Miracle-dz/UniFAR-FTUs huggingface dataset:
Caterpillars : ecological and evolutionary constraints on foraging

Part I: The constraints on foraging patterns of caterpillars. Phylogenetic constraints - J E Rawlings Foraging of caterpillars in relation to the physical environment - T M Casey Nutritional ecology: the fundamental quest for nutrients - F Slansky, Jr Body size as a constraint on foraging - D Reavey and J Lawton Foraging with finesse: caterpillar adaptations for circumventing plant defences - D Dussourd Avian predators as constraint on caterpillar foraging - B Heinrich Invertebrate predators: how they constrain caterpillar feeding strategies - E A Bernays and C B Montflor Effects of parasitoids on the foraging activities of caterpillars - R M Weseloh Effects of induced plant defences on herbivores and their pathogens - V Krischik Patterns of interaction among sedentary herbivores - H Damman. Part II: Ecological and evolutionary consequences. Transition. Caterpillar lifestyles: adaptations reflecting sets of constraints. Sociality - T D Fitzgerald. Mutualism - N Pierce Aposematism - M D Bowers. Crypsis - L Fink. Part III: Environmental variation in time and space: Transition: Sum of constraints and variation in space and time Effects of caterpillar foraging and predation on population dynamics of caterpillars - E Haukioja A tropical view - D Janzen. Temperate view - N E Stamp Biotic and abiotic constraints on foraging of arctic caterpillars - O Kukal. Part IV: Implications for pest management of foraging constraints. Transition. Synthesis of evolutionary and ecological consequences. Accounting for caterpillar foraging behaviour in forest pest management - J C Schultz. Consequences of herbivore foraging patterns on plants in agroecosystems - P Barbosa.
Divergence between passerine populations from the Malvinas - Falkland Islands and their continental counterparts: A comparative phylogeographical study

Bursts of speciation have followed colonization of remote oceanic islands by diverse taxa, a process evidenced by island endemics around the world. The present study explores whether the Malvinas – Falkland Islands (MFI), a relatively understudied archipelago off the South Atlantic coast of Patagonia, harbour endemic genetic lineages of passerine birds. Nine passerine species nest regularly in the MFI (Cinclodes antarcticus, Muscisaxicola maclovianus, Troglodytes cobbi, Cistothorus platensis, Turdus falcklandii, Anthus correndera, Melanodera melanodera, Sturnella loyca, and Carduelis barbata). Mitochondrial DNA (cytochrome c oxidase I sequences) are used to quantify and compare divergence between insular and continental populations, finding genetic patterns to vary across these nine species. Most MFI passerines do not show significant genetic differentiation from continental populations, whereas C. platensis, M. melanodera, and T. falcklandii are modestly diverged. Finally, T. cobbi differes markedly from its closest continental relative Troglodytes aedon, a result that is confirmed using nuclear and vocal data. The study also identifies broadly divergent lineages within continental populations of C. platensis and T. aedon. Taken together, these results suggest that the land bird populations of the MFI were established at different times. Troglodytes cobbi is the oldest MFI land bird, splitting from continental T. aedon during the Great Patagonian Glaciation of the Pleistocene. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ••, ••–••.
Three ways to distinguish species: using behavioural, ecological, and molecular data to tell apart two closely related ants, Camponotus renggeri and Camponotus rufipes (Hymenoptera: Formicidae)

The closely related Camponotus renggeri and Camponotus rufipes (subgenus Myrmothrix) often live in sympatry in the Brazilian ‘cerrado’ savannah, and are distinguished by nuances in their blackish body colour and by the colour of the legs. Variation in morphological characters, however, makes species separation difficult and it has been suggested that the two species should be merged into one. As appropriate species identification is essential for studies in ecology and evolutionary biology, here we examine how natural history data (habitat preference, nesting biology) and molecular tools (nuclear and mitochondrial markers) perform in distinguishing sympatric populations of C. renggeri and C. rufipes. In our study area, C. rufipes was only seen in cerrado sensu stricto (scrub of shrubs and trees), whereas C. renggeri occurred in cerrado sensu stricto and cerradao (closed woodland). Camponotus renggeri nested underground or in fallen/erect dead trunks, whereas C. rufipes constructed distinctive nests of dry straw. Nest persistence through time was higher in C. rufipes, especially in the hot/rainy season. Nest distribution was random in C. renggeri and aggregated in C. rufipes. Molecular data consistently showed that, regardless of the source of genetic variation, the uppermost hierarchical level of divergence is observed between species, unambiguously differentiating the individuals identified as C. renggeri and C. rufipes as two independent evolutionary lineages. Mitochondrial data throughout the species' geographical ranges further confirmed a consistent genetic divergence between C. renggeri and C. rufipes along their distribution in Brazil. Our integrated approach combining morphological traits with natural history and molecular data confirms that C. renggeri and C. rufipes are valid species that can be separated in our study area relatively well. © 2015 The Linnean Society of London
Morphological Analysis of Quinoa Germplasm Grown Under Lowland Desert Conditions

Twenty-eight quinoa accessions collected from the northern highlands (Andes) of Chile were assessed using eleven morphological descriptors. A complementary analysis of multivariate tools permitted a fuller understanding of interrelationships within this germplasm as it was assessed in a lowland desert environment. Through a frequency distribution, it was possible to make a general classification of accessions which were represented by plants having medium height and low grain yield. The accessions BS2 and BS1 registered the highest yields with mean values of 993.89 and 820.56 kg ha ―1 respectively. On the other hand, accession B13 stood out as having good forage potential, with relatively high values for plant weight (PW, 349 g DM) and plant height (PH) (1.91 cm). The first four principal components accounted for 70 % of the total variation among the accessions. The first PC (PC 1 ), accounting for 36 % of the total variation, included stem diameter, PW and PH with high positive, and harvest index and leaf tooth number with high negative coefficients. Principal component 2 (PC 2 ) contributed for an additional 19 % of the total variation and reflected the patterns of variation in leaf morphology all of which had high positive values. Cluster analysis allowed classification of the accessions into six discrete groups. The yield assessment in the Atacama Desert was considered low, probably due to the negative effects of the high-temperature stress around flowering. The data set presented in this study is the first report of quinoa assessed under lowland desert conditions and would assist in the development of new plant breeding programmes for quinoa in areas having similar agrocli- matic factors as the Atacama Desert.
Selection of starters for a traditional Turkish yayik butter made from yoghurt

Abstract Butter is produced from two different materials in Turkey, cream and yoghurt. The butter produced from fresh yoghurt or ‘tulum yoghurt’ (a strained yoghurt produced from cow, goat or sheep milk) is called ‘yayik butter’ and has been traditionally produced in Turkey for centuries. In this research, we attempted to isolate and identify the natural lactic acid bacteria (LAB) of yayik butter and to select the best LAB combination for butter production. Twenty samples of yayik butter were collected from Afyon, Antalya, Isparta and Konya regions in Turkey and determined to have a mean pH of 4·78±0·33, a mean titratable acidity (lactic acid) of 0·23±0·07% and a mean NaCl of 0·55±1·22%. The mean counts of LAB (log10 cfu g−1) were 2·66±0·84 and 1·72±0·82 on MRS agar at 30 and 42°C, 2·44±0·93 and 1·78±0·24 on M17 agar at 30 and 42°C, and 1·64±1·196 on Sodium Azide Leuconostoc agar at 21°C, respectively. Eighty-five different LAB isolates were obtained from 20 yayik butters and identified asStreptococcus salivarius ssp. thermophilus (21·2%), Streptococcus sp. (4·7%), Lactobacillus delbrueckii ssp. bulgaricus (20%), Lactobacillus casei ssp.casei (15·3%), Lactobacillus paracasei ssp. paracasei (2·3%),Enterococcus faecium (18·8%). Leuconostoc pseudomesenteroides (Leucono-stoc mesenteroides ssp. dextranicum) (7·1%), Leuconostoc gelidum (Leuconostoc mesenteroides ssp.mesenteroides ) (4·7%) and Weissella paramesenteroides (Leuconostoc paramesenteroides) (5·9%). Combinations of S. salivarius ssp. thermophilus S51, Lb. delbrueckii ssp.bulgaricus A42, Lb. casei ssp. casei K64, Lb. paracasei ssp. paracasei A27, andLeu. pseudomesenteroides E83 were used as starter bacteria for experimental butter production from cream. Six different groups of butters were produced using different combinations of these bacteria (B, C, D and E samples), commercial culture (F sample), and without culture (A sample). Sensory evaluations showed that the experimentally produced butter sample of group B was more acceptable than the other butters. In addition, the buttermilk of sample B had lowest fact content. LAB counts of experimental butters produced with combined cultures and commercial culture were similar (6·66±1·87–6·83±0·040 and 6·81±0·13 log10 cfu g−1 on MRS agar, respectively).
Uso da água de coco em pó (ACP®) em diferentes temperaturas como diluente de espermatozóides de capote ("Numida meleagris")

The in vitro efficiency of powdered coconut water (ACP®) as storage medium for fresh, cooled guinea fowl (Numida meleagris) sperm at 4 or 15oC compared to a commercially available medium (DC) of poultry semen was evaluated. Sperm concentration, percentage of motile spermatozoa, vigor, and morphology at baseline (T0), 2h (T2) and 24h (T24) were recorded. Average pool concentration was of 4.88±0.17 x 109 sptz/mL in the sperm and 600 x 106 sptz/mL in the final aliquots. The number of spermatozoa in the pool averaged 11.4±0.95 x109sptz/ejaculate. No treatment effect (P>0.05) on any parameter (motility, vigor and viable spermatozoa percentage) at baseline was detected between four groups (4 and 15oC in ACP® and DC). After two hours (T2), only the spermatozoa in ACP® at 4oC was always higher than the acceptable values: motility 88%, vigor 8.9 and viable spermatozoa concentration of 10.01x109 sptz/mL (P<0.05). This fact was also observed at 24h. These results suggest that ACP® at 4oC can be used in the artificial insemination in guinea fowl, because it was the best among in vitro treatments, in all storage times.
The early ontogeny of feeding in two shark species: Developmental aspects of morphology, behavior, and performance

The relationship between form, function, and biological role in determining the niche occupied by an organism depends on diverse factors. Understanding this relationship is further complicated by considering the interplay among factors over ontogeny. While much is known about the ecological and functional morphology of feeding in lower vertebrates, studies of elasmobranch feeding morphology and behavior over ontogeny are broadly lacking. In this study, the ontogeny of feeding behavior and morphology was investigated in neonatal and young-of-the-year leopard sharks Triakis semifasciata using morphometric measurements of growth and high-speed videography in a longitudinal study. Five food types were used during filming sessions to facilitate differentiation of modulation and variation over ontogeny. Functional aspects of muscle and buccal volume scaling were investigated through dissection. Size was shown to influence several kinematic variables and intraand inter-individual variability was the dominant factor contributing to variability in feeding behavior. Modulation of feeding behavior based on food size and elusivity was present for timing variables and predator motion during the strike, but not for food motion or the relative extent of buccal expansion. Allometric growth occurred in all aspects of external cranial morphology measured, resulting in a shallower head profile, anterior displacement of the mouth, and
Psychometric properties of the Adolescent Story Stem Profile

9 Introduction. 10 Method. 20 Results. 25 Discussion . 40 References . 45 Part 2: Empirical Paper . 53 Abstract . 54. 54 Introduction. 55 Method. 64 Results. 76 Discussion . 93 References . 104 Part 3: Critical Appraisal. 111 References . 123 Appendices. 125 Appendix A: UCL Research Ethics Committee Approval . 126 Appendix B: Parent and Student Information Sheets and Consent Forms 129 Appendix C: ASSP Stories and Questions . 135 Appendix D: Multiple Regression Analyses . 142
Architecture of bacterial promoters : the case of E. coli ogt promoter

The ogt gene encodes an O\(^6\)-alkylguanine DNA alkyltransferase, which is reported to repair DNA against methylation damage caused by reactive nitrogen species, which are generated during an anaerobic respiration in a presence of nitrate. This study examined transcription activation by NarL at the ogt promoter using biochemical techniques with various semi-synthetic ogt promoters. The ogt promoter has two crucial DNA sites for NarL dimers at positions -78.5 and -45.5 relative to the transcript start site. An interaction between NarL and αCTD was investigated using site-specific mutagenesis. Locations and orientations of NarL and RNA polymerase in the transcript initiation complex were also confirmed in this study. It was found that NarL, at position 45.5, is located on the different DNA helical face from αCTD, which binds to the minor groove immediately upstream the -35 element. This unrecognized promoter architecture allows residue 273 of αCTD to interact with residue 178 of NarL.
Polymorphisms in heat shock protein receptors

Extracellular heat shock protein 70 (HSP70) can act as an immunological danger signal and stimulate the activity of cytotoxic T lymphocytes and natural killer cells. Therefore, HSP70 is currently evaluated as a tool in cancer immunotherapy. We analyze polymorphisms in heat shock protein receptor genes, such as CD91 and LOX-1, which may affect immunological functions of HSP70.
The mammals of Northern Melanesia: biogeography, systematics and ecology

Northern Melanesia's mammals are poorly known, and perceived deficiencies in faunal records and taxonomic descriptions have, until now, hindered detailed analyses. I examined aspects of biogeogra- phy, systematics and ecology in the region's mammalian faunas. Generalized linear models (GLMs) were used to test for differences in rates of persistence in four orders of mammal on continental shelf islands. Ochiai and endemism indices were used to delineate regions of high endemism and influential biogeo- graphic boundaries. A non -parametric multivariate regression tree and GLMs were used to identify the influences of abiotic variables on mammalian species richness. Genetic sequencing, microsatellite geno- typing, morphological and ecological data were used to determine evolutionary relationships among the widespread insectivorous bat family, Hipposideridae. Northern Melanesia's islands support mammalian faunas that reflect the poor over -water dispersal abilities of non-volant mammals; lower rates of long - term persistence in dasyuromorphs and diprotodonts; pronounced diversification of the Family Pteropodi- dae; and comparative lack of speciation in insectivorous bat families. Analyses produced a clear hierar- chical classification of Northern Melanesia's islands based on their physical attributes and mammal assem- blages, providing the first empirical analyses of Northern Melanesia's and New Guinea's mammalian zoo- geography, and adding to biogeographic theory at both regional and local scales.
Cellular tropism and cell-to-cell fusion properties of the infectious bronchitis virus spike glycoprotein

There are numerous vaccines available for the control of infectious bronchitis virus (IBV) in poultry, however protection is short-lived and poorly cross-protective between strains. The vaccines must currently be grown in embryonated eggs, a cumbersome and expensive process. The ability to grow vaccines on a cell-line such as Vero cells would be highly advantageous. The spike (S) glycoprotein of IBV is comprised of two subunits, S1 and S2, has a vital role in virulence in vivo and is responsible for cellular tropism in vitro. This project aims to identify the amino acids present in the S glycoprotein involved in determination of cellular tropism and cell-to-cell fusion. The IBV Beaudette strain is able to replicate in both primary chick kidney (CK) cells and Vero cells, whereas the IBV M41 strain replicates in primary cells only. Recombinant IBVs with chimaeric S genes were generated using a reverse genetics system with the genomic background of Beaudette and part of the S gene from M41. Their growth characteristics and cellular tropism were investigated. The S2 subunit of Beaudette was found to be sufficient to confer the ability to grow on Vero cells and swapping just three amino acids with corresponding ones from M41 was sufficient to remove the ability of the Beaudette S glycoprotein for growth on Vero cells. Beaudette was further adapted to syncytia formation on Vero cells by serial passage and isolates were sequenced to identify amino acid changes between parent and Vero-adapted viruses that are potentially involved in cell-to-cell fusion. Understanding the way in which IBV infects host cells is vital in order to rationally design better vaccination and treatment strategies and help to reduce the prevalence of IBV infection in poultry worldwide. Using the IBV reverse genetics system, we now have the potential to grow IBV vaccines on Vero cells.
Cacti : biology and uses

List of Contributors Preface 1. Evolution and Systematics Robert S. Wallace and Arthur C. Gibson 2. Shoot Anatomy and Morphology Teresa Terrazas Salgado and James D. Mauseth 3. Root Structure and Function Joseph G. Dubrovsky and Gretchen B. North 4. Environmental Biology Park S. Nobel and Edward G. Bobich 5. Reproductive Biology Eulogio Pimienta-Barrios and Rafael F. del Castillo 6. Population and Community Ecology Alfonso Valiente Banuet and Hector Godinez-Alvarez 7. Consumption of Platyopuntias by Wild Vertebrates Eric Mellink and Monica E. Riojas-Lopez 8. Biodiversity and Conservation Thomas H. Boyle and Edward F. Anderson 9. Mesoamerican Domestication and Diffusion Alejandro Casas and Giuseppe Barbera 10.Cactus Pear Fruit Production Paolo Inglese, Filadelfio Basile, and Mario Schirra 11. Fruits of Vine and Columnar Cacti Avinoam Nerd, Noemi Tel-Zur, and Yosef Mizrahi 12. Forage, Fodder, and Animal Nutrition Ali Nefzaoui and Hichem Ben Salem 13. Nopalitos, Mucilage, Fiber, and Cochineal Carmen Saenz-Hernandez, Joel Corrales-Garcia, and Gildardo Aquino-Perez 14. Insect Pests and Diseases Helmuth G. Zimmermann and Giovanni Granata 15. Cactus Breeding and Biotechnology Brad Chapman, Candelario Mondragon Jacobo, Ronald A. Bunch, and Andrew H. Paterson Index
Rac1b Regulates the Neurotrophin-3 Mediated Neuronal Commitment of Bone Marrow Derived MIAMI Cells

of a dissertation at the University of Miami. Dissertation supervised by Paul Schiller, Ph.D. No. of pages in text. (139) Emerging trends in cell-therapy based tissue repair have focused on the renewable source of adult stem cells including human bone marrow-derived mesenchymal stromal cells (hMSCs). Due to immunomodulatory properties as well as a potential to differentiate into cells characteristic of all three germ layers, hMSCs provide a source of immature cells for utilization in cell-therapy based treatments. Marrow isolated adult multilineage inducible (MIAMI) cells are a homogeneous sub-population of hMSCs which maintain self-renewal potential during ex vivo expansion, in addition to efficiently undergoing trans-differentiation into neuron-like cells in vitro. Even though hMSCs have the potential to be used for neural tissue repair, the molecular mechanisms by which they are stimulated to become neuron-like cells have not been fully characterized. Therefore the work described herein focuses on the molecular mechanisms by which MIAMI cells undergo NT-3 dependent neuronal commitment. MIAMI cells express both the full length (FL-) and tyrosine kinase deficient (TKd-) isoforms of the NTRK3 receptor, the primary NT-3 receptor, at the protein level. NT-3 stimulation of MIAMI cells during neuronal commitment induced the phosphorylation of FL-NTRK3, degradation of TKd-NTRK3, downstream activation of the Mek1/2-Erk1/2 signaling cascade, and subsequent up-regulation of a limited number of pro-neuronal genes. These findings were verified using chemical inhibitors to block NTRK autophosphorylation (K252a) and Erk1/2 activation (U0126). TKd-NTRK3 is hypothesized to activate Rac1 upon NT-3 stimulation. Rac1 was found to suppress NT-3 stimulated Erk1/2 phosphorylation, as well as downstream gene expression, as determined using a Rac1 chemical inhibitor. Further characterization confirmed that Rac1b is the predominant Rac1 isoform in MIAMI cells. Rac1b siRNA mediated knock-down resulted in increased expression of the pro-neuronal genes NGN2, MAP2, NFH and NFL during NT-3 stimulation via regulation of Mek1/2-Erk1/2. Rac1b is also involved in NT-3 stimulated cell proliferation, as well as repression of CCND1 and CCNB1 mRNA expression. In an attempt to enhance neuronal differentiation of MIAMI cells, EGF and bFGF were used to pretreat MIAMI cells prior to NT-3 stimulated neuronal commitment. EGF/bFGF pretreatment increased NTRK3 and NTRK1 protein levels along with NT-3 stimulated Erk1/2 phosphorylation. In addition, bFGF versus EGF/bFGF pretreatment restricted the expression of the pro-neuronal transcription factors Ngn2 and Prox1 versus the neural stem cells self-renewal transcription factor Musashi-1, respectively. The culmination of this work provides a model for the NT-3 induced neuronal commitment of MIAMI cells in vitro, as well as insight into the neurogenic potential of MSCs for future applications in cell-therapy based tissue repair.