed. It is demonstrated that the invasion of the meiofaunal habitat has occurred several times independently in various euthyneuran taxa, leading to convergent adaptations previously misinterpreted as synapomorphies. The inclusion of Acochlidia extends the structural and biological diversity in pulmonates, presenting a remarkable flexibility concerning habitat choice.</p

A pilot study of the relationship between the English language abilities of a group of primary school children and their tree-drawings

This pilot study attempts to assess the correlation between language ability and a projective Tree-drawing test. The hypothesis tested is that expounded by Sandra Michel, a psychologist working with Dr. A. A. Tomatis at the Language Centre in Paris. The theory of Language from which her work derives is that put forward by A. A. Tomatis in Vers l'écoute humaine (Towards Human Hearing), (1977) and Education and Dyslexia trans . , Louise Guiney, (1972). This hypothesis states that the Tree-drawing can give a clear indication of the kind of dialogue the testee will be able and willing to use. The claims for projective Tree-drawing 'tests' or techniques have been mainly concerned with personality or psychological assessments and sometimes with intelligence testing since Charles Koch first began his work in this field in the early forties. Sandra Michel in "The Tree Test", translated by T . Brown, (unpublished paper), Tomatis Centre (Scarbrough, Ontario, 1980) discusses a Tree-drawing scale that indicates both the developmental level of the child's language ability and his/her motivation towards dialogue and communication at this level. To test this hypothesis a sample of 1094 Tree-drawings was used. The drawings were done by Primary School children of both sexes from Sub. A. to Std . 5, collected over four years of research. These drawings were studied to see if the Tree scale of drawings described by Michel did in fact occur and if they occurred in the sequence she suggests. As a result of these preliminary investigations a developmental scale was devised and proposed as a refinement of Michel's scale. Scores from these two Tree-scales were correlated with English language scores using Pearson Product Moment Correlation Coefficient and the Spearman Rank techniques. The sample for this correlation study was a group of 54 Std. 5 pupils whose English language ability was evaluated by (i) a school English Examination mark, (ii) a Questionnaire scoring receptive and expressive language behaviours and (iii) Verbal I.Q. scores. The positive correlation between these language scores and the Tree-drawing projective test scores are discussed and the implications for English language teaching and suggestions for further research mentioned

What factors drive analyst forecasts in South Africa?

In partial fulfillment of the Degree: Master of Commerce (Accountancy), University of the Witwatersrand, October 2017This research examines through the use of survey data which key factors around a companies‟ industry positioning, strategic decisions and internal qualitative capabilities, are considered by financial analysts when preparing their financial forecasts. The research covered buy-side and sell-side analysts in South Africa. The results were however found to be non-conclusive and did not align to previous research on this matter. Comparisons between analysts covering the same company were performed with consistencies found on average across all variables. It is interesting to note that when a detailed analysis and comparison was performed by individual variable for analysts covering the same company, different views on some of the variables were identified between buy-side and sell-side analysts, therefore supporting the research obtained during the literature review. It was found based on the tests performed that the factors which have an impact on forecasted financials relate to superior product/service strategy, innovation and ability to execute strategy. These variables were however noted not to be consistent across all the financial forecast factors and are contradictory to the research highlighted in the literature review as well as the outcomes of the original study, ie. There are additional factors which are considered important. Further research is recommended on analyst behaviour in South Africa.GR201

Integrative taxonomy approach to detect spatial and temporal variability of the Mediterranean benthic communities through artificial substrate units (ASUs)

Monitoring spatial and temporal changes of marine benthic communities using standardized procedures is essential to take necessary steps towards conservation of marine ecosystems. In this study we combined Artificial Substrate Units (ASUs) for sampling of benthic communities, with integrative taxonomy approach that incorporated morphological identification of organisms and COI DNA metabarcoding, to characterize the diversity of communities at three locations across the Central Mediterranean Sea (Livorno and Palinuro, Italy; Rovinj, Croatia) in 2019 and 2020. Significant differences in the communities’ structure were observed both at large spatial scale between sampled locations, and at small spatial scale (less than ten kilometers) between sites. Moreover, significant temporal variability in species richness and structure of benthic assemblages was detected, with higher richness in 2020. Revealed variability can probably be attributed to the peculiar geomorphological, oceanographical, and ecological features of locations, but also to the influence of interplaying local chemical and physical factors and biological processes such as species settlement, competition, and migration that can act at small spatial and temporal scales. The similarity in the species composition and community structure accessed by morphological and metabarcoding approaches was low,with only 16% of the species (out of 133 species identified overall) commonly detected by both approaches. This is mostly both due to a lack of data on COI sequences of numerous benthic invertebrates in the public barcoding databases on the one hand, and difficulties in detecting small and cryptic taxa through morphological analyses on the other. This suggests that combining of two approaches is required to fully describe the biodiversity of benthic assemblages. Finally, comparison of the spatial variability of the benthic communities’ structure with two approaches at different taxonomic levels, indicated that genus and family levels give results that are consistent to those obtained by the species level. This suggests that family level might be satisfactory in monitoring the spatial-temporal variability of Mediterranean hard bottom benthic communities