Miracle-dz/UniFAR-FTUs huggingface dataset:
19th century woodland structure controls stand‐scale epiphyte diversity in present‐day Scotland

Axioms developed from island biogeography theory (i.e. species–area relationships, effects of fragmentation and isolation) are central to the development of conservation strategy. Within this context, the ‘extinction debt’ hypothesis brings into question an often assumed relationship between species richness and present‐day spatial habitat structure (i.e. extent, fragmentation), suggesting instead that the richness and composition of biological communities may lag behind spatial changes in habitat. We examined evidence for an extinction debt among epiphytic lichens, a highly diverse biological group of significant conservation concern. Using sites in Scotland, we compared epiphyte species richness in smaller‐scale habitat units (aspen stands) to larger‐scale woodland structure (extent and fragmentation) measured at two spatial scales (1 km2 and 4 km2) and for two timeframes, modern (1990s to 2000s) and historic (1860s to 1880s). Species richness was positively related to woodland extent and negatively related to woodland fragmentation; however, richness was explained better by historic woodland structure at a 1‐km2 scale, than by modern woodland structure. The results indicate: (1) a coupling of stand‐scale epiphyte assembly and dynamics of the wider woodland ecosystem, and (2) a significant lag in the response of epiphyte species richness to habitat spatial structure. However, the effect of spatial habitat structure is different between species groups with contrasting traits. The effect of decreasing woodland extent on epiphyte richness is generally more severe for microlichens (comprising a greater number of rare and specialist species) than the more generalist macrolichens.
Globotriaosylceramide and globotriaosylsphingosine mediated epithelial‐to‐mesenchymal transition in kidney cells: implication for Fabry disease nephropathy (600.1)

Fabry disease is a lysosomal storage disorder caused by deficiency of α‐galactosidase A (α‐gal A), resulting in deposition of globotriaosylceramide (Gb3) in the vascular endothelium. Deacylated Gb3, globotriaosylsphingosine (lyso‐Gb3), also accumulated in the tissues of Fabry disease patients. Lyso‐Gb3 has been suggested as a candidate biomarker. According to renal and cardiac pathological findings, epithelial‐to‐mesenchymal transition (EMT) could be a possible pathogenic mechanism in Fabry disease. However, the association of EMT with Fabry disease has not been elucidated yet. Expression level of EMT markers such as E‐cadherin, N‐cadherin, β‐catenin and α‐SMA in mouse renal glomerular mesangial cell (SV40MES13) significantly increased when treated with Gb3. Whereas, in human proximal renal tubular epithelial cells (HK‐2), expression of EMT markers were significantly altered when treated with lyso‐Gb3 rather than treated with Gb3. Additionally, we observed that the activation of TGF‐β, phospho‐AKT, and PI3K were highly elevated in these cells. When we treated recombinant α‐gal A with Gb3 or lyso‐Gb3, TGF‐β expression was reversed in HK2 cells. Our study demonstrates that Gb3 and lyso‐Gb3 can potentiate EMT‐like processes through AKT/PI3K signaling pathway in HK2 and SV40MES13 cells. Moreover, these findings suggest that lyso‐Gb3, rather than Gb3 may be a crucial role nephropathy of Fabry disease by inducing EMT and may contribute to a better understanding of the renal fibrosis.
Mucosal Immunology of Human Head

001 Abstract The theme for the immune system of human head is of tripartite nature. The common mucosal immune compartment, the mononuclear phagocyte cell system and the transudate cellular and humoral factors of the systemic immunity. These compartments were covering; natural, cross-road adaptive immune events outcomes. Among which, the common mucosal immune system, which can be mapped into; CranialOral and nasal associate lymphoid tissue, conjunctiva and lachrymal associated lymphoid tissue ,Eustachian tube associate lymphoid tissue, nasopharyngeal associated lymphoid tissue as well as facial skin associated lymphoid tissue. In addition to the mononuclear phagocyte cell system and the natural immune barriers.
The Avian Erythrocyte: Its Phylogenetic Odyssey

Maturation: erythroblast to erythrocyte Erythrocyte precursors: quantitative representation in hemopoietic bone marrow Cytoskeleton Vascular system and architecture of hemopoietic bone marrow Relationship of bone marrow sinuses and erythropoiesis Erythropoiesis during embryogenesis: general plan Yolk sac erythropoiesis: early phase Germ disc: earliest commitment to erythroblast formation Ultrastructure of early yolk sac erythropoiesis Yolk sac erythropoiesis: later phase Hemopoietic stem cells and quail-chick chimeras Intraembryonic hemopoietic stem cell: origin and distribution Hepatic and splenic erythropoiesis during embryogenesis Medullary erythropoiesis during embryogenesis Circulating erythrocytes and marrow erythroblasts in the domestic chicken embryo and hatchling: quantitative aspects Embryonic erythropoiesis: an altricial passeriforme versus a precocial galliforme Hepatic erythropoiesis in the adult Thymic erythropoiesis Erythrocyte counts, hemoglobin levels and hematocrits Red cell indices (MCV, MCH, MCHC) Configuration of the erythrocyte Erythrocyte-based values and gender relationships Erythrocyte size and variations other than genderrelated Erythroid parameters and relationships with age and other conditions Erythroid profile and migratory behavior of the avian Erythrocytic picture and altitude of habitat Season and erythroid picture Interaction of erythropoiesis, egg laying, and iron metabolism Breeding cycle of a pelagic seabird Avian hemoglobins: adult and embryonic Blood volume Life span of the erythrocyte Apoptosis Erythroplastids (denucleated erythrocytes) Staining and cytochemistry Osmotic fragility Erythroid reservoir function of the spleen in fowl Telomeres Anemia Polycythemia Erythroid response to hemorrhage Phenylhydrazine-induced anemia and Heinz bodies Assessment of erythropoietic status of bone marrow Avian C-value Metals and erythropoiesis Parasitization of the erythrocyte Haemoproteus Plasmodium Leucocytozoon Babesia Aegyptianella Erythroleukemia Erythrocytes and pathologic conditions/agents Folic acid deficiency and megaloblasts Rapeseed and dimethyl disulphide Aflatoxin Prudhoe Bay crude and other oil Bacterial disease Viral disease Organophosphates Ascites syndrome Fenbendazole Antibiotics and chicks Antibiotics and chicks Immune-mediated hemolytic anemia Ethanol Hormones and erythropoiesis Avian erythrocyte: a generator of cytokines Anticoagulants: impact upon erythrocytes Table 1: Erythrocyte Counts and Related Values in Avians Appendix: Genus, Species and Other Taxa of Cited Avians and Non-Avians Glossary: Common Names of Species Cited in the Text and Tables
The generalist pollination system and reproductive success of Calluna vulgaris

Although specialist pollination systems are often thought to be the outcome of selection, wide evidence exists for generalization within plant-pollinator interactions. We studied the pollination system and reproductive success of Calluna vulgaris (L.) Hull over 3 years in an Upper Ardennes site in Belgium. A wide variety of insect visitors was recorded including Hymenoptera, Diptera, and Lepidoptera. Relative abundance of families and species of visitors varied markedly among years except for bees. Bumblebees and honeybees were the most efficient pollinators at the study site. Syrphid flies, mainly large ones, acted as important co-pollinators because of their high relative frequency. Calluna pollen was also dispersed by wind, and insect-exclusion experiments demonstrated that wind pollination contributed to reproductive success. Following open pollination, fruit set was high, ranging from 82.0 to 97.2% and independent of sampling location. Mean seed number per fruit was less than maximum potential seed number and varied strongly among sampling locations. We discuss this pollination system (generalist insect and wind) in terms of the ecological and geographical success of the species.
Contaminantes orgánicos persistentes en núcleos de sedimentos de la región sur de la Cuenca de las Californias Persistent organic pollutants in sediment cores from the southern region of the Bight of the Californias

In January 1998, four sediment cores were collected to reconstruct the history of contamination by persistent organic compounds in the southern region of the Bight of the Californias. Two groups of compounds were determined using chromatographic methods: petroleum hydrocarbons (aliphatic hydrocarbons, AHs, and polynuclear aromatic hydrocarbons, PAHs) and chlorinated hydrocarbons (pesticides and polychlorinated biphenyls, PCBs). The AHs had low concentrations, from 0.30 to 3.38 μg g–1, and presented a biogenic allocthonous origin. The PAH concentrations ranged from 0.99 to 673 ng g–1. The distribution of the alkyl homologues and the compound indices showed a clear predominance of PAHs of petrogenic origin. The chlorinated hydrocarbons presented a surface maximum, decreasing with depth to non-detectable levels. The PCB concentrations ranged from 0.18 to 7.15 ng g–1 and pesticides from 0.09 to 19.71 ng g–1. The pesticides that occurred most frequently were p,p’-DDT and its metabolites (p,p’-DDE and p,p’-DDD). Other pesticides detected were γ-chlordane and BHC isomers (α and γ). The statigraphy of the cores was carried out with molecular markers (chlorinated hydrocarbons), which were used to calculate a rate of sedimentation of 0.17 to 0.55 cm yr–1.
The relative importance of crop pests in sub-Saharan Africa.

The aim of this study was to assess the relative economic importance of insect-vectored plant diseases and other pests (harmful organisms) in each farming system of sub-Saharan Africa. The first steps were to divide sub-Saharan Africa into ten agro-ecological zones and list the major and secondary crops in each zone (Fig. 4, fold out map, and Tables 3 to 6). Through study of the literature and consultation with experts in UK and Africa, pests in each zone were then assigned to ranks indicating their relative economic importance in that zone (Tables 7 to 25, odd nos.). On this basis the most serious pests affecting each major crop were listed in order of importance for each zone (Tables 8 to 36 even nos.). By using a rudimentary scoring system, an estimate was made of the relative importance of insect-vectored plant diseases in sub-Saharan Africa as a whole. The African cassava mosaic and maize streak diseases are much the most important of such pests, followed by groundnut rosette (Table 30). A rather tentative estimate was made of the relative importance of the different zones for insect- vectored plant diseases. The two semi-arid zones appeared to have the least problems. (Table 31). The study stresses the dynamic nature of the pest situation and examines the factors likely to lead to changes in the relative importance of pests. it also summarizes the geographical features and the farming systems in each zone and their relationship to pests and their control.
Microbial alcohol dehydrogenases: identification, characterization and engineering

Keywords: alcohol dehydrogenase, laboratory evolution, rational protein engineering, Pyrococcus furiosus, biocatalysis, characterization, computational design, thermostability. Alcohol dehydrogeases (ADHs) catalyze the interconversion of alcohols, aldehydes and ketones. They display a wide variety of substrate specificities and are involved in an astonishingly wide range of metabolic processes, in all living organisms. Besides the scientific interest in ADHs, they are also attractive biocatalysts for industrial applications. Especially, their capability to catalyze chemo-, stereo-, and region-selective reactions endows them with considerable potential for a range of applications in food, pharmaceutical and fine chemicals industries. Natural enzymes are, however, optimized and often highly specialized for certain biological functions; hence, in many instances natural enzymes do not perform optimally in an industrial process. Laboratory evolution (random methods) and/or rationale-based protein engineering (design methods) can be applied to obtain enzyme variants, which are suitable for a particular industrial application. This study describes the identification, characterization and engineering of microbial ADHs. Because protein stability is an important issue for in vitro applications, thermophiles are considered a potential source of thermozymes. The genes coding for sixteen putative ADHs were identified in the genome of the hyperthermophilic archaeon Pyrococcus furiosus and a more detailed level of function prediction was attempted for all identified genes. Subsequently, fifteen of the putative ADHs were heterologously produced and an initial screening for activities was performed in which two of the putative ADHs showed activities. Next, these two ADHs, AdhD and Pf-TDH, were purified and characterized. AdhD is a member of the aldo-keto reductase superfamily and Pf-TDH is a l-threonine dehydrogenase. In addition, either laboratory evolution or rationale protein engineering was applied to improve the properties of two selected ADHs to extend their potential for industrial applications. AdhA, a thermostable ADH of P. furiosus, was engineered by laboratory evolution to improve the production of (2S,5S)-hexanediol at moderate temperatures. High-resolution 3D structures are required to perform the directed engineering of proteins. The ADH of Lactobacillus brevis (Lb-ADH) was selected because a 1.0 A resolution structure was available, and because of its potential for industrial application. Structure-based computational protein engineering was applied to adjust its cofactor specificity.
INSIGHTS INTO HEPATIC ALPHA- FETOPROTEIN GENE REGULATION DURING LIVER DEVELOPMENT AND DISEASE

OF DISSERTATION INSIGHTS INTO HEPATIC ALPHA-FETOPROTEIN GENE REGULATION DURING LIVER DEVELOPMENT AND DISEASE The liver is an essential organ for cholesterol homeostasis. If this process becomes dysregulated, cardiovascular disease (CVD) develops. Zinc-fingers and homeoboxes 2 (Zhx2) as an important hepatic gene regulator and contributes to CVD. BALB/cJ mice, with mutant Zhx2 allele, have fewer atherosclerotic plaques compared to other strains on a high fat diet. In my dissertation, I focused on the liver phenotype in BALB/cJ mice on a high-fat diet and found increased liver damage compared to wild-type Zhx2 mice. These data indicates that reduced Zhx2 in the liver leads to CVD resistance, but increases liver damage. Therefore, Zhx2 has an important role in lipid metabolism and liver function. Hepatic alpha-fetoprotein (AFP) is expressed abundantly in the fetal liver and repressed after birth regulated through three enhancers (E1, E2, and E3). E3 activity is restricted to a single layer of hepatocytes surrounding central veins (pericentral region) along with glutamine synthetase (GS). In my dissertation, I explore pericentral gene regulation in the adult liver. A GS enhancer (GS) also exhibits pericentral activity which, along with E3, is regulated by the -catenin signaling pathway. Orphan receptors, Rev-erb, Rev-erb, and ROR, contribute to E3 activity elucidating a potential mechanism for zonation.
Investigating the roles of Notch signalling during inner ear development: new insights into the dynamics of Notch activity and the functions of Delta1

The Notch signalling pathway has ubiquitous roles during inner ear development. An early phase of Notch activity, via the ligand Serrate 1 mediates lateral induction and promotes the early formation of inner ear sensory patches. In addition, Notch signalling mediated by the ligand Delta1 regulates otic neurogenesis and hair cell formation by lateral inhibition. To get new insights into the dynamics of Notch-activity during these processes, a fluorescent reporter consisting of the cis-regulatory element of the mouse Hes5 gene was introduced in the embryonic chick inner ear. In ovo electroporation was used to transfect the otic cup and to demonstrate the sensitivity of the Hes5 reporter to Notch activity. Using the retroviral vector RCAN and the Tol2 transposon system this reporter was stably integrated into the cells genome following electroporation of the otic cup. At late stages of inner ear development, the reporter was specifically activated in sensory progenitors and supporting cells but not in differentiated hair cells. The reporter was also shown to be sensitive to artificial gain- and loss-of-Notch activity. Time-lapse imaging of transfected sensory epithelia showed intercellular differences in fluorescent levels and variations over time suggesting endogenous variations of Notch activity occur within progenitor cells. Extensive proliferation and cell rearrangements could also be directly visualised at the time of hair cell differentiation. In order to test the role of lateral induction during sensory patch formation, the Hes5 regulatory element was next used to drive Delta1 expression within Notch-active cells. This created an artificial positive feedback loop mimicking the endogenous lateral induction via Serrate1. This resulted in abnormal inner ear morphogenesis and disrupted hair cell differentiation within the sensory epithelia. The inner ears transfected with the Hes5- Delta1 construct had a smaller vestibular region, cochlear defects and ectopic hair cell formation, suggesting abnormal boundary formation between sensory and non-sensory regions. Furthermore expression of Delta1 inhibited hair cell formation in trans but promoted hair cell differentiation in cis. The analysis of these effects at the single cell level provided new insights into the function of Delta1 during lateral inhibition.
Spatial prioritization of conservation management

We develop a high‐resolution conservation prioritization analysis for New Zealand's rivers and streams that simultaneously consider both the present state (representation) of ecosystems, and the prioritization of management actions designed to mitigate ongoing human impacts on their expected future state (retention). As input we used information about the geographic distributions of river ecosystem groups and their compositional similarity, species richness, present condition as compared to their estimated pristine state, and upstream and downstream connectivity. Candidate management actions included riparian planting, establishment of wetlands on tile‐drain outflows, and use of riparian buffer strips in plantation forests. The analysis, carried out at a 1‐ha resolution for a study area of 22,000 km2 in Southland, New Zealand, demonstrates a credible range of options for management intervention, particularly in lowland streams under serious threat from agricultural intensification. The proposed analysis can be replicated elsewhere for terrestrial, freshwater, or marine systems using publicly available software.
Utilization of Ascidian(Halocynthia roretzi) Tunic -3. Carotenoid Compositions of Ascidian Tunic-

Seasonal and regional variation of carotenoid contents in the muscles and tunic of the cultured ascidian(Halocynthia roretzi) was investigated. Carotenoid contents of tunic(47.87 mg/100g wet base) was much higher than that of muscles(2.35mg/100g wet base). The carotenoid contents was increased from April to August and then decreased in September. A total of 13 components were separated from the carotenoids extracted from ascidian tunic. The carotenoids of ascidian tunic accounted for followed by those of alloxanthin(), halocynthiaxanthin(), diatoxanthin(), diadinochrome(), mytilo-xanthin(), and astaxanthin().
Principles of Protein Nutrition of Ruminants

Introduction (J.M. Asplund). Structure and Function of the Ruminant Digestive Tract (J.M. Asplund). The Significance and Interpretation of Balance Methods of Determining the Utilization of Dietary Proteins (J.M. Asplund). Nitrogen Components of Forages and Feedstuffs (R.L. Reid). Amino Acid and Protein Synthesis, Turnover, and Breakdown by Ruminal Microorganisms (R.J. Wallace). Synchrony of Protein and Energy Supply to Enhance Fermentation (J.T. Huber). Absorption of Amino Acids and Peptides (K.E. Webb, Jr. and J.C. Matthews). Amino Acid and Protein Metabolism in the Whole Body and Individual Tissues of Ruminants (G.E. Lobley). The Influence of Energy on Amino Acid Supply and Utilization in the Ruminant (J.M. Asplund). The Metabolic Requirement for Amino Acids in Ruminants (J.M. Asplund). Future Research (J.M. Asplund).
Quantifying dietary pathways of proteins and lipids to tissues of a marine predator

1. Using measurements of naturally occurring stable isotopes in animal tissues is useful for monitoring diets of wide-ranging species that would otherwise be logistically difficult to evaluate. However, differential metabolic routing of macromolecules within a consumer can be problematic when using stable isotope analysis of bulk tissues to trace dietary input. 2. We used stable isotope (δ13C, δ15N) analysis to examine polar bear Ursus maritimus diet, which includes both lipid-rich blubber and the proteinaceous tissues of their marine mammal prey. Because the proportion of proteins and lipids consumed may depend on prey type and size, it was necessary to consider metabolic routing of these macromolecules separately in isotope mixing models. 3. Bayesian mixing models (MixSIR, version 1.04) were used to separately estimate protein (δ13C, δ15N) and lipid (δ13C) dietary inputs. We used existing knowledge of the relative lipid and protein intake for polar bears and isotopic information from both macromolecules to estimate overall diet composition. 4. The results for both male and female polar bears indicated that smaller prey (e.g. ringed seal Pusa hispida) contributed the largest proportion to the protein-metabolic pathway. In contrast, the largest proportion of the lipid-metabolic pathway for both sexes tended to consist of larger prey (e.g. bearded seal Erignathus barbatus). 5. The diet composition of male polar bears consisted of more large than small prey. Diet estimates for females overlapped to some degree with males but tended to consist of less large prey. 6. Synthesis and applications. Monitoring polar bear diet may help determine the effects of climate-induced environmental changes in Arctic marine ecosystems including shifts in prey composition. Additionally, tracing origins of anthropogenic pollutants is currently a priority for wildlife managers concerned with the health of marine mammals. However, our results indicate using stable isotopes to infer dietary inputs when proportions of macromolecules fluctuate amongst food sources requires the sampling and analysis of multiple tissues representing distinct macromolecular metabolic pathways. In such cases, utilizing only proteinaceous tissues for analysis will result in erroneous dietary source estimates and inaccuracies when examining trophic-level transfer of contaminants, especially those that are lipophylic.
Regulation of isoprenoid synthesis in Arabidopsis thaliana: Analysis of the GGPP branchpoint

9 List of abbreviations 13 Short prenyltransferases: an introduction 15 Alignment, mechanism and evolution 16 Enzymatic activities 25 Subcellular localization and expression patterns of short prenyltransferases 29 Predictions and mutant analysis 33 Conclusions and aims of this study 37 Material & Methods 40 List of mutant lines used in this study 40 List of oligonucleotides used in this study 41 Growth conditions of bacteria and plants 46 DNA and RNA extractions 46