Miracle-dz/UniFAR-FTUs huggingface dataset:
Genes controlling zebrafish development: Roles for Rabs and Glis.

This thesis is divided in two main sections linked by a common question concerning notochord formation and signalling. The first section describes a loss-of-function screen of zebrafish Rab proteins using antisense morpholino oligonucleotides (MO). Rab proteins are small GTPases, which constitute the largest subfamily of the Ras superfamily. There are at least 60 human Rab proteins and they are thought to be involved in every step of vesicular traffic within eukaryotic cells. I identified 63 zebrafish rab genes, but there are probably more as for fourteen human RAB genes the zebrafish counterpart was not identified in this work. The mRNA in situ localization of 20 zebrafish rabs was assessed. All 20 genes were expressed during embryonic development and 6 showed enhanced expression in certain embryonic structures, such as chordamesoderm and polster (rab1b, rab2a2 and rab18), neurons subsets (rab3c1 and rab5a1), or specific brain regions (rab5c). MO injections targeting 20 different rab proteins were carried out and 14 resulted in embryos with obvious phenotypic defects. Several of the Rab morpholino-induced phenotypes are analysed and discussed. The phenotypes observed range from defects in very early developmental processes, such as epiboly (Rab5a2), to defects in highly specialized developmental processes, such as melanophore morphology (Rab1b). Knocking down several of these proteins resulted in embryos with defects in structures with high trafficking activity, such as brain, notochord or blood (Rab7b, Rab9a, Rab14a, Rab15). The second section of the thesis describes efforts to understand the role of Gli3 protein in zebrafish development. Gli proteins are the transcription factors of the Hh signalling pathway and play a variety of roles in processes involving Hh signalling activity such as development of ventral spinal cord and limb. In the zebrafish, mutations in Gli1 and Gli2 proteins are known but no Gli3 homolog had been reported. I cloned the zebrafish gli3 gene and mapped it to linkage group 24. To analyse the loss-of-function phenotype of zebrafish Gli3 in the ventral neural tube a brief analysis of spinal cord markers was done. Using these spinal cord mariners, no obvious mispatterning phenotype was observed in zebrafish embryos injected with a MO targeting gli3. Disrupting Gli3 function in zebrafish embryos, however, resulted in a strong early phenotype. At 40% epiboly Nodal signalling is up-regulated and later in development the embryos show convergence-extension defects. Interestingly, the convergence-extension phenotype can be rescued by a short treatment with cyclopamine, a chemical inhibitor of Hh signalling.
Condition indices of Atlantic cod (Gadus morhua) biased by capturing method

In studies evaluating the condition and general health status of fish stocks, the method used for catching the fish is seldom considered as a factor of importance. In this study, condition indices were compared between cod caught in pots, gillnets, and on hooks in the same geographical area. The results showed that cod (Gadus morhua) caught on baited gear types (pots and hooks) generally displayed a lower condition and an older age (i.e. suggesting a lower growth rate) compared to cod caught in gillnets. It is unclear whether these results merely illustrate divergent behavioural responses in fish originating from one single population, or if these divergent behavioural components represent distinct subpopulations displaying different mean conditions and growth rates. Regardless of the underlying causes, the results not only show that parts of the Baltic cod stock are in extremely poor condition, they also indicate that different gear types used in the same area could target similar-sized conspecifics exhibiting large differences in condition and size-at-age. The potential impact of the difference in condition between the pots and other gear types could hamper the implementation of the cod pot as a potentially seal-safe and sustainable fishing method.
DETECTION OF BENOMYL RESISTANCE IN THE ANTHRACNOSE PATHOGEN, COLLETOTRICHUM CAPSICI

SUMMARY: Conidial isolates of Collectotrichum capsici were obtained from four field sites in Malaysia. Benomyl-resistant isolates were detected by their mycelial growth on agar containing 100 µg/ml benomyl. Resistant isolates were found at three of the four sites examined where benomyl sprays were frequently used. Large differences in the effects of benomyl on mycelial growth of sensitive and resistant isolates were demonstrated; growth of sensitive isolates were completely inhibited at 2.5 µg/ml benomyl while the resistant isolates examined, all grew on agar containing 1000 µg/ml fungicide. The benomyl-resistant isolates were cross - resistant to thiophanate-methyl and carbendazim. Benomylresistant isolates were just as pathogenic to chillies as sensitive isolates. The implication of these results and other reports of benomyl resistance in Collectotrichum are discussed in relation to disease control.
Molecular characterization and in vivo expression of hypoxia inducible factor (HIF)-1α in sea bass (Dicentrarchus labrax) exposed to acute and chronic hypoxia

Abstract Aquatic hypoxia is a frequent event and in fish a complex set of physiological and biochemical alterations are employed to cope with this environmental stress. Many of these adjustments depend to a large extent on changes in the expression of genes that encode for physiologically relevant proteins. Genes that are induced by hypoxia appear to share a common mode of transcriptional regulation. This induction depends upon activation of a transcription factor, the hypoxia inducible factor-1 (HIF-1), which is a heterodimer composed of two subunits: α and β . In this study we report first on the molecular cloning and characterization of HIF-1α in sea bass (Dicentrarchus labrax). The full-length sea bass cDNA for HIF-1α was isolated and deposited in the GenBank with accession no. DQ171936. It consists of 3317 base pairs (bp) carrying a single open-reading frame that encompasses 2265 bp of the coding region and 1052 bp of the 3’ UTR. We then utilized the real-time PCR technology to monitor dynamic changes in levels of HIF-1α tran-scripts, in response to acute and chronic hypoxic stress. The number of HIF-1α mRNA copies were significantly increased in response to both acute (1.9 mg/L, dissolved oxygen for 4 hours) and chronic (4.3 mg/L, DO for 15 days) hypoxia in sea bass, whereas it remained unchanged in fish exposed to hyperoxic (DO 13.5±1.2 mg/L, 155 % saturation) conditions. This is the first study carried out to investigate the behaviour of HIF-1α gene transcripts during hypoxia in representative of marine hypoxia-sensitive fish species.
Distributions and Congener Patterns of PCBs in Fish from Major Aquaculture Areas in the Pearl River Delta, South China

ABSTRACT The distribution and concentrations of polychlorinated biphenyls (PCBs) were determined in surface sediments and fish collected from freshwater fishponds in six major aquaculture areas of the Pearl River Delta. The concentrations of total PCBs ranged from 7.32 to 36.2 ng/g (dry weight) in sediments and 5.15 to 226 ng/g (lipid weight) in five species of fish, with higher concentrations in fishponds from two industrialized areas. Feeding habits of fishes played a significant role on the accumulation of PCBs and their homologue patterns in fish tissues, with higher concentrations in muscle and viscera of mandarin fish (Siniperca kneri), and tilapia (Tilapia mossambica) and lower in grass carp (Ctenopharyngodon idellus). In muscle, IUPAC No. 118, 138, 81/87, 153, 180, 52, 49, 99, and 44 congeners were the most dominant out of the 36 congeners measured in the present study. The contents of PCBs in fish cultivated in the Pearl River Delta were rather low when compared with the maximum concentration of total PCBs of 2.0 μg/g (wet weight), imposed by the U.S. Food and Drug Administration edible seafood. However, due to the bioaccumulation and biomagnification nature of PCBs through the food chain, continuous monitoring of PCBs as well as other Persistent Organic Pollutants in this rapidly developed region is encouraged.
The status of trace elements in lymphoma and esophageal cancer patients: A case study

Cancer is a life threatening disease. Many people die of cancer every year. Epidemiological studies suggest that alteration of trace elements in the body can contribute to the development of cancer. The aim of this study was to determine the concentration of zinc (Zn), copper (Cu), lead (Pb), Nickel (Ni), iron (Fe) and magnesium (Mg) in the blood, hair and nails of lymphoma and esophageal cancer (EC) patients in Khyber Pakhtunkhwa. The results reveal that the mean concentration of Cu, Pb and Ni increased significantly, while the concentration of Zn, Fe and Mg significantly decreased in the blood, hair and nails of lymphoma and EC patients. From this study it can be concluded that increased Pb, Cu, Ni and decreased Zn, Fe and Mg concentration in lymphoma and esophageal cancer patients suggest that these may play some role in carcinogenesis. Key Words: Trace elements, lymphoma, esophageal cancer
Beyond climate: convergence in fast evolving sclerophylls in Cape and Australian Rhamnaceae predates the mediterranean climate

Morphological convergence in mediterranean‐type ecosystems (MTEs) has long been interpreted as adaptation to climatic similarities among the five MTEs of the world. Here, we challenge this model using the globally distributed Rhamnaceae. We collected functional trait data (specific leaf area, leaf area, spinescence, leaf phenology, growth form and leaf margin type) and biome data to test for trait convergence in MTEs, for models of trait evolution and ancestral state reconstruction and for the effect of traits on speciation and extinction rates, using a phylogenetic framework. We show that leaf functional traits evolve to three optima, which correspond to (i) the edaphically specialized Australian and Cape MTEs (AC), (ii) the mediterranean‐type climates, but edaphically normal Chile, California and Mediterranean Basin (CCM) and (iii) the non‐mediterranean habitats. We find that Rhamnaceae in CCM are predominantly characterized by non‐sclerophylly, the ancestral state in Rhamnaceae, and Rhamnaceae in AC by sclerophylly. These leaf character syndromes have evolved prior to mediterranean climates in MTEs, thereby failing to be adaptive to this selective regime. However, sclerophylly evolved contemporaneously with the transitions to AC and may therefore be an adaptation to nutrient‐poor soils. The evolution of sclerophylly has contributed to increased diversification rates of Pomaderreae in Australia and Phyliceae in the Cape, by reducing extinction rates and thereby facilitating evolutionary persistence. The historical relatively stable conditions in AC are consistent with this persistence hypothesis. Synthesis. In this study, we integrate the fields of macroevolution and ecology and show that low extinction rates may not only account for the ecological, but also for the floristic dominance of sclerophylly in the hyperdiverse Australian and Cape mediterranean‐type ecosystems.
QTL dissection of yield components and morpho-physiological traits in a durum wheat elite population tested in contrasting thermo-pluviometric conditions

Abstract. Dissection of the genetic basis of the adaptive response of durum wheat to unfavourable water and temperature regimes is an important prerequisite for the selection of genotypes less vulnerable to environmental constraints. An elite durum population of 249 recombinant inbred lines was tested across 16 Mediterranean environments characterised by contrasting thermo-pluviometric conditions and, consequently, a broad range of productivity (from 0.56 to 5.88 t ha–1). Among the environmental variables investigated, soil moisture during grain filling showed the most consistent correlation with yield components and grain yield, whereas a weaker, albeit in some cases significant, association was noted with temperature at heading and thermal time during grain filling. Ear peduncle length appeared as a valid and easy-to-phenotype morphological proxy for the water available to the plant. In total, 76 quantitative trait loci (QTLs) were identified for yield components and for several morpho-physiological traits (peduncle length, the spectral reflectance index NDVI and leaf greenness at the milk-grain stage expressed in SPAD units) associated with the adaptive response of wheat to water and heat stresses. Although most of the QTLs were significant in only one or two environments, two major QTLs on chromosomes 2BL and 3BS showed consistent additive and epistatic effects on 1000-kernel weight, peduncle length, SPAD values and grain yield in half of the environments. In view of their strong phenotypic effects on kernel weight, these two QTLs are good candidates for positional cloning in order to gain a better understanding of the functional basis of their effect on the plasticity of grain weight and grain yield.
The effect of sex and deleterious mutations on fitness in Chlamydomonas

In this paper we present an experimental test of the deterministic mutation hypothesis on the evolution of sex. We studied the direct effect (i. e. before selection) of sex on offspring fitness of two strains of the unicellular alga Chlamydomonas moewusii, that had been kept in the laboratory for over 60 years. The logistic parameters r and K of each genotype, estimated in batch culture, were used as a measure of fitness. Strains were treated with uv to cause additional deleterious mutations. By comparing mean log fitness of parents and offspring in relation to the fitness difference of the parents, we tested whether and how deleterious mutations interact. No significant recombinational load was found in the offspring of the untreated strains. However, a significant negative effect of sex on log r and log K was found after crossing uv treated strains. We argue that this negative effect of sex on fitness suggests synergistic interaction, at least between the UV-induced and the naturally accumulated deleterious mutations. The latter result therefore supports the deterministic mutation hypothesis.
A comparative Method for testing Agents used in Sheep Maggot Fly Control.

Dipping or spraying sheep with various agents has for long been the principal method of maggot fly control. Although much critical and fundamental work has been carried out, the assessment of the degree of control and the length of protection afforded, has depended ultimately on field trials. There are, unfortunately, several complicating factors associated with the problem which in the past have received insufficient attention. They have often resulted in conclusions being drawn from field work which are either invalid or are not supported by adequately controlled experiments.
Daylength, Temperature and Solar Radiation Effects on the Phenology and Yield Formation of Spring Durum Wheat

Future food security will depend on crop adaptation to changing environments. We studied the limitations imposed by daylength, temperature and solar radiation on wheat yield in eight field experiments conducted at contrasting northern latitudes and involving 42 adapted spring durum wheat genotypes of divergent phenology, and reduced or without photoperiod sensitivity. Air temperatures averaged from sowing to anthesis (SA) increased from northern to southern sites, while daylength and minimum temperatures from anthesis to maturity (grain filling, GF) followed the opposite trend, due to differences in the latitude of sites. The site effect explained 96 % of the variation in the number of days SA, which was much smaller in southern sites. Average minimum daily temperatures above 6.9 °C before anthesis and below 10.8 °C during GF accompanied by photoperiods during GF of less than 14.2 h resulted in less than 14 000 kernels m−2, which was the threshold below which kernel number limited yield. Radiation during GF lower than 1.8 kJ kernel−1 day−1 limited kernel weight, which was then a constraint to the achievement of yield potential.
Distribution of Phenolic Acids in Milling Fractions of Spring Wheats

The core objective of the current research was to determine the phenolic acids through High performance liquid chromatography (HPLC) in milling fractions of spring wheats, i.e., bran, shorts, break, and reduction flour. In wheat bran, caffeic, p-coumaric, syringic, and ferulic acid ranged from 0.93 to 1.5, 24 to 32.00, 55.30 to 94, and 137.25 to 180.30 μg/g, respectively. Maximum caffeic acid (0.33 μg/g), p-coumaric acid (12.12 μg/g), and ferulic acid content (29.12 μg/g) were found in the reduction flour of Sehar-2006. Furthermore, whole wheat flour of Shafaq-2006 revealed maximum caffeic acid (1.8 μg/g), p-coumaric acid (22.3 μg/g), and syringic acid (47.07 μg/g). Since antioxidant activity is directly related with phenolic acids, it was decreased (43.26 to 74.40%) in cookies with the decrease in phenolic acids during storage. Moreover, phenolic acids hold potential to be extracted and utilized in cereal-based products for best quality and value addition.
Production of epicormic shoots on oak (Quercus robur): effects of frequency and time of pruning

The problem of epicormic shoots and their control is a common theme of oak silviculture in North America and Europe. The earliest reports are from Europe, where Pontey (1810), for example, described epicormic shoots and the knots they cause as ‘an evil of immense magnitude’. Foresters in North America began to realize the significance of epicormic shoots when virgin forests had been cleared and second growth stands were being brought under management (Kormanik and Brown, 1964). The presence of epicormic shoots on oak is regarded as undesirable because they can reduce the quality and value of timber: Hedlund (1964) described how they reduced the quality of 23 per cent of logs by two or more grades and Courraud (1987) showed how their presence affects value using French log grading rules. Even superficial epicormic shoots will suggest to timber buyers that individual knots, or clusters of them, may be present deeper in the log, resulting in lower prices being paid. The population of epicormic shoots on an oak tree is determined by three main factors: (1) the initiation of buds, (2) the release of buds from dormancy and (3) survival of epicormic shoots. Whilst it is generally accepted that most epicormic branches develop from suppressed buds which become embedded in the bark, the reasons for their release from dormancy are not well understood (Bowersox and Ward, 1968; Roussel, 1978; Wignall et al., 1987; Harmer, 1988; Wignall and Browning, 1988; Spiecker, 1996; Fontaine et al., 1997). The survival of epicormic shoots on Quercus mongolica var. grosseserrata has been studied by Yokoi and Yamaguchi (1996) who confirm that light is important; other likely factors are oak leaf roller moth (Tortrix viridana L.) and mildew (Microsphaera alphitoides Grif. Production of epicormic shoots on oak (Quercus robur): effects of frequency and time of pruning
Identificação e modelagem da autocorrelação residual no ajuste do modelo de Wood às curvas de lactação de cabras

The objective of this research was to present a methodology for identification and modeling of residual autocorrelation considering individual adjustments of the Wood's model to lactation dairy goats and evaluate the influence of such modeling in the quality of adjustment. The Wood's model was adjusted individually for lactations in three different ways, the first have assumed independence of errors (IE) for all lactations, the second have assumed autoregressives first order errors (AR1) for all lactations and the third, named (IE-AR1), was used the AR1 errors structure only for lactations that showed residual autocorrelation according to Durbin-Watson test, and the IE errors structure for the other lactations. The three ways of adjustment were compared by the percentage of convergence and the average of the mean square errors (MSE) and coefficients of determination adjusted (R2adj). The average of MSE and R2aj were very similar in the three cases of residual structure. However, the model with IE-AR1 residual structure showed a higher rate of convergence, which is an advantage, as it allows a greater number of animals are evaluated for their lactation curve. Therefore, due to the increasing convergence obtained, the fit of the Wood's model with IE-AR1 residual structure is the option most suitable for large data sets.
The Recurrent Origin of Plant Races and Species

Abstract Whereas there is increasing evidence that some polyploid taxa have multiple independent origins, little attention has been given to the possibility that taxa arising through selective processes without ploidal shifts also may be the products of recurrent evolution. I argue that there are no necessary reasons why ecologically distinct races and species could not arise from separate lineages at different times and in different places. Similarity of the genetic structure of progenitor populations combined with parallel selective pressures would make this possible, as would evolution in the direction of greatest genetic variance. Putative examples of multiple independent origins of single and multiple adaptations are reviewed. The possibility that some taxa are polyphyletic is suggested by the presence of isolated populations in different clades. I also consider the possibility of the recurrent origins of reproductive isolating mechanisms and of species. Communicating Editor: Paul Wilson
Drinking Water Quality and its Effects on Broiler Chicks Performance During Winter Season

3 Abstract: Samples of water were taken from different sources (commercial, Nile and well). Physical, chemical and bacteriological analysis of samples revealed that, levels of salinity, hardness, alkalinity, Ca, Mg, Na and K in the well water were higher than those in the Nile and commercial water. Higher levels of sulphate and chloride were found in the commercial water. Total bacterial count was higher in the Nile water than in the commercial and well water. Then an experiment was carried out to detect the effects of different sources of water on broiler chicks performance and on plasma minerals contents. Broiler chicks given Nile water had significantly increased (P 0.05).