Miracle-dz/UniFAR-FTUs huggingface dataset:
Did ‘precautionary’ 1080 baiting have a realistic potential to eradicate Red Fox (Vulpes vulpes) in Tasmania without in situ monitoring data?

Summary Anecdotal reports in 2001 suggested that the European Red Fox (Vulpes vulpes) had been deliberately released in Tasmania and thereafter an eradication programme using buried fluoroacetic acid (1080) baits was believed to be a necessary precautionary action until mid-2013. Prerequisites for the successful eradication of foxes relate to the scale of the undertaking and the ability to collect in situ data such as the distribution and abundance of the target population and measures of the efficacy of the control technique. Previously, 1080 baiting has demonstrated only limited potential as a fox eradication technique on islands when used on a scale between 685 and 2141 times smaller than Tasmania. In the absence of empirical monitoring data confirming the distribution or abundance of extant foxes, buried baiting was targeted to specific landscapes believed to be preferred by foxes. No empirical data was collected concerning the in situ effectiveness of baiting in Tasmania, yet an a priori assumption of lethal efficacy was extrapolated from four heterogeneous mainland studies to suggest that foxes would have only a 0.23 probability of surviving each bait treatment. We show that these studies were unrepresentative of Tasmanian baiting methods used and influenced by imprecise fox population surveys and misreported data. Overall, in the absence of key population monitoring and efficacy data, the ‘precautionary’ baiting strategy adopted did not have a realistic potential to eradicate fox incursions in Tasmania, nor is it an appropriate risk management strategy for other large offshore Australian islands. Contingency plans to counter fox incursions on offshore islands must address the currently inadequate technical capacity to reliably detect and monitor low-density fox populations, which is an essential component of successful fox eradication.
DNA from formalin-fixed tissue: extraction or repair? That is the question

Abstract Establishing effective DNA-based protocols for use on archival material fixed in formaldehyde (formalin) is a particularly challenging task. Formalin fixation induces cross-linking with nucleic acids and proteins, thereby reducing the amount and quality of the extracted DNA. Previous attempts have primarily focused on optimizing DNA extraction protocols. Here we focus on the use of enzymes capable of in vitro repair of DNA extracts prior to amplification of the nucleic acids by the polymerase chain reaction (PCR). The amplification success of mitochondrial DNA was greater using the repair enzyme assay (56%) than with the regular PCR assay (20%), and even more convincing results were obtained with the amplified nuclear ribosomal region (91% versus 21%). These results indicate that in vitro repair of DNA damage (depurinated sites, strand nicks and base modifications) increases the number of samples that amplify, amplify to a greater extent and amplify fewer ancillary bands and that DNA repair has been overlooked as a way of improving the efficiency of molecular methods used on formalin-fixed samples. Fidelity has not been specifically investigated, but preliminary results indicate that misincorporation is not a major problem.
Survival costs of chick rearing in black‐legged kittiwakes

1. We tested for costs of chick rearing in the black-legged kittiwake Rissa tridactyla (Linnaeus) by removing entire clutches from 149 of 405 randomly selected nests, in which one or both mates was colour-banded. After the manipulation, we monitored adult nest attendance and body condition at unmanipulated and manipulated nests, and measured the survival and fecundity of these adults the following year. 2. Late in the chick-rearing period, adults from unmanipulated nests (i.e. with chicks) went on significantly longer foraging trips, and were significantly lighter for their size, than adults from manipulated nests (i.e. without chicks). 3. Adults from unmanipulated nests also survived to the following nesting season at a significantly lower rate than those from the manipulated nests (0·898 vs. 0·953), suggesting that attempting to raise chicks can reduce life expectancy by 55%. 4. There was a tendency for adults from nests that were unmanipulated in year one to have lower reproductive success in year two, primarily because of reduced fledging success, and a higher incidence of non-breeding. 5. These findings suggest that mass loss in kittiwakes during chick rearing may not be adaptive. Raising chicks can lead to reproductive costs, and the causal mechanism appears to be a reduction in body condition. 6. We compare our results with previous brood (or clutch) size manipulation experiments that have measured adult body condition, survival and/or future fecundity. Although the empirical evidence suggests that long-lived species are more likely to experience survival costs than short-lived species, we believe the opposite may be true. We suggest that shifting the experimental protocol of cost of reproduction studies from brood enlargements (an approach taken in most prior studies) to brood reductions will provide more accurate quantifications of naturally occurring costs. 7. The cost of reproduction is one mechanism proposed to explain the reduced survival rates reported for kittiwake populations in the North Atlantic relative to those in the North Pacific ocean. Oceanographic data, however, suggest that lower food availability may limit survival of kittiwakes in the North Atlantic where a deeper mixed layer and reduced primary production combine to make conditions less favourable for this seabird during the winter months.
In Vitro Binding of Bile Acids by Rice Bran, Oat Bran, Barley and β-Glucan Enriched Barley

ABSTRACT The in vitro bile acid binding by rice bran, oat bran, dehulled barley, and β-glucan enriched barley was determined using a mixture of bile acids at a duodenal physiological pH of 6.3. Six treatments and two blank incubations were conducted testing substrates on an equal protein basis. The relative in vitro bile acid binding of the cereal brans on an equal total dietary fiber (TDF) and insoluble dietary fiber (IDF) basis considering cholestyramine as 100% bound was rice bran 45 and 49%; oat bran 23 and 30%; dehulled barley 33 and 57%; and β-glucan enriched barley 20 and 40%, respectively. Bile acid bindings on equal protein basis for the respective cereals were 68, 26, 41, and 49%. Bile acid binding by rice bran may account to a great extent for its cholesterol-lowering properties, while bile acid binding by oat bran suggests that the primary mechanism of cholesterol lowering by oat bran is not due to the bile acid binding by its soluble fiber. Bile acid binding was not proportional to the solubl.
COMPARATIVE STUDY OF NUTRITIONAL, FUNCTIONAL AND ANTINUTRITIONAL PROPERTIES OF WHITE SORGHUM BICOLOR (SORGHUM) AND PENNISETUM GLAUCUM (PEARL MILLET)

The effects of sprouting on proximate, mineral composition and functional properties of white sorghum bicolor and pennisetum glaucum were evaluated. The sorghum bicolor and pennisetum glaucum kernels obtained from Kings local market in Akure Ondo State, Nigeria and identified in the department of Agronomy Federal University of Technology, Akure were sorted and divided into two portions. The first portion was soaked for 24 hours after which it was spread on trays lined with doth and kept wet by frequent spraying of water each morning and evening for 2 days. The sprouted maize grains were oven dried at 60°C to constant weight and milled into flour. The second portion was processed into flour without sprouting, using the same method. Each of the portions was analyzed for proximate, mineral compositions and functional properties using standard methods. Sprouting of both sorghum bicolor and pennisetum glaucum grains resulted in significant increase (p<0.05) in crude protein, crude fibre, and ash content. The moisture content of sorghum bicolor increases with sprouting while that of pennisetum glaucum decreases. This decrease in the moisture content of pennisetum glaucum with sprouting implies an increase shelf life. Increase in solubility, water absorption and oil absorption capacity observed with sprouting in both sample helps in increasing the palability of the food The results showed that the sprouting process improved the nutrient composition and enhanced the functional properties of both sorghum bicolor and pennisetum glaucum with the pennisetum glaucum being found to be slightly better in terms of shelf life.
Population synchrony and environmental variation: an experimental demonstration

Understanding the causes of population synchrony is an important issue for population management. Its study in field populations involves disentangling the effects of dispersal and correlated environmental noise. Here we report on an experimental investigation of the synchronizing effects of noise in closed laboratory populations of a soil mite, Sancassania berlesei. Mite life-histories are highly plastic with respect to resource availability (which is a function of food supply and population density). By varying the food supply we imposed environmental variation. We show that (a) population synchrony is a function of environmental synchrony, (b) perceived population synchrony depends on the life-history stage counted, and (c) average population synchrony tends to be lower than environmental synchrony: even when populations were supplied with food with a correlation of 1.0, the correlation between populations was 0.63 (bootstrapped 95%CI 0.54–0.71). This supports recent theoretical work suggesting that the Moran theorem (indicating that population synchrony equals environmental synchrony) generally overestimates the population synchrony of nonlinear systems.
In vivo study of phagocytosis, intracellular survival and multiplication of Flavobacterium psychrophilum in rainbow trout, Oncorhynchus mykiss (Walbaum), spleen phagocytes

The intracellular behaviour of a Flavobacterium psychrophilum strain, ingested by spleen phagocytes of rainbow trout, Oncorhynchus mykiss, of different ages, was assessed in vivo. Three groups of rainbow trout weighing 1 g (aged 10 weeks), 25 g (aged 20 weeks) and 300 g (aged 15 months), respectively, were injected intraperitoneally with 1 × 106 cfu of a F. psychrophilum strain. It was found that only fry, aged 10 weeks, displayed clinical signs and suffered mortality. Bacteriological colony plating of different organs demonstrated that the spleen and to a lesser extent the kidney of only the fry were affected. The number of colony forming units per gram of spleen tissue increased with time. No bacteria were found in the trout aged 5 months and older. Light microscopical examination and epifluorescence microscopy revealed that the fry spleen phagocytes contained an increasing number of viable intracellular F. psychrophilum bacteria over time. Again, no bacteria were encountered in the phagocytes collected from older fish.
Ecology and biogeography of Cassia brewsteri: assessment of potential sites for cultivation

Cassia brewsteri (F. Muell.) F. Muell. ex Benth. has been identified as a potential multipurpose agroforestry species, and also as a potential source of seed galactomannans (industrial gums). In this study, the natural and cultivated distributions of C. brewsteri were used as a basis for predicting potential sites for cultivation of the tree, using the climate modelling software ANUCLIM. The natural distribution was determined by compilation of data from herbaria and from field studies. The ecological parameters of natural occurrences were characterised in terms of soil and vegetation types by sampling 113 sites throughout the natural distribution in Queensland (18.583-26.150°S, 144.750-152.750°N). In addition to the natural occurrences, a further 11 sites were identified where the tree has been grown successfully in cultivation. Failures of the tree in agroforestry trials in Thailand may be explained by high temperature as a limiting factor in the distribution of the species. Failures of the species in trials in Australia, Zimbabwe and Malawi could not be attributed to climate or soil conditions at the trial sites, indicating that further research on culture of the tree is required to achieve high survival and growth rates.
Choice Feeding as a Means of Identifying Differences in Nutritional Needs of Broiler Strains Differing in Performance Characteristics

Chickens from two broiler strains known to differ in growth rate and feed conversion (GROWTH) and in high breast meat yield (YIELD) were grown to 10 days of age on a common starter diet and from 11 to 49 days were provided single diets (control), a choice between high energy and high protein diets, or a choice between starter and finisher diets. Overall the YIELD strain had greater body weight, feed intake and breast yield than did GROWTH strain. However, the YIELD strain had better feed conversion only when offered a choice of starter and finisher diets. Birds fed single diets and Starter-Finisher diets had better body weight, feed intake, feed conversion and breast yield than those birds fed Energy-Protein diets. Birds fed both choice feeding systems selected more high energy diets than high protein diets especially during the period of 11 to 22 d of age. The YIELD strain had a preference for the high protein diet and consequently had greater protein intake and average dietary protein content than did the GROWTH strain, while the former ate more energy intake but less energy content than did the latter. Birds given choice of the energy and protein diets had less protein intake and content for all periods, whereas these birds chose less energy intake for the period of 22 to 42 d of age and a higher energy level than did birds fed the other two feeding systems. These data indicate that choice feeding systems can identify differences in performance according to the selected nutritional needs for new strains of broilers.
Partial Purification and Characterization of Chinook Salmon (Oncorhynchus tshawytscha) Calpains and an Evaluation of Their Role in Postmortem Proteolysis

: The involvement of calpains in the proteolysis of salmon muscle during refrigerated storage was investigated. Salmon m-calpain and μ-calpain were purified and partially purified, respectively. Salmon μ-calpain had similar calcium requirements and specific activity against casein as ovine m-calpain. Salmon μ-calpain had similar calcium requirements as ovine μ-calpain but a lower specific activity against casein than ovine μ-calpain. Autolysis patterns of both calpains differed from those of ovine calpains, and their activities were less than those of mammalian muscles. Calpastatin activity was relatively high and comparable to that of bovine muscles. Little proteolysis and fiber fragmentation resulted during refrigerated storage. However, proteolysis could be reproduced by incubation of myofibrils with m-calpain.
The evolution of concerted evolution

Concerted evolution is a consequence of processes that convert copies of a gene in a multigene family into the same copy. Here we ask whether this homogenization may be adaptive. Analysis of a modifier of homogenization reveals (1) that the trait is most likely to spread if interactions between deleterious mutations are not strongly synergistic; (2) that selection on the modifier is of the order of the mutation rate, hence the modifier is most likely to be favoured by selection when the species has a large effective population size and/or if the modifier affects many genes simultaneously; and (3) that linkage between the genes in the family, and between these genes and the modifier, makes invasion of the modifier easier, suggesting that selection may favour multigene families being in clustered arrays. It follows from the first conclusion that genes for which mutations may often be dominant or semi–dominant should undergo concerted evolution more commonly than others. By analysis of the mouse knockout database, we show that mutations affecting growth–related genes are more commonly associated with dominant lethality than expected by chance. We predict then that selection will favour homogenization of such genes, and possibly others that are significantly dosage dependent, more often than it favours homogenization in other genes. The first condition is almost the opposite of that required for the maintenance of sexual reproduction according to the mutation–deterministic theory. The analysis here therefore suggests that sexual organisms can simultaneously minimize both the effects of deleterious, strongly synergistically, interacting mutations and those that interact either weakly synergistically, multiplicatively, or antagonistically, assuming the latter class belong to a multicopy gene family. Recombination and an absence of homogenization are efficient in purging deleterious mutations in the former class, homogenization and an absence of recombination are efficient at minimizing the costs imposed by the latter classes.
ÜBER DIE FÄHIGKEIT DER BIENENKÖNIGIN (APIS MELLIFICA L.) ZWISCHEN ARBEITERINNEN-UND DROHNENZELLEN ZU UNTERSCHEIDEN

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. ÜBER DIE FÄHIGKEIT DER BIENENKÖNIGIN (APIS MELLIFICA L.) ZWISCHEN ARBEITERINNEN-UND DROHNENZELLEN ZU UNTERSCHEIDEN Nikolaus Koeniger
The Evolution of Viviparity in LizardsEcological, anatomical, and physiological correlates lead to new hypotheses

he birth of a relatively welldeveloped neonate-viviparity-is commonly considered a characteristic unique to mammals. However, this reproductive mode is exhibited by some species of all vertebrate classes except the jawless fishes (agnathans) and the birds. Among the reptiles, viviparity has evolved almost 100 times among the 5500 or so species of squamates (lizards and snakes). In contrast, all of the approximately 250 species of turtles, 21 species of crocodilians, and 2 species of tuatara are oviparous, producing only shelled eggs (Blackburn 1982, 1985, Shine 1985). In this article, I briefly discuss current work examining the ecological factors correlated with the evolu-
Fluorescence-guided fiber-optic micronavigation using microscopic identification of vascular boundary of liver segment and tumors

Background: The exact identification of tumor boundaries and related liver segments is especially important for liver tumor surgery. This study aimed to evaluate a new approach for vascular boundary assessment and surgical navigation based on fiber-optic microscopy and microvascular fluorescence labeling. Methods: Antibody clones with fast binding ability were identified and selected using immunofluorescence. We evaluated the endothelial capture efficacy for an anti-mouse CD31 antibody labeled with different fluorophores and different degrees of labeling ex vivo. Segment boundary identification and navigation potential using endothelial capture were explored by two different fiber-optic microscopy systems. Finally, microvasculature labeling and fiber-optic microscopy were used to identify and treat microscopic liver tumors in vivo. Results: The following monoclonal antibodies were selected: anti-mouse CD31 (clone 390), anti-mouse CD54 (YN1/1.7.4), anti-human CD31 (WM59), and anti-human CD54 (HA58). These clones showed fast binding to endothelial cells and had long half-lives. The fluorophore choice and the degree of antibody labeling did not significantly affect capture efficacy in an isolated liver perfusion model. The microvascular system was clearly identified with wide-field fiber-optic microscopy after labeling the endothelium with low doses of specific antibodies, and the specifically labeled liver segment could be microscopically dissected. High antibody doses were required for confocal laser endomicroscopy. After microscopically identifying the vascular margin in vivo, tumor thermoablation strongly reduced tumor size or totally eliminated tumors. Conclusions: We demonstrated that vascular boundaries of liver tumors and locally perfused liver segments were accurately identified and surgical micronavigation was facilitated with fiber-optic microscopy and selected endothelium-specific antibodies.
MicroRNA-1 regulates the development of osteoarthritis in a Col2a1-Cre-ERT2/GFPfl/fl-RFP-miR-1 mouse model of osteoarthritis through the downregulation of Indian hedgehog expression

The present study assessed the effects of microRNA-1 (miR-1) on the development of osteoarthritis using human tissues and a Col2a1-Cre-ERT2/GFPfl/fl-RFP-miR-1 mouse model of osteoarthritis. Human cartilage tissues (n=20) were collected for reverse transcription-quantitative polymerase chain reaction (RT-qPCR), histological analysis and immunohistochemistry experiments. A transgenic mouse model of osteoarthritis was established by subjecting Col2a1-Cre-ERT2/GFPfl/fl-RFP-miR-1 transgenic mice to anterior cruciate ligament transection (ACLT). Mice were subjected to radiography and in vivo fluorescence molecular tomography (FMT), while mouse tissues were collected for histological analysis, RT-qPCR and Safranin O staining. It was found that the miR-1 level was downregulated, whereas the levels of Indian hedgehog (Ihh), as well as those of its downstream genes were upregulated in human osteoarthritic cartilage. In the transgenic mice, treatment with tamoxifen induced miR-1, as well as collagen, type II (Col2a1) and Aggrecan (Acan) expression; however, it decreased Ihh, glioma-associated oncogene homolog (Gli)1, Gli2, Gli3, smoothened homolog (Smo), matrix metalloproteinase (MMP)-13 and collagen type X (Col10) expression. Safranin O staining revealed cartilage surface damage in the non-tamoxifen + ACLT group, compared with that in the tamoxifen + ACLT group. Histologically, an intact cartilage surface and less fibrosis were observed in the tamoxifen + ACLT group. Immunohistochemistry revealed that the protein expression of Ihh, Col10, and MMP-13 was significantly higher in the joint tissues of the non-tamoxifen + ACLT group than in those of the tamoxifen + ACLT group. However, Col2a1 expression was lower in the joint tissues of the non-tamoxifen + ACLT group than in those of the tamoxifen + ACLT group. The results of RT-qPCR and FMT further confirmed these findings. On the whole, the findings of the present study demonstrate that miR-1 expression protects against osteoarthritis-induced cartilage damage and gene expression by inhibiting Ihh signaling.
Three new Brazilian species of the land planarian Choeradoplana (Platyhelminthes: Tricladida: Geoplaninae), and an emendation of the genus

Three new Brazilian species of the neotropical land planarian genus Choeradoplana (Platyhelminthes: Tricladida: Continenticola: Geoplaninae) are described, making a total of nine species within the genus. All the new species share unique derived characters typical of the genus. Two of the new species exhibit important features representing morphological variations that were previously unknown for the genus: the dorsal cutaneous longitudinal muscle layer, as well as the ventral one, partially sunken into the parenchyma in one species, and the common ovovitelline duct approaching the copulatory apparatus ventrally in the other. As a consequence of these morphological variations, an emendation of the genus is proposed.