Miracle-dz/UniFAR-FTUs huggingface dataset:
Response of mountain Picea abies forests to stand‐replacing bark beetle outbreaks: neighbourhood effects lead to self‐replacement

Summary Large, severe disturbances drive many forest ecosystems over the long term, but pose management uncertainties when human experience with them is limited. Recent continent-scale outbreaks of bark beetles across the temperate Northern Hemisphere have raised major concerns as to whether coniferous forests will regenerate back towards pre-outbreak condition and meet possible reforestation objectives. To date, however, analyses of post-outbreak regeneration across broad spatial and temporal scales have been rare, and entirely lacking for many regions. Following a series of large, severe ( 99% overstorey mortality) outbreaks of spruce bark beetles Ips typographus in Central Europe, we capitalized on an extensive forest inventory data set (n = 615 plots across 7000 ha) to evaluate regeneration dynamics in Norway spruce Picea abies forests across the Bohemian Forest Ecosystem (spanning Germany and the Czech Republic). We asked whether neighbourhood effects (conspecific advance regeneration of spruce) would support prompt regeneration back to spruce forest, or whether the rapid, severe canopy mortality would overwhelm this influence and promote pioneer and broadleaf species. We tracked 15 years of post-outbreak regeneration dynamics (occupancy, density, height, composition) of all tree species and evaluated initial variations in successional pathway and structure. Median tree regeneration density increased from 400 trees ha−1 at the time of outbreak to 2000 trees ha−1 within a decade, and occupancy increased from 58% to 76%. The increases were driven by spruce, which primarily recruited from advance regeneration, gradually occupying greater height classes. Only one broadleaf/pioneer species increased in relative proportion, for a brief (<3-year) period before declining again. Nevertheless, both pure spruce and spruce–broadleaf stands were common and, coupled with wide variations in density and height, contributed to diverse early-successional structure. Synthesis and applications. Contrary to common expectations, spruce beetle outbreaks in Central Europe effectively promoted their host in the long term. Outbreak-affected forests are naturally self-replacing even after severe canopy mortality, when positive neighbourhood effects of conspecific advance regeneration lead to rapid replacement of the dominant species. Thus, natural regeneration may be considered among the most effective ways to meet possible reforestation objectives in forests destroyed by beetles.
The Phenotype as the Level of Selection: Cave Organisms as Model Systems

Selection operates at many levels. Robert Brandon has distinguished the question of the level of selection from the unit of selection, arguing that the phenotype is commonly the target of selection, whatever the unit of selection might be. He uses "screening off" as a criterion for distinguishing the level of selection. Cave animals show a common morphological pattern which includes hypertrophy of some structures and reduction or loss of others. In a study of a cave dwelling crustacean, Gammarus minus, we find evidence for selection for both increased antennal size and reduction of eyes. The genetic structure of the population does not support the view that the phenotype screens off the genotype in explaining the differences in fitness. Nonetheless, the results do indicate that the level of selection is at least at the level of the phenotype in both cases.
Ultrastructural, Immunohistochemical, and Biochemical Variation Amongst Symbiodinium Isolates

ii Acknowledgments . v List of Tables . vii List of Figures . viii List of Abbreviations. x I. A review of Symbiodinium symbioses with an emphasis on initiation and maintenance of the Cnidaria-Symbiodinium association . 1 II. Immunohistochemical variation amongst Symbiodinium isolates . 35 III. Ultrastructural variation amongst Symbiodinium isolates . 57 III. Ultrastructural and biochemical variation amongst Symbiodinium isolates demonstrates variation in storage molecules . 84 References . 105
The regulation of hypoxia-inducible factor (HIF-1) and the role of HIF-1 in C. elegans longevity

33 INTRODUCTION 34 MATERIAL AND METHODS 37 Strains. 37 Genome wide RNAi Screen. 37 Pegl-9:GFP expression constructs 38 Protein Blots 38 RNA extraction and quantitative RT-PCR 39 RESULTS 39 Genome wide RNAi screen 39 SKN-1 /NRF reduces HIF-1 protein levels and promotes egl-9 expression 42 DISCUSSION 45 RNAi screen identifies genes that regulate nhr-57 expression 46 SKN-1 promotes egl-9 expression, thereby inhibiting HIF-1 47 ACKNOWLEDGEMENTS 50
The Colors of Mice: A Model Genetic Network

Preface. Acknowledgments. Statement regarding the use of pictures. Statement regarding nomenclature. Part I: Introduction to the Pigmentary System. 1. Introduction to the Pigmentary System. 1.1. Introduction. 1.2. Colors of vertebrate animals. 1.3. Other pigment cells. 1.4. The epidermal melanin unit. 1.5. Mammalian hair. 1.6. Melanosome biogenesis and translocation. 1.7. Melanin. 1.8. Hair growth. 1.9. Hair growth cycles. 1.10. Embryonic development of the pigment cell lineage. 1.11. Pigment cells in culture. 1.12. Conclusion. Appendix: color loci of the mouse. Part II: The Pigmentary Loci. 2. Introduction to Mutant Pigmentary Genes. 2.1. Defects of normal melanocyte development: white spotting and graying with age. 2.2. Defects in normal melanosome development: albinism. 2.3. Transport of melanosomes to other cells: the dilute phenotype. 2.4. Pigment-type switching: from eumelanogenesis to pheomelanogenesis. 3. White Spotting and Progressive Graying. 3.1. Definitions and general background . 3.2. Pigment cell development: developmental biology. 3.3. Cellular signaling pathways for melanocytes. 3.4. Pigment phenotypes and the classical white-spotting genes. 3.5. The head, heart, ears, and eyes. 4. Albinism and the Failure of Normal Melanosome Development. 4.1. Background. 4.2. The melanosomal matrix. 4.3. The enzymes that catalyze melanogenesis. 4.4. Membrane proteins that regulate the internal milieu of the melanosome. 4.5. Protein processing and routing to the maturing melanosome. 4.6. Melanosome transport. 5. Pigment-Type Switching. 5.1. Introduction. 5.2. Yellow phenotypes. 5.3. Melanin pigment . 5.4. Melanogenesis and the eumelanin/pheomelanin switch mechanism. 5.5. Signaling the switch mechanism at the cellular level. 5.6. Yellow genes. Part III: Technology and Resources. 6. Novel Mouse Pigmentary Mutants Generated by Genetic Manipulation. 6.1. Introduction. 6.2. Mouse transgenesis: generation of genetically engineered mice. 6.3. Coat-color transgenic mice. 6.4. The coat-color mutants generated by gene targeting. 6.5. Influence of the genetic background. 6.6. Conclusions. 7. Other Species and Other Resources. 7.1. Introduction. 7.2. Resources. 7.3. Other species. References. Index.
Experimental skin carcinogenesis in mice

enzyme heterogeneity and the need to assess tissue-specific forms of the enzyme to aid in diagnostic problems. This is of great value to the technologist but should be familiar to the clinical biochemist. The clinical biochemist, however, will find the text valuable, since the author reviews the theoretical significance in intermediary metabolism, the methods of assay, the necessary reagents and the technic of one or more selected procedures, and the clinical interpreta tion of alterations from normal limits of activity, and pro vides a good bibliography for each of 28 clinically important enzymes. In addition, the appendix contains an excellent compendium of buffers which can be utilized to study enzyme reactions of clinically significant systems. Carl Alper
Investigation of cell movement and the associated cytoskeleton during chick gastrulation and somitogenesis

Cell migration involves dynamic and spatially regulated changes to the cytoskeleton. During avian gastrulation, cells ingress through the primitive streak. Previous characterisation of microtubule organisation during this process revealed the distribution of cells with polarised and radial arrays across different regions of the embryo. Interestingly, many cells organised into groups arranged in rosette-like structures. As the primitive streak regresses and the neural folds gather at the centre of the embryo, bands of paraxial mesoderm that lie either side of the neural tube separate into somites. As new somites form caudally, the more rostral somites undergo a process of morphogenesis. Each somite divides into two regions: the dermomyotome and the sclerotome. Little is known about the cytoskeletonduring this process. Signalling by the Wnt family of secreted proteins influences the fate of cells during early embryonic patterning, cell movement, and cell polarity, processes in which the cytoskeleton is noticeably modified. The microtubule and actin crosslinking factor-1/actin crosslinking factor-7 (MACF1/ACF7) protein has been implicated in Wnt signalling and, additionally, its regulation has been shown to be important in cell migration. This thesis concentrates on cellular dynamics and organisation (and the associated cytoskeleton) during chick gastrulation and somitogenesis. The aims of this project were to a) further characterise the cytoskeleton in cells that ingress into the avian primitive streak. b) Establish a published electroporation technique, which permits the targeting of different regions of the somite and subsequently observe cells (and their associated cytoskeleton) in real time. c) Determine the expression pattern for MACF1/ACF7 in chick. d) To ascertain if there is a direct role for canonical Wnt signalling in somitic myofibre orientation/organisation.
Artificial Bee Colony for Two Dimensional Protein Folding

In this study, we introduced the artificial bee colony (ABC) algorithm for the sake of improving two dimensional protein folding simulations. ABC is a novel intelligent problem solving technique under the inspiration of collective behavior on honey bees. It has better performance in function optimization problem compared with genetic algorithm, differential evolution, and particle swarm optimization. In this experiment, we compared ABC with the standard genetic algorithm and immune genetic algorithm on 4 benchmark problems with different chain lengths as 20, 36, 48, and 64. The results show that the ABC algorithm can be applied successfully to the protein folding problems based on the hydrophobic-hydrophilic lattice model, and ABC has higher success rate compared to standard genetic algorithm and immune genetic algorithm.
MUTATIONAL AND EXPRESSIONAL ANALYSIS OF A FAMILY OF SHORT CHAIN DEHYDROGENASEIREDUCTASE ENZYMES IN CA ENORHA BDITIS ELEGA NS

Our lab is interested in defining the essential gene complement of the Caenorhabditis elegans genome. To this end, the lab has created lethal mutations in over one hundred genes on the left arm of chromosome Ill. One of these genes, let-767, has been shown to be required for molting and reproduction. As well, mutants in this gene exhibit hypersensitivity to a reduction in supplemental cholesterol. There are four other closely related genes in the C. elegans genome that, together with let-767, are the focus of this project. This thesis describes the analysis of mutations and expression patterns in let767, C06B3.4, C06B3.5, F1 lA5.12, and F25G6.5. These genes are 35% 40% identical to human 17P hydroxysteroid dehydrogenase (1 7PHSD) enzymes. The closest human homolog with a well defined function is 17PHSD 3 which is required for the conversion of androstenedione to testosterone in males. I have obtained evidence of expression using RT-PCR for four of the five genes. Serial Analysis of Gene Expression (SAGE) and expressed sequence tag (EST) data from other sources confirmed these results. There is significant variation in the location of gene expression as viewed using promoter-GFP transgenics. let-767 expresses in gut, C06B3.4 in neurons and body muscle, and F25G6.5 shows expression in the pharynx. Previous characterizations of let-767 mutants, as well as RNAi experiments were meant to lend insight into a possible function for each of the genes. let-767 likely acts on a sterol derivative that is required for normal development. The other four genes do not appear to be essential, however, and may act in related metabolic pathways.
Toxicité et mode d’action du tritium seul et en mélange avec du cuivre sur l’algue verte Chlamydomonas reinhardtii

Les rejets d'effluents liquides des Centres Nucleaires de Production d'Electricite (CNPE) sont constitues d'un melange de substances stables et radioactives. L'exposition d'organismes a des substances en melange peut faire l'objet d'interactions diverses, conduisant a une augmentation ou a une diminution des effets observes. Afin d'identifier de possibles interactions dans le cas de melanges de substances caracteristiques (en termes de toxicite et de quantite) des rejets de CNPE, l'effet d'un melange binaire compose de cuivre et d'HTO a ete etudie sur le modele d'algue unicellulaire Chlamydomonas reinhardtii. Dans un premier temps, la toxicite de l'HTO a ete analysee. L'HTO s'est revelee etre peu toxique envers notre modele biologique. L'effet le plus sensible et le plus precoce est une augmentation du stress oxydant (des 40 kBq mL-1 - 0.13 µGy h-1). Lors de l'exposition des cellules algales au melange HTO/Cu, une interaction a ete revelee au niveau du stress oxydant cellulaire, celui-ci etant superieur a une simple addition de l'effet des deux substances. Cette interaction peut s'expliquer par une augmentation de l'internalisation du cuivre en presence d'HTO, mais aussi potentiellement par des interactions toxiques directes (notamment sur les processus de regulation du stress oxydatif). En conclusion, il a ete demontre que l'effet de substances stables et radioactives en melange peut etre superieur a l'addition. Bien qu'etant uniquement representative du melange binaire HTO/Cu, cette etude montre neanmoins de potentielles interactions entre substances stables et radioactives, a considerer lors de l'evaluation des risques ecologiques relatifs aux rejets de CNPE.
Modeling and targeting signal transduction pathways governing cell migration

Cell migration is a complex biophysical event that is dysregulated in a variety of human diseases including cancer. The ability of tumor cells to migrate enables cancer dissemination causing significant mortality thus making it an important therapeutic target. Motility is exhibited epigenetically by activation of numerous signaling pathways that transmit extracellular cues to the final effectors of cell movement. Such signaling switches are a part of larger and highly complex signaling (proteomic) networks that are under the control of numerous activators or inhibitors. Although majority of the proteins that are 'required' during cell motility have been identified, it is yet unclear wherein they fit within the signaling network to govern motility. Thus, a 'systems biology' approach is needed to understand the complex interplay of signaling cascades in mediating cell motility so that better therapeutic targets can be defined. We utilized a mathematical modeling approach, called decision tree analysis to map the interplay between five key signaling proteins known to regulate vital biophysical processes of fibroblast motility downstream of EGF receptor activation. Interestingly, our model identified myosin light chain (MLC) mediated cell contractility as a crucial node for maximal motility. Even more non-intuitively the decision tree model predicted that subtotal inhibition of MLC can actually increase motility. Confirmatory experiments with fibroblasts and cancer cells have shown that to be the case. Since the model proposed that total abrogation of contractility can limit cell migration, we asked if such an intervention can limit tumor invasion. Since PKCδ is implicated in EGF receptor mediated transcellular contractility, we abrogated PKCδ using pharmacological (Rottlerin) and molecular (RNAi) interventions. Such depletion of PKCδ reduced migration as well as invasiveness of prostate carcinoma cells predominantly by decreasing their contractility through myosin light chain (MLC). Additionally, activation of PKCδ correlated with human prostate cancer progression as assessed by immunohistochemistry of prostate tissue sections. In summation our studies illustrate the importance of quantitative (total versus subtotal) disruption of key signaling nodes in mediating a desired cell response. Novel computational modeling approaches are needed to identify newer molecular switches from existing proteomic networks that can be explored, using classical experimental methods, as therapeutic targets.
ZEIN NANOSPHERES FOR GENE DELIVERY

Particulates incorporating DNA provide for protection and sustained release of DNA, and thus are promising candidates for DNA delivery systems. Among the routes of administration for gene delivery, the oral route is perhaps the most appealing as it is associated with patient comfort and compliance and allows for targeting to intestinal targets for therapeutic and vaccination applications. With the goal of realizing the potential of an oral DNA delivery system, zein, a hydrophobic protein from corn that is biocompatible and degraded enzymatically, was investigated. This thesis describes the formulation of zein nanospheres encapsulating DNA by a coacervation technique and their characterization. Zein/DNA nanospheres ranged from 57.8 ± 3.9 nm to 396.8 ± 16.1 nm and from-21.8 ± 4.2 mV to-46.6 ± 1.6 mV for hydrodynamic diameter and zeta potential measured in water, respectively. Spheres formed at all ratios aggregated to some degree in PBS, with 20:1 and 40:1 zein:DNA spheres flocculating; aggregation was found to be dependent on salt concentration. DNA encapsulation efficiency was as high as 65.3 ± 1.9% with a maximum loading of 6.1 ± 0.2 mg DNA/g zein. DNA that was encapsulated and released retained its integrity. Release studies indicated that zein was degraded primary enzymatically with slow release of DNA in PBS, and faster release in pepsin containing media, and nearly instantaneous release in simulated intestinal fluid. Spheres demonstrated similar biocompatibility at high and low concentrations, and showed cellular association and evidence of internalization. Possible improvements to this delivery system include increasing loading, improving stability against aggregation, increasing resistance to enzymatic degradation, and improving internalization, nuclear localization, and transfection. The spheres formed and characterized as described in this thesis show great potential for oral gene delivery, and with judicious modification should be rendered even more likely to be applied clinically in oral gene delivery as well as tissue engineering and intramuscular injection applications. iv Acknowledgements Dr. Pannier, thank you for giving me the opportunity to work on this project. I appreciate the support and guidance you have provided throughout the last two years. Sarah, Dipika, Tadas, Tim, and Jessica thank you for being so willing to offer your friendship and assistance. Thank you to my family for your continued support and encouragement.
Age Differences in the Expression of Manual Asymmetry

Manual dexterity declines in older adults; however, the degree to which the decline is symmetrical in the two hands is less clear. In this investigation the differences between young (aged 18 to 24) and old (aged 62 to 72) men and women in the expression of manual asymmetry across several motor tasks were examined. Five motor tasks provided a broad measurement of several motor characteristics necessary for instrumental activities of daily living. The main effect of sex was not significant; therefore data from men and women were pooled. Little support was found for generalized asymmetrical performance in old adults compared to young adults across motor tasks. An age-by-hand group analysis indicated that age was related to preferred hand performance on two tasks, but when a within-subject analysis of hand differences was performed, and the speed accuracy trade off considered, differential asymmetry was seen only in the most complex, speeded task.
Comparison of experimental designs for estimating quantitative genetic parameters in fish

Four popular experimental designs for estimating variance components of additive genetic effects and (secondarily) dominance and maternal effects in fish (full-sib families, half-sib families, nested design and factorial design) were compared. The error variances of the estimators were formulated as functions of the true (hypothetical) values of genetic and environmental variances, depending on the experimental design considered, and whether the families were reared separately or mixed. Half-sib families and rectangular (many sires×few dams) factorial design were most useful for the estimation of heritability. The nested design appeared much less adequate. The minimum experimental capacity for obtaining accurate estimates was 100 lots in separate rearing or 1000 fish in mixed rearing. A larger experimental capacity is required when dominance and maternal effects as well as heritability are to be estimated because these different estimations, requiring contradictory conditions, cannot be simultaneously optimized.
Parental phase status affects the cold hardiness of progeny eggs in locusts

Summary 1. The capacity to adapt to low temperature is critical for the persistence of insect populations in heterogeneous environments. Locusts show remarkable phenotypic plasticity, termed ‘phase change’, in response to local population density. 2. In this study, the hypothesis that population density, as a social factor, affects the cold hardiness of progeny is validated in the migratory locust, Locusta migratoria, which shows remarkable density-dependent phase changes between gregarious and solitarious phases. 3. We demonstrated that eggs of gregarious and solitarious migratory locusts significantly differ not only in size and weight, but also in cold hardiness. Eggs of solitarious locusts are more resistant to cold stress compared with those of gregarious locusts, with longer 50% lethal time at different low temperatures and under different acclimation treatments of cooling rates or cold exposure time, lower upper limit of chill injury zone, and lower sum of injurious temperature resulting from temperature–time regression. The lowest cooling rate (0·05 °C min−1) yields the highest survival of cold for eggs. 4. A custom-made microarray covering 9154 unigenes of the migratory locust demonstrated quite different gene expression profiles in the two phases in response to normal or low temperature. Under cold stress, the gregarious-phase eggs have higher transcriptional levels of heat-shock proteins, DOPA decarboxylases and tyrosine hydroxylase, whereas the solitarious-phase eggs exhibit stimulated lipid metabolism and carboxylic acid transport. 5. Hybridization between the two phases showed that the cold hardiness of eggs from the hybrid with solitarious females is significantly higher than that of the hybrid with gregarious females, and the cold hardiness of eggs from each reciprocal hybrid is close to their maternal origins. These results indicate that the cold hardiness of progeny is affected by the parental phase status.