Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecological genetics of the wind-pollinated, tetraploid, Allocasuarina emuina L. Johnson (Casuarinaceae) from southeast Queensland reveals montane refugia for coastal heath during the last interglacial

Thesubtropical coastal heathlands of southeast Queensland contain many rareand threatened species and have undergone considerable habitat loss in recent years due to high levels of urbanisation. We used morphological and microsatellite markers to investigate the reproductive ecology, in relation to fire, and population genetic structure of the endangered shrub Allocasuarina emuina. Highly significant differences (P <0.001) were detected among populations for allcone-andseed-relatedmorphologicaltraits,whichrevealeddistinctnorthernandsoutherngroupsofpopulations,apattern repeated in the genetic component of the study. Results also indicated that the reproductive viability of A. emuina is more related to fire interval than population size and confirmed that seed viability declines with time since fire. The highest level of genetic diversity for the species was observed in the population on Mt Emu (AE4A; HE=0.688). Contrary to the expectations of population genetic theory, no relationship was found between the level of genetic variation and population size, density or degree of isolation, hinting that genetic diversity is being conserved as a result of polyploidy and apomixis. However, genetic signatures in the northern populations indicated that unidirectional dispersal of genetic material from the putatively refugial population on Mt Emu to the surrounding coastal plain has been occurring with recession of sea levels following the last interglacial. The findings of the study will aid in both the conservation of natural populations and translocations of A. emuina and have significant implications relating to the biogeographical history of a considerable number of co-occurring heathland taxa.
A Comparison of Channel Catfish, Ictalurus punctatus, Production in Single and Mixed Cohort Culture During Two Production Seasons

Abstract Single- and mixed-size cohorts of small (18 g) and intermediate (34 g and 60 g) fingerlings, and stocker (270-300 g) channel catfish, Ictalurus punctatus, were grown in ponds at 12,500/ha for two years. Year 1 compared single cohorts (18 g, 60 g, or stockers) to mixed-size culture of these cohorts. Year 2 compared a mixed-cohort treatment (18 g, 34 g, and carryover (CO) fish), and two, two-cohort treatments (18 g or 34 g and CO). Daily growth of 18-g fingerlings was less in triple-than single-cohort culture (0.98 g/day vs. 1.55 g/day) during Year 1. Sixty-gram fingerlings and stocker-size fish grew less (P <0.05) alone than in triple cohorts. Stockers also grew more (P <0.05) in double- than single-cohort culture. Nearly 29% of single cohort 18-g fingerlings reached marketable size (≥600 g); 14% in double cohorts, and none in triple cohort ponds. All pairwise comparisons of diet costs were significantly different during Year 1. All pairwise comparisons of yield from Year 1 were significantly different. Yield was similar among treatments during Year 2, and for the study totals. Return over fingerling and diet costs during Year 1 was greatest from single-cohort culture of stocker-size fish ($5885/ha). Return was similar among treatments during Year 2 ($6803-$7197/ha). All pairwise comparisons for the project totals were significantly (P <0.05) different. Multicohort culture produced better returns than single-cohort culture of 18-g ($1105/ha) or 60-g ($845/ha) fingerlings.
Sex size and shape differences in the lacertid community (Podarcis spp. and Archaeolacerta sp.) from the Lake Skadar region (Montenegro)

We found significant variations in the pattern of sexual dimorphism in body size and shape among and within three lacertid species (Podarcis muralis, P. melisellensis and Archaeolacerta oxycephala), which live within a very restricted area (Lake Skadar, Montenegro) and under similar ecological settings. Each species has a specific pattern of size and shape relations between the sexes that proportionally changes with increase in size of the males, contrary to the expectations of Rensch's rule. Our data do not confirm unequivocally that the level of size differences between the sexes (SSD) is affected by the body shape of two different morphotypes (cylindric vs. flattened body), or by the insularity conditions (island size, distance from mainland and the presence of syntopic lizard species). However, SSD appears to be positively correlated with clutch size at the interspecies level of comparisons.
Evolution of codon usage in bacteria

Initially, this thesis investigates patterns of intragenomic codon usage within the genome of the Delta Proteobacterium Bdellovibrio bacteriovorus. Correspondence analyses revealed the primary factor influencing codon usage within this genome to be related to translational selection. The relationship between the degree of codon usage adaptation (as given by the ‘frequency of optimal codons’ statistic) and putative gene expression level was used to look for genes with unusually high or low expression levels in B. bacteriovorus, in comparison to Escherichia coli, in order to gain further insight into the unusual lifestyle of this Delta Proteobacterium. The scope was then broadened to explore intergenomic patterns of codon usage and initially extend a study measuring the strength of selected codon usage bias across bacterial genomes (Sharp et al. 2005). A dataset of 160 fully sequenced bacterial genomes was used and the strength of selected codon usage bias was seen to vary greatly between species. A correlation was observed between (log of) generation time and the strength of selected codon usage bias with fast growing bacteria showing a higher degree of selected codon usage bias than slow growing bacteria. In bacterial species exhibiting significant levels of selected codon usage bias optimal codon choice was examined. It was observed that optimal codon choice is not always conserved across all bacterial genomes under selection but broad trends in optimal codon choice were seen to be associated with particular bacterial clades. In general, optimal codon choice was seen to be linked with differences in mutational biases among the clades, as seen by a correlation between optimal codon choice in particular clades and the G+C content of their genomes. Clades that were A+U rich (Firmicutes, Gamma Proteobacteria main clade) were seen to largely prefer codons of the form NNA/U whilst G+C rich clades (Alpha Proteobacteria, Actinobacteria and Xanthomonas species) showed preference for codons of the form NNG/C in their highly expressed genes. Finally the relationship between optimal codon usage and tRNA abundances was explored. Changes in tRNA abundances were seen to coincide with switches in optimal codon usage. Therefore, switches in codon usage and tRNA abundance are thought to be influenced by changing mutational bias within the genome as reflected by the correlation between optimal codon choice, tRNA gene complements and genomic G+C content.
Influence of laboratory cultivation on species of Rhodophyta physiological evaluations and antifungal activity against phytopathogens

O presente estudo verificou as alteracoes ocorridas na fisiologia de tres especies de Rhodophyta por meio da analise da concentracao de pigmentos e de carboidratos nao estruturais, avaliando comparativamente algas coletadas da natureza e apos 28 dias de cultivo em laboratorio. Outro objetivo do estudo foi determinar se as especies mantem o potencial antifungico apos o periodo de cultivo em laboratorio, correlacionando as mudancas ocorridas na fisiologia com as de bioatividade. Apos a realizacao de cultivo em laboratorio os resultados indicaram a tendencia de reducao nas concentracoes de pigmentos nas tres especies de macroalgas, principalmente para as ficobiliproteinas. Para os carboidratos nao estruturais nao foi observado padrao de resposta das macroalgas em relacao as condicoes avaliadas. Os extratos das macroalgas Ochtodes secundiramea e Palisada flagellifera, apos cultivo em laboratorio, apresentaram aumento significativo do potencial antifungico positivamente correlacionado com a alteracao na concentracao e nas razoes de clorofila a e pigmentos acessorios. A aplicacao de tecnicas de cultivo em laboratorio das macroalgas foi uma ferramenta eficiente para o conhecimento da fisiologia, obtencao de biomassa e de compostos com aplicacao biotecnologica, sem impactar populacoes naturais.
Temporal changes in some soil chemical properties at four depths following the surface application of lime

Abstract The effect of a surface application of lime (5000 kg/ha initially then 2500 kg/ha 1 year later) on soil properties in four soil layers was measured over 15 years on a yellow‐grey earth (Duric Palic soil). The maximum increase in soil pH occurred about 2 years after lime was initially applied in the 0–50 mm soil layer, after 5 years at 50–100 mm, after about 12 years at 100–150 mm, and was still increasing at 150–200 mm. The average rate at which soil pH increased until a maximum difference occurred was 0.57,0.15,0.04, and 0.009 pH units/year in the 0–50, 50–100, 100–150, and 150–200 mm soil layer, respectively. The average rates of soil re‐acidification (rate of decrease after reaching a maximum) were 0.075 and 0.02 pH units/year in the 0–50 and 50–100 mm layer, respectively. For exchangeable calcium (Ca), the average rate of decrease after reaching a maximum was 0.82 and 0.17 cmol(+) Ca/kg per year in the 0–50 and 50–100 mm soil layer, respectively. At this rate of decrease, lime should increase.
Interferon α/β Promotes Cell Survival by Activating Nuclear Factor κB through Phosphatidylinositol 3-Kinase and Akt*

Interferons (IFNs) play critical roles in host defense by modulating gene expression via activation of signal transducer and activator of transcription (STAT) factors. IFN-α/β also activates another transcription factor, nuclear factor κB (NF-κB), which protects cells against apoptotic stimuli. NF-κB activation requires the IFN-dependent association of STAT3 with the IFNAR1 chain of the IFN receptor. IFN-dependent NF-κB activation involves the sequential activation of a serine kinase cascade involving phosphatidylinositol 3-kinase (PI-3K) and Akt. Whereas constitutively active PI-3K and Akt induce NF-κB activation, Ly294002 (a PI-3K inhibitor), dominant-negative PI-3K, and kinase-dead Akt block IFN-dependent NF-κB activation. Moreover, dominant-negative PI-3K blocks IFN-promoted degradation of κBox α. Ly294002, a dominant-negative PI-3K construct, and kinase-dead Akt block IFN-promoted cell survival, enhancing apoptotic cell death. Therefore, STAT3, PI-3K, and Akt are components of an IFN signaling pathway that promotes cell survival through NF-κB activation.
New Chalcidoid Hymenoptera

1. Mirzagrammosoma new genus of the Elachertini. Female : With the habitus of Zagrammosoma Ashmead but the scutellmn without grooves, the vertex more elevated, elevated nearly for the length of the eyes which thus appear to be in the middle of the side of the head, the checks a little longer than the eyes. Antenme inserted about in the middle of the face, the scape compressed (about three times longer than wide at apex), also the funicle and club, as in the named genus but there are two short ring-joints. Mandibles 6- dentate. Submarginal vein distinctly broken in regularity , distinctly longer than the marginal, the postmarginal two-thirds its length. Club not very distinctly jointed. Hind tibial spur distinct, not large. Parapsidal furrows rather long, meeting the small axillre which are nearly entirely cephalad of the scutellum. Pronotum conical, as long as the scutellum which is about two-thirds the length of the scutum. Propodeum a little shorter than the scutellum, with a delicate rnedian carina and no others, the spiracle very minute. Abdomen sessile, as long as the thorax, conical. Cephalic coxre elongate. Elachertine in appearance.
Space use, habitat selection and browsing effects of red deer in Sardinia

Sound ecological data are important for the conservation of the endangered Sardinian red deer, but mainly anecdotal information is available. Deer density in Mt. Arcosu WWF Reserve was 25–26 deer/100 ha. We radiotracked 8 hinds and 2 stags. Mean annual home range size was 36.5 ha (hinds) and 65.9 ha (stags). On the rut, adult females increased their home ranges by 25% and subadult females by 80%. At birthing, female home ranges reached a minimum. Small home ranges of our deer were probably related to the mild climate and dense evergreen vegetation, providing food and cover. Hinds always moved more than stags. Site fidelity was shown to areas rich in food and cover, except on the rut. In days with tourists, mean home range size significantly increased and deer selected wooded areas, whereas they preferred open terrain in days without tourists. A stronger response to disturbance occurred during the rut and in winter, when deer were less habituated to tourists. Maximum habitat selection occurred in spring and summer, when open areas were rarely used. A lethal impact on uncommon species, because of overbrowsing, was observed on 1.3% of plants. The overall impact on vegetation was negligible, despite the great deer density.
Response of alfalfa to liming

Alfalfa is the most important forage legume at cultivated fields. In the Republic of Croatia, it is sown on 42000 ha, which is approximately 3% of total state arable land (Statisticki ljetopis, 1999). In spite of its great importance and farmer’ s interest, increasing of areas sown by alfalfa is limited primarily by soil conditions, i.e. by low soil pH reactions. The aim of the study was to evaluate the possibility to establish alfalfa at acid soil with application of different liming rates. The field experiment with application of dolomite (Agrovapno MgO: product of Kamen-Sirac, d.d. Sirac, Croatia) containing 56% CaO and 40% MgO were conducted in term of September 23, 2004 on acid soil of Bjelovar-Bilogora County (locality Pavlovac). Choice of the experimental plot was made based on previous soil test (Table 1). Four rates of dolomite and control (0, 10, 20, 30 and 40 t ha-1) were applied. The experiment was conducted by randomized block design in four replicates (basis experimental plot 20.0 m2). The statistical analysis were made according to Mead (1996) as three-factorial experiment (A = growing season ; B = haymaking ; C = liming rate). Alfalfa (cultivar Osjecanka 88 of Agricultural Institute Osijek, Croatia) was sown in term of March 25, 2005. Four cuttings of alfalfa were realized of each year of testing. For determination of hay yields, fresh mass of alfalfa was weighed. Fresh mass was oven-dried on 65 oC. Nutritional status of soil was made by extractions with AL-solution. The total amount of P and K in the leaf samples was measured by the ICP-AES technique after their microwave digestion using concentrated HNO3+H2O2. Results of this study showed that significantly increased hay yield in the second year was related to increased rate of liming. Status of phosphorus, potassium, magnesium and copper in plant was not changed by application of higher rates of lime. As we expect significant response of alfalfa to soil acidity and applied liming in next 2-3 years investigation will be continued.
Effect of sub- and supra-optimal nitrogen regimes on nutrient relations in two spring wheat cultivars differing in salinity tolerance

Summary Nutrient relations in two spring wheat cultivars differing in salinity tolerance (Sarsabz, salt tolerant and Barani-83, salt sensitive) under sub-optimal and supra-optimal levels of nitrogen were examined in a glasshouse experiment. Twenty eight-day old plants of both the cultivars were subjected to five concentrations of 56, 112, 224, 336, and 448 mg N kg −1 soil for 42 days. Both cultivars responded differently to varying soil N levels in terms of growth and seed yield. The optimum N levels were found to be 112 mg kg −1 soil for Sarsabz and 224 mg kg −1 soil for Barani-83. Barani-83 had higher uptake and accumulation of N, P, K + , and Na + in the shoots as compared to those of Sarsabz. But the utilization efficiency of these nutrients was the reverse. In contrast, higher accumulation, uptake and utilization efficiency for Ca 2+ was present in cv. Sarsabz compared with cv. Barani-83. Sub- and supra-optimal levels of N were detrimental to the growth and seed yield of Barani-83, whereas those levels proved to be inhibitory in Sarsabz only at the adult stage where seed yield was considerably affected. The better growth of Sarsabz compared to Barani-83 under normal non-saline soils supplied with sub- and supra-optimal levels of N, was found to be associated with its high utilization efficiency of N, P and K.
Molecular Analysis, Subcellular Localization and Tissue Distribution of Enzymes Involved in Uric Acid Degradation

The chain of enzymes necessary to convert uric acid to its metabolic products, urea and glyoxylic acid in vertebrates, is truncated through the successive loss of allantoicase, allantoinase and urate oxidase during evolution. In the rats, and most other animals that have urate oxidase activity, this enzyme is associated with crystalloid inclusion present within the peroxisomes in hepatocytes. We have previously shown that the absence of urate oxidase activity in man and hominoid primates is due to mutations in the gene encoding this protein. The presence of all three enzymes of uric acid catabolism in fish and amphibian liver enabled us to undertake their subcellular localization. Using specific antibodies against frog urate oxidase and allantoinase we have localized these two proteins by Immunohistochemical methods to frog liver and kidney. We demonstrated that urate oxidase is present in peroxisomes, allantoinase is localized to mitochondria and allantoicase in cytosol by protein A-gold immunocytochemical method. We have cloned the cDNA encoding allantoinase by immunoscreening a λgt11 bull-frog liver cDNA library and polymerase chain reactions. The cDNA is 2112-base pairs in length containing a 1449-bp open reading frame which correspond to a 483-residue protein. Structural analysis of the deduced protein suggested two potential transmembrane segments and also showed that it lacks a typical peroxisomal targeting signal. The protein sequence indicates the presence of a putative mitochondrial localization sequence in the amino terminus. Northern blotting revealed a single mRNA species in the liver and kidney of frog, which was confirmed by immunoblotting. The hepatic and renal specific expression of allantoinase coincides with the distribution of urate oxidase in the frog tissues. These studies clearly established that urate oxidase, allantoinase, and allantoicase the three enzymes involved in uric acid degradation are localized in different subcellular organelles in the frog liver and kidney.
A comparison of seining and electrofishing for fish community bioassessment in a mexican atlantic slope montane river

Abstract Tropical freshwater fish monitoring and conservation strategies depend on data from surveys made with a variety of sampling methodologies. These methodologies have inherent biases that can lead to different data interpretations. We compared two commonly used sampling techniques—seining and electrofishing—in the calculation of community parameters and ecosystem bioassessment in a montane river in the Gulf of Mexico drainage in the state of Veracruz, Mexico. We specifically evaluated whether seining was sufficient for fish community assessment. Electrofishing produced higher estimates of species richness (45%), diversity (∼30%), and biomass (∼80%) than seining. It also produced higher biotic integrity scores. Species' relative abundance was generally similar for species captured with both techniques, but seines failed at capturing fast-swimming and benthic species. Thus, seining alone offered an incomplete perspective on the fish community and may not be adequate for bioassessment. Our results and .
Sub‐optimal morning temperature induces photoinhibition in dense outdoor cultures of the alga Monodus subterraneus (Eustigmatophyta)

Diel changes in photosynthetic oxygen evolution and several photochemical parameters measured by chlorophyll fluorescence quenching and induction were measured in outdoor dense cultures of the alga Monodus subterraneus (Eustigmatophyta). Cultures were maintained under two temperature regimes. In one, a rise in temperature was initiated in the morning by the increase in solar radiation up to the optimal temperature of 28 °C; in the other, a heating device was used to increase the rate of warming up in early morning. Although the two cultures were maintained at the same temperature and light intensity for most of the day, cultures exposed for only a short time to suboptimal morning temperature showed a larger decrease in almost all the photosynthetic parameters. By comparing the diel changes in maximal photochemistry efficiency of photosystem II, the electron transport rate and the photochemical and non-photochemical chlorophyll fluorescence quenching of the cultures, we concluded that even a relatively short exposure to suboptimal morning temperatures induced photoinhibitory damage. The higher photochemical activity of the heated culture was also reflected in a significant increase in productivity, which was 60% higher in the morning heated cultures than in the non-heated cultures.
Crescimento in vitro e aclimatização de Cattleya loddigesii Lindley (Orchidaceae) com carvão ativado sob dois espectros luminosos

The aim of this study was to evaluate the effect of different concentrations of activated charcoal in ½ MS (half concentration of macronutrients) culture medium under two light spectra on the in vitro growth of Cattleya loddigesii seedlings. Plantlets with approximately 90 days were subcultured under eight treatments, consisting of different active charcoal concentrations (0; 0.5; 1.0 and 2.0g L-1) in ½ MS medium combined with white and red light spectra. After 180 days of germination, biometric data, fresh weight, and the level of photosynthetic pigments were evaluated. Plantlets acclimatized in a greenhouse were evaluated for survival after 120 days. Total chlorophyll, chlorophyll a, and carotenoid concentrations were higher in treatments under white light, while red light promoted greater chlorophyll b, plantlets with fewer and shorter roots, and high ex vitro mortality. The addition of 2.0g L-1 of active charcoal to the culture medium and the use of white light provided greater development efficiency both on in vitro culture and ex vitro plant survival.