Miracle-dz/UniFAR-FTUs huggingface dataset:
Defining and quantifying some on-farm factors influencing sheepmeat eating quality

This paper summarises some of the research and development being undertaken as part of Meat and Livestock Australia's Sheepmeat Eating Quality Program. Some of the main outcomes of the research are outlined: • A system for describing the consumer-defined eating quality of sheep meat is described where the sensory attributes of the cooked meat are defined on a scale of 0 to 100. • Studies over a broad range of sheep ages have shown that loin tenderness declines with increasing animal age in a predictable way but liking of flavour is less affected by age, resulting in acceptable consumer scores even for older sheep (mutton) when cuts are denuded of fat. The difference between carryover lamb and mutton for overall consumer scores is about 8 to 10 points. • The effects of animal age on sensory ratings are significant in the sucker lamb ® carryover lamb ® hogget transition. Suckers lambs have a superior consumer score with little difference between carryover lamb and hogget (for loin and outside cuts). However, loin meat from hoggets was consistently darker due to an increased content of myoglobin (the major muscle pigment). • Finishing lambs on actively growing pasture (legume/grass based) versus balanced grain-based rations did not affect consumer score of grilled denuded loins. That is, grass-finished eating quality = grain-finished eating quality. • Allowing finished lambs to lose weight for 2 weeks prior to slaughter resulted in meat with reduced muscle glycogen, increased pHu and reduced consumer scores for juiciness and liking of flavour.
Fine tuning anti-predator responses: are the costs of inducible predator defences proportional to the magnitude of the responses?

Marine population connectivity describes the likelihood that an individual of a population can disperse some distance from its natal habitat patch to settle in available downstream habitat. This connectivity is often critical for metapopulation persistence, range size expansion, and a species’ ability to cope with climate change. Unfortunately, identifying the important biophysical drivers and the resultant patterns in connectivity poses one of the greatest challenges in marine ecology. We quantify the complex interaction between the dynamic seascape and species' life history characteristics to (1) highlight the influence of key biological and physical parameters on population connectivity and (2) map the spatiotemporal patterns emerging from these interactions. We describe a spatially-explicit biophysical modelling approach that effectively quantifies population connectivity across species, from demographically relevant to evolutionarily significant scales. These population connectivity estimates are transformed into marine population networks where we apply graph-theoretic algorithms to re-evaluate connectivity, identify network-wide properties, and quantify each site’s contribution to system dynamics. Finally, we highlight multi-species dispersal corridors, semi-permeable barriers, critical stepping-stones, and the emergent spatial structure of marine population connectivity. We close with recommendations on how population connectivity estimates can be explicitly integrated within the conservation planning framework.
Genetic Epidemiology and Lipids: A Pattern So Grand and Complex

textabstractIntensive research over the course of the last several decades led to dramatic improvements in understanding, treating, and preventing cardiovascular disease. Despite this progress, cardiovascular disease remains the leading cause of mortality in both high- and low-income countries, and the leading source of morbidity in high-income countries. Lipids are well known determinants of cardiovascular disease risk; epidemiological evidence was published long ago. Total cholesterol and low-density lipoprotein cholesterol (LDL), which tend to be strongly correlated, are associated with increased disease risk. LDL can be readily oxidized, which causes inflammation and atherosclerosis to occur, and small, dense LDL particles are considered the most atherogenic lipid particles. High-density lipoprotein cholesterol (HDL), by contrast, is associated with beneficial effects, in terms of cardiovascular disease risk. Several mechanisms are likely to account for the protective consequences of increased HDL concentrations. HDL exhibits anti-inflammatory properties. Additionally, it is thought to be an anti-oxidant, helping to offset the deleterious effects of oxidized LDL. HDL is also involved in reverse cholesterol transport (i.e. the sequestration of cholesterol to the liver for metabolism), which helps to reduce the amount of circulating lipid.
DIVERSITY AND GROWTH-PROMOTING ACTIVITIES OF Bacillus sp. IN MAIZE

The aim of this paper was to evaluate biochemical activities related to promotion of plant growth of isolates of the genus Bacillus originated from areas under maize cultivation, and to evaluate the genetic similarity among the isolates using PCR-based RAPD markers. Several strains of the genera Bacillus were isolated from twenty distinct maize production areas of the State of Sao Paulo, Brazil. Forty isolates were obtained and characterized as antagonistic to plant pathogenic fungi, production of auxin (IAA), phosphate solubilization in vitro and root colonization. The potential for phosphate solubilization was not identified in any of the isolates. In addition, the majority of the isolates did not show any antagonistic effect against Fusarium oxysporum and Colletotrichum truncatum. Based on root colonization, six Bacillus isolates were selected to evaluate their growth-promotion activities in maize. All the six isolates increased root growth, while only one isolate did not promoted shoot growth and nutrient uptake in plants when compared to control. Low genetic similarity among the selected isolates was detected by RAPD analysis using eleven primers. Our results showed the utility of the in vitro selection criteria used in this study for screening of Bacillus sp. with plant growth-promoting activity, as they may reduce the number of Bacillus isolates required at the final screening stage in field.
Does proximity to conspecific adults influence the establishment of ectomycorrhizal trees in rain forest

Three ectomycorrhizal legume trees, Microberlinia bisulcata, Tetraberlinia bifoliolata and T. moreliana, form discrete groves in the southern part of Korup National Park, in southwest Cameroon and contribute c. 45–70% of stand basal area locally in a matrix of otherwise species-rich arbuscular mycorrhizal forest. A transplant experiment was performed to assess the importance of ectomycorrhizal infection associated with proximity to parents in seedling establishment of the grove-forming species. Nonectomycorrhizal seedlings of the three species were transplanted into plots of two forest types, one of high (HEM, within-grove) and one of very low (LEM, outside the grove) abundance of all three species as adult trees. For two species (T. moreliana and M. bisulcata) there was no difference in survival over 16 months, but for the third (T. bifoliolata) survival was best in HEM forest, and correlated with the basal area of adult trees of ectomycorrhizal species. Only one species (T. moreliana) increased in biomass over the experimental period; the others declined. There was no effect of forest type on overall growth of any species, but the survivors of two (T. moreliana and M. bisulcata) had heavier stems in the HEM forest. Differences in survival and growth of transplants between the three species were in accord with the ecology of the species as inferred from the frequency distributions of adult tree size in the forest. Seedlings became infected with ectomycorrhizas in both forest types; where there was a difference in extent of infection (T. moreliana) this was not related to survival or growth; and where there was a difference in survival (T. bifoliolata) this was not related to extent of infection. These results confirm that mycorrhizal inoculum associated with conspecific adults is neither a prerequisite nor a guarantee of seedling establishment, but indicates that in some circumstances there might be benefits of being close to parents. Further research is required to unravel the complexities of ectomycorrhizal community structure in this spatially and temporally heterogeneous forest, and to clarify the extent to which the various hosts share ectomycorrhizal partners.
CONCEPTION ET IMPLÉMENTATION D’UN LANGAGEDE PROGRAMMATION CONCURRENTE MODULAIRE

La programmation concurrente a memoire partagee est un modele classique de concurrence qui permet notamment de tirer parti des processeurs multicœurs aujourd’hui tres repandus dans les ordinateurs personnels. Les programmes concurrents sont sujets au probleme des interblocages, notoirement difficiles a prevoir et a eliminer, en particulier dans le cas de l’utilisation du mecanisme de synchronisation tres populaire que sont les mutex. Dans cette these nous avons travaille a rendre plus aisee la programmation avec des mutex en etudiant des methodes d’evitement des interblocages. Nous avons d’abord etudie une methode utilisant une analyse statique par un systeme de types et d’effets, puis une variante de cette methode dans un langage a typage dynamique. La seconde methode est celle que nous avons le plus developpee. Elle combine prevention et evitement des interblocages pour fournir une fonction de verrouillage sans interblocages expressive et utilisable. Nous l’avons implementee sous forme d’une bibliotheque Hop (dialecte de Scheme). Ce faisant, nous avons developpe un algorithme sans famine pour l’acquisition simultanee d’un nombre arbitraire de mutex, et identifie le concept d’interblocage asymptotique. Nous avons egalement ete amenes a proposer une optimisation des exceptions (blocs finally). Nos tests de performances semblent indiquer un impact negligeable de l’utilisation de notre biblio- theque sur des applications concurrentes reelles. La majeure partie de notre recherche pourrait etre appliquee a d’autres langages de programmation structuree tels que Java.
Signal Diversity, Sexual Selection, and Speciation

Communication is ubiquitous. Developing a framework for the diversity of signals has important consequences for understanding alternative models of sexual selection and the processes contributing to speciation. In this article we review how models of neutral evolution in the perceptual space of signal perceivers provide a first step toward constructing a framework for signal diversity. We discuss how the distinction between additive and multiplicative effects of multimodal signaling represents a second step. We then assess how signal efficiency, reliability, and the aesthetics of perceivers provide distinct mechanisms for signals to be effective, thereby partly explaining signal diversity. Understanding the relative contribution of each of these mechanisms to the effectiveness of mate choice signals unravels the relative importance of alternative models of sexual selection. It can also help to distinguish whether divergence of communication is a driver or a consequence of speciation. Throughout the review.
The screening of wheat germplasm for resistance to stripe and leaf rust in Kazakhstan using molecular markers

Resistance to stripe and leaf rusts is the most important objectives in Kazakhstan, and they are the major factor that adversely affects wheat yield and quality and finally causes considerable economic damage. This study was aimed at characterizing elite wheat germplasm from Central Asia using molecular markers linked to the Lr34/Yr18 dual rust resistance gene and to identify new wheat germplasm resistant to leaf and yellow rust. In experiment with germplasm developed from Kazakhstan and Central and West Asia yellow rust trap nursery (CIMMYT), the frequency of the csLV34b-allele linked to Lr34/Yr18 (150 bp) was low and only seven of the 42 accessions had allele diagnostic of Lr34/Yr18. Two genotypes had high level of resistance, showing immune reaction to all three rusts. Disease severity from resistance to moderate susceptible was recorded in the lines having Lr34/Yr18 genes, which is comparable to the disease severity observed on the cultivar, Cook (20MS-30MS), carrying Lr34/Yr18 genes. The molecular screening of a set of additional 51 wheat genotypes, including commercial cultivars and breeding lines from different countries, showed that the csLV34 marker was present in 20 genotypes. This allowed us to select lines that could be used for future breeding work. In all, a total of 269 lines possessed effective Lr34/Yr18 gene complex: 28 lines of F4 Almaly/Opata-85, 34 lines of Almaly/Super Kauz, 26 lines of F4 Parula/(Almaly/Anza), 23 lines of F4 Babax 1/Opata 85, and 27 lines of Madsen/Cook populations. This further validates and confirms that the STS marker csLV34 and morphological marker leaf tip necrosis are reliable in the identification of carriers of effective slow rusting Lr34/Yr18 gene. The germplasms identified are further being tested for end-used quality and could be released by NARS as varieties in the various countries of Central Asia.
Antiproliferative activity of recombinant human interferon-λ2 expressed in stably transformed BmN cells

This study aimed at the generation of a stable transformed silkworm BmN cell line which can continuously express human interferon-λ2 (IFN-λ2) gene, and investigated the antiproliferative activity of this recombinant human IFN-λ2. Silkworm BmN cells were transfected with the recombinant vector pIZT/V5-His harboring the human IFN-λ2 gene. After the BmN cells were transfected with the pIZT/V5- His- hIFN-λ2 vector, the stably transformed BmN cells expressing hIFN-λ2 gene were selected using Zeocin. Following two months of screening, the transformed BmN cell line was obtained. Stable transformed BmN cell line can be maintained at a lower Zeocin concentration. The representing 26 kDa protein band of IFN-λ2 was detected by SDS-PAGE and Western blotting. The expression level of hIFN- λ2, determined by ELISA, was about 8.142 ng in 4 × 10 5 cells. The antiproliferative activity of hIFN-λ2 was determined by MTT assay. The 50% inhibitory concentrations (IC 50 ) of the recombinant hIFN-λ2 on A549 (lung cancer cells), HL60 (acute promyelocytic leukemia cells), BEL-7402 (liver cancer cells) and M231 cells (breast cancer cells) were approximately 3.21, 2.84, 6.29 and 9.32 ng/ml, respectively. In summary, Human IFN-λ2 can be stably expressed in the transformed BmN cell line, and the expressed recombinant hIFN-λ2 demonstrated antiproliferative activity to tumor cells in vitro . Key words : Human interferon-λ2 protein, gene expression, antiproliferative activity.
Purification and Characterization of Corrinoid Compounds from a Japanese Fish Sauce

Abstract A Japanese fish sauce “Ishiru,” which was made from squid by a traditional food manufacturing process, contained the highest amounts (5.5 ± 2.3 µg/100 g) of B12 among various fish sauces tested. Two corrinoid compounds were purified from the fish sauce Ishiru and partially characterized. TLC and HPLC patterns of the main red‐colored compound, purified from the fish sauce, were identical to those of authentic vitamin B12, but minor compounds could not be identified. Fish sauce may not be suitable for use as a good vitamin B12 source, judging from the low daily intake of the sauce and occurrence of the unknown corrinoid‐compound.
Registration of a Mutant Lesquerella Genetic Stock with Cream Flower Color

A cream flower mutant of lesquerella [Lesquerella fendleri (A. Gray) S. Watson] genetic stock WCL-CF1 (Reg. no. GS13, PI 642048) was released jointly by the USDA-ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ, and the Universidad Autonoma Agraria Antonio Narro at Buenavista (UAAAN), Saltillo, Coahuila, Mexico. WCL-CF1 was derived from an accession collected in Coahuila, Mexico (A4005) during a germplasm exploration in 1999 (Salywon et al., 2005). In their monograph of the genus Lesquerella, Rollins and Shaw (1973) describe the petals of this species as yellow but sometimes with orange guidelines. All plants located at the original collection sites had wild-type yellow flowers. Flower color for this species is extremely stable and to our knowledge variation for this trait has not been reported. Plants from more than 150 L. fendleri accessions in our working collection and those in the National Plant Germplasm System (NPGS), from throughout the species range, are all yellow flowered. Seeds from the Mexico sites were increased at Phoenix, AZ, in the fall of 1999 in a field at the USDA-ARS, U.S.Water Conservation Laboratory. Screened cages with house flies (Musa domestica G. E. Rumphius) as pollinators were used to isolate accessions for the regeneration. In the spring of 2000, a single plant in a cage of 72 individuals from accession number A4005 was observed having cream flowers, while all others had yellow flowers. Controlled reciprocal crosses and self-pollinations were made between this plant and two random wild-type plants while in the field isolation cage. Flowers of all plants from the F1 generation had yellow flowers, regardless of which plant was used as the maternal parent, as were flowers of plants from self-pollinated, yellow flowered plants. Flowers of plants from the self-pollinated cream flowered plant were all cream colored, indicating that the parent plant was homozygous for this trait. F2 and selfed seeds were planted the following fall in the greenhouse. Flowers of these F2 plants fit a 3:1 ratio of yellow flowers to cream flowers indicating a recessive gene controlling the trait. S2 seed of WCL-CF1 also produced plants with all cream colored flowers. When WCL-CF1 is planted in October in Arizona, plants began flowering in early February and reached full flowering by mid-April. Plants require insect pollinators for seed-set. Oil concentration and fatty acid profile, seeds per silique, and 1000-seed weight were not significantly different between WCL-CF1 and wild types. U.S. Plant Variety Protection will be sought for WCL-CF1. Limited quantities of seed of WCL-CF1 are available for distribution to qualified researchers on written request to the corresponding author for 5 yr. Recipients of seed are asked to make appropriate recognition of the germplasm source if used in the development of a new cultivar, germplasm, parental line, or genetic stock. Requests from outside the U.S. should be accompanied by the appropriate customs control documents.
Multiple sequence alignment for phylogenetic purposes

I have addressed the biological rather than bioinformatics aspects of molecular sequence alignment by covering a series of topics that have been under-valued, particularly within the context of phylogenetic analysis. First, phylogenetic analysis is only one of the many objectives of sequence alignment, and the most appropriate multiple alignment may not be the same for all of these purposes. Phylogenetic alignment thus occupies a specific place within a broader context. Second, homology assessment plays an intricate role in phylogenetic analysis, with sequence alignment consisting of primary homology assessment and tree building being secondary homology assessment. The objective of phylogenetic alignment thus distinguishes it from other sorts of alignment. Third, I summarise what is known about the serious limitations of using phenetic similarity as a criterion for automated multiple alignment, and provide an overview of what is currently being done to improve these computerised procedures. This synthesises information that is apparently not widely known among phylogeneticists. Fourth, I then consider the recent development of automated procedures for combining alignment and tree building, thus integrating primary and secondary homology assessment. Finally, I outline various strategies for increasing the biological content of sequence alignment procedures, which consists of taking into account known evolutionary processes when making alignment decisions. These procedures can be objective and repeatable, and can involve computerised algorithms to automate much of the work. Perhaps the most important suggestion is that alignment should be seen as a process where new sequences are added to a pre-existing alignment that has been manually curated by the biologist.
Risk analysis of dissolved organic matter-mediated ultraviolet B exposure in Canadian inland waters

With depleted ozone levels and the possibility that climate change might lower dissolved organic matter (DOM) concentrations, the risk of exposure of fresh waters in Canada to ultraviolet B (UV-B) was evaluated. First, the distribution of a UV-B-sensitive zooplankton genus, Daphnia, was examined as a function of DOM concentration and maximum depth (Zmax) in 258 systems. Distribution was not restricted by UV-B, although very clear, shallow systems are underrepresented. Secondly, the depth at which 1% of surface radiance at 320 nm occurs (Z320,1%) was compared with Zmax in over 1000 aquatic systems in 15 ecozones to determine the proportions of optically clear systems (Zmax ≤ Z320,1%) and systems that may become clear (i.e., are "at risk") should DOM decrease by 50%. South of the treeline, <6% of systems were clear, with the exception of two ecozones with 10%20%. The proportion of systems at risk was 0% in most regions, with 5%9% in four regions. DOM levels appear adequate to prevent extirpation of sensit.
Transformation of E. coli and Agrobacterium and molecular analysis of transformed apple (Malus domestica) rootstock A2

This project includes two parts. The first part was transformation of Escherichia coli and Agrobacterium tumefaciens with a vector containing the GA2ox gene. The second part was molecular analyses of the apple (Malus domestica) rootstock A2 transformed with the rolC gene. The rolC and GA2ox genes are two potential genes for dwarfing plants. E. coli was transformed with a binary vector, which was supposed to contain the GA2ox and nptII genes. Transformation events were confirmed by restriction enzyme digestion and by PCR analysis, which led to the discovery that the GA2ox gene was not present in the original vector but the gus gene. A. tumefaciens was later transformed with the vector, isolated from the above transformed E. coli. Transformation of A. tumefaciens could not be confirmed by PCR analysis, even though the colonies grew well on the selectable medium containing kanamycin. In the second part of the project Southern blot was conducted to further confirm integration of the rolC and nptII genes in the transgenic clones of the apple rootstock A2 and to determine the copy number of the transgenes. The Southern results confirmed that six clones contained the nptII and rolC genes. Two of the transformed clones have a single copy of the T-DNA integrated.
Mobility of Membrane Lipids and Proteins at the Animal and Vegetal Pole of the Sea Urchin Egg

We have compared the mobility of a fluorescent lipid analogue and of fluorescently labeled membrane proteins at the animal and vegetal poles of the egg of the sea urchin Paracentrotus lividus. Translational diffusion coefficients have been measured by fluorescence microphotolysis (“photo‐bleaching”) on the egg which was rotated on its poles. Lipid and protein diffusion coefficients averaged 0.8 μm2/sec and 0.04 μm2/sec, respectively at both animal and vegetal pole of the egg. Substances which were known to animalize (Zn++) or vegetalize (Li+) the sea urchin egg had no significant effect on protein diffusion coefficients.