Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulators of hemoglobin switching in zebrafish and human models

Hemoglobin switching is a developmental process involving the dynamic transcriptional regulation of multiple globin genes. This molecular process involves multiple layer of complexity, and elucidating new mechanisms in this process will result in a more complete understanding of general gene regulation and will likely have direct clinical implications for hemoglobinopathies, such as sickle cell anemia. In this dissertation, I develop and characterize a new model for hemoglobin switching, the zebrafish. I defined and fully annotated the two zebrafish globin loci, termed major and minor loci. Both loci contain αand β-globin genes oriented in a head-to-head fashion. Characterization of the globin expression pattern precisely defined the timing of normal switching and demonstrated that zebrafish, like humans, have two globin switches. The locus control region for the major locus was identified and in conjunction with a proximal promoter was able to generate robust, erythroid-specific expression in a
Effect of heat and enzyme treatment on yield, phenolic content and antioxidant capacity of juices from chokeberry mash.

The objective of the present study was to determine the effect of different methods of chokeberry mash treatment prior to juice pressing on the yield, phenolic content, anthocyanin content and antioxidant capacity of the juice. Juice yields ranged from 63.3 to 73.9%, with maximum yield rendered by combined treatment (heat treatment +85°C for 5 min, followed by mash maceration with Pectinex BE Colour, Pectinex BE XXL, or Gammapect LC Color). Combined treatment and mash maceration with the use Gammapect LC Color was highly effective with respect to yield, polyphenol content and DPPH˙ and OH' radical scavenging activity. The highest anthocyanin content was obtained in juices produced by enzymatic maceration, particularly using Gammapect LC Color. Cyanidin-3-galactoside was the predominant anthocyanin in all juice types. The polyphenol and anthocyanin content correlated with the DPPH' and OH' radical scavenging activity.
BODY CONDITION SCORE (BCS) AND CALVING ORDER ON MILK PRODUCTION AND COMPOSITION IN ZEBU CATTLE

The present study aimed to evaluate the effect of body condition score (BCS) and calving order on milk production and composition in zebu cattle participating in an official dairy cow tournament. We analyzed milk samples from 47 Gyr, Guzerat and Red Sindhi cows, distributed into classes with respect to lactation stage, milk production, and body condition score. Means for milk composition were within standard ranges for zebu cattle, with the greatest variation recorded for fat and protein content. Fat content was higher for animals in the first month of lactation, with a mean of 5.69%, and protein content was highest after 60 days with an average of 3.55%. A positive correlation of 0.38% (p<0.05) was observed between milk fat and protein content. First calving animals exhibited lower mean milk production than those in their second calving or more. Animals with a BCS in class II demonstrated higher daily production up to 30 days of lactation. Body condition score influenced the milk production of zebu cows participating in a dairy cow competition up to the 30th day of lactation.
Simple estimators of salmonid escapement and its variance using a new area-under-the-curve method

If observed numbers of spawning salmon are plotted against sampling date, then the area under the curve (AUC) gives an estimate of spawner-days. Dividing AUC by spawner lifetime and adjusting for observer efficiency gives an estimate of spawner escapement. In particular, the trapezoidal form of AUC estimator has been widely used over the last two decades, despite the absence of a direct method for calculating its variance. For this reason, an alternative estimator of escapement was developed using a maximum likelihood (ML) model of spawner arrivals. However, this alternative has not been widely used, perhaps because of its complexity and concerns over validity of assumptions. Here, a simpler ML approach is used to estimate AUC by fitting a model directly to spawner numbers. It can be fitted using existing generalized linear modeling software and provides an explicit variance estimator for AUC and escapement. Simulations show that it has consistently higher coverage than the existing ML estimator. However,.
Adult plant resistance to powdery mildew (Erysiphe graminis)in three barley cultivars

The mechanism(s) of adult plant resistance (a.p.r.) to Erysiphe graminis f. sp. hordei were examined in two spring barley cultivars, Athos and Porthos, which possess similar identified mildew resistance genes and seedling resistance, but differential field resistance. These cultivars were compared with Golden Promise, a universally susceptible cultivar. Differential a.p.r. to a compatible race was detected as a reduction in the number and sporulation of colonies on later-formed Athos leaves. Golden Promise exhibited some a.p.r. , but much less than either Athos or Porthos. Differential a.p.r. was expressed at several infection stages, viz. appressorial formation, penetration and sporulation. Epidermal hypersensitivity occurred infrequently in all leaf position/cultivar interactions. Papillae were associated with >90% of all penetration failures. The incidence of papillae in successful penetrations at 96 h was 20% on later-formed leaves of Athos compared to c. 60% on all other leaves.
In silico modeling of Arp1 and Arp2 as targets of Photox ADP-ribosylation

Photox has been identified as an ADP-ribosylating toxin, produced by Photorhabdus luminescens, which targets actin. Recent unpublished studies have suggested that Photox may also target actin-related proteins (Arps). Herein we report possible interacting residues of actin, Arp1 and Arp2, with Photox. Both actin and Arp1 were predicted to interact with Photox in six main groups across the NAD+ binding surface whereas four interaction groups were proposed between Arp2 and Photox. The possible interactions evaluated included hydrogen bonds, salt bridges, and electrostatic and hydrophobic interactions. Our results suggest that Arp1 is a very likely target of Photox, while Arp2 is also a possible candidate; however, the possible interactions between Photox and Arp2 appear to be weaker than the possible interactions between Photox and Arp1. Understanding the various interactions of Photox and its targets may help to provide insight into its biological action, and may potentially lead to a treatment plan for similar toxin-related diseases. Keywords: ADP-ribosylating toxins; Photox (Photorhabdus luminescens); actin-related proteins (Arp1, Arp2) (targeting of); in silico modeling of protein interactions
Hygromycin as selective marker in Agrobacterium-mediated genetic transformation of indica rice MR 219.

The success of Agrobacterium-mediated genetic transformation depends on the efficiency of gene delivery, plant regeneration systems and selection agents. The effects of hygromycin B (hyg B), a selection agent that is commonly used in plant genetic transformation, on embryogenic calli and somatic embryos of indica rice var MR 219 was evaluated. Embryogenic calli and embryos were cultured on pre-regeneration medium containing hygromycin concentrations from 0 to 200 mg/litre for 12 weeks to determine the lethal dose. The potential of the hygromycin phosphotransferase (hpt) gene as the selective marker was also evaluated. The embryogenic calli was co-cultivated with the Agrobacterium strain LBA 4404 that harbours the binary vector pCAMBIA1305.2 with the hpt gene and subsequently cultured on regeneration medium with added hygromycin concentrations at 0 to 50 mg/litre. Results showed that hygromycin concentrations above 30 mg/litre strongly inhibited growth and development of non-transformed embryogenic calli and somatic embryos. Ten to 20 mg/ litre hygromycin concentrations were the most suitable concentrations used for selection of transgenic embryos or plantlets of rice MR 219 with 2.4% efficiency. Hygromycin B is a suitable selection agent and selective marker for genetic transformation of rice MR 219. Keywords: Oryza sativa L. ; somatic embryo; phosphotransferase; plant regeneration; tissue culture
A comparison of visual vs. instrumental measurement of color differences in bentgrass turf.

This study was conducted to determine: 1) if the Minolta CR-310 Chroma Meter can detect color differences among bentgrass (Agrostis stolonifera L., A. capillaris L.) cultivars maintained as a turf; 2) how the CR-310 parameters of hue angle, lightness, and chroma compare with visual color assessments; and 3) if the CR-310 can provide consistent color measurements among evaluators. Differences were detected among cultivars with respect to hue angle, lightness, and chroma. Hue angle and chroma were significantly correlated with visual color assessments when data were averaged across all evaluators. Lightness was not strongly associated with visual color assessment. Differences were found among evaluators for visual color assessment, lightness, and chroma, but not for hue angle measurements. Thus, hue angle appears to be the most consistent CR-310 parameter for measuring color of bentgrass turf. These results indicate that the CR-310 can be used to evaluate the color of bentgrass cultivars maintained as a turf and provides consistent hue angle measurements among evaluators, regardless of experience in rating turf color. The CR-310 is probably best used for measuring relative color differences and may be useful if cultivars of similar color are desired in blended turfs.
Frequent, low‐amplitude disturbances drive high tree turnover rates on a remote, cyclone‐prone Polynesian island

Aim How important are frequent, low‐intensity disturbances to tree community dynamics of a cyclone‐prone forest? We tested the following hypotheses concerning the ‘inter‐cataclysm’ period on a remote Polynesian island: (1) tree turnover would be high and recruitment rates would be significantly higher than mortality; (2) low‐intensity disturbance would result in a marginal increase in tree mortality in the short term; (3) turnover would vary among species and would be associated with plant traits linked to differences in life history; and (4) mortality and recruitment events would be spatially non‐random.
Analysis of Genetic Diversity and Phylogenetic Relationship of Kenaf Germplasm by SRAP

The genetic diversity and phylogenetic relationship were analyzed by sequence-related amplified polymorphism (SRAP) marker system on 84 varieties of kenaf (Hibiscus cannabinus L.) germplasm collected from 26 countries and regions around the world. Twenty-six of total 225 SRAP primer combinations showed polymorphisms. Analysis of 84 kenaf varieties by using the 26 polymorphic primer combinations had identified a total of 329 reproducible bands. Among them, 248 bands (75.4%) were polymorphic. The number of polymorphic fragments produced by an individual primer combination ranged from 5 to 15, with an average of 9.54 bands. DNA fragment size ranged from 300 bp to 1500 bp. Cluster analysis of the SRAP fingerprints clearly separated the 84 varieties into three distinct groups: cultivar, wild, and intermediate types. The cultivars were further delineated into four subgroups. High genetic similarity was found among varieties from the same geographic region, resulting from the fact that kenaf is a plant dominated by cross-pollination. This research indicated that SRAP molecular marker could be used to perform kenaf varieties identification, genetic diversity and phylogenetic relationship assessment, and germplasm evaluation.
Characterization of 12 new microsatellite loci in Aenictus and Neivamyrmex army ants

Here we describe 12 polymorphic microsatellite loci that were cloned and characterized for three species of army ants: the North American Neivamyrmex nigrescens , and the Asian Aenictus laeviceps and Aenictus dentatus . Observed and expected heterozygosities ranged from 0.37 to 0.97 (mean 0.70), and from 0.48 to 0.95 (mean 0.72), respectively. We observed 2–30 (mean 12) alleles per locus. These new genetic markers will be useful for studies of overall population structure and the complex pedigrees in colonies of army ants.
Avaliação de preparações antigênicas de Strongyloides stercoralis para o imunodiagnóstico da estrongiloidíase

Aqueous-soluble (AS) antigens from larvae of Strongyloides stercoralis, extracted with phosphate- buffered saline, are traditionally used for serodiagnosis of strongyloidiasis. To identify sources of antigensfor use in serodiagnosis, residual particulates from parasite larvae after aqueous extraction were solubilized with Tris-buffered 8M urea, yielding a urea-soluble (US) antigen fraction. Both AS and US antigens from S. stercoralis were evaluated by an enzyme-linked immunosorbent assay. No significalive differences were observed between AS and US antigens from the parasite regarding specific antigenic activity and cross-reactivity. lmmunoassays are highly dependent on the antigen for sensitivity and specificity. Crude extracts from S. stercoralis should be further studied, mainly in relation to antigenic fractions which could provide even more sensitive and specific results. Studies of fractionation of S. stercoralis must take into account the antigen yield of both the crude extract and fractions, since larvae of parasite are normally difficult to obtain. Considering this aspect, the results from this study are very useful, since the extraction with urea subslantialty increased the amounts of antigenic materiais normally obtained with the classical aqueous extraction.
Qualitative differences in the immune response of rabbit, mouse and sea bass,Dicentrarchus labrax, L. toPhotobacterium damselasubsp.piscicida, the causative agent of fish Pasteurellosis

Sera raised in rabbits, mice and sea bass againstPhotobacterium damselasubsp.piscicida(Ph.d.p.) cultured both in normal laboratory medium and under iron-limited conditions were analysed by Western blot. Sera collected from sea bass after injection with both live and heat-killedPh.d. p.cells were also analysed. All analysed sera reacted with two groups ofPh.d. p.cell antigens, one (an array of products) assigned as a high molecular weight group and another (lipopolysaccharide and/or lipoprotein) assigned as a low molecular weight group. Each serum tested differed in its reaction by Western blot. Cells cultured under iron-limited conditions demonstrated, both qualitatively and quantitatively, elevated immunogenicity. Great variation among the sera was evident with reference to the recognition of antigens in the high molecular weight group ofPh.d. p.products, with the sea bass serum raised against live cells demonstrating reaction against a wider range of cell material. Lipopolysaccharide and/or lipoprotein situated in the low molecular weight group products appeared to be the most immunogenic material in the bacterial cell. A 15·5 kDa antigen was recognised only from sea bass serum raised against live cells. The findings of this study are discussed in relation to future vaccine development.
Adapter Dimer Reduction in High-Throughput MicroRNA Profiling

MicroRNAs are small non-coding RNAs, approximately 19-23 nucleotides long that play a vital role in the regulation of gene expression making quantification and identification important in cellular development and differentiation between normal and diseased tissue states. Current miRNA and small RNA profiling techniques include real-time PCR, microarray and second-generation sequencing. Secondgeneration (next generation) sequencing is rapidly growing as the most high throughput method for profiling with the availability of multiplexing barcodes. Here we report a new protocol for adapter dimer reduction, which facilitates the characterization of small RNA profiles and the use of PCR barcoding to reduce bias during multiplexing.
DUAL BEHAVIOUR OF PLANTS AGAINST BACTERIAL QUORUM SENSING: INHIBITION OR EXCITATION

Bacteria use an unique and sophisticated system for regulating diverse physiological processes in function of their population size. This regulatory procedure, called “quorum sensing” (QS), depends on the synthesis and perception between bacteria of small signal molecules such as acyl-homoserine lactones (AHLs). It is now evident that plants can listen to bacterial signals and respond in sophisticated ways to the information. The anti-QS activity of the methanolic extract of 44 plant species was detected through the inhibition of the QS-related violacein pigmentation in Chromobacterium violaceum CV026 in the presence of 5 mgl-1 of C6- homoserin lactone. In addition, the ability of test plants to produce AHL-mimicking compounds that excite QS-related response in CV026 was investigated. The results revealed that the QS inhibition activity was observed in the leaves and stem extracts of tarragon (Artemisia dracunculus), radish (Raphanus sativus) and hollyhock (Althea officinalis), which repress violacein production in CV026. We have also shown that Trifolium repens contains AHL- mimicking molecules that can activate QS function in biosensor bacterium and induce violacein production in CV026. Methanolic extracts were also able to inhibit QS-regulated virulence in Pectobacterium carotovorum subsp. carotovorum on potato tubers. The results suggest that plants have quorum sensing-mimicking signals that could potentially be used for disrupting quorum sensing of associated bacteria thus controlling their infections.
Ovule and female gametophyte development in the Bromeliaceae: an embryological study of Pitcairnia encholirioides

Pitcairnia encholirioides L.B. Sm. is an endangered species endemic to the Brazilian Atlantic Forest. This species exhibits limited flowering, late seed germination, and preference for clonal growth. Because little is known about its life cycle and female gametophyte development, the ovule development, gynosporogenesis, and gynogametogenesis were analysed to advance knowledge of the species’ life cycle and structural alterations during ovule and female gametophyte development. Also, identification of embryological characters contributing to systematics of Pitcairnioideae is relevant. The ovules are anatropous, bitegmic, and crassinucellate, the gynosporogenesis is monosporic, and the female gametophyte is a Polygonum type. Different patterns in development of the integuments, nucellus, chalazal appendage, and micropylar channel indicate the potential of these characters for subfamily systematics. In the filiform apparatus, a range of glycan-directed monoclonal antibodies was used; the filiform exhibited a .
Protein phosphatase 4 is involved in the late development of Dictyostelium discoideum

A cDNA clone SSJ337 (accession no. AF161253) of 1230 bp, encoding a catalytic subunit of protein phosphatase 4, was selected as one of the clones expressed specifically in prestalk cells from a cDNA library of D. discoideum slugs. Cells transformed with a knockout construct of SSJ337 showed an aberrant and tiny fruiting-body formation with a short stalk. A knockout mutant, SSJ337KO was allowed to develop much slower than a wild-type AX2 after the post-aggregation stage. This suggested that the SSJ337 cDNA clone has played an important role especially in the later development of Dictyostelium discoideum. Results from Northern blotting, analysis showed that transcripts for SSJ337 were accumulated at 16 h to 24 h after starvation began.
Structural equation modeling of the Canadian flax (Linum usitatissimum L.) core collection for multiple phenotypic traits

Zhang, T. , Lamb, E. G. , Soto-Cerda, B. , Duguid, S. , Cloutier, S. , Rowland, G. , Diederichsen, A. and Booker, H. M. 2014. Structural equation modeling of the Canadian flax (Linum usitatissimum L.) core collection for multiple phenotypic traits. Can. J. Plant Sci. 94: 1325–1332. Flax seed yield is a complex trait that results from the inter-relationship between many crop characteristics. Structural equation modeling (SEM) is a statistical method used to determine the relationship between measured variables such as crop characteristics. Crop phenology, canopy traits, yield, and its components were included in structural equation models to determine how these crop characteristics relate to seed yield in a phenotypically diverse collection of flax germplasm. Early season vigor (scored as greater plant stand) was positively associated with canopy light interception and higher seed yield. Plant height also had a significant positive effect on seed yield. Moreover, yield components such as 1000-seed weight, number.
Multi‐dimensional Lotka–Volterra systems for carcinogenesis mutations

In the paper we consider three classes of models describing carcinogenesis mutations. Every considered model is described by the system of (n+1) equations, and in each class three models are studied: the first is expressed as a system of ordinary differential equations (ODEs), the second—as a system of reaction–diffusion equations (RDEs) with the same kinetics as the first one and with the Neumann boundary conditions, while the third is also described by the system of RDEs but with the Dirichlet boundary conditions. The models are formulated on the basis of the Lotka–Volterra systems (food chains and competition systems) and in the case of RDEs the linear diffusion is considered. The differences between studied classes of models are expressed by the kinetic functions, namely by the form of kinetic function for the last variable, which reflects the dynamics of malignant cells (that is the last stage of mutations). In the first class the models are described by the typical food chain with favourable unbounded environment for the last stage, in the second one—the last equation expresses competition between the pre‐malignant and malignant cells and the environment is also unbounded, while for the third one—it is expressed by predation term but the environment is unfavourable. The properties of the systems in each class are studied and compared. It occurs that the behaviour of solutions to the systems of ODEs and RDEs with the Neumann boundary conditions is similar in each class; i.e. it does not depend on diffusion coefficients, but strongly depends on the class of models. On the other hand, in the case of the Dirichlet boundary conditions this behaviour is related to the magnitude of diffusion coefficients. For sufficiently large diffusion coefficients it is similar independently of the class of models, i.e. the trivial solution that is unstable for zero diffusion gains stability. Copyright © 2009 John Wiley & Sons, Ltd.
Reanalysis of the biogeographical hypothesis of range expansion between robust and gracile capuchin monkeys

The data used by Lynch Alfaro et al. (2012a, Journal of Biogeography, 39, 272–288) and the biogeographical hypothesis postulated by these authors to explain the current distribution of capuchin monkeys were reanalysed including additional cytochrome b data from Sapajus xanthosternos and Sapajus flavius. Our reconstructed phylogeny placed S. xanthosternos in a monophyletic clade representing the most basal lineage of this genus. All analyses indicated polyphyletic arrangements for several capuchin species, suggesting that incomplete lineage sorting has occurred during their evolution. These results also suggest that available molecular data lack adequate variation for accurately resolving species relationships. These results suggest that the divergence of capuchin monkey genera may have occurred in the Atlantic Forest. However, a more conclusive scenario and better resolution of the species tree requires correct identification of species, data from several unlinked nuclear loci from a higher number of individuals per species, and careful analysis of ancient DNA data from museum specimens.