Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure and development of the ctenial spines on the scales of a teleost fish, the cichlid Cichlasoma nigrofasciatum

Sire, J.-Y. and Arnulf, I. 2000. Structure and development of the ctenial spines on the scales of a teleost fish, the cichlid Cichlasoma nigrofasciatum. — Acta Zoologica (Stockholm) 81: 139–158 Numerous teleost species possess ctenoid scales characterized by the presence of ctenial spines arranged in rows (the cteni) along their posterior, free margin. Whilst the morphology and function of the ctenial spines are similar to those of odontodes (extra-oral teeth), e.g. in armored catfish, their homology is questionable. To address this problem, we have studied ctenial spine development, structure, attachment to a bony support, and replacement with the aim of comparing these features to those described for odontodes. The ctenial spines have been studied in a growth series of the cichlid Cichlasoma nigrofasciatum, using light, scanning and transmission electron microscopy. Ctenial spines are entirely constituted of a collagen matrix. They lack a pulp cavity and, although their distal end can be in contact with the epidermal basal layer cells, they are not covered by an enameloid-like tissue. They are attached to the scale by means of a narrow strand of unmineralized collagen matrix acting as a ligament and allowing spines to be movable. The ctenial spines develop as prolongations of the external layer of the scale, a woven-fibroid collagen matrix, and subsequently grow by addition of parallel-fibred collagen matrix. New ctenial spines are added at the posterior scale border in waves that follow the same rhythm as the deposition of circuli in the anterior region. From the focus region to the scale border, the ctenial spines constitute lines in which only the most posterior ctenial spine is functional. The other spines that are no longer functional are not shed but resorbed from the top, and their attachment region mineralizes and thickens by deposition of new material. The remnants of spines constitute the main part of the superficial layer of the scale in which anchoring bundles attach; this region is covered afterwards by the limiting layer, a tissue devoid of collagen fibrils. Because of their tooth-like morphology (shape and size), their posterior orientation and their attachment to the scale surface, the ctenial spines resemble odontodes. Moreover, both elements perform a similar hydrodynamic function. Nevertheless, the structure and development of the ctenial spines differ completely from those of odontodes and consequently, they cannot be considered homologous elements. Ctenial spines and odontodes in teleosts provide us with a beautiful example of homoplasy; they share shape and function, but have a different origin as evidenced by their different structure and process of development.
Semiempirical modeling of abiotic and biotic factors controlling ecosystem respiration across eddy covariance sites

In this study we examined ecosystem respiration (RECO) data from 104 sites belonging to FLUXNET, the global network of eddy covariance flux measurements. The goal was to identify the main factors involved in the variability of RECO: temporally and between sites as affected by climate, vegetation structure and plant functional type (PFT) (evergreen needleleaf, grasslands, etc.). We demonstrated that a model using only climate drivers as predictors of RECO failed to describe part of the temporal variability in the data and that the dependency on gross primary production (GPP) needed to be included as an additional driver of RECO. The maximum seasonal leaf area index (LAIMAX) had an additional effect that explained the spatial variability of reference respiration (the respiration at reference temperature Tref=15 °C, without stimulation introduced by photosynthetic activity and without water limitations), with a statistically significant linear relationship (r2=0.52, P<0.001, n=104) even within each PFT. Besides LAIMAX, we found that reference respiration may be explained partially by total soil carbon content (SoilC). For undisturbed temperate and boreal forests a negative control of total nitrogen deposition (Ndepo) on reference respiration was also identified. We developed a new semiempirical model incorporating abiotic factors (climate), recent productivity (daily GPP), general site productivity and canopy structure (LAIMAX) which performed well in predicting the spatio‐temporal variability of RECO, explaining >70% of the variance for most vegetation types. Exceptions include tropical and Mediterranean broadleaf forests and deciduous broadleaf forests. Part of the variability in respiration that could not be described by our model may be attributed to a series of factors, including phenology in deciduous broadleaf forests and management practices in grasslands and croplands.
Fecundity and embryonic mortality in pigs.

Nearly all of the material described in this paper was obtained in the course of a survey undertaken by the writer jointly with Mr. R. W. Pomeroy, and carried out at the Animal Research Station, Cambridge. The purpose of the survey was to obtain information about the breeding performance of pigs, particularly sows, from a wide variety of commercial herds in East Anglia. The survey was undertaken as a preliminary to further work on prenatal mortality, mortality among young pigs before weaning, the reasons for discard of sows from breeding herds, and other problems. In the present account attention is confined to data derived from 863 animals, the reproductive tracts of which were actually examined in the fresh condition after removal from the carcass at the time of slaughter. Something of the history of 365 of them was known and it has thus been possible to relate such data as corpora lutea and embryo counts to the age of the animal or the number of litters she had borne.
Estimating jaguar population density using camera‐traps: a comparison with radio‐telemetry estimates

Reliable data on jaguar population densities are needed to propose appropriate conservation and management strategies, and camera trapping may be effective for estimating the population density of secretive large cats. I determined the population density of jaguars in the Chamela-Cuixmala Biosphere Reserve along the coast of Jalisco, Mexico, through camera trapping and capture–recapture analysis during the dry season of March to June 2008. I applied the half mean maximum distance moved (1/2MMDM) to calculate the radius of the effectively sampled area, and compared this with estimates of the effectively sampled area based on existing data on mean home range of jaguars at the study site. I found that both methods of calculating the effectively sampled area produced similar population density estimates. The widely used 1/2MMDM based on camera-trapping data produced a population density of 5.3 jaguars/100 km2, while calculation of the effectively sampled area based on mean home range produced a population density of 5 jaguars/100 km2. Despite the small size of the 131-km2 Chamela-Cuixmala Biosphere Reserve, jaguar population density was relatively high, suggesting that small, well-protected reserves can be important refuges for jaguars.
Evolutionary genetics of Drosophila ananassae: evidence for trade‐offs among several fitness traits

Correlated responses to bi-directional selection on thorax length, examined on several life-history traits and chromosome inversion polymorphisms, have revealed apparent novel trade-offs in Drosophila ananassae. We provide evidence of trade-offs between hatching time and pupal period, pupal period and egg-pupa development time, and pupal period and larval development time (LDT). Body size shows positive correlations with ovariole number, LDT and DT (egg–fly). We provide evidence of sexual dimorphism for trade-offs between longevity and body size and starvation and longevity in females only. Trade-offs between wing/thorax (W/T) ratio and longevity, W/T ratio and starvation, and DT (egg- fly) and longevity are evident in males only. Sexual dimorphism is also evident for inversion polymorphism with body size and longevity. A longevity assay suggests that low line females outlived high line females whereas high line males outlived low line males. The mean longevity in males is negatively correlated with the 2L-ST and 3R-ST arrangement frequencies whereas the 3L-ST arrangement frequency is positively correlated with the mean longevity in males but opposite arrangements are found in females. Absolute starvation resistance is negatively correlated with 2L-ST and 3R-ST chromosome arrangements and results in a trade-off between longevity and absolute starvation resistance in females. Analyses of fecundity, hatchability, and viabilities based on age intervals in both G10 and G13 suggest that the early reproduction is favoured in D. ananassae. The productivity percentage is highest in the high line and there is no effect of late reproduction on it. Overall, we provide some unravelled trade-offs and striking sex differences, which may help in understanding the life-history evolution of the species. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 90, 669–685.
Theoretical Study of the Substrate Mechanism of Ribonucleotide Reductase

The substrate mechanism of ribonucleotide reductase (RNR) is studied using a hybrid DFT method (B3LYP) with large basis sets. With models for the calculations based on recently determined X-ray structures, different mechanisms of the steps leading from a ribonucleotide to a deoxyribonucleotide are investigated. It is suggested that the transformation occurs in six steps. The role of the amino acid residues present at the active site are studied in detail. Three cysteine residues are known to be necessary for the formation of a deoxyribonucleotide, but very recently a glutamic acid residue has also been shown to be essential. The calculations indicate that this glutamic acid residue, Glu441, is important both in steps 2 and 4. In the suggested step 2, Glu441 transfers a hydrogen from the C3‘-OH group to the C2‘-OH group, and in step 4 it is proposed to participate in a cyclic transition state bridging the carbon and oxygen atoms of a keto group at C3‘. In both these steps an asparagine, Asn437, also plays .
Influence of Dietary Phosphorus Levels on Growth and Mineral Availability in Rainbow Trout.

Feeding experiment was conducted to determine the influence of dietary phosphorus levels on growth and mineral availability to juvenile rainbow trout. Mono-basic potassium phosphate was sup plemented to semipurified diet at 2, 4, 6, and 8%, in order to obtain graded dietary phosphorus (P) lev els (11.7 29.7 mg/ g). Growth, PER and NPU were not influenced by the dietary P at the level of 19.7 mg/g, but were decreased by 25.1 mg P/g or more. P, zinc (Zn) and manganese (Mn) contents in ver tebrae were significantly lowered by the diet containing P of more than 25.1 mg/g. Zn absorption was significantly influenced by the excess amount of dietary P, namely it was lowered by P at levels exceed ing 19.7 mg/g diet. The study demonstrated that excess amounts of dietary P at a level three times higher than the P re quirement lowered protein utilization and Zn absorption, induced poor growth and reduced Zn and Mn in the body of rainbow trout. It is suggested that the available P content in rainbow trout diet might be regulated to be less than 15 mg/g.
Variability studies in Okra (Abelmoschus esculentus L. Moench)

Sixty selected genotypes of okra were evaluated in one location for two years at Chatha, Jammu during 2009-10 and 2010-11. The objective was to study the genetic variability between various economically important traits for the purpose of genetic improvement. The experimental trial was laid out in a Randomized Block Design (RBD), with three replications. The data collected included Sepal size, Petal size, Flower circumference, Mature bud length, Carpel length, Pollen fertility count, pedicel length, Fruit length at marketable stage, Fruit width at marketable stage, Number of ridges per fruit, fruit length at mature stage, Number of fruits per plant, Fresh fruit weight, Length of beak, Dry fruit weight, Fruit colour, Number of seeds per fruit, Seed weight per fruit, Shelling percentage, 100 seed weight and Seed yield per plant. Analyses of variance and other genetic analyses such as genetic and phenotypic coefficient of variation, heritability and genetic advance were performed. The estimates of phenotypic coefficient of variation (PCV) were higher than genotypic coefficient of variation for all the characters. The results shows variation in all genotypes and characters. Characters such as seed yield per plant and number of fruits per plant showed high genotypic coefficient of variation, heritability and genetic advance which indicates that selection of these characters will show a positive response in improvement.
A NEW, NONRADIOACTIVE WHOLE‐MOUNT IN SITU HYBRIDIZATION PROTOCOL FOR FUCUS (PHAEOPHYTA) EMBRYOS

We present a nonradioactive protocol to localize mRNA in Fucus distichus ssp. edentatus (de la Pyl.) Powell (Phaeophyta) embryos using whole‐mount in situ hybridization. Hybridization of a digoxygenin (DIG)‐labeled oligo‐dT probe to poly A+ RNA, and DIG‐labeled riboprobes to specific mRNAs, was detected with an antibody to DIG (anti‐DIG) that was coupled to alkaline phosphatase. Our protocol, a modification of one developed for higher plants, includes a treatment of fixed embryos with specific cell‐wall‐degrading enzymes to permeabilize the cells to anti‐DIG, progressive osmotic changes to prevent plasmolysis, and a RNase A treatment to reduce nonspecific background. Using this protocol, we show the intracellular distribution of poly A+ RNA and mRNAs for actin and the fucoxanthin chlorophyll protein A (Fcp A). This method to detect mRNA localization is rapid because it does not require embedding, sectioning, or the use of radioactivity. With the availability of a variety of enzymes to degrade plant cell walls, this protocol should be applicable to many algal cells.
Aspectos da morfologia radiográfica do esqueleto, tórax e abdome do quati (Nasua nasua Linnaeus, 1766)

Thirteen adult coatis (Nasua nasua) from Zoological Park of the Federal University of Mato Grosso were chemically restrained and subjected to several radiographic procedures. Radiographs of the fore limbs, hind limbs, thorax, abdomen, neck and skull were performed. The images obtained were compared to anatomical specimens and to radiographs of dogs. Descriptions of the radiographic morphology of internal organs and skeletal structures were performed and images of the main radiographs of the species were made available. The main differences between coatis and canines members radiographic morphology were limited to the hands and feet. Coatis had 5 well developed digits with the metacarpals and metatarsals slightly shorter than the corresponding digits. This species have 7 cervical vertebrae, 15 thoracic, 5 lumbar vertebrae, and 3 sacral (fused). The frontal sinuses were larger, with cranial extension between the maxillary and nasal bones, numerous and very evident septa. The observed dentition was I 3/3, C1 / 1, P4 / 4 M2 / 2 = 40 and the main thoracic and ventral organs showed similar anatomy and radiographic features to those described for canines.
An investigation into two photostable retinoids and their use as tools to study retinoid function in vivo

All-trans retinoic acid (ATRA) is essential for embryonic development and adult homeostasis. Its study has been hindered by the fact that it can be converted to isomers upon exposure to light and because its metabolites are also bioactive molecules. Recent research has indicated that ATRA can also activate two different receptor pathways in vitro and in vivo. The present study investigates the effects of these isomers and metabolites on chick wing development using two synthetic, photostable retinoids, EC23 and EC19. These retinoids have identical structures bar the position of the terminal carboxylic acid group but surprisingly, generate different effects in vitro and in vivo, and are differentially metabolised by metabolising enzymes. EC23 mimics most of the effects of ATRA in vivo, including the novel phenotype of scapula malformation, while EC19 does not. Their phenotypes are further characterised in the text but EC23 produces a novel retinoid phenotype characterised by duplications of solely forelimb digit 1. The mechanisms behind the phenotypes generated by EC23 and EC19 are explored with respect to retinoid metabolism and localisation of ATRA binding proteins at the stage of application. Both ATRA signalling pathways are investigated at HH20 of chick embryonic development which improves our understanding of the role of retinoids in limb and embryonic development. Comparison of gene expression in response to ATRA and EC23 indicates that the metabolites and isomers of ATRA do not play a role in embryonic limb development, as well as highlighting avenues for further research into the development of the scapula and elbow. A major part of the retinoid response is to stall limb development while retinoid levels recover. By comparison with other teratogens, this may be part of a common response and be pertinent to the regulation of normal embryonic development by retinoids.
Tube-dwelling invertebrates: tiny ecosystem engineers have large effects in lake ecosystems

There is ample evidence that tube-dwelling invertebrates such as chironomids significantly alter multiple important ecosystem functions, particularly in shallow lakes. Chironomids pump large water volumes, and associated suspended and dissolved substances, through the sediment and thereby compete with pelagic filter feeders for particulate organic matter. This can exert a high grazing pressure on phytoplankton, microorganisms, and perhaps small zooplankton and thus strengthen benthic-pelagic coupling. Furthermore, intermittent pumping by tube-dwelling invertebrates oxygenates sediments and creates a dynamic, three-dimensional mosaic of redox conditions. This shapes microbial community composition and spatial distribution, and alters microbe-mediated biogeochemical functions, which often depend on redox potential. As a result, extended hotspots of element cycling occur at the oxic-anoxic interfaces, controlling the fate of organic matter and nutrients as well as fluxes of nutrients between sediments and water. Surprisingly, the mechanisms and magnitude of interactions mediated by these organisms are still poorly understood. To provide a synthesis of the importance of tube-dwelling invertebrates, we review existing research and integrate previously disregarded functional traits into an ecosystem model. Based on existing research and our models, we conclude that tube-dwelling invertebrates play a central role in controlling water column nutrient pools, and hence water quality and trophic state. Furthermore, these tiny ecosystem engineers can influence the thresholds that determine shifts between alternate clear and turbid states of shallow lakes. The large effects stand in contrast to the conventional limnological paradigm emphasizing predominantly pelagic food webs. Given the vast number of shallow lakes worldwide, benthic invertebrates are likely to be relevant drivers of biogeochemical processes at regional and global scales, thereby mediating feedback mechanisms linked to climate change.
THE INFLUENCE OF BOAR AGE ON EJACULATE QUALITY

Semen was harvested in two stages from boars aged 3, 4 and 7 years. In the first stage semen was collected at 2 and 3 day intervals and in the s econd stage after 7 days. The quality of ejaculates collected twice a week increases with boar age from 3 to 4 ye ars. After 4 years ejaculate quality is reduced. Se men collected once a week has a higher concentration an d the spermatozoa an increased motility. Sperm moti lity is remarkable especially in boars aged 5 and 7 years. A decrease in collection frequency does not alter t he dynamic of ejaculate volume and the 4 years old boars are s till the most valuable, independent of frequency. T he boars' usage for semen collection can be prolonged if the animals maintain their reproductive ability.
Asociación del valor genético del toro con caracteres productivos en vacas lecheras en Colombia

Actually, in Colombia there is not a genetic improvement program to estimate breeding values in dairy cattle. The objective of this research was to determine the association of EBV (Estimated Breeding Value) of Holstein and Jersey bulls with the phenotypic performance (milk and health traits) measured directly in their daughters in Colombia. To calculate the variance components, genetic parameters and EBV, the restricted maximum likelihood method (RMLM) using a derivative-free algorithm with the MTDFREML software, was used. The association of milk traits with the bulls EBVs was performed using a mixed model. Heritabilities for milk yield, protein percentage, fat and somatic cell score were 0.19±0.0, 0.37±0.04, 0.37±0.04 and 0.34±0.05, respectively for Holstein animals. For the Jersey were 0.20±0.0; 0.64±0.0, 0.55±0.0 and 0.14±0.26 respectively. The EBV of Holstein bulls were highly significant (p<0.01) on milk production, milk protein and milk fat content. The EBV was also found associated with somatic cell count. Similar results were found in Jersey bulls. The results showed that despite the low reliabilities estimated in Colombia assessments, the productivities are enhanced with the use of foreign genetic.
THE ECOLOGY OF PHYTOPLANKTON BLOOMS IN MORICHES BAY AND GREAT SOUTH BAY, LONG ISLAND, NEW YORK

1. The phytoplankton bloom in Great South Bay and Moriches Bay during the spring, summer, and early fall of 1952 consisted of the Chlorophyta, Nannochloris atomus and Stichococcus sp. , to the virtual exclusion of other species. These organisms persisted throughout the year, but were accompanied by minor diatom blooms during the winter and early spring.2. Growth rates of Nannochloris, Stichococcus, and the diatom, Nitzschia closterium were determined from laboratory cultures grown under various conditions of temperature, salinity, and nutrients which are peculiar to the Great South Bay-Moriches Bay area.3. Nannochloris and Stichococcus grew well in nitrogen present as nitrate, nitrite, ammonia, urea, uric acid, cystine, asparagin, and glycocoll. Nitzschia grew equally well in nitrate and nitrite, but showed poor growth in ammonia and the organic N compounds.4. Nannochloris and Stichococcus grew approximately twice as fast in media containing an N:P ratio of 5:1 as they did in media with a 15:1 ratio of the.