Miracle-dz/UniFAR-FTUs huggingface dataset:
Cumulus Cell Expansion, Its Role in Oocyte Biology and Perspectives of Measurement: A Review

Abstract Cumulus expansion of the cumulus-oocyte complex is necessary for meiotic maturation and acquiring developmental competence. Cumulus expansion is based on extracellular matrix synthesis by cumulus cells. Hyaluronic acid is the most abundant component of this extracellular matrix. Cumulus expansion takes place during meiotic oocyte maturation under in vivo and in vitro conditions. Quantification and measurement of cumulus expansion intensity is one possible method of determining oocyte quality and optimizing conditions for in vitro cultivation. Currently, subjective methods of expanded area and more exact cumulus expansion measurement by hyaluronic acid assessment are available. Among the methods of hyaluronic acid measurement is the use of radioactively labelled synthesis precursors. Alternatively, immunological and analytical methods, including enzyme-linked immunosorbent assay (ELISA), spectrophotometry, and high-performance liquid chromatography (HPLC) in UV light, could be utilized. The high sensitivity of these methods could provide a precise analysis of cumulus expansion without the use of radioisotopes. Therefore, the aim of this review is to summarize and compare available approaches of cumulus expansion measurement, respecting special biological features of expanded cumuli, and to suggest possible solutions for exact cumulus expansion analysis.
Evolutionary history of wild goat (Capra aegagrus) and the goat (C. hircus) based on the analysis of mitochondrial and nuclear DNA polymorphism: Implications for conservation and for the origin of the domestication

The goat (Capra hircus) was one of the first domesticated ungulates in Fertile Crescent more than 10,000 years ago. For investigating the evolutionary history and domestication process of this species, we studied its present genetic diversity and that of its wild progenitor, the bezoar (Capra aegagrus). Initially, the study of 2430 individuals from all over the old world allowed us to characterize the genetic diversity of domestic goats. This study included 946 new individuals from regions poorly studied until now, mainly the Fertile Crescent. The analysis concerned the HVI segment of the control region of the mtDNA. This large-scale study allowed to establish a clear nomenclature of the goat maternal haplogroups and also to assess the pertinence of defining new haplogroups. We found a large genetic diversity that was mainly distributed among goat haplogroups within geographical areas. However, even with such a huge data set, it remains difficult to understand the domestication history by the genetic analysis of domestic goats on its own. Therefore, to fully understand the domestication process, we compared the polymorphism of 487 modern bezoars from 43 localities covering most of their distribution areas to that of the 2430 goats. Based on mtDNA data, we found that 308 bezoars were close relatives to the six goat mtDNA haplogroups. They showed a higher population growth rate than other bezoars. This data supports a new two-step large-scale domestication scenario for goats. After an early phase of sustainable management of wild herds by humans (pre-domestication phase), the effective domestication took place over a large area. This area included Eastern Anatolia, the whole Zagros, the Central Iranian Plateau and the North-Eastern of Iran where wilds close-to-domestics are still present. The combined analysis of mtDNA and nuclear DNA polymorphisms for bezoars and domestic goats, demonstrated that a large genetic diversity, corresponding to a large number of mtDNA haplotypes, was captured at the initial step of the effective domestication. The first domesticated goats were able to capture most of the genetic diversity of their wild ancestors and clearly, the goats do not fit the bottleneck domestication paradigm. This scenario is very different from previous models, which call for restricted domestication centres and population bottlenecks.
Auxin Control in the Formation of Adventitious Roots

Adventitious rooting is a complex process and a key step in the vegetative propagation of economically important woody, horticultural and agricultural species, playing an important role in the successful production of elite clones. The formation of adventitious roots is a quantitative genetic trait regulated by both environmental and endogenous factors. Among phytohormones, auxin plays an essential role in regulating roots development and it has been shown to be intimately involved in the process of adventitious rooting. Great progress has been made in elucidating the auxin-induced genes and auxin signaling pathway, especially in auxin response Aux/IAA and Auxin Response Factor gene families. Although some important aspects of adventitious and lateral rooting signaling have been revealed, the intricate signaling network remains poorly understood. This review summarizes some of the current knowledge on the physiological aspects of adventitious root formation and highlights the recent progress made in the identification of putative molecular players involved in the control of adventitious rooting. Despite much has been discovered regarding the effects and regulation of auxins on plant growth since the Darwin experiments, there is much that remains unknown.
Efecto Ecotoxicológico de tres Metales Pesados Sobre el Crecimiento Radicular de Cuatro Plantas Vasculares

La evaluacion del riesgo ambiental (ERA) de los ambientes terrestres contaminados por metales pesados en el Peru requiere del empleo de organismos biologicos estandarizados, que sean sencillos, practicos, sensibles y repetibles, como las semillas de plantas superiores empleadas en bioensayos ecotoxicologicos. Por ello, el objetivo de este trabajo fue evaluar el efecto fitotoxico del Cr6+, Hg2+ y Pb2+ en forma de dicromato de potasio (K2Cr207), cloruro de mercurio (Cl2Hg) y acetato de plomo ((CH3C00)2Pb), respectivamente, sobre el crecimiento radicular de cuatro especies de plantas superiores terrestres: cebolla (Allium cepa L., Liliaceae), betarraga (Beta vulgaris L., Chenopodiaceae), arroz (Oriza sativa L., Poaceae) y rabanito (Raphanus sativus L., Brassicaceae) a 192 h (8 dias) de exposicion. Se realizaron bioensayos de toxicidad subagudos estaticos para cada metal y para cada especie de planta, usando un diseno experimental en bloques completos al azar: seis concentraciones, ocho repeticiones, con un total de 240 semillas por bioensayo. La secuencia en orden ascendente para la concentracion de inhibicion media (CI50 en mg L-1) del crecimiento radicular de las semillas a 192 h fue en la mayoria de los casos: Hg2+ > Cr6+ > Pb2+. Se analizan las perspectivas de uso para la evaluacion de suelos contaminados por metales pesados en el Peru.
Egg quality of dual-purpose hens intended for small-scale farming

The objective of the experiment was evaluation of some physical traits of egg quality in hens originating from Polish egg-type pedigree farms and destined for small-scale farming as well as in a breed of preserved chickens. 30 eggs from each of the three genetic groups (parental P55 Barred Rock strain, VH43 parental cross of V44 Rhode Island Red and H33 Leghorn strains, and the preserved Z11 Partridge Greenleg strain) were taken to analysis. The layers were maintained in the same environmental conditions and were under the same feeding regime. Analyses of egg quality were accomplished in 26th and 50th weeks of age, with an electronic EQM device. Egg weight in VH43 cross in the beginning of laying was 61.5 g and it was significantly bigger than in P55 hens (50.2 g) and Z11 hens (42 g). No statistical differences between experimental groups were found in shell thickness, shell density. Egg shell colour in P55 hens differed significantly from that in the other groups. The highest Haugh unit score (99.9) and albumen height (9.7 mm) were noted in the eggs of P55 hens in 26th weeks of age. These parameters lowered with age in all experimental groups. The highest proportion of yolk was found in the eggs of Z11 (29.5%) in 50 weeks of age. Yolk percentage increased with age in all genetic groups. Yolk colour index (La Roche) diminished with age of layers.
Harvestmen: the biology of Opiliones

Contributors Preface 1. What are harvestmen? 2. Morphology and functional anatomy 3. Phylogeny and biogeography 4. Taxonomy 5. Paleontology 6. Cytogenetics 7. Ecology 8. Foraging and food habits 9. Natural enemies 10. Defense mechanisms 11. Social behavior 12. Reproduction 13. Development 14. Eco-physiology 15. Field and laboratory methods References Taxonomic Index Subject Index
Towards fermentation of galacturonic acid-containing feedstocks with Saccharomyces cerevisiae

The ambition to reduce our current dependence on fossil transportation fuels has driven renewed interest in bioethanol. Pectin-rich feedstocks like sugar beet pulp and citrus peel, which are currently sold as cattle feed, are promising raw materials for the production of bioethanol. This thesis explores the challenges related to the fermentation of pectin-rich hydrolysates with Saccharomyces cerevisiae. Galacturonic acid is a major constituent of pectin-rich hydrolysates. Achieving efficient conversion of this compound is desired. This requires introduction of a heterologous pathway for galacturonate metabolism. In this project, we functionally expressed uronate isomerase and tagaturonate dehydrogenase, the first two enzymes of a bacterial catabolic pathway. Introduction of the entire 5-enzyme catabolic route did not result in a S. cerevisiae strain capable of galacturonic acid fermentation. Galacturonic acid will therefore remain present in the fermentation medium. It was shown that the presence of galacturonic acid negatively affects fermentation characteristics in aerobic chemostat cultivations. In addition, it was demonstrated that, especially at low pH, galacturonic acid has a drastic impact on cellular viability and galactose, arabinose and xylose consumption. As long as galacturonic acid is not consumed by S. cerevisiae, these inhibitory effects of galacturonic acid will remain a key issue in the yeast-based production of bioethanol and other products from pectin-rich feedstocks.
Dystonia and Genetics

In recent years, the identification of several new dystonia genes has provided important insights into the nature of this clinically and genetically heterogeneous disorder. Currently, about twenty different forms of monogenic dystonia are distinguished genetically and have been designated DYT 1–13; DYT 14, which has been redefined as DYT 5; and DYT 15–21 (Ozelius et al., 2011; Wider et al., 2008). Among these DYTs, ten genes have been identified using linkage analysis in families: DYT 1, 3, 5/14, 6, 8, 11, 12, 16, and 18 (See Table 1 and Figure 1) (Ozelius et al., 2011).
Genetic structure of Albizia gummifera and its local adaptation to the associated arbuscular mycorrhiza

The aim of this study was to assess genetic structure and local adaptation of Albizia gummifera to associated mycorrhiza using three populations from Uganda, Kenya and Madagascar. Using variation in chloroplast DNA sequences, estimates of genetic diversity and differentiation were obtained. Local adaptation of A. gummifera to the associated mycorrhiza was investigated by planting seed from different A. gummifera provenances into soils inoculated with soil microbial samples from respective local sites. In addition, the stability of inoculum was tested by comparing the performance of fresh and stored soils as inoculum. Four weeks after seedling emergence, height measurements were initiated and continued for six weeks. Mycorrhizas in the soil inoculum were identified using direct microscopic observation. Genetic data were analysed using GENALEX while greenhouse data were analysed using GENSTAT. The results showed that the species is genetically diverse with 14 cpDNA haplotypes identified (hTOT = 0.803), with Uganda showing most diversity (h =0813) and Kenya the least (h =0.398). Although the majority of variation was distributed within populations (75%), significant population differentiation was observed (ΦPT = 0.249, p > 0.01) and each population contained private haplotypes: Uganda (5), Madagascar (3) and Kenya (1). Greatest genetic distance was observed between Kenya and Madagascar (2.711). The lowest distance was observed between Uganda and Kenya (0.298). The diversity of the mycorrhizal community varied between sites with Ugandan fresh soils being more diverse than Kenyan fresh soils. For the old soils, fungal diversity was highest in Kenya, followed by Madagascar and then Uganda. Based on the growth performance measurements, there was no evidence of adaptation of A. gummifera provenances to local mycorrhizas though plant performance for inoculated plants was higher than that of the control. From the study, it appears that the specific kind of fungi the A. gummifera plants are exposed to is not important, although they benefit from the exposure. The tree populations seem to have genetically differentiated and transferring them to sites outside their own may pose a genetic threat. More research is however needed to ascertain adaptive differences of A. gummifera to abiotic and other biotic factors, the suitable founding genetic diversity and other factors that may affect introductions. The exact mycorrhizas that colonise the plants also need to be identified.
Combining Ability in Upland Cotton—Ginning and Fibre Characters

An 8 × 8 diallel analysis of combining ability was conducted to characterise the genetic architecture of the population and to isolate best parents for hybridization aiming to improve ginning and fibre properties in Upland cotton (Gossypium hirsutum). The variances due to general and specific combining ability, both, were significant for all the six characters, (G.O.T., seed index, lint index, fibre length, fibre strength and fibre fineness) studied. The magnitude of general combining ability variances was, however, about four to six times higher than those due to specific combining ability. A breeding plan which may mop up the additive gene effects effectively and can maintain certain degree of heterozygosity in cotton has been suggested for maximum exploitation. The Punjab strain A102 was the best general combiner for four of six characters (seed index, lint index, fibre length and fibre fineness). The per se performance of the parents had high relationship with their general combining ability effects. The genetic and geographic diversity of the parents had high association with their specific combining ability
Egg freshness detection based on digital image technology

Yolk index and air room height, two main measures for egg freshness detection, are very difficult to be accurately measured in practices. This paper investigated an image-based egg freshness detection method. The perspective image of egg was obtained by computer vision device. The characteristic regions, including the yolk region and air room region were separated from the obtained egg picture by image processing. The pixel areas and lengths of the above characteristic regions were respectively calculated and analyzed. The relative ratios of the pixel area and length of characteristic regions to that of the whole egg region were selected as characteristic parameters. It was shown that the above relative ratios increased while egg freshness reduced according to a detailed analysis. Three detection models of egg freshness were set up based on the correlations between the characteristic parameters and freshness. The test results showed that the accuracy rates of these models were 93, 94 and 92% respectively. The egg freshness detection based on image characteristic of yolk and air room was efficient and feasible.
Comparative Neurobiology in Chiroptera

These are three volumes to study systematically and comprehensively the brain structure in bats. Volume 1 contains comparisions of the macromorphology, main brain components and selected nuclei. The text is complemented by 53 tables, numerous original line drawings and photographs and one atlas of a megachiropteran and one of a microchiropteran brain. Volume 2 deals with the characteristics of brain structure in the taxonomic units and contains a comprehensive survey of the existing literature which has been organized on a taxonomic basis. Interpreting brain data with respect to taxonomic and ecoethological relationships, volume 3 provides deeper insight into the significance of the diversity of brain structure. It contains the most comprehensive and up-to-date references on chiropteran brain structure and biology presently available. This work provides immediate access to a large fund of well-organized information.
ROLES OF BIOTRANSFORMATION IN THE ANTITUMOUR ACTIVITY AND TOXICOLOGY OF THE HYPOXIA-ACTIVATED PRE- PRODRUG PR-104

Hypoxia is a characteristic of tumours and an attractive therapeutic target. PR-104, a hypoxia-activated prodrug in clinical trial, is a phosphate ester which is rapidly converted to the alcohol PR-104A, and then activated by reduction to hydroxylamine (PR-104H) and amine (PR-104M) metabolites selectively in hypoxic cells. This thesis explores the pharmacology of PR-104. The primary objectives were to define relationships between metabolic transformation of PR-104, its toxicity to normal tissues, its clearance from the body, and its antitumour activity in preclinical models. DNA damage responsible for cytotoxicity of PR-104A was characterised by comparing sensitivity of repair-defective Chinese hamster ovary cell lines with their repaircompetent counterparts. The activated metabolites PR-104H and PR-104M showed a repair profile similar to typical DNA interstrand crosslinking agents, including dependence on the ERCC1-XPF endonuclease (implicated in unhooking DNA interstrand crosslinks at blocked replication forks) and Rad51D (required for homologous recombination repair). PR-104A cytotoxicity under hypoxia is accounted for by DNA crosslinking by these reduced metabolites. This study showed that hypoxia, reductase activity, and DNA interstrand crosslink repair proficiency are key variables that interact to determine PR-104A sensitivity. PR-104 was rapidly excreted in mice, with approximately equal excretion in urine and faeces. Investigation of pathways of biotransformation in mice, rats, dogs and humans identified major species difference in biotransformation of PR-104 in that Ndealkylation and subsequent metabolites from the mercapturic acid pathway was major in rodents, while O-glucuronidation of PR-104A much more extensive in dogs and humans. The nitroreduction pathway was found in all species, with different patterns in that PR-104M was prominent in rodents but PR-104H was higher in humans. Overall, the results suggest that rodents may not be appropriate for modelling human biotransformation and toxicology of PR-104. A rapid and sensitive UHPLC-MS/MS method was developed for quantitation of the major metabolites of PR-104 in humans. Application to plasma samples from phase I clinical trials demonstrated approximately dose-linear pharmacokinetics but high variability between individuals in concentrations of the glucuronide. The species and individual difference in glucuronidation were further examined using a microsomal metabolism model. Glucuronidation was fastest in dog liver microsomes, followed by human then rodent microsomes. UGT2B7 appeared to be the only human isoform able to conjugate PR-104A, which was further confirmed by a strong correlation between UGT2B7 protein content and glucuronidation activity in microsomes from different individuals. The results suggest that differences in UGT2B7 activity may contribute to individual differences in PR-104A pharmacokinetics, and that the role of this enzyme in the toxicology of PR-104 warrants further investigation.
Stock market reaction to policy interventions

ABSTRACT We analyse stock price reactions to the announcements of monetary and fiscal policy actions in 12 stock exchanges worldwide between 1 June 2007 and 30 June 2012. While past papers have analysed the effect of policy interventions focusing on monetary policy actions (e.g. Ricci 2015), our paper focuses on stock indices either capturing the whole stock market or various industries. By estimating abnormal stock reactions around the announcement date, we show that (1) stock industry indices react to policy interventions in a different manner than the broad stock index does; (2) stock returns react negatively to restriction measures for general and non-banking sector indices; and (3) stock reaction to expansionary measures was stronger at the beginning of the financial crisis.
Wood decay in living and dead trees: A pictorial overview

Pioneering research by Alex L. Shigo and his associates has produced a series of pictorial guidelines to provide a better understanding of how trees respond to wounding and subsequent microbial infections that lead to wood decay. The purpose of this paper is to visually summarize through the use of 96 color photographs and illustrations, the varied patterns of wood discoloration and decay observed in the dissection of thousands of trees. This information has served as a conceptual framework for understanding the biochemical processes that limit the spread of wood-destroying infections initiated by wounding during the maturation of all trees. This understanding has helped those who work with forests, trees, and wood to resolve practical problems and improve the health and productivity of trees and forests.
Transcriptome and proteome analysis of xylose-metabolising Saccharomyces cerevisiae

Increasing concern about global climate warming has accelerated research into renewable energy sources that could replace fossil petroleum-based fuels and materials. Bioethanol production from cellulosic biomass by fermentation with bakers yeast Saccharomyces cerevisiae is one of the most studied areas in this field. The focus has been on metabolic engineering of S. cerevisiae for utilisation of the pentose sugars, in particular D-xylose that is abundant in the hemicellulose fraction of biomass. Introduction of a heterologous xyloseutilisation pathway into S. cerevisiae enables xylose fermentation, but ethanol yield and productivity do not reach the theoretical level. In the present study, transcription, proteome and metabolic flux analyses of recombinant xylose-utilising S. cerevisiae expressing the genes encoding xylose reductase (XR) and xylitol dehydrogenase (XDH) from Pichia stipitis and the endogenous xylulokinase were carried out to characterise the global cellular responses to metabolism of xylose. The aim of these studies was to find novel ways to engineer cells for improved xylose fermentation. The analyses were carried out from cells grown on xylose and glucose both in batch and chemostat cultures. A particularly interesting observation was that several proteins had post-translationally modified forms with different abundance in cells grown on xylose and glucose. Hexokinase 2, glucokinase and both enolase isoenzymes 1 and 2 were phosphorylated differently on the two different carbon sources studied. This suggests that phosphorylation of glycolytic enzymes may be a yet poorly understood means to modulate their activity or function. The results also showed that metabolism of xylose affected the gene expression and abundance of proteins in pathways leading to acetyl-CoA synthesis and altered the metabolic fluxes in these pathways. Additionally, the analyses
Aclerogamasus stenocornis sp.n., a fossil mite from the Baltic amber [Acari: Gamasida: Parasitidae]

Aclerogamasus stenocornis sp. n. , the eigth fossil anactinotrichid mite and the first fossil mite of Parasitidae, is described. The mite is embedded in Baltic amber and shows conspicuous shape of corniculi, palp apothele and tectum prongs. Specific and generic features are discussed in relation to extant species.